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Half of ‘Micrococcus spp.’ cases identified by conventional methods are revealed as other life-threatening bacteria with different drug susceptibility patterns by 16S ribosomal RNA gene sequencing
J Infect Chemother xxx (xxxx) xxx
Contents lists available at ScienceDirect
Journal of Infection and Chemotherapy journal homepage: http://www.elsevier.com/locate/jic
Note
Half of ‘Micrococcus spp.’ cases identified by conventional methods are revealed as other life-threatening bacteria with different drug susceptibility patterns by 16S ribosomal RNA gene sequencing Kazuhiro Noguchi, Ryosei Nishimura*, Yasuhiro Ikawa, Shintaro Mase, Yusuke Matsuda, Toshihiro Fujiki, Rie Kuroda, Raita Araki, Hideaki Maeba, Akihiro Yachie Department of Pediatrics, Kanazawa University, Kanazawa, Japan
a r t i c l e i n f o
a b s t r a c t
Article history: Received 2 September 2019 Received in revised form 17 October 2019 Accepted 29 October 2019 Available online xxx
Bacterial infection during chemotherapy is a fatal complication, therefore precise identification of the pathogenic microorganism is required for treatment. We report that 2 of 4 pediatric patients with malignancy who were diagnosed with Micrococcus spp. infection by conventional methods were finally revealed to have Kytococcus schroeteri and Kocuria marina infection by 16S ribosomal RNA gene sequence analysis (16S rRNA analysis). Although K. schroeteri is morphologically similar to Micrococcus spp., its drug susceptibility profile is quite different from that of Micrococcus spp. K. schroeteri is resistant to penicillin and cephalosporin, which are effective for Micrococcus spp. In fact, penicillin-resistant lethal pneumonia caused by K. schroeteri has been reported in compromised hosts. Based on our results, Micrococcus spp. determined by conventional methods could contain other life-threatening bacteria with different drug susceptibility patterns from Micrococcus spp. To develop an effective empirical treatment for immunocompromised hosts, accumulation of pathogen data by 16S rRNA analysis is required. © 2019 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
Keywords: 16S rRNA gene sequence analysis Micrococcus Bacterial infection Kytococcus schroeteri Kocuria marina
Bacterial infection during chemotherapy is a fatal complication and requires effective empirical therapy. Unfamiliar pathogens, which are undetectable by conventional biochemical and morphological methods, have been identified by 16S ribosomal RNA gene sequence analysis (16S rRNA analysis) [1]. However, clinical information regarding unfamiliar bacteria has not been sufficiently accumulated thus far. Here, we report that 2 of 4 pediatric patients with malignancy who were diagnosed with Micrococcus spp. infection by conventional methods were finally revealed to have Kytococcus schroeteri and Kocuria marina infection by 16S rRNA analysis. A 4-year-old girl with acute lymphoblastic leukemia (ALL) had a fever during maintenance chemotherapy. She was diagnosed with catheter-related bloodstream infection. Micrococcus spp. was
Abbreviations: ALL, acute lymphoblastic leukemia; RMS, rhabdomyosarcoma; AML, acute myeloid leukemia. * Corresponding author. Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8641, Japan. E-mail address: [email protected] (R. Nishimura).
suspected based on conventional blood culture methods, however, the colony color slightly differed from that of typical Micrococcus spp. We subsequently performed 16S rRNA analysis using bacterial DNA extracted from the colony according to the method previously reported [2] and identified Kytococcus schroeteri. As a result of this case, we hypothesized that Micrococcus spp. detected by conventional methods may be other bacteria. To test this, we performed 16S rRNA analysis of bacterial colonies that had been identified as Micrococcus spp. by conventional methods from 4 pediatric patients with malignancy (2 cases of ALL including the above case, 1 case of acute myeloid leukemia and 1 case of brain tumor) in the past 3 years in our institute [Table 1 and Fig. 1 near here]. We found that half of ‘Micrococcus spp.’ cases were other bacteria, namely K. schroeteri and Kocuria marina. K. schroeteri is a Gram-positive coccus that mainly exists on the skin as an indigenous bacterium that can cause opportunistic infection in compromised hosts. Although K. schroeteri is morphologically similar to Micrococcus spp., its drug susceptibility profile is quite different from that of Micrococcus spp [3]. K. schroeteri is resistant to penicillin and cephalosporin, which are effective for Micrococcus spp. In fact, penicillin-resistant lethal
https://doi.org/10.1016/j.jiac.2019.10.019 1341-321X/© 2019 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
Please cite this article as: Noguchi K et al., Half of ‘Micrococcus spp.’ cases identified by conventional methods are revealed as other lifethreatening bacteria with different drug susceptibility patterns by 16S ribosomal RNA gene sequencing, J Infect Chemother, https://doi.org/ 10.1016/j.jiac.2019.10.019
2
K. Noguchi et al. / J Infect Chemother xxx (xxxx) xxx
Table 1 Results of 16S rRNA gene sequencing for 4 cases diagnosed as Micrococcus spp. infection by biochemical and morphological analyses. Case
4-year-old girl
5-year-old boy
12-year-old girl
11-year-old boy
Background Colony appearancea Biological and morphological analysis 16S rRNA gene sequencing
ALL yellow Micrococcus Kytococcus schroeteri
ALL yellow Micrococcus Kocuria marina
RMS yellow Micrococcus Micrococcus
AML yellow Micrococcus Micrococcus
ALL, acute lymphoid leukemia; RMS, rhabdomyosarcoma; AML, acute myeloid leukemia. a Each colony picture is shown in Fig. 1.
case
4-year-old girl
5-year-old boy
12-year-old girl 11-year-old boy
colony
Fig. 1. Colony appearance of each cases. The difference is too slight to distinguish them by colony appearance.
pneumonia caused by K. schroeteri has been reported in compromised hosts [3]. K. schroeteri is susceptible to vancomycin, however, vancomycin becomes ineffective after the patient develops severe pneumonia [4]. K. marina is a Gram-positive coccus that also mainly exists on the skin as an indigenous bacterium, and it could be identified only by 16S rRNA analysis, similar to K. schroeteri. K. marina is resistant to penicillin G and has a different susceptibility profile than that of Micrococcus spp [5]. However, only a few cases of K. marina infection have been reported, thus, adequate antibiotic selection is unknown. According to a previous report, 3% (11/345 cases) of sepsis in pediatric cases with malignancy is caused by Micrococcus spp [6]. Based on our results, Micrococcus spp. determined by conventional methods could contain other life-threatening bacteria with different drug susceptibility patterns from Micrococcus spp. With this in mind, we propose that early initiation of vancomycin should be required when Micrococcus spp. infection is diagnosed by conventional methods. Some experts might recognize slight difference in colony color of such bacteria from those of Micrococcus spp, however most of them are indistinguishable [7,8]. In addition to 16S rRNA analysis, matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems are expected as a new identification tool of microorganisms with ease and less time if the detailed database especially for species-specific mass spectrum are available. Indeed, some cases of K. schroeteri and K. marina infection have been identified by MALDI-TOF MS [9,10]. Therefore, to develop an effective empirical treatment for immunocompromised hosts, accumulation of pathogen data by 16S rRNA analysis is required. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Authorship statement All authors meet the ICMJE authorship criteria. K.N. wrote the manuscript. R.N., Y.I., S.M., Y.M., T.F., R.K., R.A. and H.M. have
contributed to analysis and interpretation of data. A.Y. was the principal investigator and takes primary responsibility for the paper. Declaration of Competing Interest None. References [1] Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007;45(9):2761e4. [2] Clarridge 3rd JE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004;17(4):840e62. [3] Hodiamont CJ, Huisman C, Spanjaard L, van Ketel RJ. Kytococcus schroeteri pneumonia in two patients with a hematological malignancy. Infection 2010;38(2):138e40. [4] Amaraneni A, Malik D, Jasra S, Chandana SR, Garg D. Kytococcus schroeteri bacteremia in a patient with hairy cell leukemia: a case report and review of the literature. Case Rep Infect Dis 2015;2015:217307. https://doi.org/10.1155/ 2015/217307. [5] Savini V, Catavitello C, Masciarelli G, Astolfi D, Balbinot A, Bianco A, et al. Drug sensitivity and clinical impact of members of the genus Kocuria. J Med Microbiol 2010;59:1395e402. [6] Paulus SC, van Saene HK, Hemsworth S, Hughes J, Ng A, Pizer BL. A prospective study of septicaemia on a paediatric oncology unit: a three-year experience at the Royal Liverpool Children's Hospital Alder Hey, UK. Eur J Cancer 2005;41(14):2132e40. [7] Chan JF, Wong SS, Leung SS, Fan RY, Ngan AH, To KK, et al. First report of chronic implant-related septic arthritis and osteomyelitis due to Kytococcus schroeteri and a review of human K. schroeteri infections. Infection 2012;40(5):567e73. [8] Kandi V, Palange P, Vaish R, Bhatti AB, Kale V, Kandi MR, et al. Emerging bacterial infection: identification and clinical significance of Kocuria species. Cureus 2016;8(8):e731. [9] Bayraktar B, Dalgic N, Duman N, Petmezci E. First case of bacteremia caused by Kytococcus schroeteri in a child with congenital adrenal hyperplasia. Pediatr Infect Dis J 2018;37(12):e304e5. [10] Paulcrano G, Balzaretti M, Grosini A, Piacentini V, Poddighe D. First report of Kocuria marina bloodstream infection unrelated to a central venous catheter: a mini-review on an emerging and under-recognized opportunistic pathogen. Infez Med 2017;25(1):71e4.
Please cite this article as: Noguchi K et al., Half of ‘Micrococcus spp.’ cases identified by conventional methods are revealed as other lifethreatening bacteria with different drug susceptibility patterns by 16S ribosomal RNA gene sequencing, J Infect Chemother, https://doi.org/ 10.1016/j.jiac.2019.10.019
Contents lists available at ScienceDirect
Journal of Infection and Chemotherapy journal homepage: http://www.elsevier.com/locate/jic
Note
Half of ‘Micrococcus spp.’ cases identified by conventional methods are revealed as other life-threatening bacteria with different drug susceptibility patterns by 16S ribosomal RNA gene sequencing Kazuhiro Noguchi, Ryosei Nishimura*, Yasuhiro Ikawa, Shintaro Mase, Yusuke Matsuda, Toshihiro Fujiki, Rie Kuroda, Raita Araki, Hideaki Maeba, Akihiro Yachie Department of Pediatrics, Kanazawa University, Kanazawa, Japan
a r t i c l e i n f o
a b s t r a c t
Article history: Received 2 September 2019 Received in revised form 17 October 2019 Accepted 29 October 2019 Available online xxx
Bacterial infection during chemotherapy is a fatal complication, therefore precise identification of the pathogenic microorganism is required for treatment. We report that 2 of 4 pediatric patients with malignancy who were diagnosed with Micrococcus spp. infection by conventional methods were finally revealed to have Kytococcus schroeteri and Kocuria marina infection by 16S ribosomal RNA gene sequence analysis (16S rRNA analysis). Although K. schroeteri is morphologically similar to Micrococcus spp., its drug susceptibility profile is quite different from that of Micrococcus spp. K. schroeteri is resistant to penicillin and cephalosporin, which are effective for Micrococcus spp. In fact, penicillin-resistant lethal pneumonia caused by K. schroeteri has been reported in compromised hosts. Based on our results, Micrococcus spp. determined by conventional methods could contain other life-threatening bacteria with different drug susceptibility patterns from Micrococcus spp. To develop an effective empirical treatment for immunocompromised hosts, accumulation of pathogen data by 16S rRNA analysis is required. © 2019 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
Keywords: 16S rRNA gene sequence analysis Micrococcus Bacterial infection Kytococcus schroeteri Kocuria marina
Bacterial infection during chemotherapy is a fatal complication and requires effective empirical therapy. Unfamiliar pathogens, which are undetectable by conventional biochemical and morphological methods, have been identified by 16S ribosomal RNA gene sequence analysis (16S rRNA analysis) [1]. However, clinical information regarding unfamiliar bacteria has not been sufficiently accumulated thus far. Here, we report that 2 of 4 pediatric patients with malignancy who were diagnosed with Micrococcus spp. infection by conventional methods were finally revealed to have Kytococcus schroeteri and Kocuria marina infection by 16S rRNA analysis. A 4-year-old girl with acute lymphoblastic leukemia (ALL) had a fever during maintenance chemotherapy. She was diagnosed with catheter-related bloodstream infection. Micrococcus spp. was
Abbreviations: ALL, acute lymphoblastic leukemia; RMS, rhabdomyosarcoma; AML, acute myeloid leukemia. * Corresponding author. Department of Pediatrics, School of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takaramachi, Kanazawa, Ishikawa 920-8641, Japan. E-mail address: [email protected] (R. Nishimura).
suspected based on conventional blood culture methods, however, the colony color slightly differed from that of typical Micrococcus spp. We subsequently performed 16S rRNA analysis using bacterial DNA extracted from the colony according to the method previously reported [2] and identified Kytococcus schroeteri. As a result of this case, we hypothesized that Micrococcus spp. detected by conventional methods may be other bacteria. To test this, we performed 16S rRNA analysis of bacterial colonies that had been identified as Micrococcus spp. by conventional methods from 4 pediatric patients with malignancy (2 cases of ALL including the above case, 1 case of acute myeloid leukemia and 1 case of brain tumor) in the past 3 years in our institute [Table 1 and Fig. 1 near here]. We found that half of ‘Micrococcus spp.’ cases were other bacteria, namely K. schroeteri and Kocuria marina. K. schroeteri is a Gram-positive coccus that mainly exists on the skin as an indigenous bacterium that can cause opportunistic infection in compromised hosts. Although K. schroeteri is morphologically similar to Micrococcus spp., its drug susceptibility profile is quite different from that of Micrococcus spp [3]. K. schroeteri is resistant to penicillin and cephalosporin, which are effective for Micrococcus spp. In fact, penicillin-resistant lethal
https://doi.org/10.1016/j.jiac.2019.10.019 1341-321X/© 2019 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
Please cite this article as: Noguchi K et al., Half of ‘Micrococcus spp.’ cases identified by conventional methods are revealed as other lifethreatening bacteria with different drug susceptibility patterns by 16S ribosomal RNA gene sequencing, J Infect Chemother, https://doi.org/ 10.1016/j.jiac.2019.10.019
2
K. Noguchi et al. / J Infect Chemother xxx (xxxx) xxx
Table 1 Results of 16S rRNA gene sequencing for 4 cases diagnosed as Micrococcus spp. infection by biochemical and morphological analyses. Case
4-year-old girl
5-year-old boy
12-year-old girl
11-year-old boy
Background Colony appearancea Biological and morphological analysis 16S rRNA gene sequencing
ALL yellow Micrococcus Kytococcus schroeteri
ALL yellow Micrococcus Kocuria marina
RMS yellow Micrococcus Micrococcus
AML yellow Micrococcus Micrococcus
ALL, acute lymphoid leukemia; RMS, rhabdomyosarcoma; AML, acute myeloid leukemia. a Each colony picture is shown in Fig. 1.
case
4-year-old girl
5-year-old boy
12-year-old girl 11-year-old boy
colony
Fig. 1. Colony appearance of each cases. The difference is too slight to distinguish them by colony appearance.
pneumonia caused by K. schroeteri has been reported in compromised hosts [3]. K. schroeteri is susceptible to vancomycin, however, vancomycin becomes ineffective after the patient develops severe pneumonia [4]. K. marina is a Gram-positive coccus that also mainly exists on the skin as an indigenous bacterium, and it could be identified only by 16S rRNA analysis, similar to K. schroeteri. K. marina is resistant to penicillin G and has a different susceptibility profile than that of Micrococcus spp [5]. However, only a few cases of K. marina infection have been reported, thus, adequate antibiotic selection is unknown. According to a previous report, 3% (11/345 cases) of sepsis in pediatric cases with malignancy is caused by Micrococcus spp [6]. Based on our results, Micrococcus spp. determined by conventional methods could contain other life-threatening bacteria with different drug susceptibility patterns from Micrococcus spp. With this in mind, we propose that early initiation of vancomycin should be required when Micrococcus spp. infection is diagnosed by conventional methods. Some experts might recognize slight difference in colony color of such bacteria from those of Micrococcus spp, however most of them are indistinguishable [7,8]. In addition to 16S rRNA analysis, matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems are expected as a new identification tool of microorganisms with ease and less time if the detailed database especially for species-specific mass spectrum are available. Indeed, some cases of K. schroeteri and K. marina infection have been identified by MALDI-TOF MS [9,10]. Therefore, to develop an effective empirical treatment for immunocompromised hosts, accumulation of pathogen data by 16S rRNA analysis is required. This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. Authorship statement All authors meet the ICMJE authorship criteria. K.N. wrote the manuscript. R.N., Y.I., S.M., Y.M., T.F., R.K., R.A. and H.M. have
contributed to analysis and interpretation of data. A.Y. was the principal investigator and takes primary responsibility for the paper. Declaration of Competing Interest None. References [1] Janda JM, Abbott SL. 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 2007;45(9):2761e4. [2] Clarridge 3rd JE. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004;17(4):840e62. [3] Hodiamont CJ, Huisman C, Spanjaard L, van Ketel RJ. Kytococcus schroeteri pneumonia in two patients with a hematological malignancy. Infection 2010;38(2):138e40. [4] Amaraneni A, Malik D, Jasra S, Chandana SR, Garg D. Kytococcus schroeteri bacteremia in a patient with hairy cell leukemia: a case report and review of the literature. Case Rep Infect Dis 2015;2015:217307. https://doi.org/10.1155/ 2015/217307. [5] Savini V, Catavitello C, Masciarelli G, Astolfi D, Balbinot A, Bianco A, et al. Drug sensitivity and clinical impact of members of the genus Kocuria. J Med Microbiol 2010;59:1395e402. [6] Paulus SC, van Saene HK, Hemsworth S, Hughes J, Ng A, Pizer BL. A prospective study of septicaemia on a paediatric oncology unit: a three-year experience at the Royal Liverpool Children's Hospital Alder Hey, UK. Eur J Cancer 2005;41(14):2132e40. [7] Chan JF, Wong SS, Leung SS, Fan RY, Ngan AH, To KK, et al. First report of chronic implant-related septic arthritis and osteomyelitis due to Kytococcus schroeteri and a review of human K. schroeteri infections. Infection 2012;40(5):567e73. [8] Kandi V, Palange P, Vaish R, Bhatti AB, Kale V, Kandi MR, et al. Emerging bacterial infection: identification and clinical significance of Kocuria species. Cureus 2016;8(8):e731. [9] Bayraktar B, Dalgic N, Duman N, Petmezci E. First case of bacteremia caused by Kytococcus schroeteri in a child with congenital adrenal hyperplasia. Pediatr Infect Dis J 2018;37(12):e304e5. [10] Paulcrano G, Balzaretti M, Grosini A, Piacentini V, Poddighe D. First report of Kocuria marina bloodstream infection unrelated to a central venous catheter: a mini-review on an emerging and under-recognized opportunistic pathogen. Infez Med 2017;25(1):71e4.
Please cite this article as: Noguchi K et al., Half of ‘Micrococcus spp.’ cases identified by conventional methods are revealed as other lifethreatening bacteria with different drug susceptibility patterns by 16S ribosomal RNA gene sequencing, J Infect Chemother, https://doi.org/ 10.1016/j.jiac.2019.10.019