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Pathak A, Angst DC, León-Sampedro R, Hall AR. Antibiotic-degrading resistance changes bacterial community structure via species-specific responses. THE ISME JOURNAL 2023; 17:1495-1503. [PMID: 37380830 PMCID: PMC10432403 DOI: 10.1038/s41396-023-01465-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
Some bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics. We found that resistance in one community member reduced antibiotic inhibition of other species, but some benefitted more than others. Further experiments with supernatants and pure-culture growth assays showed the susceptible species profiting most from detoxification were those that grew best at degraded antibiotic concentrations (greater than zero, but lower than the starting concentration). This pattern was also observed on agar surfaces, and the same species also showed relatively high survival compared to most other species during the initial high-antibiotic phase. By contrast, we found no evidence of a role for higher-order interactions or horizontal plasmid transfer in community-level responses to detoxification in our experimental communities. Our findings suggest carriage of an antibiotic-degrading resistance mechanism by one species can drastically alter community-level responses to antibiotics, and the identities of the species that profit most from antibiotic detoxification are predicted by their intrinsic ability to survive and grow at changing antibiotic concentrations.
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Affiliation(s)
- Ayush Pathak
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland.
| | - Daniel C Angst
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland
| | - Ricardo León-Sampedro
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland
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2
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Gabana ADA, Núncio ASP, Lopes BC, de Oliveira JA, da Silva Monteiro L, de Menezes Coppola M, Furian TQ, Borges KA, Rodrigues LB, Mayer FQ. Different Multidrug-Resistant Salmonella spp. Serovars Isolated from Slaughter Calves in Southern Brazil. Curr Microbiol 2022; 80:11. [PMID: 36459239 DOI: 10.1007/s00284-022-03136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
Bovines are carriers of Salmonella spp., a relevant foodborne pathogen, acting as contamination sources in slaughterhouses. Calves are prone to infection, and antimicrobial resistance may occur in such bacteria. This study aimed to determine the prevalence and virulence determinants of Salmonella spp. recovered from calves in the Rio Grande do Sul state, Brazil. Eighty-five calves' carcasses were evaluated (leather and veal meat). Thirteen Salmonella spp. isolates (8%) from 11 animals (13%) were obtained only from leather, indicating that contamination occurred before slaughter and that the meat was safe regarding this aspect. The serotypes S. Minnesota, S. Abony, S. Cerro, and S. Gafsa were identified, and all isolates were multidrug-resistant. The isolates had at least 19 virulence-related genes, and the blaOXA-48 resistance gene was detected in three (23%). The data suggest that treating infections caused by these bacteria may be difficult in animals from these farms and can also be an extended human health problem.
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Affiliation(s)
- Alex Dall Agnol Gabana
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Adriana Souto Pereira Núncio
- Faculdade de Agronomia e Medicina Veterinária, Programa de Pós-Graduação em Bioexperimentação, Universidade de Passo Fundo, BR 285, Campus I, São José, Passo Fundo, RS, 99052-900, Brazil
| | - Bruna Correa Lopes
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Júlia Alves de Oliveira
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Luana da Silva Monteiro
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Mario de Menezes Coppola
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil
| | - Thales Quedi Furian
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9090, Agronomia, Porto Alegre, RS, 91540-000, Brazil
| | - Karen Apellanis Borges
- Centro de Diagnóstico e Pesquisa em Patologia Aviária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9090, Agronomia, Porto Alegre, RS, 91540-000, Brazil
| | - Laura Beatriz Rodrigues
- Faculdade de Agronomia e Medicina Veterinária, Programa de Pós-Graduação em Bioexperimentação, Universidade de Passo Fundo, BR 285, Campus I, São José, Passo Fundo, RS, 99052-900, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Departamento de Diagnóstico e Pesquisa Agropecuária, Instituto de Pesquisas Veterinárias Desidério Finamor, Secretaria da Agricultura, Pecuária e Desenvolvimento Rural, Estrada Municipal do Conde, 6000, Sans Souci, Eldorado do Sul, RS, 92990-000, Brazil. .,Departamento de Biologia Molecular e Biotecnologia, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500 - Agronomia, Porto Alegre, RS, 91501-970, Brazil.
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Mori N, Tada T, Oshiro S, Kuwahara-Arai K, Kirikae T, Uehara Y. A transferrable IncL/M plasmid harboring a gene encoding IMP-1 metallo-β-lactamase in clinical isolates of Enterobacteriaceae. BMC Infect Dis 2021; 21:1061. [PMID: 34645409 PMCID: PMC8513173 DOI: 10.1186/s12879-021-06758-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 10/04/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The worldwide spread of carbapenemase-producing Enterobacteriaceae (CPE) has reduced the clinical utility of carbapenems. Plasmids often play an important role in the spread of genes encoding drug-resistance factors, especially in the horizontal transfer of these genes among species of Enterobacteriaceae. This study describes a patient infected with three species of CPE carrying an identical transferrable IncL/M plasmid. METHODS Clinical isolates of CPE were collected at St. Luke's International Hospital, Tokyo, Japan, from 2015 to 2019. Three species of CPE isolates, Enterobacter cloacae, Klebsiella aerogenes and Serratia marcescens, were isolated from a patient who developed severe gallstone pancreatitis associated with bloodstream infection, with all three isolates producing IMP-1 metallo-β-lactamase. The complete sequences of the plasmids of the three isolates were determined by both MiSeq and MinION. The medical chart of this patient was retrospectively reviewed conducted to obtain relevant clinical information. RESULTS The three CPE species carried an IncL/M plasmid, pSL264, which was 81,133 bp in size and harbored blaIMP-1. The genetic environment surrounding blaIMP-1 consisted of int1-blaIMP-1-aac(6')-IIc-qacL-qacEdelta1-sul1-istB-IS21. Conjugation experiments showed that S. marcescens could transmit the plasmid to E. cloacae and K. aerogenes. In contrast, pSL264 could not transfer from E. cloacae or K. aerogenes to S. marcescens. CONCLUSION The IncL/M plasmid pSL264 harboring blaIMP-1 was able to transfer among different species of Enterobacteriaceae in a patient receiving long-term antimicrobial treatment. The worldwide emergence and spread of IncL/M plasmids harboring carbapenemase-encoding genes among species of Enterobacteriaceae is becoming a serious public health hazard.
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Affiliation(s)
- Nobuyoshi Mori
- grid.430395.8Department of Infectious Diseases, St. Luke’s International Hospital, Tokyo, Japan ,grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Tatsuya Tada
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Satoshi Oshiro
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Kyoko Kuwahara-Arai
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Teruo Kirikae
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan
| | - Yuki Uehara
- grid.258269.20000 0004 1762 2738Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421 Japan ,grid.430395.8Department of Clinical Laboratory, St. Luke’s International Hospital, Tokyo, Japan
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Davoudabadi S, Goudarzi H, Goudarzi M, Ardebili A, Faghihloo E, Sharahi JY, Hashemi A. Detection of extensively drug-resistant and hypervirulent Klebsiella pneumoniae ST15, ST147, ST377 and ST442 in Iran. Acta Microbiol Immunol Hung 2021; 69:77-86. [PMID: 34546968 DOI: 10.1556/030.2021.01562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 01/12/2023]
Abstract
In this study, we focused on the emergence of extensively drug-resistant (XDR), pandrug-resistant (PDR), and hypervirulent Klebsiella pneumoniae (hvKP) in Iran. During 2018 to 2020 a total of 52 K. pneumoniae isolates were collected from different clinical specimens. The hvKP isolates were identified by PCR amplification of virulence and capsular serotype-specific genes. Hypermucoviscous K. pneumoniae (hmKP) were identified by string test. Carbapenem-resistant hvKP (CR-hvKP), multidrug-resistant hvKP (MDR-hvKP), extensively drug-resistant hvKP (XDR-hvKP), and pandrug-resistant hvKP (PDR-hvKP) were determined by disc diffusion method, Carba-NP test and PCR method. XDR-hvKP isolates were typed by multilocus sequence typing (MLST). Among all K. pneumoniae isolates 14 (26.9%) were identified as hvKP and 78.6% (11/14) of them were hmKP however, none of the classic K. pneumoniae (cKP) isolates were hmKP. The predominant capsular serotype of hvKP was K2 (42.85%) followed by K1 (35.71%). The prevalence of MDR-hvKP, XDR-hvKP and PDR-hvKP isolates were 6 (42.9%), 5 (35.7%) and 1 (7.1%), respectively. ESBL production was found in 85.7% of hvKP isolates and most of them carried bla TEM gene (78.6%) and 6 isolates (42.9%) were CR-hvKP. Among hvKP isolates, 1 (7.1%), 2 (14.3%), 3 (21.4%), 8 (28.6%), and 11 (78.6%) carried bla NDM-6, bla OXA-48, bla CTX-M, bla SHV, and bla TEM genes, respectively. According to MLST analysis, 2, 1, 1, and 1 XDR-hvKP isolates belonged to ST15, ST377, ST442, and ST147, respectively. The occurrence of such isolates is deeply concerning due to the combination of hypervirulence and extensively drug-resistance or pandrug-resistance.
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Affiliation(s)
- Sara Davoudabadi
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Goudarzi
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdollah Ardebili
- 2 Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Faghihloo
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Yasbolaghi Sharahi
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- 1 Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Antibiotic-resistant bacteria, antibiotic resistance genes, and antibiotic residues in wastewater from a poultry slaughterhouse after conventional and advanced treatments. Sci Rep 2021; 11:16622. [PMID: 34404868 PMCID: PMC8371126 DOI: 10.1038/s41598-021-96169-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Slaughterhouse wastewater is considered a reservoir for antibiotic-resistant bacteria and antibiotic residues, which are not sufficiently removed by conventional treatment processes. This study focuses on the occurrence of ESKAPE bacteria (Enterococcus spp., S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, Enterobacter spp.), ESBL (extended-spectrum β-lactamase)-producing E. coli, antibiotic resistance genes (ARGs) and antibiotic residues in wastewater from a poultry slaughterhouse. The efficacy of conventional and advanced treatments (i.e., ozonation) of the in-house wastewater treatment plant regarding their removal was also evaluated. Target culturable bacteria were detected only in the influent and effluent after conventional treatment. High abundances of genes (e.g., blaTEM, blaCTX-M-15, blaCTX-M-32, blaOXA-48, blaCMY and mcr-1) of up to 1.48 × 106 copies/100 mL were detected in raw influent. All of them were already significantly reduced by 1–4.2 log units after conventional treatment. Following ozonation, mcr-1 and blaCTX-M-32 were further reduced below the limit of detection. Antibiotic residues were detected in 55.6% (n = 10/18) of the wastewater samples. Despite the significant reduction through conventional and advanced treatments, effluents still exhibited high concentrations of some ARGs (e.g., sul1, ermB and blaOXA-48), ranging from 1.75 × 102 to 3.44 × 103 copies/100 mL. Thus, a combination of oxidative, adsorptive and membrane-based technologies should be considered.
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Wang L, Guo L, Ye K, Yang J. Genetic characteristics of OXA-48-producing Enterobacterales from China. J Glob Antimicrob Resist 2021; 26:285-291. [PMID: 34284128 DOI: 10.1016/j.jgar.2021.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/29/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES In China, OXA-48-producing Enterobacterales have been identified sporadically, causing small-scale regional outbreaks. This study investigated the molecular epidemiology, transmission and evolution of OXA-48-producing Enterobacterales and pOXA48 from mainland China. METHODS We conducted a multicentre resistance monitoring project from 2013-2018. Genome sequencing of OXA-48-produicng isolates was performed. SNPs were analysed. Eleven isolates were selected for subsequent SMRT sequencing. Genome sequences were annotated, and alignment of the complete sequences of blaOXA-48-carrying plasmids from a subset of isolates that underwent long-read sequencing was performed. RESULTS In total, 41 OXA-48-producing Enterobacterales were included in this study (34 Klebsiella pneumoniae, 3 Escherichia coli, 3 Enterobacter cloacae complex and 1 Klebsiella oxytoca). OXA-48-produicng K. pneumoniae (OXAKp) ST383, ST147 and ST11 caused outbreaks of different scales in our hospital. OXA-48-producing E. coli ST156 and ST648, E. cloacae complex ST414 and ST418, and K. oxytoca ST34 were also identified. blaOXA-48 was embedded in a Tn1999.2 structure located in IncL plasmids with different sizes (63.58-109.14 kb). Importantly, K. pneumoniae ST11 co-producing KPC-2 and OXA-48 was identified in our hospital and it is possible that KPC-2-producing K. pneumoniae ST11 obtained the blaOXA-48-carrying plasmid during its spread. A novel 109-kb blaOXA-48-carrying IncL plasmid was identified from OXAKp ST11. Possibly, two plasmids in OXAKp ST383 were integrated to form this larger plasmid. CONCLUSION OXA-48-produicng Enterobacterales were sporadic in China. Importantly, K. pneumoniae ST11 co-producing KPC-2 and OXA-48 has emerged causing an outbreak in China. This high-risk multidrug-resistant clone exhibited high compatibility and strong integration ability with foreign resistance plasmids.
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Affiliation(s)
- Lifeng Wang
- Department of Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Ling Guo
- Department of Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Kun Ye
- Department of Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - Jiyong Yang
- Department of Laboratory Medicine, First Medical Center of Chinese PLA General Hospital, Beijing 100853, China.
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7
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Moussa J, Panossian B, Nassour E, Salloum T, Abboud E, Tokajian S. Detailed characterization of an IncFII plasmid carrying blaOXA-48 from Lebanon. J Antimicrob Chemother 2021; 75:2462-2465. [PMID: 32417901 DOI: 10.1093/jac/dkaa181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/05/2020] [Accepted: 04/12/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The spread of carbapenem-resistant Enterobacteriaceae is an important challenge and an increasing healthcare problem. OXA-48 is a class D carbapenemase that is usually localized on a conjugative plasmid belonging to the IncL incompatibility group. METHODS In this study, we used a combination of short- and long-read WGS approaches and molecular typing techniques to characterize the genetic environment of the smallest reported 27 029 bp IncFII plasmid carrying blaOXA-48 (pLAU-OXA48). RESULTS The plasmid recovered from a clinical Escherichia coli isolate was positive for blaOXA-48, which was located within the Tn6237 composite transposon. Primers targeting junctions between the IncF fragment and Tn6237 for the rapid identification of pLAU-OXA48-like plasmids were designed. CONCLUSIONS To our knowledge, this is the first report showing the complete sequence of an IncFII plasmid carrying blaOXA-48 within Tn6237 using hybrid assembly of long- and short-read sequencing.
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Affiliation(s)
- Jennifer Moussa
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
| | - Balig Panossian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
| | - Elie Nassour
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
| | - Edmond Abboud
- Laboratory Department, The Middle East Institute of Health University Center, Bsalim, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 1401, Lebanon
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8
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Mangeat T, Labouesse S, Allain M, Negash A, Martin E, Guénolé A, Poincloux R, Estibal C, Bouissou A, Cantaloube S, Vega E, Li T, Rouvière C, Allart S, Keller D, Debarnot V, Wang XB, Michaux G, Pinot M, Le Borgne R, Tournier S, Suzanne M, Idier J, Sentenac A. Super-resolved live-cell imaging using random illumination microscopy. CELL REPORTS METHODS 2021; 1:100009. [PMID: 35474693 PMCID: PMC9017237 DOI: 10.1016/j.crmeth.2021.100009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/12/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022]
Abstract
Current super-resolution microscopy (SRM) methods suffer from an intrinsic complexity that might curtail their routine use in cell biology. We describe here random illumination microscopy (RIM) for live-cell imaging at super-resolutions matching that of 3D structured illumination microscopy, in a robust fashion. Based on speckled illumination and statistical image reconstruction, easy to implement and user-friendly, RIM is unaffected by optical aberrations on the excitation side, linear to brightness, and compatible with multicolor live-cell imaging over extended periods of time. We illustrate the potential of RIM on diverse biological applications, from the mobility of proliferating cell nuclear antigen (PCNA) in U2OS cells and kinetochore dynamics in mitotic S. pombe cells to the 3D motion of myosin minifilaments deep inside Drosophila tissues. RIM's inherent simplicity and extended biological applicability, particularly for imaging at increased depths, could help make SRM accessible to biology laboratories.
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Affiliation(s)
- Thomas Mangeat
- LITC Core Facility, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Simon Labouesse
- Institut Fresnel, Aix Marseille Université, CNRS, Centrale Marseille, Marseille, France
| | - Marc Allain
- Institut Fresnel, Aix Marseille Université, CNRS, Centrale Marseille, Marseille, France
| | - Awoke Negash
- Institut Fresnel, Aix Marseille Université, CNRS, Centrale Marseille, Marseille, France
| | - Emmanuel Martin
- Molecular, Cellular & Developmental Biology (MCD), Center of Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, France
| | - Aude Guénolé
- Molecular, Cellular & Developmental Biology (MCD), Center of Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, France
| | - Renaud Poincloux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claire Estibal
- LITC Core Facility, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Anaïs Bouissou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sylvain Cantaloube
- LITC Core Facility, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Elodie Vega
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Tong Li
- Molecular, Cellular & Developmental Biology (MCD), Center of Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, France
| | - Christian Rouvière
- LITC Core Facility, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Sophie Allart
- INSERM Université de Toulouse, UPS, CNRS, Centre de Physiopathologie de Toulouse Purpan (CPTP), Toulouse, France
| | - Debora Keller
- Molecular, Cellular & Developmental Biology (MCD), Center of Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, France
| | - Valentin Debarnot
- LITC Core Facility, Centre de Biologie Integrative, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Xia Bo Wang
- Molecular, Cellular & Developmental Biology (MCD), Center of Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, France
| | - Grégoire Michaux
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) - UMR 6290, 35000 Rennes, France
| | - Mathieu Pinot
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) - UMR 6290, 35000 Rennes, France
| | - Roland Le Borgne
- Univ Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) - UMR 6290, 35000 Rennes, France
| | - Sylvie Tournier
- Molecular, Cellular & Developmental Biology (MCD), Center of Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, France
| | - Magali Suzanne
- Molecular, Cellular & Developmental Biology (MCD), Center of Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, France
| | - Jérome Idier
- LS2N, CNRS UMR 6004, 1 rue de la Noë, F44321 Nantes Cedex 3, France
| | - Anne Sentenac
- Institut Fresnel, Aix Marseille Université, CNRS, Centrale Marseille, Marseille, France
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Hashemizadeh Z, Hosseinzadeh Z, Azimzadeh N, Motamedifar M. Dissemination Pattern of Multidrug Resistant Carbapenemase Producing Klebsiella pneumoniae Isolates Using Pulsed-Field Gel Electrophoresis in Southwestern Iran. Infect Drug Resist 2020; 13:921-929. [PMID: 32280248 PMCID: PMC7125322 DOI: 10.2147/idr.s227955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/23/2020] [Indexed: 11/23/2022] Open
Abstract
Background Klebsiella pneumoniae is an important cause of healthcare-associated infection. Carbapenemases have increasingly been reported in Enterobacteriaceae, especially in K. pneumoniae. Propose The objective of this study was to determine antibiotic resistance patterns, and the molecular epidemiology of multidrug resistant K. pneumoniae isolates, obtained from hospitalized patients in Shiraz, Iran. Methods In this study, 60 K. pneumoniaeisolates were collected from Nemazee and Faghihi referral hospitals. Antibiotic susceptibility testing and MIC were performed by disk diffusion test and Epsilometer (E)-test strips, respectively. Carbapenemase genes were identified by polymerase chain reaction and sequencing. Then, clonal relationships were analyzed, using PFGE. Results Thirty-three out of 60 K. pneumoniae isolates were resistant to carbapenems. Among the isolates, 86.6% were multidrug resistant (MDR). Polymyxin B (18.3%) and tigecycline (23.3%) were shown to be the most active agents against K. pneumoniae isolates. In our study, the high prevalence of blaNDM (45%) and blaOXA-48 (10%) was detected. Conclusion The results of this study revealed the widespread carbapenemase gene between different wards in hospitals as a risk factor for treatment options. PFGE analysis showed 11 clusters and 3 singletons based on an 80% similarity level. Also, PFGE analysis showed that there were similar genetic patterns among K. pneumoniae isolates and these patterns were responsible for the distribution of infection in hospitals.
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Affiliation(s)
- Zahra Hashemizadeh
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hosseinzadeh
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Azimzadeh
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Mohammad Motamedifar
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran.,Shiraz HIV/Aids Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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10
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Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak. Antimicrob Agents Chemother 2019:AAC.01204-19. [PMID: 31591122 DOI: 10.1128/aac.01204-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Objectives. A large OXA-48 outbreak in the Netherlands involved the spread of OXA-48producing Enterobacteriaceae among at least 118 patients, suggesting horizontal transfer of this resistance gene through one or more plasmids. Elucidating transmission dynamics of resistance plasmids is hampered by the low resolution of classic typing methods. This study aimed to investigate the molecular epidemiology of plasmids carrying OXA-48 carbapenemase using a next-generation sequencing approach.Methods. A total of 68 OXA-48-producing Enterobacteriaceae isolated from the hospital outbreak, as well as 22 non-outbreak related OXA-48-producing Enterobacteriaceae from the Netherlands, Libya and Turkey were selected. Plasmids were sequenced using the Illumina Miseq platform, and read sets were assembled and analysed.Results. In all plasmids bla OXA-48 was embedded in transposon Tn1999.2 and located on a ca. 62 kb IncL/M conjugative plasmid in 14 different species. There were a maximum of 2 SNPs (single nucleotide polymorphisms) between the core sequence alignment of all plasmids. Closely related sequence variants of this plasmid were detected in non-outbreak isolates from the Netherlands and other countries. Thirty-one of 89 OXA-48-producing isolates also harboured bla CTX-M-15, which was not located on the bla OXA-48-carrying plasmid. Sequencing of four plasmids harbouring bla CTX-M15 revealed extensive plasmid heterogeneity.Conclusions. A ca 62 kb plasmid was responsible for the OXA-48 outbreak in a Dutch hospital. Our findings provide strong evidence for both within-host inter-species and between host dissemination of plasmid-based OXA-48 during a nosocomial outbreak. These findings exemplify the complex epidemiology of carbapenemase producing Enterobacteriaceae (CPE).
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11
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Lee YL, Lu MC, Shao PL, Lu PL, Chen YH, Cheng SH, Ko WC, Lin CY, Wu TS, Yen MY, Wang LS, Liu CP, Lee WS, Shi ZY, Chen YS, Wang FD, Tseng SH, Lin CN, Chen YH, Sheng WH, Lee CM, Liao MH, Hsueh PR. Nationwide surveillance of antimicrobial resistance among clinically important Gram-negative bacteria, with an emphasis on carbapenems and colistin: Results from the Surveillance of Multicenter Antimicrobial Resistance in Taiwan (SMART) in 2018. Int J Antimicrob Agents 2019; 54:318-328. [PMID: 31202925 DOI: 10.1016/j.ijantimicag.2019.06.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
Multicentre surveillance of antimicrobial susceptibility of clinically important Gram-negative bacteria (GNB) from 16 Taiwanese hospitals was performed. Escherichia coli (n = 398), Klebsiella pneumoniae (n = 346), Pseudomonas aeruginosa (n = 252) and Acinetobacter baumannii complex (ABC) (n = 188) bloodstream isolates, non-typhoidal Salmonella (n = 230) and Shigella flexneri (n = 18) from various sources were collected. Antimicrobial MICs were determined using broth microdilution. Genes encoding K. pneumoniae carbapenemases (KPCs), New Delhi metallo-β-lactamases (NDMs), Verona integron-encoded metallo-β-lactamase (VIM), OXA-48-like carbapenemase (OXA-48) as well as mcr-1-5 genes were detected by molecular methods. Rates of carbapenem non-susceptibility were 2.8%, 9.0%, 0.4%, 0%, 10.3% and 48.8% for E. coli, K. pneumoniae, Salmonella, Shigella, P. aeruginosa and ABC, respectively. For carbapenemases, one (0.3%) E. coli harboured blaNDM-1. Fifteen (4.3%), two (0.6%) and two (0.6%) K. pneumoniae contained blaKPC, blaOXA-48 and blaVIM, respectively. Two (0.5%) E. coli and fourteen (4.0%) K. pneumoniae were non-wild-type according to the colistin MIC. Among Enterobacteriaceae with a colistin MIC ≥ 2 mg/L, mcr-1 was detected in one E. coli, two K. pneumoniae and three Salmonella spp. All three mcr-1-positive Salmonella isolates were collected from community-acquired infections; none of the six mcr-1-positive Enterobacteriaceae were carbapenem-resistant. Carbapenem resistance has increased among clinically important GNB, especially among hospital-acquired infections. blaKPC, especially the blaKPC-2 variant, was detected in approximately one-half of the carbapenem-resistant K. pneumoniae isolates in this study. Although resistance rates to colistin remained low among Enterobacteriaceae, the finding of mcr-1 from different species raises concern of potential dissemination.
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Affiliation(s)
- Yu-Lin Lee
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan, and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Min-Chi Lu
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Pei-Lan Shao
- Department of Pediatrics, Hsin-Chu Branch, National Taiwan University Hospital, Hsin-Chu, Taiwan
| | - Po-Liang Lu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Hsu Chen
- Department of Internal Medicine, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Hsing Cheng
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan, and School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Chi-Ying Lin
- Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Muh-Yong Yen
- Division of Infectious Diseases, Taipei City Hospital, and National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Lih-Shinn Wang
- Division of Infectious Diseases, Department of Internal Medicine, Buddhist Tzu Chi General Hospital and Tzu Chi University, Hualien, Taiwan
| | - Chang-Pan Liu
- Division of Infectious Diseases, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan, and MacKay Medical College, New Taipei City, Taiwan
| | - Wen-Sen Lee
- Division of Infectious Diseases, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, and Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Zhi-Yuan Shi
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Shen Chen
- Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, and School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Fu-Der Wang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, and School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shu-Hui Tseng
- Center for Disease Control and Prevention, Ministry of Health and Welfare, Taiwan
| | - Chao-Nan Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, and Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yu-Hui Chen
- Infection Control Center, Chi Mei Hospital, Liouying, Taiwan
| | - Wang-Huei Sheng
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chun-Ming Lee
- Department of Internal Medicine, St Joseph's Hospital, Yunlin County, Taiwan, and MacKay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Ming-Huei Liao
- National Pingtung University of Science and Technology, Neipu, Taiwan
| | - Po-Ren Hsueh
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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12
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Düzgün AÖ, Saral A. Next-generation sequencing of plasmid carrying blaOXA-48 in Klebsiella pneumoniae from Turkey. Acta Microbiol Immunol Hung 2019; 66:261-272. [PMID: 30803252 DOI: 10.1556/030.66.2019.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A carbapenem-resistant Klebsiella pneumoniae strain was isolated in Turkey in 2012 and blaNDM-1 and blaOXA-48 genes were observed in this strain. The aim of this study was to investigate transferability of plasmid bearing blaOXA-48 in K. pneumoniae and to use whole-genome sequencing in order to understand the genetic context of plasmid. K. pneumoniae strain was used as donor in conjugation experiments. Antibiotic susceptibility profile of selected transconjugant was determined. Plasmid was isolated from transconjugant colony and was named as pKPT. Complete sequencing of the pKPT was conducted using a next-generation sequencing. Annotation of the contigs was performed using the Geneious R9, followed by finding open reading frames (ORFs) with selected web-based tools. BLAST analysis was performed at the NCBI BLAST server to determine genes showing more than 90% similarity with these ORFs. Results of antibiotic susceptibility test showed that transconjugant colony was resistant to ampicillin/sulbactam, piperacillin, and piperacillin/tazobactam. The pKPT plasmid had a length of 45,217 bp and an average G + C content of 49%. Blast analysis revealed that pKPT was included in the IncL/M incompatibility group. The pKPT was found to contain blaOXA-48 within Tn1999.2 transposon without any other antibiotic resistance gene.
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Affiliation(s)
- Azer Özad Düzgün
- 1 Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gümüşhane University, Gümüşhane, Turkey
- 2 Medicinal Plants, Traditional Medicine Practice and Research Center, Gümüşhane University, Gümüşhane, Turkey
| | - Ayşegül Saral
- 3 Department of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh University, Artvin, Turkey
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13
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Mairi A, Pantel A, Ousalem F, Sotto A, Touati A, Lavigne JP. OXA-48-producing Enterobacterales in different ecological niches in Algeria: clonal expansion, plasmid characteristics and virulence traits. J Antimicrob Chemother 2019; 74:1848-1855. [DOI: 10.1093/jac/dkz146] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Assia Mairi
- Laboratoire d’Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
| | - Alix Pantel
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
- Department of Microbiology, University Hospital Nîmes, Nîmes, France
| | - Farès Ousalem
- Institut de Biologie et de Physico-chimie, UMR826, Université de Paris Diderot, Paris, France
| | - Albert Sotto
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
- Department of Infectious Diseases, University Hospital Nîmes, Nîmes, France
| | - Abdelaziz Touati
- Laboratoire d’Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria
| | - Jean-Philippe Lavigne
- Institut National de la Santé et de la Recherche Médicale, U1047, Université Montpellier, UFR de Médecine, Nîmes, France
- Department of Microbiology, University Hospital Nîmes, Nîmes, France
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14
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Yoo JH. The Infinity War: How to Cope with Carbapenem-resistant Enterobacteriaceae. J Korean Med Sci 2018; 33:e255. [PMID: 30275806 PMCID: PMC6159103 DOI: 10.3346/jkms.2018.33.e255] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 08/28/2018] [Indexed: 01/10/2023] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are now spread worldwide. In Korea, the number of CRE isolation is rapidly increasing, and impending endemicity is a concern. To cope well with CRE, thorough infection control, such as active surveillance, early detection, strict contact precaution, cleaning the environment, and antibiotic stewardship is very important. Therapeutic options include polymyxin, tigecycline, fosfomycin or the combination of them with carbapenem, which is currently the mainstay of treatment. In addition, various combination regimens with new carbapenemase inhibitors such as avibactam, vaborbactam, or relebactam, and other classes of antimicrobials such as plazomicin and siderophore cephalosporin are in the process of evaluation.
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Affiliation(s)
- Jin-Hong Yoo
- Division of Infectious Diseases, Department of Internal Medicine, The Catholic University of Korea College of Medicine, Bucheon St. Mary's Hospital, Bucheon, Korea
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15
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In Silico Typing and Comparative Genomic Analysis of IncFII K Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles. Antimicrob Agents Chemother 2018; 62:AAC.00764-18. [PMID: 30012771 DOI: 10.1128/aac.00764-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/10/2018] [Indexed: 12/30/2022] Open
Abstract
IncFIIK plasmids are associated with the acquisition and dissemination of multiple-antimicrobial resistance in Klebsiella pneumoniae and often encountered in clinical isolates of this species. Since the phylogeny and evolution of IncFIIK plasmids remain unclear, here we performed large-scale in silico typing and comparative analysis of these plasmids in publicly available bacterial/plasmid genomes. IncFIIK plasmids are prevalent in K. pneumoniae, being found in 69% of sequenced genomes, covering 66% of sequenced STs (sequence types), but sparse in other Enterobacteriaceae IncFIIK replicons have three lineages. One IncFIIK allele could be found in distinct K. pneumoniae STs, highlighting the lateral genetic flow of IncFIIK plasmids. A set of 77 IncFIIK plasmids with full sequences were further analyzed. A pool of 327 antibiotic resistance genes or remnants were annotated in 75.3% of these plasmids. Plasmid genome comparison reiterated that they often contain other replicons belonging to IncFIA, IncFIB, IncFIIYp, IncFIIpCRY, IncR, IncL, and IncN groups and that they share a conserved backbone featuring an F-like conjugation module that has divergent components responsible for regulation and mating pair stabilization. Further epidemiological studies of IncFIIK plasmids are required due to the sample bias of K. pneumoniae genomes in public databases. This study provides insights into the evolution and structures of IncFIIK plasmids.
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16
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Pulss S, Stolle I, Stamm I, Leidner U, Heydel C, Semmler T, Prenger-Berninghoff E, Ewers C. Multispecies and Clonal Dissemination of OXA-48 Carbapenemase in Enterobacteriaceae From Companion Animals in Germany, 2009-2016. Front Microbiol 2018; 9:1265. [PMID: 29963026 PMCID: PMC6010547 DOI: 10.3389/fmicb.2018.01265] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/24/2018] [Indexed: 12/23/2022] Open
Abstract
The increasing spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a serious threat to public health. Recent studies suggested animals as a putative source of such bacteria. We investigated 19,025 Escherichia coli, 1607 Klebsiella spp. and 570 Enterobacter spp. isolated from livestock, companion animal, horse, and pet samples between 2009 and 2016 in our routine diagnostic laboratory for reduced susceptibility to carbapenems (CP) by using meropenem-containing media. Actively screened CP non-susceptible strains as well as 367 archived ESBL/AmpC-β-lactamase-producing Enterobacteriaceae were then tested for the presence of CP genes by PCRs. Among 21,569 isolates, OXA-48 could be identified as the sole carbapenemase type in 137 (0.64%) strains. The blaOXA-48 gene was located on an ∼60-kb IncL plasmid and sequence analysis revealed high similarity to reference plasmid pOXA-48a, which has been involved in the global spread of the blaOXA-48 gene in humans for many years. Klebsiella pneumoniae was the predominant OXA-48 producer (n = 86; 6.6% of all K. pneumoniae isolates), followed by E. cloacae (n = 28; 5.0%), Klebsiella oxytoca (n = 1; 0.3%), and E. coli (n = 22, 0.1%). OXA-48 was not found in livestock, but in dogs (120/3182; 3.8%), cats (13/792; 1.6%), guinea pig (1/43; 2.3%), rat (1/23; 4.3%), mouse (1/180; 0.6%), and one rabbit (1/144; 0.7%). Genotyping identified few major clones among the different enterobacteria species, including sequence types ST11 and ST15 for K. pneumoniae, ST1196 for E. coli, and ST506 and ST78 for E. cloacae, most of which were previously involved in the dissemination of multidrug-resistant strains in humans. The majority of OXA-48 isolates (n = 112) originated from a university veterinary clinic (UVC), while animals from further 16 veterinary institutions were positive. Clonal analyses suggested nosocomial events related to different species and STs in two veterinary clinics and horizontal transfer of the pOXA-48-like plasmid between bacterial species and animals. A systematic monitoring is urgently needed to assess the dissemination of CPE not only in livestock but also in companion animals and veterinary clinics.
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Affiliation(s)
- Sandra Pulss
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Inka Stolle
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany.,Institute of Microbiology, University of Veterinary Medicine Hannover, Foundation, Hanover, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Ludwigsburg, Germany
| | - Ursula Leidner
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Carsten Heydel
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Torsten Semmler
- Microbial Genomics (NG1), Robert Koch Institute, Berlin, Germany
| | - Ellen Prenger-Berninghoff
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
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17
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Slipski CJ, Zhanel GG, Bay DC. Biocide Selective TolC-Independent Efflux Pumps in Enterobacteriaceae. J Membr Biol 2018; 251:15-33. [PMID: 29063140 PMCID: PMC5840245 DOI: 10.1007/s00232-017-9992-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/04/2017] [Indexed: 02/03/2023]
Abstract
Bacterial resistance to biocides used as antiseptics, dyes, and disinfectants is a growing concern in food preparation, agricultural, consumer manufacturing, and health care industries, particularly among Gram-negative Enterobacteriaceae, some of the most common community and healthcare-acquired bacterial pathogens. Biocide resistance is frequently associated with antimicrobial cross-resistance leading to reduced activity and efficacy of both antimicrobials and antiseptics. Multidrug resistant efflux pumps represent an important biocide resistance mechanism in Enterobacteriaceae. An assortment of structurally diverse efflux pumps frequently co-exist in these species and confer both unique and overlapping biocide and antimicrobial selectivity. TolC-dependent multicomponent systems that span both the plasma and outer membranes have been shown to confer clinically significant resistance to most antimicrobials including many biocides, however, a growing number of single component TolC-independent multidrug resistant efflux pumps are specifically associated with biocide resistance: small multidrug resistance (SMR), major facilitator superfamily (MFS), multidrug and toxin extruder (MATE), cation diffusion facilitator (CDF), and proteobacterial antimicrobial compound efflux (PACE) families. These efflux systems are a growing concern as they are rapidly spread between members of Enterobacteriaceae on conjugative plasmids and mobile genetic elements, emphasizing their importance to antimicrobial resistance. In this review, we will summarize the known biocide substrates of these efflux pumps, compare their structural relatedness, Enterobacteriaceae distribution, and significance. Knowledge gaps will be highlighted in an effort to unravel the role that these apparent "lone wolves" of the efflux-mediated resistome may offer.
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Affiliation(s)
- Carmine J Slipski
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada
| | - Denice C Bay
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Rm 514C Basic Medical Sciences Bldg., 745 Bannatyne Avenue, Winnipeg, MB, R3E 0J9, Canada.
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Genetic analysis of a PER-2-producing Shewanella sp. strain harbouring a variety of mobile genetic elements and antibiotic resistance determinants. J Glob Antimicrob Resist 2017; 11:81-86. [PMID: 28760680 DOI: 10.1016/j.jgar.2017.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/07/2017] [Accepted: 06/10/2017] [Indexed: 11/23/2022] Open
Abstract
The objective of this study was to investigate the molecular mechanisms explaining the multidrug-resistant (MDR) phenotype found in a novel clinical Shewanella sp. strain (Shew256) recovered from a diabetic patient. Whole-genome shotgun sequencing was performed using Illumina MiSeq-I and Nextera XT DNA library. De novo assembly was performed with SPAdes. RAST Server was used to predict the open-reading frames and the predictions were confirmed using BLAST. Further genomic analysis was carried out using average nucleotide identity (ANI), ACT (Artemis), OrthoMCL, ARG-ANNOT, ISfinder, PHAST, tRNAscan-SE, plasmidSPAdes, PlasmidFinder and MAUVE. PCR and plasmid extraction were also performed. Genomic analysis revealed a total of 456 predicted genes unique to Shew256 compared with other Shewanella genomes. Moreover, the presence of different resistance genes, including blaPER-2, was found. A complex class 1 integron containing the ISCR1 gene, disrupted by two putative transposase genes, was identified. Furthermore, other resistance genes, a transposon containing aph(3'), insertion sequences, phages and non-coding RNAs were also found. In conclusion, evidence of acquisition of resistance genes and mobile elements that could explain the MDR phenotype were observed. This Shewanella sp. represents a prime example of how antibiotic resistance determinants can be acquired by uncommon pathogens.
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Xie L, Dou Y, Zhou K, Chen Y, Han L, Guo X, Sun J. Coexistence of blaOXA-48 and Truncated blaNDM-1 on Different Plasmids in a Klebsiella pneumoniae Isolate in China. Front Microbiol 2017; 8:133. [PMID: 28210248 PMCID: PMC5288367 DOI: 10.3389/fmicb.2017.00133] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/18/2017] [Indexed: 12/29/2022] Open
Abstract
Objectives: To describe the genetic environment, transferability, and antibiotic susceptibility of one clinical Klebsiella pneumoniae isolate harboring both blaOXA-48 and blaNDM-1 on different plasmids from a Chinese hospital. Methods: The isolate was subjected to antimicrobial susceptibility testing and multilocus sequence typing using Etest and PCR. The plasmids harboring blaOXA-48 and blaNDM-1 were analyzed through conjugation experiments, S1-nuclease pulsed-field gel electrophoresis, and hybridization with specific probes. Plasmid DNA was sequenced using Pacbio RS II and annotated using RAST. Results:K. pneumoniae RJ119, carrying both blaOXA-48 and blaNDM-1, was resistant to almost all carbapenems, cephalosporins, fluoroquinolone, and aminoglycosides and belonged to ST307. blaOXA-48 was located on a 61,748-bp IncL/M conjugative plasmid, which displayed overall nucleotide identity (99%) to pKPN-E1-Nr.7. blaNDM-1 was located on a 335,317-bp conjugative plasmid, which was a fusion of a blaNDM-1-harboring InA/C plasmid pNDM-US (140,825 bp, 99% identity) and an IncFIB plasmid pKPN-c22 (178,563 bp, 99% identity). The transconjugant RJ119-1 harboring blaNDM-1 was susceptible to carbapenem, and there was an insertion of IS10 into the blaNDM-1 gene. Conclusion: This is the first report of the coexistence of blaOXA-48 and blaNDM-1 in one K. pneumoniae clinical isolate in China. OXA-48 in RJ119 contributed to the majority to its high resistance to carbapenems, whereas NDM-1 remained unexpressed, most likely due to the insertion of IS10. Our results provide new insight for the relationship between genetic diagnosis and clinical treatment. They also indicate that increased surveillance of blaOXA-48 is urgently needed in China.
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Affiliation(s)
- Lianyan Xie
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Yi Dou
- Department of Burns and Plastic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Kaixin Zhou
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Yue Chen
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Lizhong Han
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Xiaokui Guo
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiaotong University School of Medicine Shanghai, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine Shanghai, China
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Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131. Antimicrob Agents Chemother 2016; 60:6948-6951. [PMID: 27600043 DOI: 10.1128/aac.01130-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/23/2016] [Indexed: 11/20/2022] Open
Abstract
OXA-48-like enzymes have emerged as important extended-spectrum β-lactamases/carbapenemases in Escherichia coli sequence type 131 (ST131). We report the structures of the first fully sequenced blaOXA-163 plasmid and of two other blaOXA-48 plasmids in this lineage. blaOXA-163 was located on a 71-kb IncN plasmid with other resistance genes. blaOXA-48 was present on IncL/M plasmids, genetically similar to other blaOXA-48 plasmid sequences, and consistent with interspecies/interlineage spread. The presence of blaOXA-48-like genes on epidemic plasmids in ST131 is of concern.
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Lee CR, Lee JH, Park KS, Kim YB, Jeong BC, Lee SH. Global Dissemination of Carbapenemase-Producing Klebsiella pneumoniae: Epidemiology, Genetic Context, Treatment Options, and Detection Methods. Front Microbiol 2016; 7:895. [PMID: 27379038 PMCID: PMC4904035 DOI: 10.3389/fmicb.2016.00895] [Citation(s) in RCA: 446] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 05/26/2016] [Indexed: 01/08/2023] Open
Abstract
The emergence of carbapenem-resistant Gram-negative pathogens poses a serious threat to public health worldwide. In particular, the increasing prevalence of carbapenem-resistant Klebsiella pneumoniae is a major source of concern. K. pneumoniae carbapenemases (KPCs) and carbapenemases of the oxacillinase-48 (OXA-48) type have been reported worldwide. New Delhi metallo-β-lactamase (NDM) carbapenemases were originally identified in Sweden in 2008 and have spread worldwide rapidly. In this review, we summarize the epidemiology of K. pneumoniae producing three carbapenemases (KPCs, NDMs, and OXA-48-like). Although the prevalence of each resistant strain varies geographically, K. pneumoniae producing KPCs, NDMs, and OXA-48-like carbapenemases have become rapidly disseminated. In addition, we used recently published molecular and genetic studies to analyze the mechanisms by which these three carbapenemases, and major K. pneumoniae clones, such as ST258 and ST11, have become globally prevalent. Because carbapenemase-producing K. pneumoniae are often resistant to most β-lactam antibiotics and many other non-β-lactam molecules, the therapeutic options available to treat infection with these strains are limited to colistin, polymyxin B, fosfomycin, tigecycline, and selected aminoglycosides. Although, combination therapy has been recommended for the treatment of severe carbapenemase-producing K. pneumoniae infections, the clinical evidence for this strategy is currently limited, and more accurate randomized controlled trials will be required to establish the most effective treatment regimen. Moreover, because rapid and accurate identification of the carbapenemase type found in K. pneumoniae may be difficult to achieve through phenotypic antibiotic susceptibility tests, novel molecular detection techniques are currently being developed.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Young Bae Kim
- Division of STEM, North Shore Community College, Danvers MA, USA
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University Yongin, South Korea
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Bakthavatchalam YD, Anandan S, Veeraraghavan B. Laboratory Detection and Clinical Implication of Oxacillinase-48 like Carbapenemase: The Hidden Threat. J Glob Infect Dis 2016; 8:41-50. [PMID: 27013843 PMCID: PMC4785756 DOI: 10.4103/0974-777x.176149] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Carbapenemase producing Gram-negative pathogen is of great concern for physician. The challenging aspects are treatment option and infection control. Monitoring of respective carbapenemase resistance mechanism is necessary to prevent the outbreaks. Currently, the rapid emergence of oxacillinase (OXA-48) like is alarming. Increasing frequency of OXA-48 is seen than the classical carbapenemase (KPC, NDM, IMP, and VIM) across the world. The bla OXA-48 gene is commonly identified in Escherichia coli and Klebsiella pneumoniae. The transferrable plasmid of OXA-48 is associated with rapid spread and inter-species dissemination. In general, OXA-48-like enzymes weakly hydrolyzes both carbapenem and broad spectrum cephalosporins. Except OXA-163, which effectively hydrolyze cephalosporin. This poor hydrolytic profile obscures the detection of OXA-48-like. It may go undetected in routine diagnosis and complicates the treatment option. Co-production of OXA-48-like with CTX-M-15 and other carbapenemase (NDM, VIM) leads to the emergence of multidrug resistant strains.
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Affiliation(s)
| | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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Carbapenemase-Producing Klebsiella pneumoniae in Romania: A Six-Month Survey. PLoS One 2015; 10:e0143214. [PMID: 26599338 PMCID: PMC4658179 DOI: 10.1371/journal.pone.0143214] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/02/2015] [Indexed: 01/22/2023] Open
Abstract
This study presents the first characterization of carbapenem-non-susceptible Klebsiella pneumoniae isolates by means of a structured six-month survey performed in Romania as part of an Europe-wide investigation. Klebsiella pneumoniae clinical isolates from different anatomical sites were tested for antibiotic susceptibility by phenotypic methods and confirmed by PCR for the presence of four carbapenemase genes. Genome macrorestriction fingerprinting with XbaI was used to analyze the relatedness of carbapenemase-producing Klebsiella pneumoniae isolates collected from eight hospitals. Among 75 non-susceptible isolates, 65 were carbapenemase producers. The most frequently identified genotype was OXA-48 (n = 51 isolates), eight isolates were positive for blaNDM-1 gene, four had the blaKPC-2 gene, whereas two were positive for blaVIM-1. The analysis of PFGE profiles of OXA-48 and NDM-1 producing K. pneumoniae suggests inter-hospitals and regional transmission of epidemic clones. This study presents the first description of K. pneumoniae strains harbouring blaKPC-2 and blaVIM-1 genes in Romania. The results of this study highlight the urgent need for the strengthening of hospital infection control measures in Romania in order to curb the further spread of the antibiotic resistance.
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Ma L, Wang JT, Wu TL, Siu LK, Chuang YC, Lin JC, Lu MC, Lu PL. Emergence of OXA-48-Producing Klebsiella pneumoniae in Taiwan. PLoS One 2015; 10:e0139152. [PMID: 26414183 PMCID: PMC4587373 DOI: 10.1371/journal.pone.0139152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 09/08/2015] [Indexed: 12/24/2022] Open
Abstract
The isolation of OXA-48-producing Enterobacteriaceae has increased dramatically in Mediterranean countries in the past 10 years, and has recently emerged in Asia. Between January 2012 and May 2014, a total of 760 carbapenem non-susceptible Klebsiella pneumoniae (CnSKP) isolates were collected during a Taiwan national surveillance. Carbapenemases were detected in 210 CnSKP isolates (27.6%), including 162 KPC-2 (n = 1), KPC-3, KPC-17, and NDM-1 (n = 1 each), OXA-48 (n = 4), IMP-8 (n = 18), and VIM-1 (n = 24). The four blaOXA-48 CnSKP isolates were detected in late 2013. Herein we report the emergence OXA-48-producing K. pneumoniae isolates in Taiwan. PFGE analysis revealed that the four isolates belonged to three different pulsotypes. Three isolates harboured blaCTX-M genes and belonged to MLST type ST11. In addition, the plasmids belonged to the incompatibility group, IncA/C. One isolate belonged to ST116 and the plasmid incompatibility group was non-typeable. The sequence upstream of the blaOXA-48 gene in all four isolates was identical to pKPOXA-48N1, a blaOXA-48-carrying plasmid. This is the first report of OXA-48-producing Enterobacteriaceae in Taiwan and the second report to identify blaOXA-48 on an IncA/C plasmid in K. pneumoniae. Given that three isolates belong to the same pandemic clone (ST11) and possess the IncA/C plasmid and similar plasmid digestion profile that indicated the role of clonal spread or plasmid for dissemination of blaOXA-48 gene, the emergence of OXA-48-producing K. pneumoniae in Taiwan is of great concern.
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Affiliation(s)
- Ling Ma
- National Institutes of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Jann-Tay Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tsu-Lan Wu
- Department of Clinical Pathology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - L. Kristopher Siu
- National Institutes of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan
| | - Yin-Ching Chuang
- Department of Internal Medicine and Medical Research, Chi Mei Medical Center, Tainan, Taiwan
- Department of Internal Medicine, Chi Mei Medical Center, Liouying, Tainan, Taiwan
| | - Jung-Chung Lin
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Min-Chi Lu
- Section of Infectious Diseases, Department of Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- * E-mail: (MCL); (PLL)
| | - Po-Liang Lu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail: (MCL); (PLL)
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Sotillo A, Muñoz-Vélez M, Santamaría ML, Ruiz-Carrascoso G, García-Bujalance S, Gómez-Gil R, Mingorance J. Emergence of VIM-1-producing Salmonella enterica serovar Typhimurium in a paediatric patient. J Med Microbiol 2015; 64:1541-1543. [PMID: 26384861 DOI: 10.1099/jmm.0.000170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alma Sotillo
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261, Madrid 28046, Spain
| | - Marta Muñoz-Vélez
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261, Madrid 28046, Spain
| | - Manuel López Santamaría
- Servicio de Cirugía Pediátrica, Hospital Universitario La Paz, Paseo de La Castellana, 261, Madrid 28046, Spain
| | - Guillermo Ruiz-Carrascoso
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261, Madrid 28046, Spain
| | - Silvia García-Bujalance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261, Madrid 28046, Spain
| | - Rosa Gómez-Gil
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261, Madrid 28046, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261, Madrid 28046, Spain
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Complete Sequence of a blaOXA-48-Harboring IncL Plasmid from an Enterobacter cloacae Clinical Isolate. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01076-15. [PMID: 26383652 PMCID: PMC4574381 DOI: 10.1128/genomea.01076-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report a 63,584-bp conjugative IncL plasmid (pUR17313-1) from an Enterobacter cloacae clinical isolate, containing a blaOXA-48 gene. The plasmid sequence also carried important mobile genetic elements involved in the spread of antibiotic resistance, namely, the Tn1999.2 composite transposon, which enclosed blaOXA-48-, integrase-, and transposase-encoding genes.
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Diversity and Global Distribution of IncL/M Plasmids Enabling Horizontal Dissemination of β-Lactam Resistance Genes among the Enterobacteriaceae. BIOMED RESEARCH INTERNATIONAL 2015; 2015:414681. [PMID: 26236726 PMCID: PMC4510254 DOI: 10.1155/2015/414681] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 06/22/2015] [Indexed: 02/07/2023]
Abstract
Antibiotic resistance determinants are frequently associated with plasmids and other mobile genetic elements, which simplifies their horizontal transmission. Several groups of plasmids (including replicons of the IncL/M incompatibility group) were found to play an important role in the dissemination of resistance genes encoding β-lactamases. The IncL/M plasmids are large, broad host range, and self-transmissible replicons. We have identified and characterized two novel members of this group: pARM26 (isolated from bacteria inhabiting activated sludge from a wastewater treatment plant) and pIGT15 (originating from a clinical strain of Escherichia coli). This instigated a detailed comparative analysis of all available sequences of IncL/M plasmids encoding β-lactamases. The core genome of these plasmids is comprised of 20 genes with conserved synteny. Phylogenetic analyses of these core genes allowed clustering of the plasmids into four separate groups, which reflect their antibiotic resistance profiles. Examination of the biogeography of the IncL/M plasmids revealed that they are most frequently found in bacteria of the family Enterobacteriaceae originating from the Mediterranean region and Western Europe and that they are able to persist in various ecological niches even in the absence of direct antibiotic selection pressure.
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Willemsen I, van Esser J, Kluytmans-van den Bergh M, Zhou K, Rossen JW, Verhulst C, Verduin K, Kluytmans J. Retrospective identification of a previously undetected clinical case of OXA-48-producing K. pneumoniae and E. coli: the importance of adequate detection guidelines. Infection 2015; 44:107-10. [PMID: 26062812 DOI: 10.1007/s15010-015-0805-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/29/2015] [Indexed: 12/01/2022]
Abstract
INTRODUCTION The laboratory detection of OXA-48-carbapenemase-producing Enterobacteriaceae is difficult, as minimum inhibition concentrations for carbapenems are often below the clinical breakpoint. In 2011, the Dutch national guideline for the detection of highly resistant micro-organisms was issued, which includes recommendations on the use of carbapenem screening breakpoints for the detection of carbapenemase-producing Enterobacteriaceae. MATERIALS AND METHODS During a validation study of the Check-MDR CT103 microarray (Check-Points, Wageningen, The Netherlands) in 2013, an OXA-48-like carbapenemase gen was identified in two isolates that were previously obtained from a patient with non-Hodgkin lymphoma in 2007. Whole-genome sequencing (WGS) and subsequent BLAST Ringe Image Generator (BRIG) analysis were performed to establish the presence of OXA-48 carbapenemase encoding plasmids and their similarity. RESULTS This case report describes the first documented OXA-48-producing Klebsiella pneumonia (ST648) and Escherichia coli (ST866) in the Netherlands. A similar IncL/M plasmid was identified in both strains, suggesting within-patient horizontal transfer. CONCLUSION This case illustrates that OXA-48-carbapenemase-producing Enterobacteriaceae can be unnoticed without adequate laboratory detection procedures. Our observation stresses the importance of uniform and adequate laboratory methods for the timely and accurate detection of important antimicrobial resistance.
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Affiliation(s)
- Ina Willemsen
- Laboratory for Microbiology and Infection Control, Amphia Hospital, PO Box 90158, 4800 RK, Breda, The Netherlands.
| | - Joost van Esser
- Department for internal medicine, Amphia Hospital, Breda, The Netherlands
| | - Marjolein Kluytmans-van den Bergh
- Amphia Academy Infectious Disease Foundation, Amphia Hospital, Breda, The Netherlands.,Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Kai Zhou
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John W Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carlo Verhulst
- Laboratory for Microbiology and Infection Control, Amphia Hospital, PO Box 90158, 4800 RK, Breda, The Netherlands
| | - Kees Verduin
- Laboratory for Microbiology and Infection Control, Amphia Hospital, PO Box 90158, 4800 RK, Breda, The Netherlands
| | - Jan Kluytmans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, PO Box 90158, 4800 RK, Breda, The Netherlands.,Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
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First report of an OXA-48-producing multidrug-resistant Proteus mirabilis strain from Gaza, Palestine. Antimicrob Agents Chemother 2015; 59:4305-7. [PMID: 25896692 DOI: 10.1128/aac.00565-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/11/2015] [Indexed: 01/11/2023] Open
Abstract
We report the first multidrug-resistant Proteus mirabilis strain producing the carbapenemase OXA-48 (Pm-OXA-48) isolated at Al-Shifa hospital in Gaza, Palestine. Draft genome sequencing of Pm-OXA-48 identified 16 antimicrobial resistance genes, encoding resistance to β-lactams, aminoglycosides, fluoroquinolones, phenicols, streptothricin, tetracycline, and trimethoprim-sulfamethoxazole. Complete sequencing of the bla(OXA-48)-harboring plasmid revealed that it is a 72 kb long IncL/M plasmid, harboring carbapenemase gene bla(OXA-48), extended spectrum β-lactamase gene bla(CTX-M-14), and aminoglycoside resistance genes strA, strB, and aph(3')-VIb.
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30
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Brañas P, Villa J, Viedma E, Mingorance J, Orellana MA, Chaves F. Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in a hospital in Madrid: Successful establishment of an OXA-48 ST11 clone. Int J Antimicrob Agents 2015; 46:111-6. [PMID: 25914088 DOI: 10.1016/j.ijantimicag.2015.02.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 01/05/2023]
Abstract
Here we report a retrospective clinical and molecular study conducted in a tertiary care facility in southern Madrid, Spain, from January 2009 to February 2014 to investigate the epidemiology of carbapenemase-producing Klebsiella pneumoniae (CPKp). Carbapenemase genes were identified in 97 non-duplicate K. pneumoniae isolates, including 59 harbouring blaOXA-48, 37 harbouring blaVIM-1 and 1 harbouring blaKPC-2. Pulsed-field gel electrophoresis (PFGE) analysis verified the presence of 20 different clonal types, whilst multilocus sequence typing (MLST) assigned the isolates to eight sequence types (STs). A gradual increase was noted in the number of CPKp isolated, ranging from 0.8% in 2009 to 4.3% in 2013. A large outbreak was also identified, initiated in 2013 owing to a blaOXA-48 and blaCTX-M-15 co-producing ST11 clone and involving a total of 44 patients. Whole-genome sequencing was used to characterise the resistome of a representative isolate from this outbreak. Bioinformatics analysis revealed the presence of 121 genes related to antibiotic and antiseptic resistance, mutations in the ompk35 and ompk36 genes, and the presence of the blaOXA-48 gene on a 62 811bp IncL/M-type plasmid as part of a Tn1999.2 composite transposon. These results portray the increasing trend in carbapenemase-producing isolates in this hospital and highlight the successful establishment of a blaOXA-48 and blaCTX-M-15 co-producing ST11 clone that has led to the displacement of previous circulating clones.
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Affiliation(s)
- Patricia Brañas
- Servicio de Microbiología Clínica, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jennifer Villa
- Servicio de Microbiología Clínica, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Esther Viedma
- Servicio de Microbiología Clínica, Hospital Universitario 12 de Octubre, Madrid, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Mingorance
- Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain; Hospital Universitario la Paz, IdiPAZ, Madrid, Spain
| | - M Angeles Orellana
- Servicio de Microbiología Clínica, Hospital Universitario 12 de Octubre, Madrid, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Chaves
- Servicio de Microbiología Clínica, Hospital Universitario 12 de Octubre, Madrid, Spain; Spanish Network for the Research in Infectious Diseases (REIPI RD12/0015), Instituto de Salud Carlos III, Madrid, Spain.
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Preston KE, Hitchcock SA, Aziz AY, Tine JA. The complete nucleotide sequence of the multi-drug resistance-encoding IncL/M plasmid pACM1. Plasmid 2014; 76:54-65. [PMID: 25291385 DOI: 10.1016/j.plasmid.2014.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/20/2014] [Accepted: 08/29/2014] [Indexed: 11/25/2022]
Abstract
The 89,977 bp nucleotide sequence of pACM1, isolated from a 1993 outbreak strain of cephalosporin-resistant Klebsiella oxytoca, has been completed and assigned GenBank accession number KJ541681. The plasmid has a single 31,842 bp mosaic multi-drug resistance-encoding (MDR) region comprising the mer resistance module of Tn1696, two integrons with a total of seven cassettes, one complete copy each of IS1R and IS26, and the bla(SHV-5)-carrying Tn2003 (with defective IS26 termini), all within a Tn1721-like element inserted into the mucB gene of the IncL/M plasmid backbone. The Tn1721-Tn1696 combination resembles sequence found in the chromosomal MDR islands of some Acinetobacter baumannii isolates. Among the completely sequenced IncL/M resistance plasmids, the Tn1721-based MDR region is unique, but data from older studies suggest that this type of plasmid was widespread in the 1990s. Since resistance gene dosage is affected by plasmid copy number (PCN), we used a relatively simple new "efficiency-corrected" qPCR assay to measure the PCN of pACM1. There are approximately three copies per chromosome in an Escherichia coli DH5α host, and two in the original Klebsiella oxytoca isolate. We could not find similar PCN data for other medically important plasmids for comparison. The study of this plasmid property and its effect on resistance levels should be facilitated in the future by the availability of qPCR instruments and complete genome sequences.
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Affiliation(s)
- Karen E Preston
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA.
| | - Sandra A Hitchcock
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA; Hudson Valley Community College, 80 Vandenburgh Ave., Troy, NY 12180, USA
| | - Abdullah Y Aziz
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA; Hudson Valley Community College, 80 Vandenburgh Ave., Troy, NY 12180, USA
| | - John A Tine
- Center for Functional Genomics, University at Albany, SUNY, 1 Discovery Dr., Rensselaer, NY 12144-3452, USA
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Draft Whole-Genome Sequence of OXA-48-Producing Multidrug-Resistant Klebsiella pneumoniae KP_ST11_OXA-48. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00737-14. [PMID: 25081259 PMCID: PMC4118062 DOI: 10.1128/genomea.00737-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We present the draft genome sequence of a blood culture isolate of OXA-48-producing Klebsiella pneumoniae (sequence type 11 [ST11]) obtained in the course of a hospital outbreak in Spain. Sequence analysis showed 121 genes related to antibiotic and antiseptic resistance, including blaOXA-48, which was located in an IncL/M plasmid.
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Beyrouthy R, Robin F, Dabboussi F, Mallat H, Hamzé M, Bonnet R. Carbapenemase and virulence factors of Enterobacteriaceae in North Lebanon between 2008 and 2012: evolution via endemic spread of OXA-48. J Antimicrob Chemother 2014; 69:2699-705. [DOI: 10.1093/jac/dku181] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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34
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IS1R-mediated plasticity of IncL/M plasmids leads to the insertion of bla OXA-48 into the Escherichia coli Chromosome. Antimicrob Agents Chemother 2014; 58:3785-90. [PMID: 24752261 DOI: 10.1128/aac.02669-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The OXA-48 carbapenemase is mainly encoded by ∼ 62-kb IncL/M plasmids. However, chromosome-mediated genes have been observed in Escherichia coli isolates. In this work, we investigated the genetic environment of OXA-48 in members of the family Enterobacteriaceae (n = 22) to understand how the OXA-48-encoding gene is transferred into the E. coli chromosome. The OXA-48-encoding gene was located within intact Tn1999.2 transposons in the ∼ 62-kb plasmids or within a truncated variant of Tn1999.2 for the OXA-48-encoding genes located in the chromosomes of E. coli bacteria. The analysis of the Tn1999.2 genetic environment revealed an inverted orientation of the transposon in five ∼ 62-kb plasmids (5/14 [35%]) and in all chromosome inserts (n = 8). The sequencing of pRA35 plasmid showed that this orientation of Tn1999.2 and the acquisition of an IS1R insertion sequence generated a 21.9-kb IS1R-based composite transposon encoding OXA-48 and designated Tn6237. The sequencing of a chromosomal insert encoding OXA-48 also revealed this new transposon in the E. coli chromosome. PCR mapping showed the presence of this element in all strains harboring an OXA-48-encoding chromosomal insert. However, different insertion sites of this transposon were observed in the E. coli chromosome. Overall, these findings indicate a plasticity of the OXA-48 genetic environment mediated by IS1R insertion sequences. The insertion sequences can induce the transfer of the OXA-encoding gene into E. coli chromosomes and thereby promote its persistence and expression at low levels.
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Power K, Wang J, Karczmarczyk M, Crowley B, Cotter M, Haughton P, Lynch M, Schaffer K, Fanning S. Molecular analysis of OXA-48-carrying conjugative IncL/M-like plasmids in clinical isolates of Klebsiella pneumoniae in Ireland. Microb Drug Resist 2014; 20:270-4. [PMID: 24520822 DOI: 10.1089/mdr.2013.0022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This study characterized an IncL/M-like plasmid containing a bla(OXA-48)-encoding gene from a clinical isolate of Klebsiella pneumoniae, denoted as E71T. Investigation of this plasmid sequence identified unique regions of interest along with conserved regions detected in eight other clinical carbapenem-resistant isolates. A 63-kb plasmid (pE71T) from K. pneumoniae E71T was sequenced and found to be highly similar to the recently published K. pneumoniae pOXA-48a (JN626286). Two copies of the insertion sequence element IS1R were identified, one of which was located adjacent to the bla(OXA-48)-encoding gene forming part of a composite transposon Tn1999.2 and the second located 16-kb downstream. Plasmid profiling and PCR assays confirmed that the pE71T backbone was conserved among the eight other clinical bla(OXA-48)-positive isolates, and in all cases, the OXA-48 genes were part of the Tn1999.2 composite transposon. This is the first report of a bla(OXA-48) and IS1R arrangement-containing plasmid in Ireland.
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Affiliation(s)
- Karen Power
- 1 UCD Centre for Molecular Innovation & Drug Discovery, School of Public Health, Physiotherapy & Population Science, University College Dublin , Dublin, Ireland
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