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Pitout JDD, Peirano G, Matsumura Y, DeVinney R, Chen L. Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance. Antimicrob Agents Chemother 2024; 68:e0133923. [PMID: 38193668 PMCID: PMC10869336 DOI: 10.1128/aac.01339-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.
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Affiliation(s)
- Johann D. D. Pitout
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Yasufumi Matsumura
- Kyoto University Graduate School of Medicine, Pretoria, Gauteng, South Africa
| | | | - Liang Chen
- Meridian Health Center for Discovery and Innovation, Kyoto, Japan
- Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
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Ba X, Guo Y, Moran RA, Doughty EL, Liu B, Yao L, Li J, He N, Shen S, Li Y, van Schaik W, McNally A, Holmes MA, Zhuo C. Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone. Nat Commun 2024; 15:494. [PMID: 38216585 PMCID: PMC10786849 DOI: 10.1038/s41467-023-43854-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/22/2023] [Indexed: 01/14/2024] Open
Abstract
Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children's hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the blaOXA-181-bearing X3 plasmid, but carries a F-type plasmid containing blaNDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence.
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Affiliation(s)
- Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Yingyi Guo
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Emma L Doughty
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Baomo Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Likang Yao
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiahui Li
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Nanhao He
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Yang Li
- Department of Clinical Laboratory, Children's Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom.
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
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Chen L, Peirano G, Yen K, Wang B, Terlecky A, DeVinney R, Kreiswirth BN, Pitout JDD. CRISPR-Cas9-mediated IncF plasmid curing in extraintestinal pathogenic Escherichia coli. Microbiol Spectr 2024; 12:e0369223. [PMID: 38018989 PMCID: PMC10783119 DOI: 10.1128/spectrum.03692-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Understanding the role of IncF plasmids in the success of drug-resistant bacteria has far-reaching implications for tackling antibiotic resistance. The study's use of a novel CRISPR-Cas9-mediated plasmid-curing system provides a precision tool for dissecting the specific impact of IncF plasmids on ExPEC clones, especially high-risk, multidrug-resistant strains like ST131, ST1193, and ST410. The study offers a crucial stepping stone for future research into understanding how these plasmids influence more complex aspects of bacterial behavior, such as cell invasion and in vivo fitness.
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Affiliation(s)
- Liang Chen
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Gisele Peirano
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Kelly Yen
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
| | - Bingjie Wang
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Austin Terlecky
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
| | - Rebekah DeVinney
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack-Meridian Health, Nutley, New Jersey, USA
- Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Johann D. D. Pitout
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
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Tao G, Tan H, Chen Q. The First Report of Escherichia coli and Klebsiella pneumoniae Strains That Produce Both NDM-5 and OXA-181 in Jiangsu Province, China. Infect Drug Resist 2023; 16:3245-3255. [PMID: 37249963 PMCID: PMC10225149 DOI: 10.2147/idr.s412678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/18/2023] [Indexed: 05/31/2023] Open
Abstract
Objective The aim of this study was to analyze the genetic characteristics of three Enterobacteriaceae strains (one strain of Escherichia coli and two strains of Klebsiella pneumoniae) that produce both the NDM-5 and OXA-181 carbapenemases in pediatric patients. Methods Carbapenem-resistant Enterobacteriaceae (CRE) strains were collected from the Children's Hospital Affiliated to Nanjing Medical University in 2022. Resistance genes were detected by PCR. CRE strains that produced both the blaNDM-5 and blaOXA-181 genes were further characterized by antimicrobial susceptibility testing, multilocus sequence typing (MLST), plasmid conjugation assay, S1 nuclease-PFGE, Southern blotting and whole-genome sequencing. Results Three Enterobacteriaceae strains carrying both the blaNDM-5 and blaOXA-181 resistance genes were screened. MLST results showed that the strain of Escherichia coli carrying both blaNDM-5 and blaOXA-181 was ST410; the two strains of Klebsiella pneumoniae with both blaNDM-5 and blaOXA-181 were ST2601 and ST759. Conjugation assays showed that the plasmids harboring the blaNDM-5 and blaOXA-181 genes were self-transmissible. S1-PFGE and Southern blotting showed that the blaNDM-5 and blaOXA-181 genes were located on the plasmid with the size of about 60kb~. The genotyping results showed that the plasmid types were ColKP3 and IncX3. Conclusion This is the first report of Enterobacteriaceae strains that produce both NDM-5 and OXA-181 isolated from pediatric patients in China. Active infection control measures are urgently needed to prevent the spread of bacteria in children.
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Affiliation(s)
- Guixiang Tao
- Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Hua Tan
- Department of Clinical Laboratory, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
| | - Qian Chen
- Institute of Pediatrics, Children’s Hospital of Nanjing Medical University, Nanjing, People’s Republic of China
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Xiao R, Li Y, Liu X, Ding Y, Lai J, Li Y, Kang W, Zou P, Wang J, Du Y, Zhang J, Wang Y. Antibiotic susceptibility of Escherichia coli isolated from neonates admitted to neonatal intensive care units across China from 2015 to 2020. Front Cell Infect Microbiol 2023; 13:1183736. [PMID: 37325509 PMCID: PMC10267875 DOI: 10.3389/fcimb.2023.1183736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023] Open
Abstract
Background Escherichia coli is one of the most common pathogens causing neonatal infections. Recently, the incidence and drug resistance of E. coli have increased, posing a major threat to neonatal health. The aim of this study was to describe and analyze the antibiotic resistance and multilocus sequence typing (MLST) characteristics of E. coli derived from infants admitted to neonatal intensive care units (NICUs) across China. Methods In this study, 370 strains of E. coli from neonates were collected. E. coli isolated from these specimens were subjected to antimicrobial susceptibility testing (by broth microdilution method) and MLST. Results The overall resistance rate was 82.68%, with the highest rate of methicillin/sulfamethoxazole (55.68%) followed by cefotaxime (46.22%). Multiple resistance rate was 36.74%, 132 strains (35.68%) had extended-spectrum β-lactamase (ESBL) phenotype and 5 strains (1.35%) had insensitivity to the tested carbapenem antibiotics. The resistance of E. coli isolated from different pathogenicity and different sites of infections varied, strains derived from sputum were significantly more resistant to β-lactams and tetracyclines. Currently, the prevalence spectrum in NICUs was dominated by ST1193, ST95, ST73, ST69 and ST131 across China. And the multidrug resistance of ST410 was the most severe. ST410 had the highest resistance rate to cefotaxime (86.67%), and its most common multidrug resistance pattern was β-lactams + aminoglycosides + quinolones + tetracyclines + sulfonamides. Conclusions Substantial proportions of neonatal E. coli isolates were severely resistant to commonly administered antibiotics. MLST results can suggest the prevalent characteristics of antibiotic resistance in E. coli with different ST types.
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Affiliation(s)
- Ruiqi Xiao
- Capital Institute of Pediatrics, Beijing, China
| | - Ying Li
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Xiaowei Liu
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yijun Ding
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Jidong Lai
- Department of Neonatology, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yangfang Li
- Department of Neonatology, Children’s Hospital of Kunming, Kunming, Yunnan, China
| | - Wenqing Kang
- Neonatal Intensive Care Unit, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou, Henan, China
| | - Peicen Zou
- Capital Institute of Pediatrics, Beijing, China
| | - Jie Wang
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yue Du
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Jinjing Zhang
- Department of Neonatology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yajuan Wang
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
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Pitout JD, Peirano G, DeVinney R. The contributions of multidrug resistant clones to the success of pandemic extra-intestinal Pathogenic Escherichia coli. Expert Rev Anti Infect Ther 2023; 21:343-353. [PMID: 36822840 DOI: 10.1080/14787210.2023.2184348] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
INTRODUCTION High-risk multidrug (MDR) clones have played essential roles in the global emergence and spread of antimicrobial resistance (AMR), especially among Extra-intestinal Escherichia coli (ExPEC). AREAS COVERED Successful global ExPEC MDR clones are linked with the acquisition of fluoroquinolone resistance, CTX-M enzymes, and with carbapenemases. This article described the underlying mechanisms of fluoroquinolone resistance, the acquisition of CTX-M and carbapenemase genes among three global ExPEC high-risk MDR clones, namely i) ST1193 as being an example of a fluoroquinolone resistant clone. ii) ST131 as an example of a fluoroquinolone resistant and CTX-M clone. iii) ST410 as an example of a fluoroquinolone resistant, CTX-M and carbapenemase clone. This article also highlighted the contributions of these MDR determinants in the evolution of these high-risk MDR clones. EXPERT OPINION There is an enormous public health burden due to E. coli MDR high-risk clones such as ST1193, ST131 and ST410. These clones have played pivotal roles in the global spread of AMR. Sparse information is available on which specific features of these high-risk MDR clones have enabled them to become such successful global pathogens in relative short time periods.
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Affiliation(s)
- Johann Dd Pitout
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada.,University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- University of Calgary, Calgary, Alberta, Canada.,Dynalife Laboratories, University of Calgary, Calgary, Alberta, Canada
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Pitout JDD, Chen L. The Significance of Epidemic Plasmids in the Success of Multidrug-Resistant Drug Pandemic Extraintestinal Pathogenic Escherichia coli. Infect Dis Ther 2023; 12:1029-1041. [PMID: 36947392 PMCID: PMC10147871 DOI: 10.1007/s40121-023-00791-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing blaCTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A "plasmid-replacement" clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.
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Affiliation(s)
- Johann D D Pitout
- Cummings School of Medicine, University of Calgary, #9, 3535 Research Road NW, Calgary, AB, T2L 2K8, Canada.
- Dynacare Laboratories, Alberta, Canada.
- University of Pretoria, Pretoria, Gauteng, South Africa.
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Hackensack Meridian School of Medicine, Nutley, NJ, USA
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Nobrega D, Peirano G, Matsumura Y, Pitout JDD. Molecular Epidemiology of Global Carbapenemase-Producing Citrobacter spp. (2015-2017). Microbiol Spectr 2023; 11:e0414422. [PMID: 36847542 PMCID: PMC10101073 DOI: 10.1128/spectrum.04144-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
The emergence of carbapenem resistance is a significant public health concern. The rate of infections caused by carbapenemase-producing Citrobacter spp., particularly C. freundii, is increasing. Concomitantly, comprehensive global genomic data on carbapenemase-producing Citrobacter spp. are scarce. We used short read whole-genome sequencing to describe the molecular epidemiology and international distribution of eighty-six carbapenemase-producing Citrobacter spp. obtained from two surveillance programs (2015 to 17). The common carbapenemases were KPC-2 (26%), VIM-1 (17%), IMP-4 (14%) and NDM-1 (10%). C. freundii and C. portucalensis were the principal species. C. freundii consisted of multiple clones obtained mainly from Colombia (with KPC-2), the United States (with KPC-2, -3), and Italy (with VIM-1). Two dominant C. freundii clones were identified: ST98 was linked with blaIMP-8 from Taiwan and blaKPC-2 from the United States, and ST22 was linked with blaKPC-2 from Colombia and blaVIM-1 from Italy. C. portucalensis consisted mainly of two clones: ST493 with blaIMP-4 which was limited to Australia, and ST545 with blaVIM-31 which was limited to Turkey. Class I integron (In916) with blaVIM-1 was circulating between multiple sequence types (STs) in Italy, Poland, and Portugal. In73 with blaIMP-8 was circulating between various STs in Taiwan, while In809 with blaIMP-4 was circulating between different STs in Australia. The global carbapenemase-producing Citrobacter spp. population is dominated by diverse STs with different characteristics and varied geographical distribution and thus requires continued monitoring. Ongoing genomic surveillance should use methodologies able to distinguish between C. freundii and C. portucalensis. IMPORTANCE Citrobacter spp. are gaining recognition as important causes of hospital-acquired infections in humans. Among Citrobacter spp., carbapenemase-producing strains are cause of utmost concern to health care services globally due to their ability to resist therapy with virtually any beta-lactam antibiotic. Here, we described the molecular characteristics of a global collection of carbapenemase-producing Citrobacter spp. C. freundii and C. portucalensis were the most common species among Citrobacter spp. with carbapenemases from this survey. Importantly, C. portucalensis was misidentified as C. freundii when using Vitek 2.0/MALDI-TOF MS (matrix-assisted laser desorption/ionization-time of flight mass spectrometry) phenotypic identification, which has important implications for future surveys. Among C. freundii, we identified two dominant clones: ST98 with blaIMP-8 from Taiwan and blaKPC-2 from the United States, and ST22 with blaKPC-2 from Colombia and blaVIM-1 from Italy. As for C. portucalensis, the dominant clones consisted of ST493 with blaIMP-4 from Australia and ST545 with blaVIM-31 from Turkey.
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Affiliation(s)
- Diego Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Gisele Peirano
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Johann D. D. Pitout
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, South Africa
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