- Email: [email protected]
Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting
Journal of Hospital Infection xxx (2017) 1e6 Available online at www.sciencedirect.com
Journal of Hospital Infection journal homepage: www.elsevierhealth.com/journals/jhin
Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting M.I. Garvey a, *, C.W. Bradley a, K.L. Holden a, P. Hewins a, S.-L. Ngui b, R. Tedder b, P. Jumaa a, E. Smit a, c a
University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK Blood Borne Virus Unit, Microbiology Service Colindale, Public Health England, London, UK c Public Health England Birmingham Laboratory, Birmingham Heartlands Hospital, Birmingham, UK b
A R T I C L E
I N F O
Article history: Received 19 December 2016 Accepted 9 January 2017 Available online xxx Keywords: Hepatitis C NS5B genome sequencing Infection prevention and control Bloodborne transmission
S U M M A R Y
Hepatitis C virus (HCV) infection is a major health burden worldwide. A patient with no history of HCV infection while on a renal unit was found to seroconvert to HCV. Here we report the use of sequencing to postulate how transmission of HCV occurred in a healthcare setting, and how this guided our outbreak investigation. Based on infection control inspections the transmission event was surmised to be due to ward environmental contamination with blood and subsequent inoculation from intravenous interventions on the patient acquiring HCV. We discuss the interventions put in place in response to the outbreak investigation findings. Sequencing of healthcare-acquired HCV infections should be undertaken as routine practice in outbreak investigations. ª 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.
Introduction Hepatitis C virus (HCV) is a significant human pathogen and is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma.1,2 Most people affected live in resource-limited regions such as Asia, Africa, and the Middle East. It is estimated that around 214,000 individuals are chronically infected with HCV in the UK.3,4 There are several risk factors for haemodialysis patients acquiring HCV infection,
* Corresponding author. Address: University Hospitals Birmingham NHS Foundation Trust, Infection Control, Clinical Laboratory Services, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston, Birmingham B15 2GW, UK. Tel.: þ44 (0)121 371 3787. E-mail address: [email protected] (M.I. Garvey).
including lifestyle risk factors, treatment-related infections, haemodialysis procedures, and non-compliance by healthcare workers to standard precautions.1,5 Preventing the transmission of HCV remains a key priority for reducing the burden of disease and subsequent sequelae of HCV-related disease in England.4 Typing of HCV isolates is of specific clinical interest, as the genotype is a marker of the likelihood of a response to therapy and serves as a guideline for the duration of treatment, although this is becoming clinically less important with the advent of pangenotypic direct-acting antiviral agents.6,7 Genotyping is also useful for investigating outbreaks of infections and for understanding the epidemiology of this virus.7 Several methods targeting different regions of the HCV genome have been used for assessing genotypes.7 The most accurate method
http://dx.doi.org/10.1016/j.jhin.2017.01.002 0195-6701/ª 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved. Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
2
M.I. Garvey et al. / Journal of Hospital Infection xxx (2017) 1e6
is to sequence an appropriate coding region that is divergent enough to allow the discrimination of types and subtypes.7e9 In this report we examine the usefulness of sequencing to identify the source of an HCV transmission event in a healthcare setting and how this focused the outbreak investigation.
Methods Design An outbreak control team (OCT) was convened comprising representatives from the hospital infection control team, director for infection prevention and control, senior renal medical and nursing staff, satellite dialysis nursing and management staff, Public Health England consultant in communicable disease and control, a member of each from the communication and risk compliance teams, and a consultant virologist. Outbreak management was based on national guidance for communicable diseases and expert knowledge of the outbreak team.10
Genotyping by sequencing was undertaken to compare the seroconverter’s virus to these five chronically infected HCV patients receiving dialysis who had temporal overlap with the seroconverter. Sequencing was performed by restriction fragment length polymorphism and NS5B sequencing as previously described.9 Analysis of the sequences was performed as previously described.9 Phylogenetic studies of a 328-nucleotide fragment of the NS5B sub-genomic region permitted genotypic comparisons of relatedness to be made. NS5B sequencing of the newly acquired HCV seroconverter revealed a genetically similar HCV in a patient under the care of UHB, which was designated the index case (Figure 1). The number of single nucleotide polymorphism (SNP) differences between the index and seroconverter was low at five polymorphisms, all of which were present as nucleotide mixtures, resulting in a homology of 98.5%; this high level of identity is consistent with a transmission event having occurred between them. A strong characteristic of HCV infection is its significant genetic diversity,
Setting University Hospitals Birmingham (UHB) NHS Foundation Trust is a major teaching hospital in Birmingham, UK, and provides clinical services to nearly one million patients every year. The dialysis unit at UHB consists of 32 beds with 1200 patients on haemodialysis and 130 patients on peritoneal dialysis.
Seroconverter Index patient
Results Case (seroconverter) A patient with end-stage renal disease requiring haemodialysis at a West Midlands regional dialysis centre was admitted to UHB due to suspected infection associated with a tunnelled dialysis line. During admission the patient spiked a temperature while on dialysis and was treated with antibiotics, the source of infection being the line which was removed. Routine blood testing of haemodialysis patients for bloodborne viruses is undertaken every three months; this was the case for the seroconverter. Five months after admission routine blood tests were positive for HCV antibody and HCV RNA. The patient had never tested positive for any bloodborne virus previously. The patient had no risk factors for HCV and a healthcareassociated transmission event was suspected. It was hypothesized that the HCV transmission event had occurred during the patient’s hospital admission based on a slight rise in alanine transaminase two months later. An OCT was convened to investigate the HCV seroconversion.
Typing The OCTs first approach was to identify with reasonable certainty where the infection had come from, i.e. identify an index case. If the OCT were not successful in identifying an index case, then all staff would have been screened for HCV. There were five other patients with chronic HCV who either dialysed at the regional dialysis centre or who were dialysing at the same time as the seroconverter was dialysing at UHB.
10.1 10
8
6
4
2
0
Nucleotide substitution per 100 residues
Figure 1. Phylogenetic tree of hepatitis C virus comparing selected patients at University Hospitals Birmingham NHS Foundation Trust. The difference in number of single nucleotide polymorphisms between the index and seroconverter was low at five polymorphisms, resulting in a homology of 98.5%; this high level of identity is consistent with a transmission event having occurred.
Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
Index discharged
63
the consequence of the absence of proofreading activity in RNA-dependent RNA polymerase, and the high level of viral replication during its life cycle.11 The mean frequency of nucleotide alterations occurring in HCV RNA is calculated at between 1.4 103 and 1.9 103 substitutions per nucleotide per year.11 As such, five or more changes during the time from infection from the index case till sequencing would be expected.11 As no stored blood from the seroconverter’s earlier negative bloodborne virus screens taken during previous UHB admissions were available for HCV RNA testing, it was not possible to pinpoint when the infection occurred.
3
62 61 60 59 58 57 56 Discharged
55 54 53 52 51
Timeline
50 49
The index case had chronic kidney disease requiring haemodialysis and been diagnosed with chronic HCV infection more than 10 years ago. In light of the sequencing data, epidemiology studies revealed that the index patient and the seroconverter had been on ward A at the same time (Figure 2). Both patients had received haemodialysis at UHB on three separate days (Figure 2). As the index patient had been identified, the OCT then explored the routes of possible transmission.
48 47 46 45 Admitted
PM bed AM bed 22 39
43 42 41 40 39
PM bed AM bed 30 32
44
Infection control-related outcomes e haemodialysis review
38 37 36 35 Index
32 31 30 29 28 27 26 25 Bed 24,1
24 23 22 21 20 19 18 17 16 15 14 13 12
Haemodialysis machines The two patients received haemodialysis on different machines, in different rooms, and cared for by different staff, so this was ruled out as a source of transmission. No other invasive procedures were performed on the patients during this time.
11 10 Bed 27
9 8 7 6 5 2 1 0
Bed 4
3
Index admitted
4
Unit inspection Inspection of the dialysis unit revealed hand hygiene audits of 59%. Based on the World Health Organization ‘five moments of hand hygiene’ the opportunity that was most missed was before touching a patient.15 The technique of hand hygiene was also not appropriate; for example, the use of alcohol gel was often rushed and not adequate. Educational sessions and
Day
33
Patients Patients who received dialysis at the same time as the index case are routinely screened for bloodborne viruses; none of this patient group has tested positive for HCV at present.12e14 Rescreening for HCV of all the patients dialysing with the serconverter at the regional dialysis centre and also all the patients admitted during the index patient’s stay revealed no secondary HCV cases. No additional follow-up of patients was required as all haemodialysis patients are screened for bloodborne viruses.
Seroconversion HCV+VE
34
Healthcare workers The OCT reviewed the timeline of healthcare workers who had looked after the case patients to identify whether there were links between the patients that could have been a source of transmission. Different healthcare professionals cared for these patients when they had received haemodialysis. No healthcare workers reported needlestick injuries or any clinical incidents during the time these patients had been receiving haemodialysis. None of the healthcare workers caring for the patients had ever reported needlestick injuries.
Figure 2. Timeline of the two patients involved in the HCV transmission: both the index and seroconverter. Admission and discharge dates are shown as well as any dialysis and phlebotomy procedures during the inpatient stay of both patients. The index case timeline is shown above the x-axis; the seroconverter timeline is shown below the x-axis. Diamonds represent admission and discharge dates; circles represent dialysis dates; triangles represent phlebotomy interventions. PM, afternoon; AM, morning; HCV, hepatitis C virus; þVE, positive; IV, intravenous.
M.I. Garvey et al. / Journal of Hospital Infection xxx (2017) 1e6
Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
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M.I. Garvey et al. / Journal of Hospital Infection xxx (2017) 1e6
daily hand hygiene audits were put in place to improve hand hygiene compliance. Personal protective equipment (PPE) usage was another issue: when staff removed PPE such as gloves and aprons, on occasions they did not decontaminate their hands. Educational sessions around usage of PPE were put into place to improve compliance with correct use. Environmental and equipment cleanliness was also an issue, as the environment and equipment were often found to be soiled. In some instances, blood was seen on pieces of high-risk equipment such as haemodialysis machines. A new procedure for the external decontamination of the dialysis machines has been developed with checklists/documentation for assurance. A standard operating procedure for decontamination of dialysis machines has been developed and implemented. Routine monitoring of equipment cleanliness has been implemented as practice on the unit. Training concerning bloodborne viruses for the staff was found to be outdated and medical staff did not receive specific bloodborne virus training. Bespoke education sessions for the medical teams have been undertaken with an updated teaching package. The package is included in the renal medical team’s annual infection control training. Conclusion Haemodialysis was unlikely to be the route of transmission, as no links between the patients could be identified.
Infection control related outcomes e ward A Patients All patients located on ward A during the same period as the index case were screened for HCV. For this group of patients currently none has tested positive for HCV. Healthcare workers The outbreak team decided that only staff who reported needlestick injuries during the index case’s stay on ward A would be screened for HCV. In total, three staff reported needlestick injuries during this time, all screening negative for HCV. All other healthcare staff would not be screened as the source of transmission for an infected healthcare worker was thought to be highly unlikely, as we had identified an index patient. All staff since 2007 undertaking exposure-prone procedures were screened for HCV, making an infected healthcare worker an extremely unlikely route of transmission in this investigation.12e14 Ward environment In light of the fact that the index case and seroconverter were on ward A at the same time, the ward was subjected to an infection control inspection by infection prevention nurses and an external renal dialysis nurse (Figure 1). The inspections consisted of visiting the areas on three occasions, making observations of practice including dialysis, environmental cleanliness, and hand hygiene practice. Ward inspection Inspection of ward A revealed similar issues as raised in the dialysis unit. Hand hygiene audits of 62.5% were obtained with hand hygiene moment 2 most missed. PPE usage was an issue when staff removed PPE without decontaminating their hands: the environment and equipment were found to be soiled with blood. All the corrective actions put in place on the dialysis unit
were rolled out to ward A. Educational and training sessions to ward A on hand hygiene increased hand hygiene compliance. Teaching concerning PPE usage improved compliance in decontaminating hands after glove removal. Monitoring of equipment cleanliness with particular attention to the blood gas machine, blood glucose monitors, equipment trolleys including phlebotomy trolley, and observation machines improved cleanliness, with no blood staining being observed in the preceding month. In addition, daily cleanliness checks which were implemented for patient bathrooms, consultation room, clinical rooms, and window sills improved cleanliness with no blood staining being observed in the preceding month. During the infection control inspections, aseptic technique (AT) trays were found to be used for multiple invasive blood procedures; for example, phlebotomy and cannulation, administration of intravenous products, and carrying of phlebotomy equipment to the patient’s bedside. AT trays would then be cleaned and reused throughout ward A. It was noted that these trays were often soiled with blood and not cleaned adequately before reuse, providing a mechanism of transmission of blood containing HCV. Differently coloured AT trays for all procedures involving blood are now used throughout ward A to eliminate this risk. From the epidemiological investigations, it was noted that the index patient had a high viral load (12,249,540 IU/mL of HCV RNA). When the timings for the invasive blood procedures were reviewed e for example administration of IV antibiotics e the seroconverter was usually dealt with after the index case. These procedures were carried out by the same member of staff, who tested negative for HCV. The staff member’s practice was audited and reviewed, with the only change being the use of differently coloured AT trays for all procedures involving blood. Conclusion The source of HCV transmission was suspected to be on ward A. The authors hypothesize that inappropriate hygiene standards in parenteral treatment leading to viral hepatitis transmission may be the likely source of transmission.
Discussion HCV is an established parenteral cause of viral hepatitis; infection may cause chronic hepatitis, potentially leading to cirrhosis, decompensated cirrhosis, and hepatocellular carcinoma.1,16 There are several risk factors for haemodialysis patients acquiring HCV infection. We identified multiple routes of potential transmission from poor hand hygiene, inappropriate PPE usage, environmental cleanliness issues, and possible issues with regard to invasive blood procedure practice using reusable AT trays. Molecular evolutionary analyses have been used to assess genetic similarities and to investigate transmission of clinical pathogens.6 A number of studies have shown that phylogenetic tree analysis of individual HCV RNA isolates provides a clear documentation of patientepatient transmission of HCV occurring within healthcare settings.17,18 Our results suggest that use of NS5B sequencing may reduce ambiguity regarding potential transmission events in hospitals and consequently inform infection prevention efforts about the direction and sequence of transmission. A patient with end-stage renal failure receiving haemodialysis was found to acquire HCV. No risk factors for HCV
Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
M.I. Garvey et al. / Journal of Hospital Infection xxx (2017) 1e6 infection were identified and a healthcare transmission event was suspected. Epidemiological investigation supported a healthcare-associated mode of transmission e an observation that was supported by the results of sequencing. On investigation, an index patient was identified who had spent time on the same ward as the patient who had acquired HCV. From infection control inspections on ward A, multiple failures in standard infection prevention and control precautions could have facilitated the spread of infection. At UHB we found issues on the dialysis unit and ward A with hand hygiene, inappropriate PPE, environment and equipment cleanliness with soiling of blood. On ward A we found that multiply invasive procedures involving blood (for example, cannulation, administration of intravenous or injectable medications) included the reuse of AT trays which were often inadequately cleaned, in some instances being soiled with blood. In the European food hygiene regulations, food safety management procedures are based on the principles of hazard analysis and critical control points.19 For the preparation of food the use of a colour coding system is used to prevent cross-contamination.19 At UHB this principle has been adapted and differently coloured AT trays are now used for separate invasive procedures involving blood, to avoid cross-contamination. A new cleaning checklist for these AT trays is also in place. From the epidemiological investigations it was noted that the index patient had a high viral load and often had an invasive procedure involving blood (such as administration of antibiotics) before the seroconverter. Despite the fact that the exact route or routes of infection were not identified, the authors hypothesize, that inappropriate hygiene standards in parenteral treatment led to viral hepatitis transmission. The index patient had a high HCV viral load; previous studies have concluded that, when there are high plasma levels of HCV RNA in patients and/or staff, only a fraction of blood or wound secretions from these infected individuals is required to transmit HCV to other patients.20 Previous reports have found HCV infection in dialysis units, hospital wards, surgical wards, and outpatient clinics.5,20 The most frequent infection prevention and control failures were use of multi-dose drug vials, reuse of equipment for capillary blood sampling, endomyocardial biopsy, and multiple mistakes in standard precaution compliance.1,4 Basic infection control practice towards bloodborne viruses needs consideration at all times, especially in a high-risk setting such as haemodialysis.1,5 In conclusion, our work shows that even in the twenty-first century, transmission events of healthcare-associated HCV infection may occur. Even when appropriate facilities are provided, there is no assurance that healthcare workers will not mishandle medical consumables and comply with basic good hygiene. Our experience demonstrates the importance of continuing audit of clinical practices in hospitals, as well as the need for microbiological vigilance in higher-risk units.
Acknowledgements We thank the Infection Prevention and Control Team and staff in the renal team at the University Hospitals Birmingham NHS Foundation Trust; also G. Kelly, lead dialysis nurse for Smethwick satellite unit, for help with the infection control inspections. Conflict of interest statement None declared.
5
Funding sources None.
References 1. Webster DP, Klenerman P, Dusheiko GM. Hepatitis C. Lancet 2015;385:1124e1135. 2. Bull RA, Eltahla AA, Rodrigo C, et al. A method for near full-length amplification and sequencing for six hepatitis C virus genotypes. BMC Genomics 2016;17:247. 3. Mohd Hanafiah K, Groeger J, Flaxman AD, Wiersma ST. Global epidemiology of hepatitis C virus infection: new estimates of age-specific antibody to HCV seroprevalence. Hepatology 2013;57:1333e1342. 4. Public Health England. Hepatitis C in the UK. 2015. Available at: https://www.gov.uk/government/uploads/system/uploads/ attachment_data/file/448710/NEW_FINAL_HCV_2015_IN_THE_ UK_REPORT_28072015_v2.pdf [last accessed January 2017]. 5. Duong CM, McLaws ML. An investigation of an outbreak of hepatitis C virus infections in a low-resourced hemodialysis unit in Vietnam. Am J Infect Control 2016;44:560e566. 6. Quer J, Gregori J, Rodrı´guez-Frias F, et al. High-resolution hepatitis C virus subtyping using NS5B deep sequencing and phylogeny, an alternative to current methods. J Clin Microbiol 2015;53:219e226. 7. Murphy DG, Willems B, Deschenes M, Hilzenrat N, Mousseaub R, Sabbah S. Use of sequence ananlysis of the NS5B region for routine genotyping of hepatitis C virus with reference to C/E and 50 untranslated region sequences. J Clin Microbiol 2007;45:1102e1112. 8. Laperche S, Lunel F, Izopet J, et al. Comparison of hepatitis C virus NS5b and 50 noncoding gene sequencing method in a multicenter study. J Clin Microbiol 2005;42:733e739. 9. May S, Ngui SL, Collins S, et al. Molecular epidemiology of newly acquired hepatitis C infections in England 2008e2011: genotype, phylogeny and mutation analysis. J Clin Virol 2015;64:6e11. 10. Public Health England. Communicable disease outbreak management. Operational guidance. 2014. Available at: https://www. gov.uk/government/uploads/system/uploads/attachment_data/ file/343723/12_8_2014_CD_Outbreak_Guidance_REandCT_2__2_. pdf [last accessed January 2017]. 11. Nasu A, Marusawa H, Ueda Y, et al. Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing. PLoS One 2011;6:e24907. 12. Tomkins SE, Rice BD, Roy K, Cullen B, Ncube FM. Universal treatment success among healthcare workers diagnosed with occupationally acquired acute hepatitis C. J Hosp Infect 2015;89:69e71. 13. Health and Safety Executive. Advisory Committee on dangerous pathogens protection against blood-borne infections in the workplace: HIV and hepatitis. Available at: http://www.hse.gov. uk/biosafety/diseases/bbv.pdf [last accessed January 2017]. 14. European Association for the Study of the Liver. EASL Clinical Practice Guidelines: management of hepatitis C virus infection. J Hepatol 2014;60:92e420. 15. World Health Organization. Guidelines on hand hygiene in health Care. First Global Patient Safety Challenge e Clean Care is Safer Care. 2009. Available at: http://apps.who.int/iris/bitstream/ 10665/44102/1/9789241597906_eng.pdf [last accessed January 2017]. 16. Scheel TK, Rice CM. Understanding the hepatitis C virus life cycle paves the way for highly effective therapies. Nat Med 2013;19:837e849. 17. Kokubo S, Horii T, Yonekawa O, Ozawa N, Mukaide M. A phylogenetic-tree analysis elucidating nosocomial transmission of hepatitis C in a haemodialysis unit. J Viral Hep 2002;9:450e454. 18. Abacioglu YH, Bacaksiz F, Bahar IH, Simmonds P. Molecular evidence of nosocomial transmission of hepatitis C virus in a
Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
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haemodialysis unit. Eur J Clin Microbiol Infect Dis 2000;19: 182e186. 19. Food Standards Agency. Safe catering e your guide to making food safely. 2015. https://www.food.gov.uk/sites/default/files/ multimedia/pdfs/pdf-ni/safe-catering.pdf [last accessed January 2017].
20. Ross RS, Viazov S, Gross T, Hofmann F, Siepp HM, Roggendorf M. Transmission of hepatitis C virus from a patient to an anesthesiology assistant to five patients. N Engl J Med 2000;343:1851e1854.
Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
Journal of Hospital Infection journal homepage: www.elsevierhealth.com/journals/jhin
Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting M.I. Garvey a, *, C.W. Bradley a, K.L. Holden a, P. Hewins a, S.-L. Ngui b, R. Tedder b, P. Jumaa a, E. Smit a, c a
University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital Birmingham, Edgbaston, Birmingham, UK Blood Borne Virus Unit, Microbiology Service Colindale, Public Health England, London, UK c Public Health England Birmingham Laboratory, Birmingham Heartlands Hospital, Birmingham, UK b
A R T I C L E
I N F O
Article history: Received 19 December 2016 Accepted 9 January 2017 Available online xxx Keywords: Hepatitis C NS5B genome sequencing Infection prevention and control Bloodborne transmission
S U M M A R Y
Hepatitis C virus (HCV) infection is a major health burden worldwide. A patient with no history of HCV infection while on a renal unit was found to seroconvert to HCV. Here we report the use of sequencing to postulate how transmission of HCV occurred in a healthcare setting, and how this guided our outbreak investigation. Based on infection control inspections the transmission event was surmised to be due to ward environmental contamination with blood and subsequent inoculation from intravenous interventions on the patient acquiring HCV. We discuss the interventions put in place in response to the outbreak investigation findings. Sequencing of healthcare-acquired HCV infections should be undertaken as routine practice in outbreak investigations. ª 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.
Introduction Hepatitis C virus (HCV) is a significant human pathogen and is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma.1,2 Most people affected live in resource-limited regions such as Asia, Africa, and the Middle East. It is estimated that around 214,000 individuals are chronically infected with HCV in the UK.3,4 There are several risk factors for haemodialysis patients acquiring HCV infection,
* Corresponding author. Address: University Hospitals Birmingham NHS Foundation Trust, Infection Control, Clinical Laboratory Services, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston, Birmingham B15 2GW, UK. Tel.: þ44 (0)121 371 3787. E-mail address: [email protected] (M.I. Garvey).
including lifestyle risk factors, treatment-related infections, haemodialysis procedures, and non-compliance by healthcare workers to standard precautions.1,5 Preventing the transmission of HCV remains a key priority for reducing the burden of disease and subsequent sequelae of HCV-related disease in England.4 Typing of HCV isolates is of specific clinical interest, as the genotype is a marker of the likelihood of a response to therapy and serves as a guideline for the duration of treatment, although this is becoming clinically less important with the advent of pangenotypic direct-acting antiviral agents.6,7 Genotyping is also useful for investigating outbreaks of infections and for understanding the epidemiology of this virus.7 Several methods targeting different regions of the HCV genome have been used for assessing genotypes.7 The most accurate method
http://dx.doi.org/10.1016/j.jhin.2017.01.002 0195-6701/ª 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved. Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
2
M.I. Garvey et al. / Journal of Hospital Infection xxx (2017) 1e6
is to sequence an appropriate coding region that is divergent enough to allow the discrimination of types and subtypes.7e9 In this report we examine the usefulness of sequencing to identify the source of an HCV transmission event in a healthcare setting and how this focused the outbreak investigation.
Methods Design An outbreak control team (OCT) was convened comprising representatives from the hospital infection control team, director for infection prevention and control, senior renal medical and nursing staff, satellite dialysis nursing and management staff, Public Health England consultant in communicable disease and control, a member of each from the communication and risk compliance teams, and a consultant virologist. Outbreak management was based on national guidance for communicable diseases and expert knowledge of the outbreak team.10
Genotyping by sequencing was undertaken to compare the seroconverter’s virus to these five chronically infected HCV patients receiving dialysis who had temporal overlap with the seroconverter. Sequencing was performed by restriction fragment length polymorphism and NS5B sequencing as previously described.9 Analysis of the sequences was performed as previously described.9 Phylogenetic studies of a 328-nucleotide fragment of the NS5B sub-genomic region permitted genotypic comparisons of relatedness to be made. NS5B sequencing of the newly acquired HCV seroconverter revealed a genetically similar HCV in a patient under the care of UHB, which was designated the index case (Figure 1). The number of single nucleotide polymorphism (SNP) differences between the index and seroconverter was low at five polymorphisms, all of which were present as nucleotide mixtures, resulting in a homology of 98.5%; this high level of identity is consistent with a transmission event having occurred between them. A strong characteristic of HCV infection is its significant genetic diversity,
Setting University Hospitals Birmingham (UHB) NHS Foundation Trust is a major teaching hospital in Birmingham, UK, and provides clinical services to nearly one million patients every year. The dialysis unit at UHB consists of 32 beds with 1200 patients on haemodialysis and 130 patients on peritoneal dialysis.
Seroconverter Index patient
Results Case (seroconverter) A patient with end-stage renal disease requiring haemodialysis at a West Midlands regional dialysis centre was admitted to UHB due to suspected infection associated with a tunnelled dialysis line. During admission the patient spiked a temperature while on dialysis and was treated with antibiotics, the source of infection being the line which was removed. Routine blood testing of haemodialysis patients for bloodborne viruses is undertaken every three months; this was the case for the seroconverter. Five months after admission routine blood tests were positive for HCV antibody and HCV RNA. The patient had never tested positive for any bloodborne virus previously. The patient had no risk factors for HCV and a healthcareassociated transmission event was suspected. It was hypothesized that the HCV transmission event had occurred during the patient’s hospital admission based on a slight rise in alanine transaminase two months later. An OCT was convened to investigate the HCV seroconversion.
Typing The OCTs first approach was to identify with reasonable certainty where the infection had come from, i.e. identify an index case. If the OCT were not successful in identifying an index case, then all staff would have been screened for HCV. There were five other patients with chronic HCV who either dialysed at the regional dialysis centre or who were dialysing at the same time as the seroconverter was dialysing at UHB.
10.1 10
8
6
4
2
0
Nucleotide substitution per 100 residues
Figure 1. Phylogenetic tree of hepatitis C virus comparing selected patients at University Hospitals Birmingham NHS Foundation Trust. The difference in number of single nucleotide polymorphisms between the index and seroconverter was low at five polymorphisms, resulting in a homology of 98.5%; this high level of identity is consistent with a transmission event having occurred.
Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
Index discharged
63
the consequence of the absence of proofreading activity in RNA-dependent RNA polymerase, and the high level of viral replication during its life cycle.11 The mean frequency of nucleotide alterations occurring in HCV RNA is calculated at between 1.4 103 and 1.9 103 substitutions per nucleotide per year.11 As such, five or more changes during the time from infection from the index case till sequencing would be expected.11 As no stored blood from the seroconverter’s earlier negative bloodborne virus screens taken during previous UHB admissions were available for HCV RNA testing, it was not possible to pinpoint when the infection occurred.
3
62 61 60 59 58 57 56 Discharged
55 54 53 52 51
Timeline
50 49
The index case had chronic kidney disease requiring haemodialysis and been diagnosed with chronic HCV infection more than 10 years ago. In light of the sequencing data, epidemiology studies revealed that the index patient and the seroconverter had been on ward A at the same time (Figure 2). Both patients had received haemodialysis at UHB on three separate days (Figure 2). As the index patient had been identified, the OCT then explored the routes of possible transmission.
48 47 46 45 Admitted
PM bed AM bed 22 39
43 42 41 40 39
PM bed AM bed 30 32
44
Infection control-related outcomes e haemodialysis review
38 37 36 35 Index
32 31 30 29 28 27 26 25 Bed 24,1
24 23 22 21 20 19 18 17 16 15 14 13 12
Haemodialysis machines The two patients received haemodialysis on different machines, in different rooms, and cared for by different staff, so this was ruled out as a source of transmission. No other invasive procedures were performed on the patients during this time.
11 10 Bed 27
9 8 7 6 5 2 1 0
Bed 4
3
Index admitted
4
Unit inspection Inspection of the dialysis unit revealed hand hygiene audits of 59%. Based on the World Health Organization ‘five moments of hand hygiene’ the opportunity that was most missed was before touching a patient.15 The technique of hand hygiene was also not appropriate; for example, the use of alcohol gel was often rushed and not adequate. Educational sessions and
Day
33
Patients Patients who received dialysis at the same time as the index case are routinely screened for bloodborne viruses; none of this patient group has tested positive for HCV at present.12e14 Rescreening for HCV of all the patients dialysing with the serconverter at the regional dialysis centre and also all the patients admitted during the index patient’s stay revealed no secondary HCV cases. No additional follow-up of patients was required as all haemodialysis patients are screened for bloodborne viruses.
Seroconversion HCV+VE
34
Healthcare workers The OCT reviewed the timeline of healthcare workers who had looked after the case patients to identify whether there were links between the patients that could have been a source of transmission. Different healthcare professionals cared for these patients when they had received haemodialysis. No healthcare workers reported needlestick injuries or any clinical incidents during the time these patients had been receiving haemodialysis. None of the healthcare workers caring for the patients had ever reported needlestick injuries.
Figure 2. Timeline of the two patients involved in the HCV transmission: both the index and seroconverter. Admission and discharge dates are shown as well as any dialysis and phlebotomy procedures during the inpatient stay of both patients. The index case timeline is shown above the x-axis; the seroconverter timeline is shown below the x-axis. Diamonds represent admission and discharge dates; circles represent dialysis dates; triangles represent phlebotomy interventions. PM, afternoon; AM, morning; HCV, hepatitis C virus; þVE, positive; IV, intravenous.
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daily hand hygiene audits were put in place to improve hand hygiene compliance. Personal protective equipment (PPE) usage was another issue: when staff removed PPE such as gloves and aprons, on occasions they did not decontaminate their hands. Educational sessions around usage of PPE were put into place to improve compliance with correct use. Environmental and equipment cleanliness was also an issue, as the environment and equipment were often found to be soiled. In some instances, blood was seen on pieces of high-risk equipment such as haemodialysis machines. A new procedure for the external decontamination of the dialysis machines has been developed with checklists/documentation for assurance. A standard operating procedure for decontamination of dialysis machines has been developed and implemented. Routine monitoring of equipment cleanliness has been implemented as practice on the unit. Training concerning bloodborne viruses for the staff was found to be outdated and medical staff did not receive specific bloodborne virus training. Bespoke education sessions for the medical teams have been undertaken with an updated teaching package. The package is included in the renal medical team’s annual infection control training. Conclusion Haemodialysis was unlikely to be the route of transmission, as no links between the patients could be identified.
Infection control related outcomes e ward A Patients All patients located on ward A during the same period as the index case were screened for HCV. For this group of patients currently none has tested positive for HCV. Healthcare workers The outbreak team decided that only staff who reported needlestick injuries during the index case’s stay on ward A would be screened for HCV. In total, three staff reported needlestick injuries during this time, all screening negative for HCV. All other healthcare staff would not be screened as the source of transmission for an infected healthcare worker was thought to be highly unlikely, as we had identified an index patient. All staff since 2007 undertaking exposure-prone procedures were screened for HCV, making an infected healthcare worker an extremely unlikely route of transmission in this investigation.12e14 Ward environment In light of the fact that the index case and seroconverter were on ward A at the same time, the ward was subjected to an infection control inspection by infection prevention nurses and an external renal dialysis nurse (Figure 1). The inspections consisted of visiting the areas on three occasions, making observations of practice including dialysis, environmental cleanliness, and hand hygiene practice. Ward inspection Inspection of ward A revealed similar issues as raised in the dialysis unit. Hand hygiene audits of 62.5% were obtained with hand hygiene moment 2 most missed. PPE usage was an issue when staff removed PPE without decontaminating their hands: the environment and equipment were found to be soiled with blood. All the corrective actions put in place on the dialysis unit
were rolled out to ward A. Educational and training sessions to ward A on hand hygiene increased hand hygiene compliance. Teaching concerning PPE usage improved compliance in decontaminating hands after glove removal. Monitoring of equipment cleanliness with particular attention to the blood gas machine, blood glucose monitors, equipment trolleys including phlebotomy trolley, and observation machines improved cleanliness, with no blood staining being observed in the preceding month. In addition, daily cleanliness checks which were implemented for patient bathrooms, consultation room, clinical rooms, and window sills improved cleanliness with no blood staining being observed in the preceding month. During the infection control inspections, aseptic technique (AT) trays were found to be used for multiple invasive blood procedures; for example, phlebotomy and cannulation, administration of intravenous products, and carrying of phlebotomy equipment to the patient’s bedside. AT trays would then be cleaned and reused throughout ward A. It was noted that these trays were often soiled with blood and not cleaned adequately before reuse, providing a mechanism of transmission of blood containing HCV. Differently coloured AT trays for all procedures involving blood are now used throughout ward A to eliminate this risk. From the epidemiological investigations, it was noted that the index patient had a high viral load (12,249,540 IU/mL of HCV RNA). When the timings for the invasive blood procedures were reviewed e for example administration of IV antibiotics e the seroconverter was usually dealt with after the index case. These procedures were carried out by the same member of staff, who tested negative for HCV. The staff member’s practice was audited and reviewed, with the only change being the use of differently coloured AT trays for all procedures involving blood. Conclusion The source of HCV transmission was suspected to be on ward A. The authors hypothesize that inappropriate hygiene standards in parenteral treatment leading to viral hepatitis transmission may be the likely source of transmission.
Discussion HCV is an established parenteral cause of viral hepatitis; infection may cause chronic hepatitis, potentially leading to cirrhosis, decompensated cirrhosis, and hepatocellular carcinoma.1,16 There are several risk factors for haemodialysis patients acquiring HCV infection. We identified multiple routes of potential transmission from poor hand hygiene, inappropriate PPE usage, environmental cleanliness issues, and possible issues with regard to invasive blood procedure practice using reusable AT trays. Molecular evolutionary analyses have been used to assess genetic similarities and to investigate transmission of clinical pathogens.6 A number of studies have shown that phylogenetic tree analysis of individual HCV RNA isolates provides a clear documentation of patientepatient transmission of HCV occurring within healthcare settings.17,18 Our results suggest that use of NS5B sequencing may reduce ambiguity regarding potential transmission events in hospitals and consequently inform infection prevention efforts about the direction and sequence of transmission. A patient with end-stage renal failure receiving haemodialysis was found to acquire HCV. No risk factors for HCV
Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002
M.I. Garvey et al. / Journal of Hospital Infection xxx (2017) 1e6 infection were identified and a healthcare transmission event was suspected. Epidemiological investigation supported a healthcare-associated mode of transmission e an observation that was supported by the results of sequencing. On investigation, an index patient was identified who had spent time on the same ward as the patient who had acquired HCV. From infection control inspections on ward A, multiple failures in standard infection prevention and control precautions could have facilitated the spread of infection. At UHB we found issues on the dialysis unit and ward A with hand hygiene, inappropriate PPE, environment and equipment cleanliness with soiling of blood. On ward A we found that multiply invasive procedures involving blood (for example, cannulation, administration of intravenous or injectable medications) included the reuse of AT trays which were often inadequately cleaned, in some instances being soiled with blood. In the European food hygiene regulations, food safety management procedures are based on the principles of hazard analysis and critical control points.19 For the preparation of food the use of a colour coding system is used to prevent cross-contamination.19 At UHB this principle has been adapted and differently coloured AT trays are now used for separate invasive procedures involving blood, to avoid cross-contamination. A new cleaning checklist for these AT trays is also in place. From the epidemiological investigations it was noted that the index patient had a high viral load and often had an invasive procedure involving blood (such as administration of antibiotics) before the seroconverter. Despite the fact that the exact route or routes of infection were not identified, the authors hypothesize, that inappropriate hygiene standards in parenteral treatment led to viral hepatitis transmission. The index patient had a high HCV viral load; previous studies have concluded that, when there are high plasma levels of HCV RNA in patients and/or staff, only a fraction of blood or wound secretions from these infected individuals is required to transmit HCV to other patients.20 Previous reports have found HCV infection in dialysis units, hospital wards, surgical wards, and outpatient clinics.5,20 The most frequent infection prevention and control failures were use of multi-dose drug vials, reuse of equipment for capillary blood sampling, endomyocardial biopsy, and multiple mistakes in standard precaution compliance.1,4 Basic infection control practice towards bloodborne viruses needs consideration at all times, especially in a high-risk setting such as haemodialysis.1,5 In conclusion, our work shows that even in the twenty-first century, transmission events of healthcare-associated HCV infection may occur. Even when appropriate facilities are provided, there is no assurance that healthcare workers will not mishandle medical consumables and comply with basic good hygiene. Our experience demonstrates the importance of continuing audit of clinical practices in hospitals, as well as the need for microbiological vigilance in higher-risk units.
Acknowledgements We thank the Infection Prevention and Control Team and staff in the renal team at the University Hospitals Birmingham NHS Foundation Trust; also G. Kelly, lead dialysis nurse for Smethwick satellite unit, for help with the infection control inspections. Conflict of interest statement None declared.
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Funding sources None.
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Please cite this article in press as: Garvey MI, et al., Use of genome sequencing to identify hepatitis C virus transmission in a renal healthcare setting, Journal of Hospital Infection (2017), http://dx.doi.org/10.1016/j.jhin.2017.01.002