Escherichia coli ST131: The Quintessential Example of an International Multiresistant High-Risk Clone

CHAPTER FOUR

Escherichia coli ST131: The Quintessential Example of an International Multiresistant High-Risk Clone Amy J. Mathers*, Gisele Peiranox, { and Johann D.D. Pitoutx, {, jj, 1 *University of Virginia, Charlottesville, VA, USA x Division of Microbiology, Calgary Laboratory Services, University of Calgary, Calgary, AB, Canada { Departments of Pathology & Laboratory Medicine, University of Calgary, Calgary, AB, Canada jj Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada 1 Corresponding author: E-mail: [email protected]

Contents 1. Introduction 2. Extraintestinal Pathogenic E. coli 3. Expanded-Spectrum b-Lactamases 3.1 CTX-M b-Lactamases 3.2 AmpC b-Lactamases or Cephalosporinases 3.3 NDM b-Lactamases 4. OXA-48-like b-Lactamases 5. International Multiresistant High-Risk Clones 6. Escherichia coli ST131 6.1 Initial Studies Pertaining to E. coli ST131 6.2 Plasmids Associated with E. coli ST131 6.3 Recent Developments Pertaining to ST131 6.3.1 6.3.2 6.3.3 6.3.4 6.3.5

110 111 113 114 116 117 119 120 123 123 127 129

Epidemiology and Clinical Issues Population Biology O16:H5 H41 Lineage Virulence ST131 and Carbapenemases

129 130 132 133 133

6.4 Does ST131 Qualify as an International Multiresistant High-Risk Clone? 6.4.1 6.4.2 6.4.3 6.4.4 6.4.5 6.4.6

Global Distribution Association with Antimicrobial Resistance Mechanisms Ability to Colonize Human Hosts Effective Transmission among Hosts Enhanced Pathogenicity and Fitness Causing Severe and/or Recurrent Infections

7. Rapid Methods for the Detection of E. coli ST131 7.1 Multilocus Sequence Typing Advances in Applied Microbiology, Volume 90 ISSN 0065-2164 http://dx.doi.org/10.1016/bs.aambs.2014.09.002

134 135 135 136 136 137 137

138 138 © 2015 Elsevier Inc. All rights reserved.

109

j

110

Amy J. Mathers et al.

7.2 Pulsed Field Gel Electrophoresis 7.3 Repetitive Sequence-Based PCR Typing 7.4 Polymerase Chain Reaction 7.5 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry 8. Summary References

139 139 140 141 142 143

Abstract Escherichia coli ST131emerged during the early to mid-2000s is an important human pathogen, has spread extensively throughout the world, and is responsible for the rapid increase in antimicrobial resistance among E. coli. ST131 is known to cause extraintestinal infections, being fluoroquinolone resistant, and is associated with ESBL production most often due to CTX-M-15. Recent molecular epidemiologic studies using wholegenome sequencing and phylogenetic analysis have demonstrated that the H30 ST131 lineage emerged in early 2000s that was followed by the rapid expansion of its sublineages H30-R and H30-Rx. Escherichia coli ST131 clearly has all of the essential characteristics that define a high-risk clone and might be the quintessential example of an international multiresistant high-risk clone. We urgently need rapid costeffective detection methods for E. coli ST131, as well as well-designed epidemiological and molecular studies to understand the dynamics of transmission, risk factors, and reservoirs for ST131. This will provide insight into the emergence and spread of this multiresistant sequence type that will hopefully lead to information essential for preventing the spread of ST131.

1. INTRODUCTION The global spread of antimicrobial resistance was recently identified by the World Health Organization (WHO) as one of the three greatest threats to human health (America, 2010). In April 2014, the WHO released a report entitled, “Antimicrobial resistance: global report on surveillance 2014” (Organization, 2014b). The report focused on antibiotic resistance in seven different bacteria responsible for common, serious diseases such as bloodstream infections (BSIs), diarrhea, pneumonia, urinary tract infections (UTIs), and gonorrhea. It states that antimicrobial resistance to common bacteria has reached alarming levels in many parts of the world and that in some settings, few, if any, of the available treatment options remain effective for common infections. Specifically for Escherichia coli the report states the following (Organization, 2014b): “Resistance to one of the most widely used antibacterial agents (i.e., the fluoroquinolones) for the treatment of UTIs caused by E. coli is very widespread. In the 1980s, when the

The Quintessential Example of an International Multiresistant High-Risk Clone

111

fluoroquinolones were first introduced, resistance was virtually zero. Today, there are countries in many parts of the world where this treatment is now ineffective in more than half of patients.” Another important finding of the 2014 WHO report is that surveillance for antibacterial resistance is neither coordinated nor harmonized and there are many gaps in information on bacteria of major public health importance (Organization, 2014b). The report also reveals that key tools to tackle antibiotic resistance, such as basic systems to track and monitor the problem, do not exist in many countries. The spread of multiresistant bacteria is problematic for the medical community at large since it undermines empirical treatment regimens by delaying the administration of appropriate antibiotic therapy and by reducing the options for appropriate treatment. This contributes to increased patient mortality and morbidity (Schwaber et al., 2006). One of the most urgent areas of drug resistance is the rapid evolution of extended-spectrum cephalosporin and carbapenem resistance in Enterobacteriaceae which has spread globally and rapidly in the last decade (Organization, 2014a). This epidemic comes at a time when Moore’s law has enabled analysis of big data combined with rapid massively parallel whole-genome sequencing which has given us a glimpse of molecular epidemiology in ways that were not feasible 10 years ago (GE, 1965; Reuter et al., 2013). This will likely enable the scientific community to determine the global dissemination for these genes of resistance and the successful plasmids and clones which carry them in ways not previously possible. Hopefully this new insight can yield urgently needed clues about how to go about prioritizing tactics to limit the devastating spread of multidrugresistant Enterobacteriaceae.

2. EXTRAINTESTINAL PATHOGENIC E. COLI Escherichia coli is an incredibly diverse bacterial species that shows considerable metabolic versatility with the ability to colonize numerous animal hosts. Escherichia coli is part of the nonpathogenic commensal bacteria that forms part of the normal intestinal flora of humans and various animals (Kaper, Nataro, & Mobley, 2004). However, several variants of E. coli had been described that cause infections of the gastrointestinal system (referred to as intestinal pathogenic E. coli). Intestinal pathogenic E. coli strains are generally divided into those that cause diarrhea by: (1) expressing heatlabile or heat-stable toxin (enterotoxigenic E. coli (ETEC)) or Shiga toxin

112

Amy J. Mathers et al.

(Shiga toxin-producing E. coli (STEC), including enterohemorrhagic E. coli (EHEC)); (2) invading the intestinal mucosa (enteroinvasive E. coli (EIEC)); (3) causing attaching and effacing lesions in the intestinal mucosa (enteropathogenic E. coli (EPEC)); and (4) other less well-defined mechanisms (e.g., enteroaggregative E. coli (EaggEC)) (Nataro & Kaper, 1998). Whereas ETEC, EIEC, EPEC, and EaggEC remain important causes of diarrhea among children in developing countries, the most prevalent intestinal pathogenic E. coli strains in developed countries are STEC/EHEC. The most common EHEC, E. coli O157:H7, is usually community-acquired via contaminated food or water. A newly recognized clonal lineage belonging to serotype O104:H4 that carries virulence traits of both EHEC and EaggEC was responsible for a massive outbreak of bloody diarrhea, hemolytic–uremic syndrome, and death in Germany in 2011 that was traced to contaminated bean sprouts (Buchholz et al., 2011). Escherichia coli isolates that have the ability to cause infections outside the gastrointestinal system are referred to as extraintestinal pathogenic E. coli (ExPEC) isolates (Pitout, 2012a). ExPEC incorporates the following variants: avian pathogenic E. coli, uropathogenic E. coli (UPEC), and those isolates responsible for septicemia and neonatal meningitis (Kaper et al., 2004). The presence to several putative virulence genes has been positively linked with the pathogenicity of ExPEC. Phylogenetic analyses have shown that intestinal E. coli and ExPEC fall into four main phylogenetic groups namely A, B1, B2, and D (Herzer, Inouye, Inouye, & Whittam, 1990). ExPEC belongs mainly to group B2 and, to a lesser extent, to group D, while intestinal commensal isolates tend to belong to groups A and B1. ExPEC isolates exhibit considerable genome diversity and possess a broad range of virulence-associated factors including toxins, adhesions, lipopolysaccharides, polysaccharide capsules, proteases, and invasins that are frequently encoded by pathogenic islands and other mobile DNA islands. It seems that these putative virulence factors contribute to fitness (e.g., iron-uptake systems, bacteriocins, proteases, adhesins) of ExPEC and increase the adaptability, competitiveness, and ability to colonize the human body rather than being typical virulence factors directly involved in infection (Mokady, Gophna, & Ron, 2005). ExPEC is the most important cause of lower UTIs and systemic infections in humans (Mandell, Douglas, Bennett, & Dolin, 2005). The systemic infections include upper UTIs, bacteremia, nosocomial pneumonia, cholecystitis, cholangitis, peritonitis, cellulitis, osteomyelitis, infectious arthritis, and neonatal meningitis (Wiles, Kulesus, & Mulvey, 2008). ExPEC is also

The Quintessential Example of an International Multiresistant High-Risk Clone

113

the most common Gram-negative bacterium associated with BSIs in both developed and developing countries. ExPEC is the primary cause of community-acquired UTIs, with an estimated 20% of women over the age of 18 years suffering from a UTI during their lifetime (Foxman, 2010). The UPEC variant is responsible for 70–95% of community-onset UTIs and approximately 50% of nosocomial UTIs, hence accounting for substantial morbidity, mortality, and medical expenses (Foxman, 2010). Recurrent or relapsing UTIs are especially problematic in many individuals. The primary reservoir of UPEC is believed to be the human intestinal tract and isolates act as opportunistic pathogens that employ diverse repertoire of virulence factors to colonize and infect the urinary tract in an ascending fashion (Foxman, 2010). However, community-onset clonal outbreaks of UTIs, possibly due to the consumption of food contaminated with UPEC, have also been described (Wiles et al., 2008). Additionally, there is some evidence that UPEC isolates can also be transmitted via sexual activities (Wiles et al., 2008). During the 1990s and early 2000s, antibiotic therapy with the thirdgeneration cephalosporins or fluoroquinolones was considered the treatment of choice for serious infections due to ExPEC (Pitout, 2012b). However, fluoroquinolone-resistant and extended-spectrum b-lactamase (ESBL)-producing E. coli have increased significantly during the mid-tolate 2000s and in certain areas of the world, a significant proportion of nosocomial and community E. coli isolates are resistant to these important antimicrobial classes (Pitout, 2012a). The ESBL pandemic in E. coli is mostly due to CTX-M b-lactamases (especially CTX-M-15) and these enzymes have become the most prevalent and widespread types of ESBLs in the world (Pitout, 2012b).

3. EXPANDED-SPECTRUM b-LACTAMASES Antibiotic therapy with the oxyimino-cephalosporins (i.e., cefotaxime, ceftazidime, ceftriaxone, and cefepime) is considered as one of the most important treatment of choice for serious infections due to ExPEC (Pitout, 2012b). The development of resistance to the carbapenems among Enterobacteriaceae is of special concern to the medical community at large, because these agents are often the last line of effective therapy available for the treatment of serious infections due to these bacteria (Pitout, 2012b). Among ExPEC, the production of b-lactamases remains the most important mediator to b-lactam resistance. Several different schemes have

114

Amy J. Mathers et al.

been traditionally used for classification of b-lactamases. The molecular or Ambler classification is based on the amino acid sequence and divides b-lactamases into classes (e.g., class A, C, and D enzymes utilize serine for b-lactam hydrolysis, whereas the class B metalloenzymes require divalent zinc ions for substrate hydrolysis) (Bush & Jacoby, 2010). The functional or Bush Jacoby classification uses substrate and inhibitor profiles to divide blactamases into three groups: group 1 (i.e., cephalosporinases), group 2 (i.e., serine b-lactamases), and group 3 (i.e., metallo-b-lactamases (MBLs)) (Bush & Jacoby, 2010). For the sake of simplicity we will use the term “expanded-spectrum” blactamases in this chapter to stipulate those enzymes with activity against the oxyimino-cephalosporins, monobactams (i.e., aztreonam), and/or the carbapenems. These enzymes consist of the plasmid-mediated or imported Amp C b-lactamases (e.g., cephamycin (CMY) types), ESBLs (e.g., CTX-M types), and carbapenemases (e.g., KPC types, MBLs, e.g., VIM, IPM, and NDM types, and the oxacilinases, e.g., OXA-48-like enzymes). The production of expanded-spectrum b-lactamases often results in broad-spectrum resistance to most of the b-lactam antibiotics and ExPEC with these enzymes are often multiresistant to a variety of other classes of antibiotics (Pitout, 2012a). The NDM and OXA-48 are the most common carbapenemases among nosocomial and community isolates of ExPEC, whereas the VIM, IPM, and KPC b-lactamases are not yet commonly encountered in this specie (Nordmann & Poirel, 2014). Infections with carbapenemase-producing ExPEC have most often been associated with visiting and being hospitalized in endemic areas such as the Indian subcontinent for NDMs and North Africa or Turkey for OXA-48 (van der Bij & Pitout, 2012).

3.1 CTX-M b-Lactamases The most well-known of the expanded-spectrum b-lactamases were first described in 1983 and have been named the ESBLs. These enzymes have the ability to hydrolyze the penicillins, cephalosporins, and monobactams, but not the CMYs and carbapenems, and are inhibited by b-lactamase inhibitors such as clavulanic acid, sulbactam, and tazobactam (Paterson & Bonomo, 2005). Although ESBLs have been identified in a range of Enterobacteriaceae, they are most often present in E. coli and Klebsiella pneumoniae. The majority of ESBLs identified in clinical isolates during the 1980s and 1990s were the SHV or TEM types, which evolved from parent enzymes such as TEM-1, -2, and SHV-1 (Paterson & Bonomo, 2005). A different

The Quintessential Example of an International Multiresistant High-Risk Clone

115

type of ESBL, named CTX-M (i.e., active against CefoTaXime) b-lactamases, that originated from environmental Kluyvera spp., gained prominence in the 2000s with reports of clinical isolates of E. coli producing these enzymes from Europe, Africa, Asia, South and North America (Canton & Coque, 2006). Since the mid-2000s CTX-M b-lactamases have also been identified in different members of the Enterobacteriaceae as well as nonEnterobacteriaceae, but remain especially common in E. coli, and had become the most widespread and common type of ESBL identified worldwide (Pitout & Laupland, 2008). The CTX-Ms belong to the molecular class A or functional group 2 blactamases, and include at least six lineages (i.e., CTX-M-1, CTX-M-2, CTX-M-8, CTX-M-9, CTX-M-25, and KLUC) that differ from each other by 10% amino acid homology (Canton & Coque, 2006). The majority of blaCTX-M genes are carried on conjugative plasmids that belong to incompatibility groups circulating in Enterobacteriaceae (e.g., IncFII, IncN, and IncK types) (D’Andrea, Arena, Pallecchi, & Rossolini, 2013). Insertion sequences (IS) (e.g., ISEcp1 or ISCR1) are able to capture and mobilize blaCTX-M genes but also provide strong promoters for high-level expression of the b-lactamase. The CTX-M-type enzymes are inhibited by most commercial b-lactamase inhibitors (e.g., clavulanate, sulbactam, and tazobactam), including the new inhibitor avibactam (D’Andrea et al., 2013). Inhibitor-resistant variants of CTX-M-type enzymes have not yet been reported. Currently, the most widespread and prevalent type of CTX-M enzyme among human clinical isolates of E. coli is CTX-M-15. Escherichia coli producing this enzyme often belongs to the sequence type (ST) named ST131 and to a lesser extent to clonal complexes STC405 and STC38 ST38 (Peirano & Pitout, 2010). It seems that the intercontinental dissemination of these STs have played a major role in the worldwide emergence of CTX-M-15-producing E. coli (more details are provided in the high-risk clone section). CTX-M-producing Enterobacteriaceae are important causes of hospitaland community-onset UTIs, bacteremia, and intra-abdominal infections (Canton & Coque, 2006). The risk factors associated with infections caused by CTX-M-producing E. coli include the following: repeated UTIs, underlying renal pathology, previous antibiotics including cephalosporins and fluoroquinolones, previous hospitalization, nursing home residents, older males and females, diabetes mellitus, underlying liver pathology, and international travel to high-risk areas such as the Indian subcontinent (Rodriguez-Bano &

116

Amy J. Mathers et al.

Pascual, 2008). The spread of CTX-M-type ESBLs has been very efficient and not limited to health care settings, but has also involved the community, livestock and companion animals, wildlife, and the environment (NicolasChanoine, Bertrand, & Madec, 2014). Studies have also shown high transmission rates of E. coli with blaCTX-Ms within households (Hilty et al., 2012). Global surveys have illustrated an alarming trend of associated resistance to other classes of antimicrobial agents among CTX-M-producing E. coli that includes trimethoprim-sulfamethoxazole, tetracycline, gentamicin, tobramycin, and ciprofloxacin (Pitout & Laupland, 2008). This has important clinical implications because the fluoroquinolones and trimethoprimsulfamethoxazole are popular oral treatment options for community-onset UTIs. Fortunately, fosfomycin, and nitrofurantoin retain sufficient activity against a high percentage of E. coli that produce CTX-Ms (D’Andrea et al., 2013). It is evident today that CTX-M-producing E. coli is a major player in the world of antimicrobial resistance. A report from the Infectious Diseases Society of America listed ESBL-producing E. coli as a priority drug-resistant microbe to which new therapies are urgently needed (Talbot et al., 2006). The CTX-M pandemic has significantly contributed to the rapid global increase of cephalosporins resistance among Enterobacetriaceae with subsequent increase in carbapenem usage. As such, bacteria with CTX-M b-lactamases should be regarded as a major target for surveillance, infection control, and fundamental investigation in the field of microbial drug resistance.

3.2 AmpC b-Lactamases or Cephalosporinases Enterobacteriaceae with inducible cephalosporinases or AmpC b-lactamases such as Enterobacter cloacae, Citrobacter freundii, Serratia marcescens, Morganella morganii, and Providencia stuartii can develop resistance to the oxyiminocephalosporins and 7-a-methoxy-cephalosporins (i.e., CMYs, e.g., cefoxitin, cefotetan) and monobactams (e.g., aztreonam) by overproducing their chromosomal AmpC b-lactamase (Jacoby, 2009). In Klebsiella spp., Salmonella spp., and P. mirabilis, which lack chromosomal b-lactamases, this type of resistance is usually mediated by plasmid encoded or imported AmpC b-lactamases (Hanson, 2003). Escherichia coli is different in that it possesses genes encoding for chromosomal noninducible AmpC b-lactamases that are regulated by weak promoters and strong attenuators resulting in low amounts of the cephalosporinase (Philippon, Arlet, & Jacoby, 2002). Surveys of resistance mechanisms in CMY-resistant E. coli have identified several

The Quintessential Example of an International Multiresistant High-Risk Clone

117

promoter or attenuator mutations, which resulted in the upregulation and production of the naturally occurring chromosomal AmpC b-lactamases (Forward et al., 2001). Occasionally, CMY-resistant E. coli can also produce plasmid-mediated or imported AmpC b-lactamases (Jacoby, 2009). AmpC b-lactamases at high levels hydrolyze penicillins, most cephalosporins, CMYs, and monobactams, but not the fourth-generation cephalosporins (e.g., cefepime) and carbapenems. Resistance to the fourth-generation cephalosporins is caused by point mutations in AmpC b-lactamases and is called extended-spectrum cephalosporinases. AmpC enzymes are not inhibited by “classical” b-lactamase inhibitors such as clavulanic acid, sulbactam, and tazobactam although boronic acids and cloxacillin have shown to be good inhibitors (Doi & Paterson, 2007). The genes are typically encoded on large plasmids containing additional antibiotic resistance genes that are responsible for multiresistant phenotype, leaving few therapeutic options (Philippon et al., 2002). Just like ESBL-producing bacteria, E. coli with plasmid-mediated AmpC enzymes have mostly been responsible for nosocomial outbreaks on a worldwide basis during the late 1980s and 1990s, although the risk factors associated with infection are not as well defined as those associated with ESBL-producing bacteria (Philippon et al., 2002). In a study reported from Korea, patients infected by plasmid-mediated AmpC-producing organisms had similar clinical features and outcomes to those patients infected with TEM- or SHV-related ESBL producers (Pai et al., 2004). It seems that CMY-2 (active on cephaycins) is the most common imported AmpC b-lactamase reported in Enterobacteriaceae (especially E. coli and Salmonella spp.) from different areas of the world (Jacoby, 2009). Hospital surveys from Asia, North America, and Europe have shown that the DHA types of cephamycinases are mostly present in Klebsiella spp. from Asia, CMY are present in E. coli from Asia, North America, and Europe while FOX are present in Klebsiella spp. from North America and Europe (Alvarez, Tran, Chow, & Jacoby, 2004; Li et al., 2008; Moland et al., 2006; Mulvey et al., 2005; Woodford et al., 2007).

3.3 NDM b-Lactamases A new type of MBL, named NDM (i.e., New Delhi metallo-b-lactamases), was described in 2009 in K. pneumoniae and E. coli recovered from a Swedish patient who was hospitalized in New Delhi, India (Yong et al., 2009). NDMs have the ability to hydrolyze a wide variety of b-lactams, including the penicillins, cephalosporins, and carbapenems, but not the monobactams

118

Amy J. Mathers et al.

(i.e., aztreonam), and are inhibited by metal chelators such as EDTA. NDM1 shares very little identity with other MBLs, the most similar being VIM-1/ VIM-2 with only 32.4% amino acid identity. Since the first description of NDM-1, more than eight variants of this enzyme have been described, the majority of them originated from Asia (Nordmann & Poirel, 2014). The majority of NDM-1-producing bacteria are broadly resistant to various drug classes and also carry a diversity of other resistance mechanisms (e.g., to aminoglycosides and fluoroquinolones), which leaves limited treatment options (Nordmann, Naas, & Poirel, 2011). These additional mechanisms include the following: plasmid-mediated AmpC b-lactamases (especially CMY types), ESBLs (especially CTX-M-15), different carbapenemases (e.g., OXA-48-, VIM-, KPC-types), 16S RNA methylases, plasmid-mediated quinolone resistance determinants to quinolones, macrolide-modifying esterases, and rifampicin-modifying enzymes. Consequently, Enterobacteriaceae with NDMs remain only susceptible to colistin, fosfomycin, and tigecycline (Nordmann & Poirel, 2014). Kumarasamy, Toleman, and Walsh (2010), provide compelling evidence that NDM-producing Enterobacteriaceae (mostly K. pneumoniae and E. coli) are widespread in India and Pakistan. They also found that many U.K. patients infected with NDM-producing bacteria had recently traveled to India to undergo several types of medical procedures. The patients presented with a variety of hospital- and community-associated infections with UTIs being the most common clinical syndrome. Recent reports from the subcontinent (including India, Pakistan, and Bangladesh) show that the distribution of NDM b-lactamases among Enterobacteriaceae are widespread through these countries (Castanheira, Deshpande, et al., 2011; Castanheira, Mendes, Woosley, & Jones, 2011; Lascols et al., 2011): e.g., a hospital in Varanasi in Northern India identified NDM-1 prevalence rate of 6% among E. coli (n ¼ 528) from outpatients and hospitalized patients between February 2010 and July 2010 (Seema, Ranjan Sen, Upadhyay, & Bhattacharjee, 2011), 7% among E. coli from a major hospital in Mumbai, India (Deshpande et al., 2010), whereas 15% (30/200) of in- and outpatients in Rawalpindi, Pakistan, carried E. coli with NDM-1 in their gut flora (Perry et al., 2011). The prevalence of asymptomatic fecal carriage is estimated to be between 5% and 15% in these countries (Nordmann & Poirel, 2014). Since 2010, Enterobacteriaceae with NDMs have been reported worldwide from patients with an epidemiological link to the Indian subcontinent (Nordmann, Poirel, Walsh, & Livermore, 2011). The impact of intercontinental travels as a source of spread of NDM producers has been extensively

The Quintessential Example of an International Multiresistant High-Risk Clone

119

reported and these enzymes are now one of the most common carbapenemases identified in countries such as the Canada, the United Kingdom, and France (Nordmann & Poirel, 2014). Recent findings suggest that the Balkan states, North Africa, and the Middle East might act as secondary reservoirs for the spread of NDMs, which may or may not initially have reached these countries from the Indian subcontinent (Nordmann & Poirel, 2014). Enterobacteriaceae (especially K. pneumoniae and E. coli) with NDMs have been recovered from many clinical settings, reflecting the disease spectra of these opportunistic bacteria, including hospital- and community-onset UTIs, septicemia, pulmonary infections, peritonitis, device-associated infections, and soft tissue infections (Castanheira, Deshpande, et al., 2011; Nordmann, Naas, & Poirel, 2011; Nordmann, Poirel, et al., 2011). The frequent identification of NDMs within E. coli is of special concern because this organism is the most common cause of communityand hospital-onset UTIs, and diarrhea [88]. NDM-1-positive bacteria have been recovered from the gut flora of travelers returning from the Indian subcontinent and undergoing microbiological investigation for unrelated diarrheal symptoms (Leverstein-Van Hall et al., 2010). There is also widespread environmental contamination by NDM-1-positive bacteria in New Delhi (Walsh, Weeks, Livermore, & Toleman, 2011).

4. OXA-48-LIKE b-LACTAMASES The Ambler class D b-lactamases are commonly referred to as OXAs (i.e., “oxacillinases”) and comprises over 400 enzymes and some variants possess carbapenemase activity. These enzymes (also referred to as carbapenem-hydrolyzing class D b-lactamases or CHDLs) do not hydrolyze efficiently the oxyimino-cephalosporins or the monobactams (the exception being OXA-163) (Nordmann, Naas, et al., 2011). The CHDLs possess weak carbapenemase activity that does not confer high-level resistance to carbapenems if not associated to other factors, such as permeability defects. The majority of CHDL variants have been identified in Acinetobacter spp., but OXA-48 and its derivatives (i.e., OXA-163, OXA-181, OXA-204, and OXA-232) are most often encountered in Enterobacteriaceae (Poirel, Bonnin, & Nordmann, 2012). OXA-48 was first identified in 2003 from K. pneumoniae isolated in Turkey (Poirel, Heritier, Tolun, & Nordmann, 2004) and since then, bacteria that produce these b-lactamases have been important causes of nosocomial outbreaks in this country (Carrer et al., 2010). The first report

120

Amy J. Mathers et al.

of OXA-48-producing K. pneumoniae outside Turkey was in 2007 from Belgium (Cuzon et al., 2008) and bacteria that produce OXA-48 have rapidly spread to several Belgian hospitals (Glupczynski et al., 2012). Since then Enterobacteriaceae with OXA-48 have disseminated throughout Europe, and it seems that Turkey and North African countries (especially Morocco and Tunisia (Nordmann, Naas, et al., 2011)) are the main reservoir for these infections. Subsequently several nosocomial outbreaks OXA48-producing K. pneumoniae, E. coli, and E. cloacae have been reported in France, Germany, Switzerland, Spain, the Netherlands, and the United Kindgom (Poirel et al., 2012). The spread of OXA-48 is mostly due to a mobile 62.5-kb plasmid that belongs to the Inc L/M replicon group, as well as the presence of Tn1999 (Poirel et al., 2012). Interestingly, the 62.5-kb plasmid does not carry additional resistance genes. This plasmid has the ability to transfer efficiently to other enterobacterial species. OXA-48-like enzymes have mostly been identified in K. pneumoniae and E. coli to a lesser extent and are not inhibited by metal chelators such as EDTA or “classical” b-lactamases inhibitors such as clavulanic acid or tazobactam. The production of ESBLs and/or permeability barriers in bacteria that coproduces OXA-48 will increase the level of resistance to the cephalosporins and carbapenems (Nordmann, Naas, et al., 2011). Several point mutant variants of OXA-48, most often in K. pneumoniae, had recently been reported. These include OXA-163, OXA-181, OXA204, and OXA-232 (Nordmann & Poirel, 2014). OXA-163 differs from the other OXA-48-like enzymes in that its carbapenemase activity is low compared with enhanced hydrolysis of the oxyimino-cephalosporins providing isolates with these enzymes-resistant phenotypes similar to those bacteria with ESBL. OXA-163 was originally identified from enterobacterial isolates (E. cloacae and K. pneumoniae) recovered in Argentina, and it seems that Enterobacteriaceae with these OXAs are common in this South American country (Nordmann & Poirel, 2014).

5. INTERNATIONAL MULTIRESISTANT HIGH-RISK CLONES Many different definitions have been used in the medical literature to describe the different patterns of resistance found in multidrug-resistant (MDR) Enterobacteriaceae. We will use the recent definition of MDR Enterobacteriaceae that was adopted by the European Center for Disease

The Quintessential Example of an International Multiresistant High-Risk Clone

121

Prevention and Control (Magiorakos et al., 2012). This states that an MDR Enterobacteriaceae isolate is nonsusceptible to at least one agent in more than three antimicrobial categories that include the following: aminoglycosides, cephalosporins (divided into three groups), CMYs, antipseudomonal penicillins with b-lactamase inhibitors, penicillins, penicillins and b-lactamase inhibitors, monobactams, carbapenems, folate pathway inhibitors, glycylcyclines, fluoroquinolones, phenicols, phosphonic acids, polymyxins, and tetracyclines. A bacterial clone refers to the progeny of one bacterial cell through asexual reproduction implying that the same clonal lineage are very closely related isolates that have recently diverged from a common ancestor (Dijkshoorn, Ursing, & Ursing, 2000). However, bacterial genomes are plastic and are subjected to genome rearrangements (i.e., deletions, IS, etc.) and, to a variable extent, to localized recombinational events. Thus, bacterial isolates assigned to the same clone may not be identical, as the recent descendants of the same common ancestor may differ somewhat in genotype (Spratt, 2004). Therefore, the strict definition of a clone tends to be loosened slightly in bacteriology, and clones are defined as isolates that are indistinguishable, or highly similar, using a particular molecular typing procedure. It has become well established that all isolates of pathogenic species are not equal, and that in a typical pathogenic species there are a small number of clones that are greatly overrepresented among those isolates recovered from disease or from a particular type of infection. The term clone has also become useful in epidemiology, particularly in the study of the relationships between isolates from different geographical areas. In this chapter, the term clone refers to any bacterium propagated from a single colony isolated at a specific time and place showing common phylogenetic origins, i.e., phenotypic or genotypic traits characterized by typing methods showing it to belong to the same group. According to such a definition, the most precise way to characterize clones would be to perform whole-genome sequencing, which is increasingly being applied to study infectious disease transmission. Short of whole-genome sequencing, however, multilocus sequence typing (MLST) is one highly reproducible method that is commonly applied to genotype E. coli. With this genotyping method, E. coli strains are assigned an ST with a numerical designation, according to two widely used and standardized schemes of Achtman and Pasteur, respectively. The Achtman scheme uses the following seven housekeeping genes: adk (adenylate kinase), fumC (fumarate hydratase), gyrB (DNA gyrase), icd (isocitrate/isopropylmalate dehydrogenase), mdh (malate dehydrogenase),

122

Amy J. Mathers et al.

purA (adenylosuccinate dehydrogenase), recA (ATP/GTP binding motif) (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli). The Pasteur MLST scheme uses the following eight housekeeping genes: dinB (DNA polymerase), icdA (isocitrate dehydrogenase), pabB(p-aminobenzoate synthase), polB (polymerase PolII), putP (proline permease), trpA (tryptophan synthase subunit A), trpB (tryptophan synthase subunit B), and uidA (beta-glucuronidase) (http://www.pasteur.fr/recherche/genopole/ PF8/mlst/EColi.html). MLST uses sequence variation in a number of housekeeping genes to define STs, and is an excellent tool for evolutionary studies to show common ancestry lineages among bacteria. Relatedness between isolates when using MLST and is based on polymorphisms within strongly conserved “housekeeping” genes. MLST enables the epidemiology associated with bacteria to be evaluated and can be used to track the population biology of a species, defining the clones within a particular species as an “ST” (Sullivan, Diggle, & Clarke, 2005). It has led to the definition of major STs and the recognition of successful widespread international antimicrobialresistant STs. Although MLST is useful for demonstrating phylogenetic relationships of a large collection of bacterial lineages, it does not have the discriminatory power to show genetic changes in strains during transmissions that occur over a short time period (e.g., outbreaks) (Bryant, Chewapreecha, & Bentley, 2012). A more discriminating test is pulsed field gel electrophoresis (PFGE), which is another widely used method for genotyping E. coli (Sabat et al., 2013). PFGE forms the basis for national and international surveillance systems, such as the PulseNet in the United States and PulseNet International (http://www.cdc.gov/pulsenet/). PFGE is often used to trace contaminated food products during outbreaks or epidemics. A “successful” bacterial clone is an extremely effective vehicle for the dissemination of genetic resistance elements (i.e., genes, integrons, transposons, and plasmids) for the following reasons (Woodford, Turton, & Livermore, 2011): first, all of the hosted resistance elements are transmitted vertically (i.e., from mother to daughter cells) by virtue of the clone’s propensity to spread and hence its increasing prevalence; second, a successful clone has multiple opportunities to act as a donor and to transfer its resistance elements horizontally to other isolates, species, or genera. International multiresistant high-risk clones are defined as clones with a global distribution and showing enhanced ability to colonize, spread, and persist in a variety of niches (Baquero, Tedim, & Coque, 2013). High-risk

The Quintessential Example of an International Multiresistant High-Risk Clone

123

clones have acquired certain adaptive traits that increase their pathogenicity and survival skills accompanied with the acquisition of antibiotic resistance determinants. They have the tenacity and flexibility to accumulate and exchange resistance and virulence genes to other isolates. High-risk clones have contributed to the spread of different plasmids, genetic platforms, and resistance genes among Gram-negative bacteria and play a very important role in global spread of antibiotic resistance (Woodford et al., 2011). Examples of some multiresistant high-risk clones among Enterobacteriaceae are E. coli ST38, ST131, ST155, ST393, ST405, and ST648; and K. pneumoniae ST14, ST37, ST147, and ST258 (Baquero et al., 2013). It is possible that these high-risk clones possess biological factors that provide them with increased “fitness,” giving them a competitive advantage over other ExPEC that reside in the same niche (Riley, 2014). These factors may allow them to outcompete other strains and become the predominant bacterial population in that niche, from which they spread, the spread being facilitated by antimicrobial drug selective pressures in health care settings or food animal husbandry, other human activities, or contaminated vehicles. Thus, their biological “fitness” might enable high-risk clone and their lineages to eventually acquire drug resistance. To summarize: To qualify as an international multiresistant high-risk clone, clones must have the following characteristics: (1) Global distribution, (2) Association with various antimicrobial resistance determinants, (3) Ability to colonize and persist in hosts for long periods of time, (4) Effective transmission among hosts, (5) Showing enhanced pathogenicity and fitness, and (6) Cause severe and or recurrent infections.

6. ESCHERICHIA COLI ST131 6.1 Initial Studies Pertaining to E. coli ST131 In the mid-2000s, PFGE analyses of E. coli isolates with CTX-M-15 in the United Kingdom and Canada identified a pulsotype cluster with less than 80% similarity, designated clone A in the United Kingdom and clones 15A, 15AR (related to A) in Canada (Pitout et al., 2007; Woodford et al., 2004). Because these PFGE patterns did not satisfy the criteria for relatedness outlined by Tenover et al. (1995), these isolates were initially not recognized to belong to a related lineage. In 2008, E. coli ST, ST131 with blaCTX-M-15 was simultaneously identified in nine countries that spanned three continents (Coque et al., 2008; Nicolas-Chanoine et al., 2008). This ST was

124

Amy J. Mathers et al.

present in several countries including Spain, France, Canada (including isolates from PFGE clones 15A and 15AR), Portugal, Switzerland, Lebanon, India, Kuwait, and Korea (Coque et al., 2008; Nicolas-Chanoine et al., 2008). Clone A from the United Kingdom also turned out to be ST131 (Lau et al., 2008). ST131 belonged to serotype O25b:H4 and the highly virulent phylogenetic group B2 while harboring MDR IncFII types of plasmids harboring blaCTX-M-15 (Coque et al., 2008; Nicolas-Chanoine et al., 2008). These two initial studies showed that ST131 had emerged predominantly in the community but seemingly independent in different parts of the world spanning three continents at the same time. Their findings suggested that the emergence of ST131 could be either due to the ingestion of contaminated food/water sources and/or is being imported into various countries via returning travelers. Subsequently, ST131 with CTX-M-15 was described in the United Kingdom (Lau et al., 2008), Italy (Cagnacci, Gualco, Debbia, Schito, & Marchese, 2008), Turkey (Yumuk, Afacan, Nicolas-Chanoine, Sotto, & Lavigne, 2008), Croatia (Literacka et al., 2009), Japan (Suzuki et al., 2009), the United States (Johnson JR, 2008), and Norway (Naseer et al., 2009). Escherichia coli that belong to ST131 but without CTX-M-producing b-lactamases have been isolated from stools of healthy volunteers in Paris, France (Leflon-Guibout et al., 2008), and among isolates without ESBLs causing UTIs in Canada (Johnson et al., 2009). CTX-M-15-producing E. coli that belongs to ST131 had been identified in isolates recovered from the community (Arpin et al., 2009), hospital (Oteo et al., 2009), and nursing homes settings (Rooney et al., 2009), and interestingly, in a companion animal (Pomba, da Fonseca, Baptista, Correia, & Martinez–Martinez, 2009). Why did CTX-M-15-producing E. coli emerge simultaneously in different continents as a cause of community-associated infections? Studies from Calgary, Canada, and Auckland, New Zealand, have shed some light on this intriguing question. The publication from New Zealand describes a series of patients that presented to an Auckland hospital with communityassociated genito-UTIs due to CTX-M-15-producing E. coli. All the patients lacked the traditional risk factors associated with UTIs but had a history of travel to or recent emigration from the Indian subcontinent (Freeman et al., 2008). A Canadian study demonstrated that returning travelers from areas such as the Indian subcontinent (i.e., India, Pakistan), Africa, and Middle East, had a high risk of presenting with community-associated UTIs (including urosepsis) caused by CTX-M-producing E. coli (Laupland, Church,

The Quintessential Example of an International Multiresistant High-Risk Clone

125

Vidakovich, Mucenski, & Pitout, 2008). A follow-up study by the same group of investigators showed that this high risk of infection was mostly due to the acquisition of E. coli ST131 that produces CTX-M-15 (Pitout, Campbell, et al., 2009a). A different study from Calgary over an 8-year period (2000–2007) showed that E. coli clone ST131 that produces CTX-M-15 had emerged as an important cause of community-onset bacteremia during the latter part of the study period (i.e., 1/18 (5%) of ESBL-producing E. coli isolated from blood between 2000 and 2003 were ST131 as opposed to 20/49 (41%) isolated between 2004 and 2007 (Pitout, Campbell, et al., 2009b)). In that study, ST131 (as compared to other ESBL-producing E. coli) was more likely to be resistant to several classes of antibiotics, more likely to produce the aminoglycoside-modifying enzyme aac(6’)-Ib-cr, and more likely to cause community-acquired BSIs including urosepsis. These initial studies suggest that the sudden worldwide increase of community-associated CTX-M-15-producing E. coli was associated with the distribution of ST131. Since reports from India indicated that more than 70% of E. coli collected from the community are ESBL producers (Hawser et al., 2009), it is conceivable that foreign travel to high-risk areas such as the Indian subcontinent potentially played an initial important role in spreading across different continents (van der Bij & Pitout, 2012). The high incidence of spread associated with CTX-M-15-producing E. coli could have achieved by at least two possible ways: the spread of an epidemic clone (such as ST131) with selective advantages (as multiple antibiotic resistance and enhanced virulence factors) between different hospitals, long-term care facilities, and the community; or the horizontal transfer of plasmids or genes that carry blaCTX-M-15 alleles. The literature, during the late 2000s, suggests that the spread of CTX-M-15 E. coli is mostly due to ST131 but plasmid transfer also seems to be important in certain places. The global distribution of ST131 reflected repeated selection of local variants that have acquired certain IncFII resistance plasmids encoding for CTX-Ms (Novais et al., 2012). Johnson and colleagues gave some insight into the early origin of ST131 in North America (Johnson et al., 2009). They studied 199 trimethoprimsulfamethoxazole-resistant and fluoroquinolone-resistant E. coli isolated from urines in Canada during 2002–2004 and identified ST131 in 23% of isolates and nearly all were fluoroquinolone-resistant (i.e., 99%) but, notably, remained susceptible to the cephalosporins (i.e., only 2% of ST131 in that study were resistant to the cephalosporins) (Johnson et al., 2009).

126

Amy J. Mathers et al.

One of the first in vitro studies that investigated the virulence factors of ST131 among 127 E. coli from the 2007 SENTRY and Meropenem Yearly Susceptibility Test Information Collection surveillance programs across the United States was performed by Johnson, Johnston, Clabots, Kuskowski, and Castanheira (2010). Overall 54 (i.e., 17%) belonged to ST131, but interestingly this ST included 52% of isolates that showed resistance to 3 antimicrobial classes. ST131 had a significant higher aggregate virulence score that other E. coli and certain virulence factors such as uropathogenicspecific protein (usp); outer membrane protein (ompT); secreted autotransporter toxin (sat), aerobactin receptor (iutA), and pathogenicity island marker (malX) were associated with this ST. Their results showed that ST131 had distinctive virulence profiles and concluded that the combination of antimicrobial resistance and virulence may be responsible for the epidemiological success of this ST. Subsequent similar studies from different investigators have shown similar virulence profiles among ST131 (NicolasChanoine et al., 2014). Of special interest is the absence of classical ExPEC virulence factors (i.e., pap (P fimbriae), cnF1 (cytoxic nectizing factor), and hlyD (a-hemolysin) among isolates than belong to ST131. The precise role of these virulence factors remains to be elucidated; however, it is possible that certain putative virulence factors possibly contribute to the fitness of ST131. Factors such as sat, iutA, malX, usp, iha, hra, and ompT might increase the adaptability, competitiveness, and the ability to efficiently colonize the human body than being directly involved in the pathogenesis of infection (Dobrindt, 2005). PFGE analysis has shown that E. coli ST131 is not a single entity and can be subdivided into different pulsotypes. Studies have shown that ST131 with similar pulsotypes (i.e., >80% relatedness) can be present in different regions or countries (Gibreel et al., 2012; Nicolas-Chanoine et al., 2008; Novais et al., 2012). A study that included ST131 isolates from Canada, the United States, Brazil, the Netherlands, France, the United Arab Emirates, India, South Africa, and New Zealand identified 15 distinct pulsotypes among ST131; 43% of the isolates belonged to four pulsotypes that was present in seven of the nine countries (Peirano et al., 2014). However, the same studies have also shown that ST131 with different pulsotypes (<80% relatedness) can be present in the same location (Gibreel et al., 2012; NicolasChanoine et al., 2008; Peirano et al., 2014). Johnson and colleagues studied 579 ST131 from various countries and diverse sources (humans, animals, and the environment) that spanned from 1967 to 2009 (Johnson, NicolasChanoine, et al., 2012). They concluded that ST131 is highly diverse at

The Quintessential Example of an International Multiresistant High-Risk Clone

127

the pulsotype level but a small number of pulsotypes predominate internationally and these high-frequency pulsotypes had emerged within the last decade (Johnson, Nicolas-Chanoine, et al., 2012). A study from Calgary, Canada, over an 11-year period (2000–2010) had shown that a distinct pulsotype of ST131 (named A5 in that study) was responsible for the significant increase of ESBL-producing E. coli causing BSIs since 2007 (Peirano, van der Bij, Gregson, & Pitout, 2012). Although ST131 first came to attention because of its association with ESBL-producing E. coli strains, in particular, those expressing CTX-M15, most ST131 isolates are ESBL-negative, but resistant to the fluoroquinolones with associated resistance to the aminoglycosides and/or trimethoprim-sulfamethoxazole (Nicolas-Chanoine et al., 2014). Global surveillance studies show that ST131 is actually a fluoroquinoloneresistant clone but is also strongly associated with CTX-M-15 (Banerjee & Johnson, 2014).

6.2 Plasmids Associated with E. coli ST131 Plasmids are extra chromosomal elements of circular DNA present in bacteria, which replicate independently of the host genome. Horizontal transfer of antibiotic resistance plasmids through conjugation is an important mechanism for the spread of antimicrobial drug resistance genes. Epidemic resistance plasmids that belong to incompatibility [Inc] groups with F replicons (named IncF) have the ability to acquire resistance genes and then rapidly disseminate among Enterobacteriaceae (Carattoli, 2009). Three IncF plasmids (i.e., pEK499, pEK516, and pEK204) were obtained in the United Kingdom and were the first plasmids from ST131 to be completely sequenced (Woodford et al., 2009). Plasmid pEK499 is a fusion of two replicons of types FII and FIA. It harbored 185 predicted genes, including 10 conferring resistance to 8 different classes of antibiotics. Most of the antibiotic resistance genes, other than blaTEM-1, were clustered in a 25-kb region. This region included blaCTX-M-15 and blaOXA-1, together with genes responsible for the plasmid-mediated quinolone resistance determinant aac(60 )-Ib-cr that causes resistance to the aminoglycosides amikacin and tobramycin as well as ciprofloxacin and norfloxacin. Other resistance determinants such mph(A), catB4, and tetA were also sequenced. These genes are responsible for macrolides, chloramphenicol, and tetracycline resistance, respectively. A 1.8-kb class I integron was also present within this multiresistance region and carried dfrA7, aadA5, and sulI conferring resistance to trimethoprim, streptomycin, and sulfonamide

128

Amy J. Mathers et al.

respectively. pEK499 encode for four systems for postsegregation killing that is responsible for stable plasmid inheritance. These factors include hok-mok postsegregation killing protein and modulator, the pemI-pemK toxin-antitoxin system, the vagC-vagD virulence-associated genes, and the ccdA-ccdB toxin-antitoxin system. These systems would be responsible for the persistence of pEK499 among ST131 even in the absence of antibiotic selection pressure. Plasmid pEK516 belonged to IncFII and harbors 103 predicted genes, seven of which are clustered in a 22-kb region that consist of the following antimicrobial resistance determinants: blaCTX-M-15, blaOXA-1 blaTEM-1, aac(60 )-Ib-cr, aac (3)-II (responsible for resistance to gentamicin), catB4, and tetA. The pEK516 and pEK499 plasmids display 75% DNA sequence homology, despite pEK516 being 45% smaller than pEK499. The pEK516 plasmid carries the two addiction systems, pemI-pemK and hok-mok, and, unlike pEK499, it also carries the type I partitioning locus parM and the stbB gene, responsible for ensuring stable plasmid inheritance. Plasmid pEK204 from a Belfast belongs to a different incompatibility group IncI1, harbors 112 predicted genes, and because it is a broadspectrum plasmid, it can be easily transferred between isolates via in vitro conjugation. pEK204 carries only two resistance genes, blaCTX-M-3 andblaTEM-1. An ISEcp1 element was identified 128 bp upstream from the blaCTX-M-3 gene. None of the known systems for ensuring stable plasmid inheritance and postsegregation killing has been identified in pEK204. This followed by several molecular epidemiology studies investigating ST131 from different parts of the world and showed that IncF plasmids with FIA-FII replicons are most often associated with blaCTX-M-15 (Nicolas-Chanoine et al., 2014). This suggests that IncF plasmids using postsegregation killing systems have played an essential role in the dissemination of the blaCTX-M-15 within E. coli ST131. Escherichia coli ST131 can also contain IncF plasmids encoding b-lactamases other than CTX-M-15, such as CTX-M-14, SHV-2, and SHV-12 while CTX-M-15-containing plasmids can belong to IncI1, IncN, and IncA/C incompatibility groups as well as be on pir-type plasmids (Nicolas-Chanoine et al., 2014). To summarize: The blaCTX-M-15 gene has mainly been found on certain IncF plasmids (especially those with FIA-FII replicons) in ST131 (Doumith, Dhanji, Ellington, Hawkey, & Woodford, 2012), whereas Inc plasmids with different replicons have been identified in non-ST131 ExPEC (Shin, Choi, & Ko, 2012). Some IncF plasmids encode for multiple virulence

The Quintessential Example of an International Multiresistant High-Risk Clone

129

determinants that confer significant selective advantages for the ST131 host (Zong, 2013) and contribute to bacterial fitness through their virulence and antimicrobial resistance determinants (Villa, Garcia-Fernandez, Fortini, & Carattoli, 2010).

6.3 Recent Developments Pertaining to ST131 The prevalence of ST131 among human clinical E. coli isolates varies by geographic region and host population. Recent surveillance studies have shown that the overall prevalence ranges from 12.5% to nearly 30% of all E. coli clinical isolates (Banerjee & Johnson, 2014). ST131 remains being overpresented among antimicrobial-resistant ExPEC; recent global surveillance has shown that ST131 consistently accounts for approximately 70– 80% of fluoroquinolone-resistant isolates, and for 50–60% of ESBL-producing isolates, but for only 0–7% of fluoroquinolonesusceptible isolates (Banerjee & Johnson, 2014). 6.3.1 Epidemiology and Clinical Issues Like other ExPEC isolates, ST131 causes a variety of extraintestinal infections, including bacteremia, pneumonia, and urinary tract, intraabdominal, and wound infections. ST131 is strongly associated with community-onset infections in patients with regular contact with the health care settings. This was illustrated with infections due to ESBL-producing isolates (Peirano et al., 2012) as well as a population-based cohort study from the United States (Banerjee, Johnston, Lohse, Porter, et al., 2013). Interestingly, E. coli ST131 has not been responsible for large nosomial outbreaks such as intensive care units. Infections with ST131 are most common among the elderly and this ST has a high prevalence among residents in nursing homes and long-term care facilities (Banerjee, Johnston, Lohse, Porter, et al., 2013). ST131 has also been detected in nonhuman sources, such as companion animals, other animals, food sources, and the environment (Nicolas-Chanoine et al., 2014). However, the prevalence of ST131 colonization and infection is substantially greater among humans than among nonhuman hosts (Platell, Johnson, Cobbold, & Trott, 2011). It seems that the ST131 pandemic is primarily a human-based phenomenon and that ST131 has adapted to human hosts. There is a clear association between previous antibiotic consumption and colonization followed by infection due to ST131. Antimicrobial agents that have most often been implicated to select for ST131 infections include the fluoroquinolones and cephalosporins (Banerjee, Johnston, Lohse, Porter,

130

Amy J. Mathers et al.

et al., 2013). The high prevalence of ST131 in environments with extensive antimicrobial use, such as health care settings, nursing homes, and long-term care centers indirectly supports the idea that antimicrobial use facilitates the selection ST131. 6.3.2 Population Biology The most prevalent lineage within ST131 is named H30 because it contains the H30 variant of the type 1 fimbrial adhesin gene fimH (Johnson et al., 2013). The H30 lineage was identified through subtyping of over 1000 historical and recent E. coli isolates (both ST131 and non-ST131) using a combination of typing strategies, including sequencing of fimH, gyrA, and parC, MLST, and PFGE (Johnson et al., 2013). Investigators observed that the H30 ST131 lineage comprised approximately half of all recent fluoroquinolone-resistant E. coli isolates from different geographical regions and sources. This lineage was rare among fluoroquinolone-susceptible ST131 isolates (<1%). The H30 lineage first appeared in 2000 and expanded rapidly after that. The close genetic similarity of most H30 isolates suggested that they originate from a single fimH30-carrying ancestor. This indicated that the dramatic emergence of fluroquinolone-resistant ST131 isolates has been driven by clonal expansion and dissemination of the H30 lineage rather than by independent acquisition of fluoroquinolone resistance genes among different isolates. Further support for this conclusion was provided by the finding of a tight linkage between the H30 ST131 lineage and a single fluoroquinolone resistance-conferring gyrA and -parC allele combination, despite evidence for widespread horizontal transfer of gyrA and parC alleles among other lineages (Johnson et al., 2013). A polymerase chain reaction (PCR)-based assay that detects fimH30-specific single-nucleotide polymorphisms (SNPs) is available to rapidly and cost effectively detect the H30 lineage (Colpan et al., 2013). An important sublineage within H30, called H30-Rx because of its more extensive antimicrobial resistance profile, was identified by Price et al. using whole-genome sequencing and phylogentic analysis (Price et al., 2013). Those investigators analyzed 524 ST131 isolates collected between 1967 and 2011 using PFGE and found that fluoroquinolone-resistant, fluoroquinolone-susceptible, CTX-M-positive, CTX-M-negative, H30 lineage, non-H30 lineage isolates showed different and intermixing types of pulsotypes. This suggested that fluoroquinolone-resistant and CTX-M genes were repeatedly acquired in a horizontal fashion. However, when 105 of

The Quintessential Example of an International Multiresistant High-Risk Clone

131

these isolates underwent whole-genome sequencing and SNP analysis to reconstruct the phylogeny of ST131, both fluoroquinolone resistance and blaCTX-M-15 were shown to be almost entirely confined to the H30 lineage. Moreover, within H30, those H30 isolates with blaCTX-M-15 formed a discrete sublineage, named H30-Rx, that was separated from ESBL-negative fluoroquinolone-resistant H30 isolates by three core genome SNPs (Price et al., 2013). This indicates that the H30 ST131 lineage comprises a series of nested sublineages, all derived from a single common fluoroquinolonesusceptible H30 ancestor (Banerjee & Johnson, 2014). Within H30, the fluoroquinolone-resistant sublineage, named H30-R, encompasses nearly all fluoroquinolone-resistant ST131 isolates, whereas within H30-R, the H30-Rx sublineage consists of the vast majority of ST131 isolates with blaCTX-M-15 (Price et al., 2013). This clonal structure results in a continuum of antimicrobial resistance among the H30-associated sublineages, from the most susceptible, H30 (fluoroquinolone susceptible, CTX-M-negative), to the more resistant H30-R (fluoroquinolone resistant, CTX-M-negative), to the most extensively resistant, H30-Rx (fluoroquinolone resistant, CTX-M-positive). Whole-genome sequencing has indicated that the clonal expansion of the H30 lineage is the most dominant and important vehicle for the rising prevalence of fluoroquinolone resistance and blaCTX-M-15 among ST131 and in E. coli overall. These results were later confirmed by Petty and colleagues (Petty et al., 2014). The prevalence and resistance phenotypes of the H30, H30-R, and H30-Rx ST131 sublineages were first described in populations within the United States. Among E. coli clinical isolates from U.S. veterans from 2011, ST131 accounted for 78% and 64%, respectively, of fluoroquinolone-resistant and ESBL-producing E. coli but only 7% of fluoroquinolone-susceptible isolates. Among these ST131 isolates, the H30 ST131 sublineages accounted for 95% and 98% of fluoroquinoloneresistant and ESBL-producing isolates, respectively but only 12.5% of fluoroquinolone-susceptible isolates (Colpan et al., 2013). Similarly, in a case–control study conducted in the Chicago region, approximately half of ESBL-producing E. coli isolates were ST131, and of those ST131 isolates, 98% were H30 and 92% were H30-Rx (Banerjee, Robicsek, et al., 2013). In a population-based study of consecutively collected E. coli isolates in Minnesota, the prevalence of ST131 H30 sublineages varied with patient age and type of infection. ST131 that did not belong to the H30 lineage were

132

Amy J. Mathers et al.

more common among young patients, whereas H30 lineage was mostly present among patients older than 50 years (Banerjee, Johnston, Lohse, Chattopadhyay, et al., 2013). In a multicenter study that analyzed >1600 ExPEC isolates, CH clonotype 40-30 (corresponding to the H30 lineage of ST131) was the most prevalent clonotype overall and was statistically associated with recurrent or persistent UTIs and sepsis (Tchesnokova et al., 2013). The whole-genome sequencing study from Price and colleagues observed that sepsis was significantly associated with the H30-Rx sublineage (Price et al., 2013). A population-based surveillance study from Calgary, Canada, over an 11-year period (2000–2010) showed that the influx of the H30-Rx sublineage toward the latter part of the study period was responsible for the increase in ST131 and fluoroquinolone-resistant E. coli responsible for BSIs in that region (Peirano & Pitout, 2014). That study also identified the association of H30-Rx sublineage with primary sepsis, upper UTIs as a complication of prostate biopsies, and the presence of aac(6’)-lb-cr. 6.3.3 O16:H5 H41 Lineage Some ST131 isolates are positive for serotype O16:H5 that are well separated from the more prominent O25b:H4 ST131 clade. The O16 and O25b subsets within ST131 are identified as representing distinct STs according to the Pasteur Institute (but not the Achtman) MLST scheme (Banerjee & Johnson, 2014). The O16 ST131 isolates uniformly contain the fimH41 allele, whereas the majority of O25b:H4 ST131 isolates have the fimH30 allele, some contain the fimH22 and fimH35 alleles with the remainder have one of several rarer fimH alleles (Peirano et al., 2014). O16 ST131 isolates also have distinct combinations of gyrA and parC alleles compared with other ST131 isolates (Johnson et al., 2014). The O16 ST131 H41 lineage is not detected by a commonly used PCR screening assay for ST131 that targets the O25 rfb variant and pabB. A recent rapid PCR screening test was published combining the O16 rfb variant with the ST131-specific alleles of mdh and gyrB (Johnson et al., 2014). The O16 H41 lineage accounted for 1–5% of the E. coli isolates and had higher rates of resistance to trimethoprim-sulfamethoxazole and gentamicin than the H30 ST131 (Johnson et al., 2014) Fluoroquinolone resistance and the presence of ESBLs was not associated with the O16 H41 lineage. Among a global collection of ESBL-producing ST131, the O16 H41 lineage was associated with blaCTX-M-14 and susceptibility to the fluoroquinolones (Peirano et al., 2014).

The Quintessential Example of an International Multiresistant High-Risk Clone

133

6.3.4 Virulence Blanco and colleagues recently introduced a classification system for ST131 into four groups or virotypes (i.e., A, B, C, and D) that is based on the distribution of four distinctive virulence factors namely afa FM955459 (Afa/Dr adhesion), iroN (catecholate siderophore receptor), ibeA (invasion of brain endothelium), and sat (secreted autotransporter toxin) (Blanco et al., 2013). They reported that virotypes A and B were associated with multidrug resistance, the presence of CTX-M-15 and the plasmid-mediated quinolone determinant aac(6’)-lb-cr. Virotype C had a global distribution (i.e., was present in Spain, France, Portugal, Switzerland, the United States, Canada, Korea, and Lebanon) and was statistically associated with higher frequency of infection (Blanco et al., 2013). A study by Banerjee and colleagues determined the prevalence of ST131 and its sublineages among 267 E. coli from the Chicago region (Banerjee, Robicsek, et al., 2013). The authors were able to show that the H30-R and H30-Rx sublineages were more antimicrobial resistant and had distinctive virulence profiles when compared to non-H30 ST131 isolates. Interestingly, the H30-Rx sublineage had the highest virulence scores implying greater virulence potential and possibly explaining its high prevalence (Banerjee, Robicsek, et al., 2013). 6.3.5 ST131 and Carbapenemases The development of resistance to the carbapenems among E. coli is of special concern to the medical community at large, because these agents are often the last line of effective therapy available for the treatment of serious infections due to these bacteria (Pitout, 2012b). Most important among E. coli is the recognition of isolates that harbor carbapenemases responsible for resistance to the carbapenems. These enzymes include class A (i.e., KPC types), class B or the MBLs (i.e., VIM, IPM, and NDM types), and class D OXAs (i.e., OXA enzymes) (Nordmann, Naas, et al., 2011). The NDM and OXA48 are the most common carbapenemases among nosocomial and community isolates of E. coli, while the VIM, IPM, and KPC b-lactamases are not yet commonly encountered in this specie (Nordmann & Poirel, 2014). Infections with carbapenemase-producing E. coli have most often been associated with visiting and being hospitalized in endemic areas such as the Indian subcontinent for NDMs and North Africa or Turkey for OXA-48 (van der Bij & Pitout, 2012). Due to the unprecedented global success of ST131, the presence of carbapenemases among ST131 has been carefully monitored by molecular

134

Amy J. Mathers et al.

epidemiologists and the presence of blaNDM was first identified in ST131 during 2010 from patients in Chicago and Paris, respectively (Bonnin, Poirel, Carattoli, & Nordmann, 2012; Peirano, Schreckenberger, & Pitout, 2011). Both patients had previously visited the Indian subcontinent. This was followed by case reports of ST131 with blaVIM from Italy (Mantengoli et al., 2011), ST131 with blaKPC from Ireland (Morris et al., 2011), France (Naas, Cuzon, Gaillot, Courcol, & Nordmann, 2011), the United States (Kim et al., 2012), Italy (Accogli et al., 2014), Taiwan (Ma et al., 2013), China (Cai, Zhang, Hu, Zhou, & Chen, 2014), ST131 with blaOXA-48 from the United Kingdom (Dimou, Dhanji, Pike, Livermore, & Woodford, 2012), Ireland (Morris et al., 2012), Algeria (Agabou et al., 2014), Spain (Fernandez, Montero, Fleites, & Rodicio, 2014), and with blaIMP from Taiwan (Yan, Tsai, & Wu, 2012). The largest collection of ST131 with carbapenemases was recently reported from Pittsburgh, USA (O’Hara et al., 2014). The authors characterized 20 isolates of KPC-producing E. coli: 60% belonged to the ST131 H30 lineage while the blaKPC was associated with IncFIIk replicons. A recent study from the SMART and AstraZeneca global surveillance programs has shown that 35% of 116 carbapenemase-producing E. coli belonged to ST131 that was associated with fluoroquinolone resistance, the presence of blaKPC, H30 lineage and virotype C (Gisele et al., 2014). ST131 was present in Argentina, China, Colombia, Ecuador, India, Italy, Jordan, Morocco, Panama, the Philippines, Puerto Rico, Thailand, Turkey, the United Arab Emirates, the United States, and Vietnam. Escherichia coli ST131 with carbapenemases poses a significant new public health threat due to its global distribution and association with the very dominant H30 lineage. This study is of special concern because it documents resistance to “last resort” antibiotics (i.e., carbapenems), in most regions of the world to a common pathogen (i.e., Escherichia coli) in a very successful ST (i.e., ST131).

6.4 Does ST131 Qualify as an International Multiresistant High-Risk Clone? The pandemic emergence of E. coli ST131, and specifically its H30-R and H30-Rx sublineages, occurred over less than 10 years. It is a remarkable success story rivaling the global pandemics caused by clones within methicillin resistant Staphylococcus aureus and Streptococcus pneumoniae.

The Quintessential Example of an International Multiresistant High-Risk Clone

135

6.4.1 Global Distribution Escherichia coli ST131 was initially described among isolates with blaCTX-M-15 from the following countries: Canada, France, Switzerland, Portugal, Spain, Kuwait, Lebanon, India, and Korea (Coque et al., 2008; Nicolas-Chanoine et al., 2008). Subsequently, ST131 had been identified among ESBL, nonESBL, and fluoroquinolone-resistant and fluoroquinolone-susceptible E. coli from all corners of the world (Nicolas-Chanoine et al., 2014). If investigators decide to determine the presence of ST131 among E. coli isolates collected from human sources, they will most likely detect ST131 among their collection. Escherichia coli ST131 has a true global distribution and is present on all continents except Antarctica. 6.4.2 Association with Antimicrobial Resistance Mechanisms Escherichia coli ST131 is known to be associated with fluoroquinolone resistance and ESBL production most often due to CTX-M-15 (Banerjee, Robicsek, et al., 2013; Colpan et al., 2013; Peirano et al., 2012). Population genetics has indicated that the fluoroquinolone resistance in the ST131 H30 lineage is mostly due to gyrA1AB and parC1aAB mutations in topoisomerase II and IV, respectively (Johnson et al., 2013). The gyrA1AB and parC1aAB mutations are present in 71% of fluoroquinolone-resistant and 62% of ESBL E. coli from various Veterans Administration hospitals in the United States (Colpan et al., 2013). ST131 is associated with the presence of the plasmid-mediated quinolone resistance determinant aac(6’)-lb-cr (Peirano & Pitout, 2010). This resistance determinant caused decreased susceptibility to the fluroquinolones, ciprofloxacin and norfloxacin as well as has resistance to the aminoglycosides, tobramycin and amikacin. Various expanded-spectrum b-lactamases (e.g., CTX-Ms, CMYs, SHVs, TEMs) have been detected in ST131 (Nicolas-Chanoine et al., 2014); CTX-M-15 in combination with TEM-1 and OXA-30 being by far the commonest. Due to the unprecedented global success of ST131, the presence of carbapenemases had been carefully monitored by molecular epidemiologists but has mostly been limited to case reports from several countries (Nicolas-Chanoine et al., 2014). Other resistance determinants that have been characterized in ST131 include mph(A) (resistance to the macrolides), catB4 (resistance to chloramphenicol), tetA (resistance to tetracycline), dfrA7 (resistance to trimethoprim), aadA5 (resistance to streptomycin), and sulI (resistance to

136

Amy J. Mathers et al.

sulfonamides). Therefore, isolates that belong to ST131 are most often nonsusceptible to the cephalosporins, monobactams, fluroquinolones, trimethoprim-sulfamethoxazole, and the aminoglycosides (NicolasChanoine et al., 2014). 6.4.3 Ability to Colonize Human Hosts Because intestinal colonization with ExPEC is believed to be a prerequisite for extraintestinal infection, it is possible that the enhanced ability to colonize the intestinal tract is partly responsible for the widespread dissemination of ST131. In a mouse model of intestinal colonization, an ST131 isolate surpassed other commensal E. coli isolates mixed in a 1:1 ratio and administered enterally into streptomycin-pretreated mice. Although that study was limited by its evaluation of only a single ST131 isolate, it provided some evidence that some ST131 isolates have the ability to efficiently colonize the intestine, bladder, and kidney of mice (Vimont et al., 2012). It is unclear whether the prevalence or duration of intestinal colonization in humans is different for ST131 compared to other E. coli isolates including the more successful ST131 sublineages (i.e., H30-R and H30-Rx) compared to other ST131 sublineages (e.g., H41, H35, and H22). In studies of the prevalence of ST131 carriage among individuals colonized specifically with ESBL-producing E. coli, ST131 colonization rates have varied greatly by patient population, from nearly 10–44% of ESBL producers (Nicolas-Chanoine et al., 2014). Some studies have evaluated the prevalence of ST131 among fecal E. coli and found that the prevalence of ST131 varied from of 0–25% (Banerjee & Johnson, 2014). As expected, the prevalence of E. coli ST131 among ESBL-producing or fluoroquinolone-resistant E. coli stool isolates are higher and vary considerably with the population studied, geographical regions, host characteristics, and the time frame when the study was completed. 6.4.4 Effective Transmission among Hosts The transmission of ST131 had previously been documented between different household family members (father to daughter; daughter to mother; sister to sister) and companion animals (dogs and cats in particular) (Banerjee & Johnson, 2014; Nicolas-Chanoine et al., 2014). A study from Switzerland has shown that ST131 were more likely to be transmitted between members of the same household than within the hospital setting (Hilty et al., 2012). Recent evidence suggests the spread of a

The Quintessential Example of an International Multiresistant High-Risk Clone

137

CTX-M-15-producing ST131 isolate within a French day care center, where seven children had intestinal colonization with the same strain (Blanc et al., 2014). It seems that the effective transmission of E. coli ST131 isolates, between members of the same household, play an essential role in the communitywide dissemination of this ST. However, whether ST131 is more efficiently transmitted than other E. coli isolates is unknown and deserves further study. 6.4.5 Enhanced Pathogenicity and Fitness It is possible that the globally increasing prevalence of ST131 among clinical isolates is also occurring because ST131 strains are more virulent than other E. coli isolates, giving it a fitness advantage. Studies that determined the maximal growth rate and the ability of ST131 to produce bioflim had suggested that this ST has a high metabolic potential, most likely enhancing its fitness and ability to establish intestinal colonization (Kudinha et al., 2013). In vivo studies that investigated the virulence potential of ST131 in animal models indicated that this ST kills mice (Johnson, Porter, Zhanel, Kuskowski, & Denamur, 2012), but are less virulent when compared to non-ST131 E. coli in the Caenorhabditis elegans and zebra fish embryo models (Lavigne et al., 2012). In several molecular epidemiological studies, ST131 always has a greater number of virulence factor genes (i.e., higher aggregate virulence scores) than other comparably antimicrobial-resistant E. coli isolates (Johnson et al., 2010; Van der Bij, Peirano, Pitondo-Silva, & Pitout, 2012). Moreover, within ST131, the H30, non-H30, and H30-Rx sublineages have characteristic virulence profiles that are distinct from those of non-H30 ST131 E. coli, conceivably conferring enhanced virulence (Banerjee, Robicsek, et al., 2013). 6.4.6 Causing Severe and/or Recurrent Infections It is unclear if ST131 cause more severe infections than other ExPEC E. coli but data suggest that ST131 is more likely to cause upper UTIs than lower UTIs (Banerjee & Johnson, 2014). In a series of studies from Australia, ST131 accounted for 30% of pyelonephritis isolates among E. coli isolates from women, versus only 13% of cystitis isolates and 4% of fecal isolates, and similar prevalence trends were seen among men and children (Kudinha et al., 2013). A study from the United Kingdom showed similar results where the prevalence of ST131 was 21% among bacteremia isolates as compared to only 7% among urinary isolates (Alhashash, Weston, Diggle, & McNally, 2013).

138

Amy J. Mathers et al.

Whether ST131 is associated with worse clinical outcomes than other E. coli strains is unclear, since some studies suggest that ST131 is more likely to cause persistent or recurrent UTIs (Banerjee, Johnston, Lohse, Porter, et al., 2013) while others have found no difference in outcomes of infections with ST131 versus other E. coli isolates (Chung et al., 2012). The H30-Rx lineage of ST131 has exhibited epidemiological associations with sepsis (Price et al., 2013). When investigators adjusted for host factors, no differences in cure or mortality were found in patients with infections due to ST131 and those with infections due to other E. coli strains (Tchesnokova et al., 2013). To summarize: Escherichia coli ST131 clearly has all of the essential characteristics that defines a high-risk clone. In fact this ST might be the quintessential example of an international multiresistant high-risk clone.

7. RAPID METHODS FOR THE DETECTION OF E. COLI ST131 Due to the unprecedented success of E. coli ST131, several investigators have designed rapid methods for the detection of this ST to aid molecular epidemiology and surveillance studies. Such technique facilitated enhanced surveillance for ST131. These include PCR, PFGE, DiversiLab repetitive PCR typing and more recently matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS). Next-generation sequencing (NGS) is an emerging technology with considerable promise for clinical microbiology (Pallen, Loman, & Penn, 2010). This technique uses PCR to amplify individual DNA molecules that are immobilized on a solid surface, enabling molecules to be sequenced in parallel, leading to decreased costs and rapid turnaround times (Koser et al., 2012). NGS yields all of the available DNA information in a single rapid step and provide a high-resolution, accurate, and reproducible means to determine the core genome of organisms that can be used for typing. Several ST131 isolates have undergone NGS (Price et al., 2013) and it is likely that this technique combined with user-friendly rapid bioinformatics will become the gold standard for the identification of ST131 in the near future.

7.1 Multilocus Sequence Typing MLST is a sequence-based typing method that examines the nucleotide sequences of several (i.e., six to ten) housekeeping genes (Sullivan et al., 2005).

The Quintessential Example of an International Multiresistant High-Risk Clone

139

This makes it suitable for continuous surveillance and is excellent for comparing data generated independently from different laboratories via open-sourced Web-based databases. MLST is ideal for tracking and investigating antimicrobial-resistant bacteria and their clones or STs to show common ancestry lineages among bacteria (Sullivan et al., 2005). Unfortunately, MLST is expensive; time consuming but it remains the gold standard for the detection of ST131. There are two MLST schemes that are often used to identify E. coli ST131. The Achtman scheme (http://mlst.warwick.ac.uk/ mlst/dbs/Ecoli) uses the gene sequences of seven housekeeping genes (i.e., adk, fumC, gyrB, icd, mdh, purA, and recA). The Pasteur institute (http://www.pasteur.fr/recherche/genopole/PF8/mlst/EColi.html) uses eight housekeeping genes (i.e., dinB, icdA, pabB, polB, putB, trpA, trpB, and uidA). The scheme from the Pasteur institute tends to distinguish different STs among ST131. Most investigators use the Achtman MLST scheme to routinely identify ST131.

7.2 Pulsed Field Gel Electrophoresis PFGE is considered as the gold standard for typing of medically important bacteria during outbreak investigations (Tenover et al., 1995). This method is based on the specific digestion (or cutting) of bacterial DNA into fragments of varying sizes, followed by the separation of these DNA fragments into fingerprints by gel electrophoresis. PFGE is excellent for identifying different clones responsible for recent or ongoing outbreaks. Unfortunately, PFGE is labor intensive and time consuming (it takes days to get results) and only delivers the best results when performed by a technologist with extensive technical experience in this method. Moreover, the comparison of data generated in different laboratories remains a challenge when using PFGE. PFGE was extensively used during the late 2000s to recognize isolates that belonged to ST131 (Pitout, Gregson, Campbell, & Laupland, 2009). However, PFGE is not a very good method to identify ST131, because this ST consists of different pulsotypes that display high levels of interlineage genetic variation. ST131 often displays less than 80% similarity and often does not satisfy the criteria for relatedness outlined by Tenover et al. (Johnson, Nicolas-Chanoine, et al., 2012).

7.3 Repetitive Sequence-Based PCR Typing Two separate studies from Canada and the United Kingdom evaluated the ability of the DiversiLab fingerprinting kit, a type of repetitive element

140

Amy J. Mathers et al.

PCR, to identify E. coli ST131 (Lau et al., 2010; Pitout, Campbell, et al., 2009a). The DiversiLab system allowed the discrimination of ST131 isolates from other E. coli STs. With an analysis time of <4 h between receipt of a cultured organism and provision of a typing result, the system offers results on a real-time basis. The DiversiLab system is unfortunately rather expensive and this prohibited the widespread utilization of this technique for the recognition of ST131.

7.4 Polymerase Chain Reaction PCR-based techniques offer rapid and inexpensive methodologies (when compared to MLST that is) to identify E. coli ST131 and are the most popular approaches used to screen for ST131 among a large number of E. coli isolates. The PCR screening methods are based on the detection of SNPs of O serogroups and housekeeping genes specific for ST131 (NicolasChanoine et al., 2014). Several PCR screening methods are widely available to determine whether an E. coli isolate belongs to the ST131 lineage. These techniques include a specific-allele PCR of the 50 portion of the rfb locus that identify the allele specific for O25b (Clermont, Johnson, Menard, & Denamur, 2007). Other methods make use of the so-called “ST131-specific” alleles of genes used in the MLST methods designed by Achtman and the Pasteur Institute. For example, Clermont and colleagues described a specific-allele ST131 PCR based on SNPs of the pabB gene from the Pasteur Institute MLST scheme (Clermont et al., 2009). Johnson and colleagues designed a sequencing method based on ST131-associated SNPs of the mdh and gyrB genes included in Achtman MLST scheme (Johnson et al., 2009). A novel and rapid form of sequence typing based on sequencing of the fumC and fimH loci (called CH or clono typing) identified the H30 ST131 lineage as clonotype CH 40-30 (Weissman et al., 2012). Blanco and colleagues designed a triplex PCR that was based on the detection of O25b (O25b rfb allele), with the 30 end of the blaCTX-M-15 and the afa/draBC virulence factor (Blanco et al., 2009). A recent PCR screening test was published combining the O16 rfb variant with the ST131-specific alleles of mdh and gyrB that can distinguish between the two serogroups of ST131, namely O25b (fimH30) and O16 (fimH41) (Johnson et al., 2014). PCR methods are also available for the identification of the fimH30 lineage and the H30-Rx sublineage (Banerjee, Robicsek, et al., 2013; Johnson

The Quintessential Example of an International Multiresistant High-Risk Clone

141

et al., 2014, 2013). The identification of the H30-Rx sublineage requires an additional sequencing step to be performed. Just a caution: PCR-based screening of E. coli ST131 may infrequently identify isolates that belong to the 131Clonal Complex as ST131 and very rarely can misidentify non-ST131 E. coli as ST131.

7.5 Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry MALDI-TOF MS is a high-throughput methodology based on the identification of the mass-to-charge ratio of peptides and small proteins, most of which are ribosomal (Clark, Kaleta, Arora, & Wolk, 2013). It has been increasingly adopted by clinical microbiology laboratories all over the world for quick and reliable microbial identification at the species level based on the comparison of mass spectral fingerprints (obtained from single colonies or crude extracts) with previously established reference databases. MALDI-TOF MS is a promising tool for the identification of bacteria because it is a rapid, inexpensive, and accurate system. The use of MALDI-TOF MS for bacterial typing is based on the principle that sequence variations within a given taxa or subspecies level will be translated into corresponding protein or peptide sequences, and supported by a similar clustering obtained from either mass spectral data or genomic sequences, highlighting the usefulness of peak patterns as taxonomic markers (Lartigue, 2013). The simplicity and low cost advantages associated with MALDI-TOF MS and its potential application on a large-scale basis might be useful to enable timely and appropriate diagnosis, infection control, and individual patient-management decisions. Two studies have been published that evaluated MALDI-TOF MS for the identification of E. coli ST131. The study from Japan used FlexAnalysis to distinguish ST131 (O25b and O16 serotypes) from other STs (Matsumura et al., 2014). With FlexAnalysis, a peak of 9720 Da detected the ST131-whole group with a sensitivity of 97.0% and a specificity of 91.5% at a cutoff value of 8.0. The study from Portugal showed that MALDI-TOF MS fingerprinting analysis was able to discriminate between ST131, ST69, ST405, ST39 and between phylogenetic group B2 ST131 from other phylogenetic group B2 that did not belong to ST131 (Novais et al., 2014). MALDI-TOF is a promising tool for the detection of E. coli ST131 that might be available for routine use in the near future.

142

Amy J. Mathers et al.

8. SUMMARY Escherichia coli ST131 is as an important human pathogen, has spread extensively throughout the world, and is responsible for the rapid increase in the prevalence of antimicrobial resistance among E. coli (Peirano & Pitout, 2010). ST131 is known to cause extraintestinal infections, being fluoroquinolone resistant, and is associated with ESBL production most often due to CTX-M-15 (Nicolas-Chanoine et al., 2014). Escherichia coli ST131 has received comparatively less attention than other antimicrobial-resistant pathogens. Retrospective molecular surveillance studies have shown that ST131 with blaCTX-M-15 was rare among E. coli during the early 2000s, but was present in different parts of the world. This was followed by an explosive increase during the mid-to-late 2000s (NicolasChanoine et al., 2014). The reasons for the sudden increase are not clear or well understood. Recent molecular epidemiologic studies utilizing advanced technologies such as whole-genome phylogenetic analysis have demonstrated that the H30 ST131 lineage emerged in 2000, followed by rapid expansion of its sublineages H30-R and H30-Rx. This dramatically changed the population structure of E. coli in general and created the most prevalent and extensive antimicrobial-resistant human-associated E. coli lineages in the world (Banerjee & Johnson, 2014). With its combination of multidrug resistance and ecological success, H30 ST131 counters the hypothesis that increased antimicrobial resistance entails a significant fitness cost. This is most likely the best example of an international multiresistant high-risk clone. The widespread use of antimicrobials has likely contributed to the emergence and spread of ST131. The strong association between H30 ST131 and fluroquinolone resistance suggests that use of fluoroquinolones has driven the expansion of the H30 ST131 lineage. Likewise, use of the oxyiminocephalosporins cephalosporins may have driven the expansion of H30-Rx sublineage, which is strongly associated with CTX-M-15. In vivo studies suggest that fluoroquinolone-resistant E. coli may undergo compensatory mutations and be as fit as fluoroquinolon-susceptible isolates (Riley, 2014). The use of fluoroquinolones will create selection pressure that gives these isolates the opportunity to become effective intestinal colonizer. To prescribe more effective empirical antimicrobial therapy, clinicians will require increased awareness about ST131 and its high prevalence and extensive antimicrobial resistance capabilities and which patients are at risk for infection with this ST. Clinical risk factors on its own may fail to identify

The Quintessential Example of an International Multiresistant High-Risk Clone

143

many patients with ST131. Therefore the medical community needs rapid and cost-effective diagnostic tests that have the ability to detect ST131 and its lineages. This approach may lead to more timely and appropriate antimicrobial therapy that can improve clinical outcomes. Additionally, vaccines that target H30-associated antigens, and other H30-specific interventions directed toward the intestinal tract (or, in women, vaginal colonization), may reduce the reservoir of asymptomatic individuals colonized with ST131, in turn reducing the number of infected patients. The medical community can ill afford to ignore E. coli ST131 because this ST and its sublinegaes is now a major threat to public health due to its worldwide distribution and association with multidrug resistance that has recently included the production of carbapenemases. We urgently need rapid cost-effective detection methods for E. coli ST131 (Matsumura et al., 2014; Novais et al., 2014), as well as well-designed epidemiological and molecular studies to understand the dynamics of transmission, risk factors, and reservoirs for ST131. This will provide insight into the emergence and spread of this multiresistant ST that will hopefully lead to information essential for preventing the spread of ST131.

REFERENCES Accogli, M., Giani, T., Monaco, M., Giufre, M., Garcia-Fernandez, A., Conte, V., et al. (2014). Emergence of Escherichia coli ST131 sub-clone H30 producing VIM-1 and KPC-3 carbapenemases. Italy Journal of Antimicrobial Chemotherapy, 69(8), 2293–2296. http://dx.doi.org/10.1093/jac/dku132. Agabou, A., Pantel, A., Ouchenane, Z., Lezzar, N., Khemissi, S., Satta, D., et al. (2014). First description of OXA-48-producing Escherichia coli and the pandemic clone ST131 from patients hospitalised at a military hospital in Algeria. European Journal of Clinical Microbiology and Infectious Diseases, 33(9), 1641–1646. http://dx.doi.org/10.1007/s10096-0142122-y. Alhashash, F., Weston, V., Diggle, M., & McNally, A. (2013). Multidrug-resistant Escherichia coli bacteremia. Emerging Infectious Diseases, 19(10), 1699–1701. http://dx.doi.org/ 10.3201/eid1910.130309. Alvarez, M., Tran, J. H., Chow, N., & Jacoby, G. A. (2004). Epidemiology of conjugative plasmid-mediated AmpC beta-lactamases in the United States. Antimicrobial Agents and Chemotherapy, 48(2), 533–537. America, I. D. S.o (2010). The 10  ’20 Initiative: pursuing a global commitment to develop 10 new antibacterial drugs by 2020. Clinical Infectious Diseases, 50(8), 1081–1083. http:// dx.doi.org/10.1086/652237. Arpin, C., Quentin, C., Grobost, F., Cambau, E., Robert, J., Dubois, V., et al. (2009). Nationwide survey of extended-spectrum {beta}-lactamase-producing Enterobacteriaceae in the French community setting. Journal of Antimicrobial and Chemotherapy, 63(6), 1205–1214. http://dx.doi.org/10.1093/jac/dkp108. dkp108 [pii]. Banerjee, R., & Johnson, J. R. (2014). A new clone sweeps clean: the enigmatic emergence of Escherichia coli sequence type 131. Antimicrobial Agents and Chemotherapy, 58(9), 4997–5004. http://dx.doi.org/10.1128/AAC.02824-14.

144

Amy J. Mathers et al.

Banerjee, R., Johnston, B., Lohse, C., Chattopadhyay, S., Tchesnokova, V., Sokurenko, E. V., et al. (2013). The clonal distribution and diversity of extraintestinal Escherichia coli isolates vary according to patient characteristics. Antimicrobial Agents and Chemotherapy, 57(12), 5912–5917. http://dx.doi.org/10.1128/AAC.01065-13. Banerjee, R., Johnston, B., Lohse, C., Porter, S. B., Clabots, C., & Johnson, J. R. (2013a). Escherichia coli sequence type 131 is a dominant, antimicrobial-resistant clonal group associated with healthcare and elderly hosts. Infection Control and Hospital Epidemiology, 34(4), 361–369. http://dx.doi.org/10.1086/669865. Banerjee, R., Robicsek, A., Kuskowski, M. A., Porter, S., Johnston, B. D., Sokurenko, E., et al. (2013b). Molecular epidemiology of Escherichia coli sequence type 131 and its H30 and H30-Rx subclones among extended-spectrum-beta-lactamase-positive and -negative E. coli clinical isolates from the Chicago Region, 2007 to 2010. Antimicrobial Agents and Chemotherapy, 57(12), 6385–6388. http://dx.doi.org/10.1128/AAC.01604-13. Baquero, F., Tedim, A. P., & Coque, T. M. (2013). Antibiotic resistance shaping multi-level population biology of bacteria. Frontiers in Microbiology, 4, 15. http://dx.doi.org/ 10.3389/fmicb.2013.00015. Blanc, V., Leflon-Guibout, V., Blanco, J., Haenni, M., Madec, J. Y., Rafignon, G., et al. (2014). Prevalence of day-care centre children (France) with faecal CTX-M-producing Escherichia coli comprising O25b:H4 and O16:H5 ST131 strains. Journal of Antimicrobial Chemotherapy, 69(5), 1231–1237. http://dx.doi.org/10.1093/jac/dkt519. Blanco, M., Alonso, M. P., Nicolas-Chanoine, M. H., Dahbi, G., Mora, A., Blanco, J. E., et al. (2009). Molecular epidemiology of Escherichia coli producing extended-spectrum {beta}-lactamases in Lugo (Spain): dissemination of clone O25b:H4-ST131 producing CTX-M-15. Journal of Antimicrobial Chemotherapy, 63(6), 1135–1141. http:// dx.doi.org/10.1093/jac/dkp122. Blanco, J., Mora, A., Mamani, R., Lopez, C., Blanco, M., Dahbi, G., &, Spanish Group for Nosocomial, I. (2013). Four main virotypes among extended-spectrum-beta-lactamaseproducing isolates of Escherichia coli O25b:H4-B2-ST131: bacterial, epidemiological, and clinical characteristics. Journal of Clinical Microbiology, 51(10), 3358–3367. http:// dx.doi.org/10.1128/JCM.01555-13. Bonnin, R. A., Poirel, L., Carattoli, A., & Nordmann, P. (2012). Characterization of an IncFII plasmid encoding NDM-1 from Escherichia coli ST131. PLoS One, 7(4), e34752. http://dx.doi.org/10.1371/journal.pone.0034752. Bryant, J., Chewapreecha, C., & Bentley, S. D. (2012). Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences. Future Microbiology, 7(11), 1283–1296. http://dx.doi.org/10.2217/fmb.12.108. Buchholz, U., Bernard, H., Werber, D., Bohmer, M. M., Remschmidt, C., Wilking, H., et al. (2011). German outbreak of Escherichia coli O104:H4 associated with sprouts. The New England Journal of Medicine, 365(19), 1763–1770. http://dx.doi.org/10.1056/ NEJMoa1106482. Bush, K., & Jacoby, G. A. (2010). Updated functional classification of beta-lactamases. Antimicrobial Agents and Chemotherapy, 54(3), 969–976. http://dx.doi.org/10.1128/ AAC.01009-09. Cagnacci, S., Gualco, L., Debbia, E., Schito, G. C., & Marchese, A. (2008). European emergence of ciprofloxacin-resistant Escherichia coli clonal groups O25:H4-ST 131 and O15: K52:H1 causing community-acquired uncomplicated cystitis. Journal of Clinical Microbiology, 46(8), 2605–2612. http://dx.doi.org/10.1128/JCM.00640-08. JCM.00640-08 [pii]. Cai, J. C., Zhang, R., Hu, Y. Y., Zhou, H. W., & Chen, G. X. (2014). Emergence of Escherichia coli sequence type 131 isolates producing KPC-2 carbapenemase in China. Antimicrobial Agents and Chemotherapy, 58(2), 1146–1152. http://dx.doi.org/10.1128/ AAC.00912-13.

The Quintessential Example of an International Multiresistant High-Risk Clone

145

Canton, R., & Coque, T. M. (2006). The CTX-M beta-lactamase pandemic. Current Opinion in Microbiology, 9(5), 466–475. http://dx.doi.org/10.1016/j.mib.2006.08.011. S1369-5274(06)00134-2 [pii]. Carattoli, A. (2009). Resistance plasmid families in Enterobacteriaceae. Antimicrobial Agents and Chemotherapy, 53(6), 2227–2238. http://dx.doi.org/10.1128/AAC.0170708. Carrer, A., Poirel, L., Yilmaz, M., Akan, O. A., Feriha, C., Cuzon, G., et al. (2010). Spread of OXA-48-encoding plasmid in Turkey and beyond. Antimicrob Agents Chemother, 54(3), 1369–1373. http://dx.doi.org/10.1128/AAC.01312-09. AAC.01312-09 [pii]. Castanheira, M., Deshpande, L. M., Mathai, D., Bell, J. M., Jones, R. N., & Mendes, R. E. (2011a). Early dissemination of NDM-1- and OXA-181-producing Enterobacteriaceae in Indian hospitals: report from the SENTRY Antimicrobial Surveillance Program, 2006–2007. Antimicrobial Agents and Chemotherapy, 55(3), 1274–1278. http:// dx.doi.org/10.1128/AAC.01497-10. Castanheira, M., Mendes, R. E., Woosley, L. N., & Jones, R. N. (2011b). Trends in carbapenemase-producing Escherichia coli and Klebsiella spp. from Europe and the Americas: report from the SENTRY antimicrobial surveillance programme (2007–09). Journal of Antimicrobial Chemotherapy, 66(6), 1409–1411. http://dx.doi.org/10.1093/ jac/dkr081. Chung, H. C., Lai, C. H., Lin, J. N., Huang, C. K., Liang, S. H., Chen, W. F., et al. (2012). Bacteremia caused by extended-spectrum-beta-lactamase-producing Escherichia coli sequence type ST131 and non-ST131 clones: comparison of demographic data, clinical features, and mortality. Antimicrobial Agents and Chemotherapy, 56(2), 618–622. http:// dx.doi.org/10.1128/AAC.05753-11. Clark, A. E., Kaleta, E. J., Arora, A., & Wolk, D. M. (2013). Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clinical Microbiology Reviews, 26(3), 547–603. http://dx.doi.org/ 10.1128/CMR.00072-12. Clermont, O., Dhanji, H., Upton, M., Gibreel, T., Fox, A., Boyd, D., et al. (2009). Rapid detection of the O25b-ST131 clone of Escherichia coli encompassing the CTX-M15-producing strains. Journal of Antimicrobial and Chemotherapy, 64(2), 274–277. http:// dx.doi.org/10.1093/jac/dkp194. Clermont, O., Johnson, J. R., Menard, M., & Denamur, E. (2007). Determination of Escherichia coli O types by allele-specific polymerase chain reaction: application to the O types involved in human septicemia. Diagnostic Microbiology and Infectious Disease, 57(2), 129–136. http://dx.doi.org/10.1016/j.diagmicrobio.2006.08.007. Colpan, A., Johnston, B., Porter, S., Clabots, C., Anway, R., Thao, L., et al. (2013). Escherichia coli sequence type 131 (ST131) subclone H30 as an emergent multidrug-resistant pathogen among US veterans. Clinical Infectious Diseases, 57(9), 1256–1265. http:// dx.doi.org/10.1093/cid/cit503. Coque, T. M., Novais, A., Carattoli, A., Poirel, L., Pitout, J., Peixe, L., et al. (2008). Dissemination of clonally related Escherichia coli strains expressing extended-spectrum beta-lactamase CTX-M-15. Emerging Infectious Diseases, 14(2), 195–200. http://dx.doi.org/ 10.3201/eid1402.070350. Cuzon, G., Naas, T., Bogaerts, P., Glupczynski, Y., Huang, T. D., & Nordmann, P. (2008). Plasmid-encoded carbapenem-hydrolyzing beta-lactamase OXA-48 in an imipenemsusceptible Klebsiella pneumoniae strain from Belgium. Antimicrobial Agents and Chemotherapy, 52(9), 3463–3464. http://dx.doi.org/10.1128/AAC.00543-08. AAC.00543-08 [pii]. D’Andrea, M. M., Arena, F., Pallecchi, L., & Rossolini, G. M. (2013). CTX-M-type betalactamases: a successful story of antibiotic resistance. International Journal of Medical Microbiology, 303(6–7), 305–317. http://dx.doi.org/10.1016/j.ijmm.2013.02.008.

146

Amy J. Mathers et al.

Deshpande, P., Rodrigues, C., Shetty, A., Kapadia, F., Hedge, A., & Soman, R. (2010). New Delhi Metallo-beta lactamase (NDM-1) in Enterobacteriaceae: treatment options with carbapenems compromised. Journal of the Association Physicians of India, 58, 147–149. Dijkshoorn, L., Ursing, B. M., & Ursing, J. B. (2000). Strain, clone and species: comments on three basic concepts of bacteriology. Journal of Medical Microbiology, 49(5), 397–401. Dimou, V., Dhanji, H., Pike, R., Livermore, D. M., & Woodford, N. (2012). Characterization of Enterobacteriaceae producing OXA-48-like carbapenemases in the UK. Journal of Antimicrobial and Chemotherapy, 67(7), 1660–1665. http://dx.doi.org/10.1093/jac/ dks124. Dobrindt, U. (2005). (Patho-)Genomics of Escherichia coli. International Journal of Medical Microbiology, 295(6–7), 357–371. http://dx.doi.org/10.1016/j.ijmm.2005.07.009. Doi, Y., & Paterson, D. L. (2007). Detection of plasmid-mediated class C beta-lactamases. International Journal of Infectious Diseases, 11(3), 191–197. http://dx.doi.org/10.1016/ j.ijid.2006.07.008. S1201-9712(06)00200-1 [pii]. Doumith, M., Dhanji, H., Ellington, M. J., Hawkey, P., & Woodford, N. (2012). Characterization of plasmids encoding extended-spectrum beta-lactamases and their addiction systems circulating among Escherichia coli clinical isolates in the UK. Journal of Antimicrobial Chemotherapy, 67(4), 878–885. http://dx.doi.org/10.1093/jac/dkr553. dkr553 [pii]. Fern
andez, J., Montero, I., Fleites, A., & Rodicio, M. R. (2014). Cluster of Escherichia coli producing a plasmid-mediated OXA-48 beta-Lactamase in a Spanish hospital in 2012. Journal of Clinical Microbiology, 52(9), 3414–3417. http://dx.doi.org/10.1128/JCM.01271-14. Forward, K. R., Willey, B. M., Low, D. E., McGeer, A., Kapala, M. A., Kapala, M. M., et al. (2001). Molecular mechanisms of cefoxitin resistance in Escherichia coli from the Toronto area hospitals. Diagnostic Microbiology and Infectious Disease, 41(1–2), 57–63. S07328893(01)00278-4 [pii]. Foxman, B. (2010). The epidemiology of urinary tract infection. Nature Reviews Urology, 7(12), 653–660. http://dx.doi.org/10.1038/nrurol.2010.190. Freeman, J. T., McBride, S. J., Heffernan, H., Bathgate, T., Pope, C., & Ellis-Pegler, R. B. (2008). Community-onset genitourinary tract infection due to CTX-M-15-Producing Escherichia coli among travelers to the Indian subcontinent in New Zealand. Clinical Infectious Diseases, 47(5), 689–692. http://dx.doi.org/10.1086/590941. GE, M. (1965). Cramming more components onto integrated circuits. Electronics, 38(8), 1–4. Gibreel, T. M., Dodgson, A. R., Cheesbrough, J., Fox, A. J., Bolton, F. J., & Upton, M. (2012). Population structure, virulence potential and antibiotic susceptibility of uropathogenic Escherichia coli from Northwest England. Journal of Antimicrobial Chemotherapy, 67(2), 346–356. http://dx.doi.org/10.1093/jac/dkr451. dkr451 [pii]. Gisele, Peirano, Patricia A, Bradford, Krystyna M, Kazmierczak, Robert E, Badal, Meredith, Hackel, Daryl J, Hoban, et al. (2014). Global Incidence of CarbapenemaseProducing Escherichia coli ST131. Emerging Infectious Diseases, 20(11), 1928–1931. Glupczynski, Y., Huang, T. D., Bouchahrouf, W., Rezende de Castro, R., Bauraing, C., Gerard, M., et al. (2012). Rapid emergence and spread of OXA-48-producing carbapenem-resistant Enterobacteriaceae isolates in Belgian hospitals. International Journal of Antimicrobial Agents, 39(2), 168–172. http://dx.doi.org/10.1016/j.ijantimicag.2011.10.005. S0924-8579(11)00423-7 [pii]. Hanson, N. D. (2003). AmpC beta-lactamases: what do we need to know for the future? Journal of Antimicrobial Chemotherapy, 52(1), 2–4. http://dx.doi.org/10.1093/jac/dkg284. dkg284 [pii]. Hawser, S. P., Bouchillon, S. K., Hoban, D. J., Badal, R. E., Hsueh, P. R., & Paterson, D. L. (2009). Emergence of high levels of extended-spectrum-beta-lactamase-producing

The Quintessential Example of an International Multiresistant High-Risk Clone

147

gram-negative bacilli in the Asia-Pacific region: data from the Study for Monitoring Antimicrobial Resistance Trends (SMART) program, 2007. Antimicrobial Agents and Chemotherapy, 53(8), 3280–3284. http://dx.doi.org/10.1128/AAC.00426-09. AAC.00426-09 [pii]. Herzer, P. J., Inouye, S., Inouye, M., & Whittam, T. S. (1990). Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. Journal of Bacteriology, 172(11), 6175–6181. Hilty, M., Betsch, B. Y., Bogli-Stuber, K., Heiniger, N., Stadler, M., Kuffer, M., et al. (2012). Transmission dynamics of extended-spectrum beta-lactamase-producing Enterobacteriaceae in the tertiary care hospital and the household setting. Clinical Infectious Diseases, 55(7), 967–975. http://dx.doi.org/10.1093/cid/cis581. Jacoby, G. A. (2009). AmpC beta-lactamases. Clinical Microbiology Reviews, 22(1), 161–182. http://dx.doi.org/10.1128/CMR.00036-08. Table of Contents. Johnson, J. R., Clermont, O., Johnston, B., Clabots, C., Tchesnokova, V., Sokurenko, E., et al. (2014). Rapid and specific detection, molecular epidemiology, and experimental virulence of the O16 subgroup within Escherichia coli sequence type 131. Journal of Clinical Microbiology, 52(5), 1358–1365. http://dx.doi.org/10.1128/JCM.03502-13. Johnson, J. R., Johnston, B., Clabots, C., Kuskowski, M. A., & Castanheira, M. (2010). Escherichia coli sequence type ST131 as the major cause of serious multidrug-resistant E. coli infections in the United States. Clinical Infectious Diseases, 51(3), 286–294. http://dx.doi.org/10.1086/653932. Johnson, J. B., Jr., Jorgensen, J. H., Lewis, J., II, Robicsek, A., Menard, M., Clabots, C., et al. (2008). CTX-M-15-producing E. coli in the United States: predominance of sequence type ST131 (O25:H4). In Paper presented at the Proceedings of the Forty-eighth Interscience Conference on antimicrobial agents and Chemotherapy,, Washington. Johnson, J. R., Menard, M., Johnston, B., Kuskowski, M. A., Nichol, K., & Zhanel, G. G. (2009). Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002 to 2004. Antimicrobial Agents and Chemotherapy, 53(7), 2733–2739. http://dx.doi.org/10.1128/AAC.00297-09. Johnson, J. R., Nicolas-Chanoine, M. H., Debroy, C., Castanheira, M., Robicsek, A., Hansen, G., et al. (2012a). Comparison of Escherichia coli ST131 pulsotypes, by epidemiologic traits, 1967–2009. Emerging Infectious Diseases, 18(4), 598–607. http://dx.doi.org/ 10.3201/eid1804.111627. Johnson, J. R., Porter, S. B., Zhanel, G., Kuskowski, M. A., & Denamur, E. (2012b). Virulence of Escherichia coli clinical isolates in a murine sepsis model in relation to sequence type ST131 status, fluoroquinolone resistance, and virulence genotype. Infectious Immunity, 80(4), 1554–1562. http://dx.doi.org/10.1128/IAI.06388-11. Johnson, J. R., Tchesnokova, V., Johnston, B., Clabots, C., Roberts, P. L., Billig, M., et al. (2013). Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli. Journal of Infectious Diseases, 207(6), 919–928. http://dx.doi.org/10.1093/infdis/ jis933. Kumarasamy, K. K., Toleman, M. A., Walsh, T. R., Bagaria, J., Butt, F., Balakrishnan, R., et al. (2010). Emergence of a new antibiotic resistance in India, Pakistan and the UK: end of conventional antibiotics? Lancet Infectious Diseases, 10(9), 597–602. Kaper, J. B., Nataro, J. P., & Mobley, H. L. (2004). Pathogenic Escherichia coli. Nature Reviews Microbiology, 2(2), 123–140. http://dx.doi.org/10.1038/nrmicro818. Kim, Y. A., Qureshi, Z. A., Adams-Haduch, J. M., Park, Y. S., Shutt, K. A., & Doi, Y. (2012). Features of infections due to Klebsiella pneumoniae carbapenemase-producing Escherichia coli: emergence of sequence type 131. Clinical Infectious Diseases, 55(2), 224–231. http://dx.doi.org/10.1093/cid/cis387. Koser, C. U., Ellington, M. J., Cartwright, E. J., Gillespie, S. H., Brown, N. M., Farrington, M., et al. (2012). Routine use of microbial whole genome sequencing in

148

Amy J. Mathers et al.

diagnostic and public health microbiology. PLoS Pathogens, 8(8), e1002824. http:// dx.doi.org/10.1371/journal.ppat.1002824. Kudinha, T., Johnson, J. R., Andrew, S. D., Kong, F., Anderson, P., & Gilbert, G. L. (2013). Escherichia coli sequence type 131 as a prominent cause of antibiotic resistance among urinary Escherichia coli isolates from reproductive-age women. Journal of Clinical Microbiology, 51(10), 3270–3276. http://dx.doi.org/10.1128/JCM.01315-13. Lartigue, M. F. (2013). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for bacterial strain characterization. Infection, Genetics, and Evolution, 13, 230–235. http://dx.doi.org/10.1016/j.meegid.2012.10.012. Lascols, C., Hackel, M., Marshall, S. H., Hujer, A. M., Bouchillon, S., Badal, R., et al. (2011). Increasing prevalence and dissemination of NDM-1 metallo-beta-lactamase in India: data from the SMART study (2009). Journal of Antimicrobial Chemotherapy, 66(9), 1992–1997. http://dx.doi.org/10.1093/jac/dkr240. Lau, S. H., Cheesborough, J., Kaufmann, M. E., Woodford, N., Dodgson, A. R., Dodgson, K. J., et al. (2010). Rapid identification of uropathogenic Escherichia coli of the O25:H4-ST131 clonal lineage using the DiversiLab repetitive sequence-based PCR system. Clinical Microbiology and Infection, 16(3), 232–237. http://dx.doi.org/ 10.1111/j.1469-0691.2009.02733.x. Lau, S. H., Kaufmann, M. E., Livermore, D. M., Woodford, N., Willshaw, G. A., Cheasty, T., et al. (2008). UK epidemic Escherichia coli strains A–E, with CTX-M-15 beta-lactamase, all belong to the international O25:H4-ST131 clone. Journal of Antimicrobial Chemotherapy, 62(6), 1241–1244. http://dx.doi.org/10.1093/jac/dkn380. dkn380 [pii]. Laupland, K. B., Church, D. L., Vidakovich, J., Mucenski, M., & Pitout, J. D. (2008). Community-onset extended-spectrum beta-lactamase (ESBL) producing Escherichia coli: importance of international travel. Journal of Infection, 57(6), 441–448. http:// dx.doi.org/10.1016/j.jinf.2008.09.034. Lavigne, J. P., Vergunst, A. C., Goret, L., Sotto, A., Combescure, C., Blanco, J., et al. (2012). Virulence potential and genomic mapping of the worldwide clone Escherichia coli ST131. PLoS One, 7(3), e34294. http://dx.doi.org/10.1371/journal.pone.0034294. Leflon-Guibout, V., Blanco, J., Amaqdouf, K., Mora, A., Guize, L., & NicolasChanoine, M. H. (2008). Absence of CTX-M enzymes but high prevalence of clones, including clone ST131, among fecal Escherichia coli isolates from healthy subjects living in the area of Paris, France. Journal of Clinical Microbiology, 46(12), 3900–3905. http:// dx.doi.org/10.1128/JCM.00734-08. JCM.00734-08 [pii]. Leverstein-Van Hall, M. A., Stuart, J. C., Voets, G. M., Versteeg, D., Tersmette, T., & Fluit, A. C. (2010). Global spread of New Delhi metallo-beta-lactamase 1. The Lancet Infectious Diseases, 10(12), 830–831. http://dx.doi.org/10.1016/S1473-3099(10)70277-2. Li, Y., Li, Q., Du, Y., Jiang, X., Tang, J., Wang, J., et al. (2008). Prevalence of plasmidmediated AmpC beta-lactamases in a Chinese university hospital from 2003 to 2005: first report of CMY-2-Type AmpC beta-lactamase resistance in China. Journal of Clinical Microbiology, 46(4), 1317–1321. http://dx.doi.org/10.1128/JCM.00073-07. JCM.00073-07 [pii]. Literacka, E., Bedenic, B., Baraniak, A., Fiett, J., Tonkic, M., Jajic-Bencic, I., et al. (2009). blaCTX-M genes in Escherichia coli strains from Croatian hospitals are located in new (blaCTX-M-3a) and widely spread (blaCTX-M-3a, blaCTX-M-15) genetic structures. Antimicrobial Agents and Chemotherapy, 53(4), 1630–1635. http://dx.doi.org/ 10.1128/AAC.01431–08. AAC.01431-08 [pii]. Magiorakos, A. P., Srinivasan, A., Carey, R. B., Carmeli, Y., Falagas, M. E., Giske, C. G., et al. (2012). Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired

The Quintessential Example of an International Multiresistant High-Risk Clone

149

resistance. Clinical Microbiology and Infection, 18(3), 268–281. http://dx.doi.org/10.1111/ j.1469-0691.2011.03570.x. Mandell, G. L., Douglas, R. G., Bennett, J. E., & Dolin, R. (2005). Mandell, Douglas, and Bennett’s principles and practice of infectious diseases (6th ed.). New York: Churchill Livingstone. Mantengoli, E., Luzzaro, F., Pecile, P., Cecconi, D., Cavallo, A., Attala, L., et al. (2011). Escherichia coli ST131 producing extended-spectrum beta-lactamases plus VIM-1 carbapenemase: further narrowing of treatment options. Clinical Infectious Diseases, 52(5), 690–691. http://dx.doi.org/10.1093/cid/ciq194. Ma, L., Siu, L. K., Lin, J. C., Wu, T. L., Fung, C. P., Wang, J. T., et al. (2013). Updated molecular epidemiology of carbapenem-non-susceptible Escherichia coli in Taiwan: first identification of KPC-2 or NDM-1-producing E. coli in Taiwan. BMC Infectious Diseases, 13, 599. http://dx.doi.org/10.1186/1471-2334-13-599. Matsumura, Y., Yamamoto, M., Nagao, M., Tanaka, M., Machida, K., Ito, Y., et al. (2014). Detection of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 and ST405 clonal groups by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Journal of Clinical Microbiology, 52(4), 1034–1040. http://dx.doi.org/ 10.1128/JCM.03196-13. Mokady, D., Gophna, U., & Ron, E. Z. (2005). Virulence factors of septicemic Escherichia coli strains. Interantional Journal of Medicine Microbiology, 295(6–7), 455–462. Moland, E. S., Hanson, N. D., Black, J. A., Hossain, A., Song, W., & Thomson, K. S. (2006). Prevalence of newer beta-lactamases in gram-negative clinical isolates collected in the United States from 2001 to 2002. Journal of Clinical Microbiology, 44(9), 3318–3324. http://dx.doi.org/10.1128/JCM.00756-06. Morris, D., Boyle, F., Ludden, C., Condon, I., Hale, J., O’Connell, N., et al. (2011). Production of KPC-2 carbapenemase by an Escherichia coli clinical isolate belonging to the international ST131 clone. Antimicrobial Agents and Chemotherapy, 55(10), 4935–4936. http://dx.doi.org/10.1128/AAC.05127-11. Morris, D., McGarry, E., Cotter, M., Passet, V., Lynch, M., Ludden, C., et al. (2012). Detection of OXA-48 carbapenemase in the pandemic clone Escherichia coli O25b:H4-ST131 in the course of investigation of an outbreak of OXA-48-producing Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy, 56(7), 4030–4031. http:// dx.doi.org/10.1128/AAC.00638-12. Mulvey, M. R., Bryce, E., Boyd, D. A., Ofner-Agostini, M., Land, A. M., Simor, A. E., et al. (2005). Molecular characterization of cefoxitin-resistant Escherichia coli from Canadian hospitals. Antimicrobial Agents and Chemotherapy, 49(1), 358–365. http://dx.doi.org/ 10.1128/AAC.49.1.358-365.2005. Naas, T., Cuzon, G., Gaillot, O., Courcol, R., & Nordmann, P. (2011). When carbapenemhydrolyzing beta-lactamase Kpc meets Escherichia coli ST131 in France. Antimicrobial Agents and Chemotherapy, 55(10), 4933–4934. http://dx.doi.org/10.1128/AAC.00719-11. Naseer, U., Haldorsen, B., Tofteland, S., Hegstad, K., Scheutz, F., Simonsen, G. S., et al. (2009). Molecular characterization of CTX-M-15-producing clinical isolates of Escherichia coli reveals the spread of multidrug-resistant ST131 (O25:H4) and ST964 (O102:H6) strains in Norway. APMIS, 117(7), 526–536. http://dx.doi.org/10.1111/j.16000463.2009.02465.x. APM2465 [pii]. Nataro, J. P., & Kaper, J. B. (1998). Diarrheagenic Escherichia coli. Clinical Microbiology Reviews, 11(1), 142–201. Nicolas-Chanoine, M. H., Bertrand, X., & Madec, J. Y. (2014). Escherichia coli ST131, an intriguing clonal group. Clinical Microbiology Reviews, 27(3), 543–574. http:// dx.doi.org/10.1128/CMR.00125-13. Nicolas-Chanoine, M. H., Blanco, J., Leflon-Guibout, V., Demarty, R., Alonso, M. P., Canica, M. M., et al. (2008). Intercontinental emergence of Escherichia coli clone O25:

150

Amy J. Mathers et al.

H4-ST131 producing CTX-M-15. Journal of Antimicrobial Chemotherapy, 61(2), 273–281. http://dx.doi.org/10.1093/jac/dkm464. Nordmann, P., Naas, T., & Poirel, L. (2011a). Global spread of Carbapenemase-producing Enterobacteriaceae. Emerging Infectious Diseases, 17(10), 1791–1798. http://dx.doi.org/ 10.3201/eid1710.110655. Nordmann, P., & Poirel, L. (2014). The difficult-to-control spread of carbapenemase producers in Enterobacteriaceae worldwide. Clinical Microbiology and Infection, 20(9), 821–830. http://dx.doi.org/10.1111/1469-0691.12719. Nordmann, P., Poirel, L., Walsh, T. R., & Livermore, D. M. (2011b). The emerging NDM carbapenemases. Trends in Microbiology, 19(12), 588–595. http://dx.doi.org/10.1016/ j.tim.2011.09.005. S0966-842X(11)00177-6 [pii]. Novais, A., Pires, J., Ferreira, H., Costa, L., Montenegro, C., Vuotto, C., et al. (2012). Characterization of globally spread Escherichia coli ST131 isolates (1991 to 2010). Antimicrobial Agents and Chemotherapy, 56(7), 3973–3976. http://dx.doi.org/10.1128/AAC.0047512. AAC.00475-12 [pii]. Novais, A., Sousa, C., de Dios Caballero, J., Fernandez-Olmos, A., Lopes, J., Ramos, H., et al. (2014). MALDI-TOF mass spectrometry as a tool for the discrimination of highrisk Escherichia coli clones from phylogenetic groups B2 (ST131) and D (ST69, ST405, ST393). European Journal of Clinical Microbiology and Infectious Diseases, 33(8), 1391–1399. http://dx.doi.org/10.1007/s10096-014-2071-5. O’Hara, J. A., Hu, F., Ahn, C., Nelson, J., Rivera, J. I., Pasculle, A. W., et al. (2014). Molecular epidemiology of KPC-producing Escherichia coli: Occurrence of ST131-fimH30 subclone harboring pKpQIL-like IncFIIk plasmid. Antimicrobial Agents and Chemotherapy, 58(7), 4234–4237. http://dx.doi.org/10.1128/AAC.02182-13. Organization, W. H. (2014a). In L. Hiliary Cadman (Ed.), Antimicrobial resistance a global report on Surviellence (1st ed.). (pp. 1–257). 20 Avenue Appia, 1211 Geneva 27, Switzerland: World Health Organization. Organization, W. H. (2014b). Antimicrobial resistance: Global report on surveillance 2014. Retrieved June 2014, from World Heath Organization http://www.who.int/ drugresistance/documents/surveillancereport/en/. Oteo, J., Diestra, K., Juan, C., Bautista, V., Novais, A., Perez-Vazquez, M., et al. (2009). Extended-spectrum beta-lactamase-producing Escherichia coli in Spain belong to a large variety of multilocus sequence typing types, including ST10 complex/A, ST23 complex/A and ST131/B2. International Journal of Antimicrobial Agents, 34(2), 173–176. http://dx.doi.org/10.1016/j.ijantimicag.2009.03.006. S0924-8579(09)00117-4 [pii]. Pai, H., Kang, C. I., Byeon, J. H., Lee, K. D., Park, W. B., Kim, H. B., et al. (2004). Epidemiology and clinical features of bloodstream infections caused by AmpC-type-beta-lactamase-producing Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy, 48(10), 3720–3728. http://dx.doi.org/10.1128/AAC.48.10.3720-3728.2004. Pallen, M. J., Loman, N. J., & Penn, C. W. (2010). High-throughput sequencing and clinical microbiology: progress, opportunities and challenges. Current Opinion in Microbiology, 13(5), 625–631. http://dx.doi.org/10.1016/j.mib.2010.08.003. S1369-5274(10) 00117-7 [pii]. Paterson, D. L., & Bonomo, R. A. (2005). Extended-spectrum beta-lactamases: a clinical update. Clinical Microbiology Reviews, 18(4), 657–686. http://dx.doi.org/10.1128/ CMR.18.4.657-686.2005. Peirano, G., & Pitout, J. D. (2010). Molecular epidemiology of Escherichia coli producing CTX-M beta-lactamases: the worldwide emergence of clone ST131 O25:H4. International Journal of Antimicrobial Agents, 35(4), 316–321. http://dx.doi.org/10.1016/ j.ijantimicag.2009.11.003. Peirano, G., & Pitout, J. D. (2014). Fluoroquinolone-resistant Escherichia coli sequence type 131 isolates causing bloodstream infections in a canadian region with a centralized

The Quintessential Example of an International Multiresistant High-Risk Clone

151

laboratory system: rapid emergence of the H30-Rx sublineage. Antimicrobial Agents and Chemotherapy, 58(5), 2699–2703. http://dx.doi.org/10.1128/AAC.00119-14. Peirano, G., Schreckenberger, P. C., & Pitout, J. D. (2011). Characteristics of NDM1-producing Escherichia coli isolates that belong to the successful and virulent clone ST131. Antimicrobial Agents and Chemotherapy, 55(6), 2986–2988. http://dx.doi.org/ 10.1128/AAC.01763-10. Peirano, G., van der Bij, A. K., Freeman, J. L., Poirel, L., Nordmann, P., Costello, M., et al. (2014). Characteristics of Escherichia coli sequence type 131 isolates that produce extended-spectrum beta-lactamases: global distribution of the H30-Rx sublineage. Antimicrobial Agents and Chemotherapy, 58(7), 3762–3767. http://dx.doi.org/10.1128/ AAC.02428-14. Peirano, G., van der Bij, A. K., Gregson, D. B., & Pitout, J. D. (2012). Molecular epidemiology over an 11-year period (2000 to 2010) of extended-spectrum beta-lactamase-producing Escherichia coli causing bacteremia in a centralized Canadian region. Journal of Clinical Microbiology, 50(2), 294–299. http://dx.doi.org/10.1128/JCM.06025-11. Perry, J. D., Naqvi, S. H., Mirza, I. A., Alizai, S. A., Hussain, A., Ghirardi, S., et al. (2011). Prevalence of faecal carriage of Enterobacteriaceae with NDM-1 carbapenemase at military hospitals in Pakistan, and evaluation of two chromogenic media. Journal of Antimicrobial Chemotherapy, 66(10), 2288–2294. http://dx.doi.org/10.1093/jac/dkr299. dkr299 [pii]. Petty, N. K., Ben Zakour, N. L., Stanton-Cook, M., Skippington, E., Totsika, M., Forde, B. M., et al. (2014). Global dissemination of a multidrug resistant Escherichia coli clone. Proceedings of the National Academy of Sciences of the United States of America, 111(15), 5694–5699. http://dx.doi.org/10.1073/pnas.1322678111. Philippon, A., Arlet, G., & Jacoby, G. A. (2002). Plasmid-determined AmpC-type betalactamases. Antimicrobial Agents and Chemotherapy, 46(1), 1–11. Pitout, J. D. (2012a). Extraintestinal pathogenic Escherichia coli: a combination of virulence with antibiotic resistance. Frontiers in Microbiology, 3, 9. http://dx.doi.org/10.3389/ fmicb.2012.00009. Pitout, J. D. (2012b). Extraintestinal pathogenic Escherichia coli: an update on antimicrobial resistance, laboratory diagnosis and treatment. Expert Review of Anti-infective Therapy, 10(10), 1165–1176. http://dx.doi.org/10.1586/eri.12.110. Pitout, J. D., Campbell, L., Church, D. L., Wang, P. W., Guttman, D. S., & Gregson, D. B. (2009a). Using a commercial DiversiLab semiautomated repetitive sequence-based PCR typing technique for identification of Escherichia coli clone ST131 producing CTX-M-15. Journal of Clinical Microbiology, 47(4), 1212–1215. http://dx.doi.org/10.1128/ JCM.02265-08. Pitout, J. D., Campbell, L., Church, D. L., Wang, P. W., Guttman, D. S., & Gregson, D. B. (2009b). Using a Commercial DiversiLabTM Semi automated repetitive sequence-based PCR typing technique for the identification of Escherichia coli clone ST131 producing CTX-M-15. Journal of Clinical Microbiology, 47(4), 1212–1215. http://dx.doi.org/ 10.1128/JCM.02265–08. JCM.02265-08 [pii]. Pitout, J. D., Church, D. L., Gregson, D. B., Chow, B. L., McCracken, M., Mulvey, M. R., et al. (2007). Molecular epidemiology of CTX-M-producing Escherichia coli in the Calgary Health Region: emergence of CTX-M-15-producing isolates. Antimicrobial Agents and Chemotherapy, 51(4), 1281–1286. http://dx.doi.org/10.1128/AAC.01377-06. Pitout, J. D., Gregson, D. B., Campbell, L., & Laupland, K. B. (2009). Molecular characteristics of extended-spectrum-beta-lactamase-producing Escherichia coli isolates causing bacteremia in the Calgary Health Region from 2000 to 2007: emergence of clone ST131 as a cause of community-acquired infections. Antimicrobial Agents and Chemotherapy, 53(7), 2846–2851. http://dx.doi.org/10.1128/AAC.00247-09.

152

Amy J. Mathers et al.

Pitout, J. D., & Laupland, K. B. (2008). Extended-spectrum beta-lactamase-producing Enterobacteriaceae: an emerging public-health concern. Lancet Infectious Disease, 8(3), 159–166. http://dx.doi.org/10.1016/S1473-3099(08)70041-0. Platell, J. L., Johnson, J. R., Cobbold, R. N., & Trott, D. J. (2011). Multidrug-resistant extraintestinal pathogenic Escherichia coli of sequence type ST131 in animals and foods. Veterinary Microbiology, 153(1–2), 99–108. http://dx.doi.org/10.1016/j.vetmic.2011.05.007. Poirel, L., Bonnin, R. A., & Nordmann, P. (2012). Genetic features of the widespread plasmid coding for the carbapenemase OXA-48. Antimicrobial Agents and Chemotherapy, 56(1), 559–562. http://dx.doi.org/10.1128/AAC.05289-11. AAC.05289-11 [pii]. Poirel, L., Heritier, C., Tolun, V., & Nordmann, P. (2004). Emergence of oxacillinasemediated resistance to imipenem in Klebsiella pneumoniae. Antimicrobial Agents and Chemotherapy, 48(1), 15–22. Pomba, C., da Fonseca, J. D., Baptista, B. C., Correia, J. D., & Martinez-Martinez, L. (2009). Detection of the pandemic O25-ST131 human virulent Escherichia coli CTX-M15-producing clone harboring the qnrB2 and aac(6’)-Ib-cr genes in a dog. Antimicrobial Agents and Chemotherapy, 53(1), 327–328. http://dx.doi.org/10.1128/AAC.00896-08. AAC.00896-08 [pii]. Price, L. B., Johnson, J. R., Aziz, M., Clabots, C., Johnston, B., Tchesnokova, V., et al. (2013). The epidemic of extended-spectrum-beta-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. mBio, 4(6), e00377–00313. http://dx.doi.org/10.1128/mBio.00377-13. Reuter, S., Ellington, M. J., Cartwright, E. J., K€ oser, C. U., T€ or€ ok, M. E., Gouliouris, T., et al. (2013). Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology. JAMA Internal Medicine, 173(15), 1397–1404. http:// dx.doi.org/10.1001/jamainternmed.2013.7734. Riley, L. W. (2014). Pandemic lineages of extraintestinal pathogenic Escherichia coli. Clinical Microbiology and Infection, 20(5), 380–390. http://dx.doi.org/10.1111/1469-0691.12646. Rodriguez-Bano, J., & Pascual, A. (2008). Clinical significance of extended-spectrum betalactamases. Expert Review of Anti-infective Therapy, 6(5), 671–683. http://dx.doi.org/ 10.1586/14787210.6.5.671. Rooney, P. J., O’Leary, M. C., Loughrey, A. C., McCalmont, M., Smyth, B., Donaghy, P., et al. (2009). Nursing homes as a reservoir of extended-spectrum beta-lactamase (ESBL)producing ciprofloxacin-resistant Escherichia coli. Journal of Antimicrobial Chemotherapy, 64(3), 635–641. http://dx.doi.org/10.1093/jac/dkp220. dkp220 [pii]. Sabat, A. J., Budimir, A., Nashev, D., Sa-Leao, R., van Dijl, J., Laurent, F., et al. (2013). Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Eurosurveillance, 18(4), 20380. Schwaber, M. J., Navon-Venezia, S., Kaye, K. S., Ben-Ami, R., Schwartz, D., & Carmeli, Y. (2006). Clinical and economic impact of bacteremia with extended- spectrum-betalactamase-producing Enterobacteriaceae. Antimicrobial Agents and Chemotherapy, 50(4), 1257–1262. http://dx.doi.org/10.1128/AAC.50.4.1257-1262.2006, 50/4/1257 [pii]. Seema, K., Ranjan Sen, M., Upadhyay, S., & Bhattacharjee, A. (2011). Dissemination of the New Delhi metallo-beta-lactamase-1 (NDM-1) among Enterobacteriaceae in a tertiary referral hospital in north India. Journal of Antimicrobial and Chemotherapy, 66(7), 1646–1647. http://dx.doi.org/10.1093/jac/dkr180. dkr180 [pii]. Shin, J., Choi, M. J., & Ko, K. S. (2012). Replicon sequence typing of IncF plasmids and the genetic environments of blaCTX-M-15 indicate multiple acquisitions of blaCTX-M-15 in Escherichia coli and Klebsiella pneumoniae isolates from South Korea. Journal of Antimicrobial Chemotherapy, 67(8), 1853–1857. http://dx.doi.org/10.1093/jac/dks143. dks143 [pii]. Spratt, B. G. (2004). Exploring the concept of clonality in bacteria. Methods in Molecular Biology, 266, 323–352. http://dx.doi.org/10.1385/1-59259-763-7:323.

The Quintessential Example of an International Multiresistant High-Risk Clone

153

Sullivan, C. B., Diggle, M. A., & Clarke, S. C. (2005). Multilocus sequence typing: data analysis in clinical microbiology and public health. Molecular Biotechnology, 29(3), 245–254. http://dx.doi.org/10.1385/MB:29:3:245. MB:29:3:245 [pii]. Suzuki, S., Shibata, N., Yamane, K., Wachino, J., Ito, K., & Arakawa, Y. (2009). Change in the prevalence of extended-spectrum-beta-lactamase-producing Escherichia coli in Japan by clonal spread. Journal of Antimicrobial Chemotherapy, 63(1), 72–79. http://dx.doi.org/ 10.1093/jac/dkn463. dkn463 [pii]. Talbot, G. H., Bradley, J., Edwards, J. E., Jr., Jr., Gilbert, D., Scheld, M., & Bartlett, J. G. (2006). Bad bugs need drugs: an update on the development pipeline from the Antimicrobial Availability Task Force of the Infectious Diseases Society of America. Clinical Infectious Diseases, 42(5), 657–668. http://dx.doi.org/10.1086/499819. CID38405 [pii]. Tchesnokova, V., Billig, M., Chattopadhyay, S., Linardopoulou, E., Aprikian, P., Roberts, P. L., et al. (2013). Predictive diagnostics for Escherichia coli infections based on the clonal association of antimicrobial resistance and clinical outcome. Journal of Clinical Microbiology, 51(9), 2991–2999. http://dx.doi.org/10.1128/JCM.00984-13. Tenover, F. C., Arbeit, R. D., Goering, R. V., Mickelsen, P. A., Murray, B. E., Persing, D. H., et al. (1995). Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. Journal of Clinical Microbiology, 33(9), 2233–2239. Van der Bij, A. K., Peirano, G., Pitondo-Silva, A., & Pitout, J. D. (2012). The presence of genes encoding for different virulence factors in clonally related Escherichia coli that produce CTX-Ms. Diagnostic Microbiology and Infectious Disease, 72(4), 297–302. http:// dx.doi.org/10.1016/j.diagmicrobio.2011.12.011. van der Bij, A. K., & Pitout, J. D. (2012). The role of international travel in the worldwide spread of multiresistant Enterobacteriaceae. Journal of Antimicrobial Chemotherapy, 67(9), 2090–2100. http://dx.doi.org/10.1093/jac/dks214. Villa, L., Garcia-Fernandez, A., Fortini, D., & Carattoli, A. (2010). Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants. Journal of Antimicrobial Chemotherapy, 65(12), 2518–2529. http://dx.doi.org/10.1093/jac/dkq347. Vimont, S., Boyd, A., Bleibtreu, A., Bens, M., Goujon, J. M., Garry, L., et al. (2012). The CTX-M-15-producing Escherichia coli clone O25b: H4–ST131 has high intestine colonization and urinary tract infection abilities. PLoS One, 7(9), e46547. http://dx.doi.org/ 10.1371/journal.pone.0046547. Walsh, T. R., Weeks, J., Livermore, D. M., & Toleman, M. A. (2011). Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infectious Diseases, 11(5), 355–362. http://dx.doi.org/10.1016/S1473-3099(11)70059-7. Weissman, S. J., Johnson, J. R., Tchesnokova, V., Billig, M., Dykhuizen, D., Riddell, K., et al. (2012). High-resolution two-locus clonal typing of extraintestinal pathogenic Escherichia coli. Applied Environmental Microbiology, 78(5), 1353–1360. http:// dx.doi.org/10.1128/AEM.06663-11. Wiles, T. J., Kulesus, R. R., & Mulvey, M. A. (2008). Origins and virulence mechanisms of uropathogenic Escherichia coli. Experimental and Molecular Pathology, 85(1), 11–19. http:// dx.doi.org/10.1016/j.yexmp.2008.03.007. Woodford, N., Carattoli, A., Karisik, E., Underwood, A., Ellington, M. J., & Livermore, D. M. (2009). Complete nucleotide sequences of plasmids pEK204, pEK499, and pEK516, encoding CTX-M enzymes in three major Escherichia coli lineages from the United Kingdom, all belonging to the international O25:H4-ST131 clone. Antimicrobial Agents and Chemotherapy, 53(10), 4472–4482. http://dx.doi.org/10.1128/ AAC.00688-09. Woodford, N., Reddy, S., Fagan, E. J., Hill, R. L., Hopkins, K. L., Kaufmann, M. E., et al. (2007). Wide geographic spread of diverse acquired AmpC beta-lactamases among

154

Amy J. Mathers et al.

Escherichia coli and Klebsiella spp. in the UK and Ireland. Journal of Antimicrobial Chemotherapy, 59(1), 102–105. http://dx.doi.org/10.1093/jac/dkl456. dkl456 [pii]. Woodford, N., Turton, J. F., & Livermore, D. M. (2011). Multiresistant Gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance. FEMS Microbiology Reviews, 35(5), 736–755. http://dx.doi.org/10.1111/j.15746976.2011.00268.x. Woodford, N., Ward, M. E., Kaufmann, M. E., Turton, J., Fagan, E. J., James, D., et al. (2004). Community and hospital spread of Escherichia coli producing CTX-M extended-spectrum beta-lactamases in the UK. Journal of Antimicrobial Chemotherapy, 54(4), 735–743. http://dx.doi.org/10.1093/jac/dkh424. Yan, J. J., Tsai, L. H., & Wu, J. J. (2012). Emergence of the IMP-8 metallo-beta-lactamase in the Escherichia coli ST131 clone in Taiwan. Interanational Journal of Antimicrobial Agents, 40(3), 281–282. http://dx.doi.org/10.1016/j.ijantimicag.2012.05.011. Yong, D., Toleman, M. A., Giske, C. G., Cho, H. S., Sundman, K., Lee, K., et al. (2009). Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrobial Agents and Chemotherapy, 53(12), 5046–5054. http://dx.doi.org/10.1128/AAC.00774-09. AAC.00774-09 [pii]. Yumuk, Z., Afacan, G., Nicolas-Chanoine, M. H., Sotto, A., & Lavigne, J. P. (2008). Turkey: a further country concerned by community-acquired Escherichia coli clone O25-ST131 producing CTX-M-15. Journal of Antimicrobial Chemotherapy, 62(2), 284–288. http://dx.doi.org/10.1093/jac/dkn181. dkn181 [pii]. Zong, Z. (2013). Complete sequence of pJIE186-2, a plasmid carrying multiple virulence factors from a sequence type 131 Escherichia coli O25 strain. Antimicrobial Agents and Chemotherapy, 57(1), 597–600. http://dx.doi.org/10.1128/AAC.01081-12. AAC.01081-12 [pii].