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Lerminiaux N, Mitchell R, Bartoszko J, Davis I, Ellis C, Fakharuddin K, Hota SS, Katz K, Kibsey P, Leis JA, Longtin Y, McGeer A, Minion J, Mulvey M, Musto S, Rajda E, Smith SW, Srigley JA, Suh KN, Thampi N, Tomlinson J, Wong T, Mataseje L. Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021. Antimicrob Agents Chemother 2023; 67:e0086023. [PMID: 37971242 PMCID: PMC10720558 DOI: 10.1128/aac.00860-23] [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: 06/30/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
Abstract
Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.
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Affiliation(s)
| | | | | | - Ian Davis
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - Chelsey Ellis
- The Moncton Hospital, Moncton, New Brunswick, Canada
| | - Ken Fakharuddin
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Susy S. Hota
- University Health Network, Toronto, Ontario, Canada
| | - Kevin Katz
- North York General Hospital, Toronto, Ontario, Canada
| | - Pamela Kibsey
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
| | - Jerome A. Leis
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yves Longtin
- Jewish General Hospital, Montréal, Québec, Canada
| | | | - Jessica Minion
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Sonja Musto
- Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Ewa Rajda
- McGill University Health Centre, Montréal, Québec, Canada
| | | | - Jocelyn A. Srigley
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
| | | | - Nisha Thampi
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Titus Wong
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Laura Mataseje
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - on behalf of the Canadian Nosocomial Infection Surveillance Program
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
- Public Health Agency of Canada, Ottawa, Ontario, Canada
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
- The Moncton Hospital, Moncton, New Brunswick, Canada
- University Health Network, Toronto, Ontario, Canada
- North York General Hospital, Toronto, Ontario, Canada
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Jewish General Hospital, Montréal, Québec, Canada
- Sinai Health, Toronto, Ontario, Canada
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
- Health Sciences Centre, Winnipeg, Manitoba, Canada
- McGill University Health Centre, Montréal, Québec, Canada
- University of Alberta Hospital, Edmonton, Alberta, Canada
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
- The Ottawa Hospital, Ottawa, Ontario, Canada
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
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Fernandez JE, Seth-Smith HMB, Nordmann P, Egli A, Endimiani A, Perreten V. Intra- and Interspecies Spread of a Novel Conjugative Multidrug Resistance IncC Plasmid Coharboring blaOXA-181 and armA in a Cystic Fibrosis Patient. Microbiol Spectr 2022; 10:e0312122. [PMID: 36154665 PMCID: PMC9603557 DOI: 10.1128/spectrum.03121-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/09/2022] [Indexed: 01/04/2023] Open
Abstract
A novel multidrug resistance conjugative 177,859-bp IncC plasmid pJEF1-OXA-181 coharboring the carbapenemase-coding blaOXA181 and the aminoglycoside resistance 16S rRNA methyltransferase-coding armA genes was detected in two unrelated Escherichia coli gut isolates of ST196 and ST648, as well as two ST35 Klebsiella pneumoniae gut and sputum isolates of a cystic fibrosis patient. The armA gene was located within the antimicrobial resistance island ARI-A and the blaOXA181 gene, which was preceded by IS903 and ISEcp1Δ was inserted within the transfer genes region without affecting conjugation ability. Comparative plasmid analysis with other related IncC plasmids showed the presence of blaOXA181, as well as its integration site, are thus far unique for these types of plasmids. This study illustrates the potential of a promiscuous multidrug resistance plasmid to acquire antibiotic resistance genes and to disseminate in the gut of the same host. IMPORTANCE Colocalization of carbapenemases and aminoglycoside resistance 16S rRNA methylases on a multidrug resistance conjugative plasmid poses a serious threat to public health. Here, we describe the novel IncC plasmid pJEF1-OXA-181 cocarrying blaOXA-181 and armA as well as several other antimicrobial resistance genes (ARGs) in different Enterobacterales isolates of the sputum and gut microbiota of a cystic fibrosis patient. IncC plasmids are conjugative, promiscuous elements which can incorporate accessory antimicrobial resistance islands making them key players in ARGs spread. This plasmid was thus far unique among IncC plasmids to contain a blaOXA-181 which was integrated in the transfer gene region without affecting its conjugation ability. This study highlights that new plasmids may be introduced into a hospital through different species hosted in one single patient. It further emphasizes the need of continuous surveillance of multidrug-resistant bacteria in patients at risk to avoid spread of such plasmids in the health care system.
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Affiliation(s)
- Javier E. Fernandez
- Division of Molecular bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Helena M. B. Seth-Smith
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Patrice Nordmann
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Division of Molecular bacterial Epidemiology and Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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3
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Moser AI, Keller PM, Campos-Madueno EI, Poirel L, Nordmann P, Endimiani A. A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC bla NDM-1- and armA-carrying Plasmid. Pathog Immun 2022; 6:119-134. [PMID: 34988342 PMCID: PMC8714174 DOI: 10.20411/pai.v6i2.482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background. Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes. Methods. We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies. Results. All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene. Conclusions. The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad-host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.
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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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Sun M, Xiao W, Xu Q. IncN1 ST7 Epidemic Plasmid Carrying blaIMP-4 in One ST85-Type Klebsiella oxytoca Clinical Isolate with Porin Deficiency. Infect Drug Resist 2021; 14:3827-3835. [PMID: 34566416 PMCID: PMC8458025 DOI: 10.2147/idr.s330362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/07/2021] [Indexed: 01/07/2023] Open
Abstract
Purpose Klebsiella oxytoca is an opportunistic pathogen causing nosocomial infections. This study was designed to characterize the genomic features of a carbapenem-resistant K. oxytoca strain and analyze its molecular characteristics. Materials and Methods The strain wzx-IMP was isolated from the blood of a 2-year-old girl diagnosed with acute myeloid leukemia-M7. Species identification was performed, and the minimal inhibitory concentration of the strain was measured. Multilocus sequence typing was performed to identify the subtypes of K. oxytoca. The transfer capacity of the blaIMP-4-harboring plasmid was investigated by conjugation experiments, and the genome characteristics of the strain were examined using whole-genome sequencing. Results wzx-IMP belongs to the ST85 type and is resistant to imipenem and meropenem, which harbored the blaIMP-4 gene. The blaIMP-4 gene was located in an IS26-associated class 1 integron of pwzx_IMP, which contains conserved IncN1-type backbone regions with a replication gene and its accessory structure for plasmid replication. The blaIMP-4-carrying plasmid in wzx-IMP was successfully transferred to Escherichia coli EC600 by conjugation. Whole-genome sequencing showed that the wzx-IMP isolate included the blaOXY-1-1 gene, accompanied by OmpK36 absence. Conclusion We report an ST85-type carbapenem-resistant K. oxytoca strain, which produces blaIMP-4 located in an IncN1-type plasmid and accompanied by OmpK36 porin deficiency.
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Affiliation(s)
- Mingyue Sun
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
| | - Weiqiang Xiao
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
| | - Qingxia Xu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
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5
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Cassone M, Linder M, Shin CJ, Mantey J, Gibson K, Lansing B, Mody L. Not too close! impact of roommate status on MRSA and VRE colonization and contamination in Nursing Homes. Antimicrob Resist Infect Control 2021; 10:104. [PMID: 34225783 PMCID: PMC8258944 DOI: 10.1186/s13756-021-00972-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/22/2021] [Indexed: 11/10/2022] Open
Abstract
Multiple room occupancy is common in Nursing Homes (NHs), and its role in transmission of antibiotic-resistant pathogens is unclear. We investigated prevalence of patient colonization and environmental contamination with vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) in NH roommates, compared it with expected prevalence, and determined specific body and environmental sites that may act as sources of roommate colonization. Roommate contamination was associated with index patient's colonization (relative risk (RR): 2.57 (95% CI 1.04-6.37)) for MRSA, and index patient's immediate environment contamination for VRE (RR: 3.60 (95% CI 1.59-8.12)). When specific index patient sites associated with roommate colonization were investigated, the side table (Fisher's p = 0.029 and 0.047 for VRE and MRSA, respectively) and the nurse call button (p = 0.001 and 0.052) stood out, together with patient hands in the case of VRE (p = 0.026). Future studies should be carried out to establish whether these sites should be a specific target of infection prevention campaigns in NHs with multiple occupancy rooms.
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Affiliation(s)
- Marco Cassone
- Division of Geriatric and Palliative Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 3023 BSRB, 109 Zina Pitcher Place48109, USA.
| | - Meghan Linder
- School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Oregon Health Authority, Portland, OR, USA
| | - Cheon Jee Shin
- Division of Geriatric and Palliative Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 3023 BSRB, 109 Zina Pitcher Place48109, USA.,University of Louisville, Louisville, KY, USA
| | - Julia Mantey
- Division of Geriatric and Palliative Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 3023 BSRB, 109 Zina Pitcher Place48109, USA
| | - Kristen Gibson
- Division of Geriatric and Palliative Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 3023 BSRB, 109 Zina Pitcher Place48109, USA
| | - Bonnie Lansing
- Division of Geriatric and Palliative Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 3023 BSRB, 109 Zina Pitcher Place48109, USA
| | - Lona Mody
- Division of Geriatric and Palliative Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 3023 BSRB, 109 Zina Pitcher Place48109, USA.,Geriatric Research and Education Clinical Center, VA Ann Arbor, Ann Arbor, MI, USA
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6
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Osei Sekyere J, Reta MA. Global evolutionary epidemiology and resistome dynamics of Citrobacter species, Enterobacter hormaechei, Klebsiella variicola, and Proteeae clones. Environ Microbiol 2021; 23:7412-7431. [PMID: 33415808 DOI: 10.1111/1462-2920.15387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022]
Abstract
Citrobacter spp., Enterobacter hormaechei subsp., Klebsiella variicola and Proteae tribe members are rarely isolated Enterobacterales increasingly implicated in nosocomial infections. Herein, we show that these species contain multiple genes encoding resistance to important antibiotics and are widely and globally distributed, being isolated from human, animal, plant, and environmental sources in 67 countries. Certain clones and clades of these species were internationally disseminated, serving as reservoirs and mediums for the global dissemination of antibiotic resistance genes. As they can easily transmit these genes to more pathogenic species, additional molecular surveillance studies should be undertaken to identify and contain these antibiotic-resistant species.
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Affiliation(s)
- John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Prinshof, Pretoria, Gauteng, South Africa
| | - Melese Abate Reta
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Prinshof, Pretoria, Gauteng, South Africa
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7
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Conlan S, Lau AF, Deming C, Spalding CD, Lee-Lin S, Thomas PJ, Park M, Dekker JP, Frank KM, Palmore TN, Segre JA. Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy. mBio 2019; 10:e00652-19. [PMID: 31594809 PMCID: PMC6786864 DOI: 10.1128/mbio.00652-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Antibiotics, which are used both to prevent and to treat infections, are a mainstay therapy for lifesaving procedures such as transplantation. For this reason, and many others, increased antibiotic resistance among human-associated pathogens, such as the carbapenem-resistant Enterobacteriaceae species, is of grave concern. In this study, we report on a hematopoietic stem cell transplant recipient in whom cultures detected the emergence of carbapenem resistance and spread across five strains of bacteria that persisted for over a year. Carbapenem resistance in Citrobacter freundii, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae was linked to a pair of plasmids, each carrying the Klebsiella pneumoniae carbapenemase gene (blaKPC). Surveillance cultures identified a carbapenem-susceptible strain of Citrobacter freundii that may have become resistant through horizontal gene transfer of these plasmids. Selection of a multidrug-resistant Klebsiella pneumoniae strain was also detected following combination antibiotic therapy. Here we report a plasmid carrying the blaKPC gene with broad host range that poses the additional threat of spreading to endogenous members of the human gut microbiome.IMPORTANCE Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.
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Affiliation(s)
- Sean Conlan
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Anna F Lau
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Clay Deming
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | | | - Pamela J Thomas
- National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA
| | - Morgan Park
- National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA
| | - John P Dekker
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Karen M Frank
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Tara N Palmore
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Julia A Segre
- National Human Genome Research Institute, Bethesda, Maryland, USA
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8
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Infection prevention and control practices related to carbapenemase-producing Enterobacteriaceae (CPE) in acute-care hospitals in Ontario, Canada. Infect Control Hosp Epidemiol 2019; 40:1006-1012. [PMID: 31244458 DOI: 10.1017/ice.2019.173] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To determine infection prevention and control (IPAC) practices for carbapenemase-producing Enterobacteriaceae (CPE), an emerging threat, at acute-care hospitals in Ontario, Canada. DESIGN A descriptive cross-sectional survey. METHODS We surveyed IPAC directors and managers at all acute-care hospitals in Ontario, Canada, to gather information on IPAC practices related to CPE, including admission screening, other patient screening, environmental testing, use of precautions to prevent transmission, and outbreak management. RESULTS Of 116 acute-care hospitals, 105 (91%) responded. Admission screening included patients previously colonized or infected with CPE (n = 64, 61%), patients recently hospitalized outside of Canada (Indian subcontinent, n = 62, 59%; other countries, n = 56, 53%), and patients recently hospitalized in Canada (n = 22, 21%). Fifty-one hospitals (49%) screened patients for colonization during an outbreak. Almost all hospitals (n = 101, 96%) used precautions to prevent transmission from patients with CPE colonization or infection; most hospitals (n = 54, 53%) continued precautions indefinitely. Few hospitals (n = 19, 18%) performed environmental cultures. Eight hospitals (8%) reported at least 1 outbreak, and 6 hospitals (6%) reported transmission from sink or shower drains to patients. CONCLUSIONS Variability in practices may result from lack of evidence and challenges in updating guidelines as evidence emerges. A coordinated approach to slow the emergence of CPE should be considered in our population.
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9
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Faccone D, Albornoz E, Tijet N, Biondi E, Gomez S, Pasterán F, Vazquez M, Melano RG, Corso A. Characterization of a multidrug resistant Citrobacter amalonaticus clinical isolate harboring blaNDM-1 and mcr-1.5 genes. INFECTION GENETICS AND EVOLUTION 2019; 67:51-54. [DOI: 10.1016/j.meegid.2018.10.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 10/12/2018] [Accepted: 10/26/2018] [Indexed: 10/28/2022]
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10
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Xu H, Wang X, Yu X, Zhang J, Guo L, Huang C, Jiang X, Li X, Feng Y, Zheng B. First detection and genomics analysis of KPC-2-producing Citrobacter isolates from river sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 235:931-937. [PMID: 29358148 DOI: 10.1016/j.envpol.2017.12.084] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/22/2017] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
The wide spread of carbapenemase-producing Enterobacteriaceae (CPE) in the environment is an emerging environmental issue with potentially-serious public health implications. However, carbapenemase-producing Citrobacter from environment has rarely been investigated. Here we report the isolation and comparative genomics of carbapenemase-producing Citrobacter isolates from river sediment in China. Potential CPE was isolated by selective MacConkey agar plates containing 2 mg/L meropenem. The presence of carbapenemase genes was detected by PCR and sequencing. The clonal relatedness of Klebsiella pneumoniae carbapenemase (KPC-2)-producing Citrobacter isolates was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Plasmid analysis of KPC-2-producing Citrobacter isolates was performed by S1-PFGE, Southern blotting, and whole genome sequencing. A total of four KPC-2-producing Citrobacter and three Aeromonas isolates were recovered from 54 sediment cultures of Shifeng River. Notably, all KPC-producing isolates were isolated from sampling sites near a waste water treatment plant. Antimicrobial susceptibility testing showed that three of the four sequenced isolates (C1710, C191, and C196) resistant to multiple antibiotics. Genotyping and pan-genome analyses revealed that the C191 and C196 C. freundii isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaKPC-2 gene is located on either IncF or IncN3 plasmids in all isolates. The blaKPC-2 gene of C1710, C181 and C191 was successfully transferred with E. coli EC600 as the recipient strain. In silico analysis further suggested that pKPC-191 is a novel IncF plasmid, with 99% identity to two previously described IncFII plasmids at 71% coverage. We report here the presence of diverse conjugative blaKPC-2 plasmids from environmental Citrobacter isolates, which poses the possible dissemination of antimicrobial resistance into clinical isolates. To our knowledge, this is the first study to culture and characterize KPC-2-producing Citrobacter isolates from river sediments in China.
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Affiliation(s)
- Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xin Wang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China; School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Xiao Yu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Zhang
- Division of Respiratory Diseases, Guangdong General Hospital, Guangzhou, China
| | - Lihua Guo
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Huang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiawei Jiang
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xuewen Li
- School of Public Health, Shandong University, Jinan, China
| | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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11
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Anes J, Hurley D, Martins M, Fanning S. Exploring the Genome and Phenotype of Multi-Drug Resistant Klebsiella pneumoniae of Clinical Origin. Front Microbiol 2017; 8:1913. [PMID: 29109700 PMCID: PMC5660112 DOI: 10.3389/fmicb.2017.01913] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/20/2017] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae is an important nosocomial pathogen with an extraordinary resistant phenotype due to a combination of acquired resistant-elements and efflux mechanisms. In this study a detailed molecular characterization of 11 K. pneumoniae isolates of clinical origin was carried out. Eleven clinical isolates were tested for their susceptibilities, by disk diffusion and broth microdilution and interpreted according to CLSI guidelines. Efflux activity was determined by measuring the extrusion of ethidium bromide and biofilm formation was assessed following static growth in Müeller-Hinton and minimal media M9 broths at two temperatures and time points. Template DNA from all 11 isolates was extracted and sequenced. The study collection was found to be resistant to several (extended-spectrum beta-lactam) ESBL-type compounds along with several (fluoro)quinolones (FQ). Resistance to tetracycline accounted for 55% of the study collection (n = 6) and three of the 11 isolates were resistance to carbapenems. Genotyping identified blaCTX-M-15 (82%), blaSHV-12 (55%), and blaTEM-1B (45%) ESBL encoding genes and FQ resistance was associated the presence of the oqxAB operon, identified in 10 of the 11 isolates and qnrB gene in one isolate. The polymorphisms detected in the quinolone resistance-determining regions (QRDRs) were associated with isolates of the clonal group CG15. Sequence types (ST) identified were representative of previously described clonal groups including CG258 (n = 7), CG15 (n = 3), and CG147 (n = 1). Plasmid replicon type databases were queried indicating the presence of IncFII and IncFIB replicon types in the majority of the isolates (91%), followed by IncFIA (45%), and IncR (45%). Two of the 11 isolates were found positive for yersiniabactin siderophore-encoding genes. No differences in the ability to efflux ethidium bromide were identified. Biofilm formation was stronger when the isolates were grown under stressed conditions at 37°C for a period up to 96 h. These data confirm the fact that well-recognized clonal groups of K. pneumoniae of importance to human health carries a diverse repertoire of antimicrobial resistance determinants, particularly related to critically important drugs in the ESBL and FQ classes. The capacity of most isolates to form strong biofilms, when stressed under laboratory-simulated conditions, supports the risk to human health associated with nosocomial infections deriving from indwelling medical devices.
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Affiliation(s)
- João Anes
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Daniel Hurley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Marta Martins
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
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12
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Botts RT, Apffel BA, Walters CJ, Davidson KE, Echols RS, Geiger MR, Guzman VL, Haase VS, Montana MA, La Chat CA, Mielke JA, Mullen KL, Virtue CC, Brown CJ, Top EM, Cummings DE. Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland. Front Microbiol 2017; 8:1922. [PMID: 29067005 PMCID: PMC5641379 DOI: 10.3389/fmicb.2017.01922] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Self-transmissible and mobilizable plasmids contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance. The objective of this study was to capture and characterize self-transmissible and mobilizable resistance plasmids from a coastal wetland impacted by urban stormwater runoff and human wastewater during the rainy season. Four plasmids were captured, two self-transmissible and two mobilizable, using both mating and enrichment approaches. Plasmid genomes, sequenced with either Illumina or PacBio platforms, revealed representatives of incompatibility groups IncP-6, IncR, IncN3, and IncF. The plasmids ranged in size from 36 to 144 kb and encoded known resistance genes for most of the major classes of antibiotics used to treat Gram-negative infections (tetracyclines, sulfonamides, β-lactams, fluoroquinolones, aminoglycosides, and amphenicols). The mobilizable IncP-6 plasmid pLNU-11 was discovered in a strain of Citrobacter freundii enriched from the wetland sediments with tetracycline and nalidixic acid, and encodes a novel AmpC-like β-lactamase (blaWDC-1), which shares less than 62% amino acid sequence identity with the PDC class of β-lactamases found in Pseudomonas aeruginosa. Although the IncR plasmid pTRE-1611 was captured by mating wetland bacteria with P. putida KT2440 as recipient, it was found to be mobilizable rather than self-transmissible. Two self-transmissible multidrug-resistance plasmids were also captured: the small (48 kb) IncN3 plasmid pTRE-131 was captured by mating wetland bacteria with Escherichia coli HY842 where it is seemed to be maintained at nearly 240 copies per cell, while the large (144 kb) IncF plasmid pTRE-2011, which was isolated from a cefotaxime-resistant environmental strain of E. coli ST744, exists at just a single copy per cell. Furthermore, pTRE-2011 bears the globally epidemic blaCTX-M-55 extended-spectrum β-lactamase downstream of ISEcp1. Our results indicate that urban coastal wetlands are reservoirs of diverse self-transmissible and mobilizable plasmids of relevance to human health.
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Affiliation(s)
- Ryan T Botts
- Department of Mathematical, Information and Computer Sciences, Point Loma Nazarene University, San Diego, CA, United States
| | - Brooke A Apffel
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - C J Walters
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Kelly E Davidson
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Ryan S Echols
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Michael R Geiger
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Victoria L Guzman
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Victoria S Haase
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Michal A Montana
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Chip A La Chat
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Jenna A Mielke
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Kelly L Mullen
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Cierra C Virtue
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Celeste J Brown
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Eva M Top
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - David E Cummings
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
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13
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Tijet N, Faccone D, Rapoport M, Seah C, Pasterán F, Ceriana P, Albornoz E, Corso A, Petroni A, Melano RG. Molecular characteristics of mcr-1-carrying plasmids and new mcr-1 variant recovered from polyclonal clinical Escherichia coli from Argentina and Canada. PLoS One 2017; 12:e0180347. [PMID: 28678874 PMCID: PMC5498056 DOI: 10.1371/journal.pone.0180347] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/14/2017] [Indexed: 11/18/2022] Open
Abstract
We have characterized nine mcr-1-harboring plasmids from clinical Escherichia coli isolates previously described in Argentina and Canada. Three of these plasmids carried a mcr-1-variant called here mcr-1.5. All these E. coli isolates were not clonally related and were recovered in different years and locations. However, their mcr-1-harboring plasmids showed high identity among them and to others characterized in other countries, which strongly suggests that this plasmid-type is playing an important role in spreading this mechanism of resistance to polymyxins.
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Affiliation(s)
- Nathalie Tijet
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Diego Faccone
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Melina Rapoport
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Christine Seah
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Fernando Pasterán
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Paola Ceriana
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Ezequiel Albornoz
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Alejandro Petroni
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Roberto G. Melano
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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14
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Jiang X, Yin Z, Yin X, Fang H, Sun Q, Tong Y, Xu Y, Zhang D, Feng J, Chen W, Song Y, Wang J, Chen S, Zhou D. Sequencing of blaIMP-Carrying IncN2 Plasmids, and Comparative Genomics of IncN2 Plasmids Harboring Class 1 Integrons. Front Cell Infect Microbiol 2017; 7:102. [PMID: 28424761 PMCID: PMC5371602 DOI: 10.3389/fcimb.2017.00102] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/15/2017] [Indexed: 12/23/2022] Open
Abstract
This work presents the complete nucleotide sequences of p0801-IMP from Klebsiella pneumoniae, p7121-IMP from K. oxytoca, and p17285-IMP from Citrobacter freundii, which are recovered from three different cases of nosocomial infection. These three plasmids represent the first fully sequenced blaIMP-carrying IncN2 plasmids. Further comparative genomics analysis of all the five integron-carrying IncN2 plasmids p0801-IMP, p7121-IMP, p17285-IMP, pJIE137, and p34983-59.134kb indicates that they possess conserved IncN2 backbones with limited genetic variations with respect to gene content and organization. Four class 1 integrons (blaIMP-1-carrying In1223 in p0801-IMP/p7121-IMP, blaIMP-8-carrying In655 in p17285-IMP, In27 in pJIE137, and In1130 in p34983-59.134kb), two insertion sequence-based transposition units (ISEcp1-orfRA1-14 in p17285-IMP, and ISEcp1-blaCTX-M-62-Δorf477-orfRA1-14 in pJIE137), and a novel Tn1696-related transposon Tn6325 carrying In1130 in p34983-59.134kb are indentified in the plasmid accessory regions. In1223 and In655 represent ancestral Tn402-associated integrons, while In27 and In1130 belong to complex class 1 integrons. The relatively small IncN2 backbones are able to integrate different mobile elements which carry various resistance markers, promoting the accumulation and spread of antimicrobial resistance genes among enterobacterial species.
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Affiliation(s)
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
| | - Xiuyun Yin
- Department of Clinical Laboratory, The 307th Hospital of the People's Liberation ArmyBeijing, China
| | - Haihong Fang
- Anhui Medical UniversityHefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical UniversityHefei, China
| | - Defu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China.,College of Food Science and Project Engineering, Bohai UniversityJinzhou, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijing, China
| | - Yajun Song
- Anhui Medical UniversityHefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
| | - Jinglin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
| | - Shuiping Chen
- Department of Clinical Laboratory, The 307th Hospital of the People's Liberation ArmyBeijing, China
| | - Dongsheng Zhou
- Anhui Medical UniversityHefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijing, China
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15
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Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Citrobacter freundii at a Tertiary Acute Care Facility in Miami, Florida. Infect Control Hosp Epidemiol 2016; 38:320-326. [PMID: 27923418 DOI: 10.1017/ice.2016.273] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To describe the investigation and control of a rare cluster of Klebsiella pneumoniae carbapenemase-producing Citrobacter freundii in a hospital in southern Florida. METHODS An epidemiologic investigation, review of infection prevention procedures, and molecular studies including whole genome sequencing were conducted. RESULTS An outbreak of K. pneumoniae carbapenemase-3-producing C. freundii was identified at a tertiary hospital in Florida in 2014. Of the 6 cases identified, 3 occurred in the same intensive care unit and were caused by the same clone. For 2 of the 3 remaining cases, the isolates had low carbapenem minimum inhibitory concentrations and were unrelated by whole genome sequencing. As a response to the outbreak, supplementary environmental cleaning was implemented, including closure and terminal cleaning of the unit where the 3 cases clustered, in addition to the infection control bundle already in place at the time. No further cases were identified after these additional interventions. CONCLUSIONS Although C. freundii is not a species that commonly demonstrates carbapenem resistance, our findings suggest that carbapenemase-producing C. freundii may be underdetected even when active surveillance is in place and has a potential to cause hospital outbreak. Infect Control Hosp Epidemiol 2017;38:320-326.
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16
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Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC. Antimicrob Agents Chemother 2016; 60:3767-78. [PMID: 27067320 PMCID: PMC4879409 DOI: 10.1128/aac.00464-16] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/03/2016] [Indexed: 01/01/2023] Open
Abstract
The recent widespread emergence of carbapenem resistance in Enterobacteriaceae is a major public health concern, as carbapenems are a therapy of last resort against this family of common bacterial pathogens. Resistance genes can mobilize via various mechanisms, including conjugation and transposition; however, the importance of this mobility in short-term evolution, such as within nosocomial outbreaks, is unknown. Using a combination of short- and long-read whole-genome sequencing of 281 blaKPC-positive Enterobacteriaceae isolates from a single hospital over 5 years, we demonstrate rapid dissemination of this carbapenem resistance gene to multiple species, strains, and plasmids. Mobility of blaKPC occurs at multiple nested genetic levels, with transmission of blaKPC strains between individuals, frequent transfer of blaKPC plasmids between strains/species, and frequent transposition of blaKPC transposon Tn4401 between plasmids. We also identify a common insertion site for Tn4401 within various Tn2-like elements, suggesting that homologous recombination between Tn2-like elements has enhanced the spread of Tn4401 between different plasmid vectors. Furthermore, while short-read sequencing has known limitations for plasmid assembly, various studies have attempted to overcome this by the use of reference-based methods. We also demonstrate that, as a consequence of the genetic mobility observed in this study, plasmid structures can be extremely dynamic, and therefore these reference-based methods, as well as traditional partial typing methods, can produce very misleading conclusions. Overall, our findings demonstrate that nonclonal resistance gene dissemination can be extremely rapid, presenting significant challenges for public health surveillance and achieving effective control of antibiotic resistance.
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17
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Ahn S, Sung JY, Kim H, Kim MS, Hwang Y, Jong S, Seo Y, Ha E, Park ES, Choi JY, Yong D, Lee K. Molecular Epidemiology and Characterization of Carbapenemase-ProducingEnterobacteriaceaeIsolated at a University Hospital in Korea during 4-Year Period. ANNALS OF CLINICAL MICROBIOLOGY 2016. [DOI: 10.5145/acm.2016.19.2.39] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Sunyoung Ahn
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Ji Yeon Sung
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Hyunsoo Kim
- Department of Laboratory Medicine, National Police Hospital, Seoul, Korea
| | - Myung Sook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Younjee Hwang
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Sori Jong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Younghee Seo
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
| | - Eunjin Ha
- Department of Infection Control, Severance Hospital, Seoul, Korea
| | - Eun Suk Park
- Department of Infection Control, Severance Hospital, Seoul, Korea
| | - Jun Yong Choi
- Department of Infection Control, Severance Hospital, Seoul, Korea
- Division of Infectious Diseases,Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
- Department of Infection Control, Severance Hospital, Seoul, Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance,Yonsei University College of Medicine, Seoul, Korea
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