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Izdebski R, Biedrzycka M, Urbanowicz P, Żabicka D, Gniadkowski M. Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp., Poland. Emerg Infect Dis 2023; 29:1618-1626. [PMID: 37486192 PMCID: PMC10370858 DOI: 10.3201/eid2908.230199] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
We sequenced all nonduplicate 934 VIM/IMP carbapenemase-producing Enterobacterales (CPE) reported in Poland during 2006-2019 and found ≈40% of the isolates (n = 375) were Enterobacter spp. During the study period, incidence of those bacteria gradually grew in nearly the entire country. The major factor affecting the increase was clonal spread of several E. hormaechei lineages responsible for multiregional and interregional outbreaks (≈64% of all isolates), representing mainly the pandemic sequence type (ST) 90 or the internationally rare ST89 and ST121 clones. Three main VIM-encoding integron types efficiently disseminated across the clone variants (subclones) with various molecular platforms. Those variants were predominantly Pseudomonas aeruginosa-derived In238-like elements, present with IncHI2+HI2A, IncFII+FIA, IncFIB, or IncN3 plasmids, or chromosomal genomic islands in 30 Enterobacter STs. Another prevalent type, found in 34 STs, were In916-like elements, spreading in Europe recently with a lineage of IncA-like plasmids.
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2
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Domingues CPF, Rebelo JS, Dionisio F, Nogueira T. Multi-Drug Resistance in Bacterial Genomes-A Comprehensive Bioinformatic Analysis. Int J Mol Sci 2023; 24:11438. [PMID: 37511196 PMCID: PMC10380340 DOI: 10.3390/ijms241411438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance is presently one of the greatest threats to public health. The excessive and indiscriminate use of antibiotics imposes a continuous selective pressure that triggers the emergence of multi-drug resistance. We performed a large-scale analysis of closed bacterial genomes to identify multi-drug resistance considering the ResFinder antimicrobial classes. We found that more than 95% of the genomes harbor genes associated with resistance to disinfectants, glycopeptides, macrolides, and tetracyclines. On average, each genome encodes resistance to more than nine different classes of antimicrobial drugs. We found higher-than-expected co-occurrences of resistance genes in both plasmids and chromosomes for several classes of antibiotic resistance, including classes categorized as critical according to the World Health Organization (WHO). As a result of antibiotic-resistant priority pathogens, higher-than-expected co-occurrences appear in plasmids, increasing the potential for resistance dissemination. For the first time, co-occurrences of antibiotic resistance have been investigated for priority pathogens as defined by the WHO. For critically important pathogens, co-occurrences appear in plasmids, not in chromosomes, suggesting that the resistances may be epidemic and probably recent. These results hint at the need for new approaches to treating infections caused by critically important bacteria.
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Affiliation(s)
- Célia P F Domingues
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
| | - João S Rebelo
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Francisco Dionisio
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Teresa Nogueira
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE, Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- INIAV-National Institute for Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
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3
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Bitar I, Papagiannitsis CC, Kraftova L, Marchetti VM, Petinaki E, Finianos M, Chudejova K, Zemlickova H, Hrabak J. Implication of different replicons in the spread of the VIM-1-encoding integron, In110, in Enterobacterales from Czech hospitals. Front Microbiol 2023; 13:993240. [PMID: 36687644 PMCID: PMC9845580 DOI: 10.3389/fmicb.2022.993240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
Background VIM metallo-β-lactamases are enzymes characterized by the ability to hydrolyze all β-lactams. Usually, bla VIM-like genes are carried by class 1 integrons. In the Czech Republic, only sporadic cases of VIM-producing Enterobacterales have been reported in which those isolates carried the VIM-1 carbapenemase-encoding integron In110. However, during 2019-2020, an increased number was reported. Therefore, the aim of the current study was to characterize the genetic elements involved in the increased spread of bla VIM genes. Materials and methods 32 VIM-producing Enterobacterales collected between 2019 and 2020 were subjected to: antimicrobial susceptibility testing, integron analysis, and short reads sequencing. Based on the results, 19 isolates were selected as representative and sequenced using Sequel I platform. Results The 32 VIM-producing isolates exhibited variations in the MICs of carbapenems. Based on short-read data, 26 of the 32 sequenced isolates harbored the bla VIM-1 allele while six isolates carried the bla VIM-4 gene. The most prevalent was the In110 integron (n = 24) and two isolates carried the In4873 class 1 integron. The bla VIM-4 allele was identified in class 1 integrons In1174 (n = 3), In416 (n = 1), In2143 (n = 1) and In2150. Long reads sequencing revealed that the bla VIM was carried by: pKPC-CAV1193-like (n = 6), HI1 (pNDM-CIT; n = 4), HI2 (n = 3), FIB (pECLA; n = 2) and N (n = 1) incompatibility groups. Two bla VIM-carrying plasmids could not be typed by the database, while another one was integrated into the chromosome. Conclusion We observed the spread of VIM-encoding integrons, mainly of In110, among Enterobacterales isolated from Czech hospitals, but also an increased number of novel elements underlining the ongoing evolution.
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Affiliation(s)
- Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia,*Correspondence: Ibrahim Bitar, ✉
| | | | - Lucie Kraftova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Vittoria Mattioni Marchetti
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Efthymia Petinaki
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Marc Finianos
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Helena Zemlickova
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czechia,Department of Medical Microbiology, 3rd Faculty of Medicine, Charles University, Prague, Czechia
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
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4
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Emeraud C, Petit C, Gauthier L, Bonnin RA, Naas T, Dortet L. Emergence of VIM-producing Enterobacter cloacae complex in France between 2015 and 2018. J Antimicrob Chemother 2022; 77:944-951. [PMID: 35045171 DOI: 10.1093/jac/dkab471] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES To genetically characterize VIM-producing Enterobacter cloacae complex (ECC) isolates recovered in France from 2015 to 2018. METHODS WGS, species determination, MLST, clonal relationship and genetic characterization were performed on 149 VIM-producing ECC isolates. RESULTS Among VIM-producing Enterobacterales, the prevalence of ECC increased drastically from 6% in 2012 to 52% in 2018. The most prevalent species were Enterobacter hormaechei subsp. hoffmannii (40.9%), E. hormaechei subsp. steigerwaltii (21.5%), E. hormaechei subsp. xiangfangensis (14.8%) and ECC clade S (17.4%). Major STs were ST-873 (17.5%), ST-66 (12.1%), ST-78 (9.4%), ST-419 (8.1%), ST-145 (4.7%), ST-50 (4.0%), ST-118 (4.0%) and ST-168 (4.0%). Finally, six different integrons were identified, with some being specific to a given blaVIM variant (In916 with blaVIM-1-aacA4'-aphA15-aadA1-catB2 and In416 with blaVIM-4-aacA7-dfrA1b-aadA1b-smr2 genes). CONCLUSIONS This study demonstrated the genetic diversity among VIM-producing ECC isolates, indicating that their spread is not linked to a single clone.
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Affiliation(s)
- Cécile Emeraud
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Caroline Petit
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Lauraine Gauthier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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5
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Blackwell GA, Doughty EL, Moran RA. Evolution and dissemination of L and M plasmid lineages carrying antibiotic resistance genes in diverse Gram-negative bacteria. Plasmid 2020; 113:102528. [PMID: 32781088 DOI: 10.1016/j.plasmid.2020.102528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/04/2020] [Accepted: 07/08/2020] [Indexed: 11/19/2022]
Abstract
Conjugative, broad host-range plasmids of the L/M complex have been associated with antibiotic resistance since the 1970s. They are found in Gram-negative bacterial genera that cause human infections and persist in hospital environments. It is crucial that these plasmids are typed accurately so that their clinical and global dissemination can be traced in epidemiological studies. The L/M complex has previously been divided into L, M1 and M2 subtypes. However, those types do not encompass all diversity seen in the group. Here, we have examined 148 complete L/M plasmid sequences in order to understand the diversity of the complex and trace the evolution of distinct lineages. The backbone sequence of each plasmid was determined by removing translocatable genetic elements and reversing their effects in silico. The sequence identities of replication regions and complete backbones were then considered for typing. This supported the distinction of L and M plasmids and revealed that there are five L and eight M types, where each type is comprised of further sub-lineages that are distinguished by variation in their backbone and translocatable element content. Regions containing antibiotic resistance genes in L and M sub-lineages have often formed by initial rare insertion events, followed by insertion of other translocatable elements within the inceptive element. As such, islands evolve in situ to contain genes conferring resistance to multiple antibiotics. In some cases, different plasmid sub-lineages have acquired the same or related resistance genes independently. This highlights the importance of these plasmids in acting as vehicles for the dissemination of emerging resistance genes. Materials are provided here for typing plasmids of the L/M complex from complete sequences or draft genomes. This should enable rapid identification of novel types and facilitate tracking the evolution of existing lineages.
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Affiliation(s)
- Grace A Blackwell
- EMBL-EBI, Wellcome Genome Campus, Hinxton, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Emma L Doughty
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, UK
| | - Robert A Moran
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, UK.
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6
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Sadek M, Soliman AM, Nariya H, Shimamoto T, Shimamoto T. Genetic Characterization of Carbapenemase-Producing Enterobacter cloacae Complex and Pseudomonas aeruginosa of Food of Animal Origin from Egypt. Microb Drug Resist 2020; 27:196-203. [PMID: 32598213 DOI: 10.1089/mdr.2019.0405] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The increasing spread of carbapenem resistance is a serious global public health concern that negatively affects human and animal health. In this study we characterized the carbapenemase production in gram-negative bacteria isolated from different meat and meat products in Egypt. Phenotypic and genotypic susceptibility testing were investigated. Two Enterobacter cloacae complex strains, isolated from kofta and beef burger, and one Pseudomonas aeruginosa isolated from minced meat, were found to harbor VIM-1 and VIM-2, respectively. These isolates showed multidrug resistance phenotype. The phenotypic carbapenemase production was confirmed with Carba NP test in addition to modified Hodge test, modified carbapenem inactivation method, and ethylenediaminetetraacetic acid inhibition test. The blaVIM-1 gene in both non-clonally related E. cloacae complex strains was part of a class 1 integron that also carried other resistance gene cassettes such as aacA7, dfrA1, ΔaadA, and smr. This integron was uncommonly disrupted by the insertion sequence ISPa21, located on a self-conjugative plasmid of either the A/C or HI2 incompatibility group with a size of >93 kb. The blaVIM-2 gene was identified within a class 1 integron, followed downstream by resistance genes aadB and blaOXA-10. The transfer of blaVIM-2 gene from P. aeruginosa failed, suggesting that this gene was located on the chromosome. Further studies are needed to screen the dissemination of carbapenemase-producing bacteria in both the environment and food chain.
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Affiliation(s)
- Mustafa Sadek
- Food Hygiene and Control, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt.,Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Ahmed M Soliman
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan.,Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Hirofumi Nariya
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Toshi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tadashi Shimamoto
- Laboratory of Food Microbiology and Hygiene, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
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7
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Beyrouthy R, Barets M, Marion E, Dananché C, Dauwalder O, Robin F, Gauthier L, Jousset A, Dortet L, Guérin F, Bénet T, Cassier P, Vanhems P, Bonnet R. Novel Enterobacter Lineage as Leading Cause of Nosocomial Outbreak Involving Carbapenemase-Producing Strains. Emerg Infect Dis 2019; 24:1505-1515. [PMID: 30014838 PMCID: PMC6056098 DOI: 10.3201/eid2408.180151] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We investigated unusual carbapenemase-producing Enterobacter cloacae complex isolates (n = 8) in the novel sequence type (ST) 873, which caused nosocomial infections in 2 hospitals in France. Whole-genome sequence typing showed the 1-year persistence of the epidemic strain, which harbored a blaVIM-4 ST1-IncHI2 plasmid, in 1 health institution and 2 closely related strains harboring blaCTX-M-15 in the other. These isolates formed a new subgroup in the E. hormaechei metacluster, according to their hsp60 sequences and phylogenomic analysis. The average nucleotide identities, specific biochemical properties, and pangenomic and functional investigations of isolates suggested isolates of a novel species that had acquired genes associated with adhesion and mobility. The emergence of this novel Enterobacter phylogenetic lineage within hospitals should be closely monitored because of its ability to persist and spread.
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8
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Hurst JJ, Oliver JP, Schueler J, Gooch C, Lansing S, Crossette E, Wigginton K, Raskin L, Aga DS, Sassoubre LM. Trends in Antimicrobial Resistance Genes in Manure Blend Pits and Long-Term Storage Across Dairy Farms with Comparisons to Antimicrobial Usage and Residual Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2405-2415. [PMID: 30707579 DOI: 10.1021/acs.est.8b05702] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The use of antimicrobials by the livestock industry can lead to the release of unmetabolized antimicrobials and antimicrobial resistance genes (ARG) into the environment. However, the relationship between antimicrobial use, residual antimicrobials, and ARG prevalence within manure is not well understood, specifically across temporal and location-based scales. The current study determined ARG abundance in untreated manure blend pits and long-term storage systems from 11 conventional and one antimicrobial-free dairy farms in the Northeastern U.S. at six times over one-year. Thirteen ARGs corresponding to resistance mechanisms for tetracyclines, macrolides-lincosamides, sulfonamides, aminoglycosides, and β-lactams were quantified using a Custom qPCR Array or targeted qPCR. ARG abundance differed between locations, suggesting farm specific microbial resistomes. ARG abundance also varied temporally. Manure collected during the winter contained lower ARG abundances. Overall, normalized ARG concentrations did not correlate to average antimicrobial usage or tetracycline concentrations across farms and collection dates. Of the 13 ARGs analyzed, only four genes showed a higher abundance in samples from conventional farms and eight ARGs exhibited similar normalized concentrations in the conventional and antimicrobial-free farm samples. No clear trends were observed in ARG abundance between dairy manure obtained from blend pits and long-term storage collected during two drawdown periods (fall and spring), although higher ARG abundances were generally observed in spring compared to fall. This comprehensive study informs future studies needed to determine the contributions of ARGs from dairy manure to the environment.
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Affiliation(s)
- Jerod J Hurst
- Department of Chemistry , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
| | - Jason P Oliver
- Department of Animal Sciences , Cornell University , Ithaca , New York 14850 , United States
| | - Jenna Schueler
- Department of Environmental Science & Technology , University of Maryland , College Park , Maryland 20742 , United States
| | - Curt Gooch
- Department of Animal Sciences , Cornell University , Ithaca , New York 14850 , United States
| | - Stephanie Lansing
- Department of Environmental Science & Technology , University of Maryland , College Park , Maryland 20742 , United States
| | - Emily Crossette
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Krista Wigginton
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Diana S Aga
- Department of Chemistry , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
| | - Lauren M Sassoubre
- Department of Civil, Structural, and Environmental Engineering , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
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9
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Impact of co-carriage of IncA/C plasmids with additional plasmids on the transfer of antimicrobial resistance in Salmonella enterica isolates. Int J Food Microbiol 2018; 271:77-84. [DOI: 10.1016/j.ijfoodmicro.2018.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/22/2017] [Accepted: 01/19/2018] [Indexed: 11/22/2022]
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10
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Zhou K, Yu W, Shen P, Lu H, Wang B, Rossen JWA, Xiao Y. A novel Tn1696-like composite transposon (Tn6404) harboring bla IMP-4 in a Klebsiella pneumoniae isolate carrying a rare ESBL gene bla SFO-1. Sci Rep 2017; 7:17321. [PMID: 29229976 PMCID: PMC5725488 DOI: 10.1038/s41598-017-17641-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/29/2017] [Indexed: 11/29/2022] Open
Abstract
Genetic determinants of a clinical Klebsiella pneumoniae isolate (KP1814) coproducing IMP-4 and a rare ESBL gene SFO-1 was investigated. KP1814 belongs to a novel sequence type (ST) assigned to ST2270. WGS identified four circular DNA sequences in KP1814, including two multidrug-resistance (MDR) plasmids, one virulence plasmid, and one circular form. The MDR plasmid pKP1814-1 (299.9 Kb) is untypeable, and carries two large mosaic multiresistance regions (MRRs). blaSFO-1 and blaIMP-4 co-exists on MRR1, and blaSFO-1 is associated with an IS/Tn-independent genetic context. blaIMP-4 is carried by a novel In804-like integron (intlI-blaIMP-4-Kl.pn.I3-qacG2-aacA4-catB3∆) associated with a novel Tn1696-like transposon (designed Tn6404) flanked by IS5075. The other MDR plasmid pKP1814-3 is a 95,701-bp IncFII plasmid, and is a hybrid of a Shigella flexneri plasmid pSF07201 and an E. coli plasmid pCA08. All resistance genes of pKP1814-3 were detected in a ~16-kb IS26-flanked composite transposon carried by a Tn5396 transposon. The circular form (18.3 Kb) was composed of two parts belonging to pKP1814-1 and pKP1814-3, respectively. The plasmid pKP1814-2, carrying multiple virulence factors, encodes IncFIBK and IncFIIK replicons with a size of 187,349 bp. The coexistence of MDR and virulence plasmids largely enhances the bacterial fitness in the host and environment.
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Affiliation(s)
- Kai Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China
| | - Wei Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China.,Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China
| | - Haifeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China
| | - Baohong Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China
| | - John W A Rossen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital of Medicine School, Zhejiang University, Hangzhou, China.
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11
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Sonnevend Á, Yahfoufi N, Ghazawi A, Jamal W, Rotimi V, Pál T. Contribution of horizontal gene transfer to the emergence of VIM-4 carbapenemase producer Enterobacteriaceae in Kuwait. Infect Drug Resist 2017; 10:469-478. [PMID: 29263683 PMCID: PMC5724420 DOI: 10.2147/idr.s149321] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae encountered in countries of the Arabian Peninsula usually produce OXA-48-like and New Delhi metallo-beta-lactamases (NDM) carbapenemases. However, a temporary increase in VIM-4-producing, clonally unrelated Enterobacteriaceae strains was described earlier in a Kuwaiti hospital. We investigated the genetic support of blaVIM-4 in six Klebsiella pneumoniae strains, one Escherichia coli, and one Enterobacter cloacae strain and compared it to that of VIM-4-producing isolates from other countries of the region. Five K. pneumoniae strains and the E. coli strain from Kuwait carried an ~165 kb IncA/C-type plasmid indistinguishable by restriction fragment length polymorphism. The complete sequence of one of them (pKKp4-VIM) was established. pKKp4-VIM exhibited extensive similarities to episomes pKP-Gr642 carrying blaVIM-19 encountered in Greece and to the partially sequenced pCC416 harboring blaVIM-4 detected in Italy. In other countries of the region, the only similar plasmid was the one detected in the isolate from the UAE. In all Kuwaiti strains, irrespective of the species and their VIM plasmids, the blaVIM-4 gene was located within the same integron structure (In416), different from those of other countries of the region. Our data show that the spread of this IncA/C plasmid and particularly that of the In416 integron caused a considerable, albeit temporary, increase in the rate of mostly clonally unrelated VIM-producing Enterobacteriaceae strains of multiple species. Monitoring of such events is of high importance as the interference with the spread of mobile genetic elements may represent a formidable challenge to infection control.
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Affiliation(s)
- Ágnes Sonnevend
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
| | - Nour Yahfoufi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
| | - Wafaa Jamal
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Vincent Rotimi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Tibor Pál
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, UAE
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12
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Papagiannitsis CC, Dolejska M, Izdebski R, Giakkoupi P, Skálová A, Chudějová K, Dobiasova H, Vatopoulos AC, Derde LPG, Bonten MJM, Gniadkowski M, Hrabák J. Characterisation of IncA/C2 plasmids carrying an In416-like integron with the blaVIM-19 gene from Klebsiella pneumoniae ST383 of Greek origin. Int J Antimicrob Agents 2015; 47:158-62. [PMID: 26795022 DOI: 10.1016/j.ijantimicag.2015.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/29/2015] [Accepted: 12/01/2015] [Indexed: 11/30/2022]
Abstract
The complete nucleotide sequences of three multidrug resistance (MDR) IncA/C-like plasmids from Enterobacteriaceae isolates carrying the VIM-type carbapenemase-encoding integrons In4863 (blaVIM-19-aacA7-dfrA1-ΔaadA1-smr2) or In4873 (blaVIM-1-aacA7-dfrA1-ΔaadA1-smr2) were determined, which are the first In416-like elements identified in Greece. Plasmids pKP-Gr642 and pKP-Gr8143 were from Klebsiella pneumoniae ST383 isolates, whereas plasmid pEcl-Gr4873 was from an Enterobacter cloacae ST88 isolate. Sequencing showed that pKP-Gr642 (162787bp) and pKP-Gr8143 (154395bp) consisted of the type 1 IncA/C2 conserved backbone, the blaCMY-2-like gene-containing region, and the ARI-B (with the sul2 gene) and ARI-A (with a class 1 integron) resistance islands, like the plasmid pUMNK88_161 from the USA. The third plasmid, pEcl-Gr4873 (153958bp), exhibited extensive similarity with the type 2 IncA/C2 plasmid pR55 from France. pEcl-Gr4873 carried only one resistance island of a hybrid transposon structure inserted in a different location to ARI-A in type 1 A/C2 plasmids. In all three plasmids, the In416-like integrons In4863 or In4873 were identified within non-identical class II transposon structures. All three In416-like-carrying regions presented significant similarities with the MDR region of the IncA/C2 plasmid pCC416 from Italy, carrying the prototype In416 integron (blaVIM-4-aacA7-dfrA1-ΔaadA1-smr2). These findings provided the basis for speculations regarding the evolution of IncA/C2 plasmids with In416-like integrons, and confirmed the rapid evolution of some IncA/C2 plasmid lineages. Considering the broad host range of IncA/C2 molecules, it seems that pKP-Gr642, pKP-Gr8143 and pEcl-Gr4873 plasmids might support the diffusion of In416-like integrons among Enterobacteriaceae.
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Affiliation(s)
- Costas C Papagiannitsis
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic; Biomedical Center, Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic.
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | | | - Panagiota Giakkoupi
- Department of Microbiology, National School of Public Health, Athens, Greece
| | - Anna Skálová
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic
| | - Kateřina Chudějová
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic
| | - Hana Dobiasova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | | | | | | | | | - Jaroslav Hrabák
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic; Biomedical Center, Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic
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13
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Papagiannitsis CC, Izdebski R, Baraniak A, Fiett J, Herda M, Hrabák J, Derde LPG, Bonten MJM, Carmeli Y, Goossens H, Hryniewicz W, Brun-Buisson C, Gniadkowski M, Grabowska A, Nikonorow E, Dautzenberg MJ, Adler A, Kazma M, Navon-Venezia S, Malhotra-Kumar S, Lammens C, Legrand P, Annane D, Chalfine A, Giamarellou H, Petrikkos GL, Nardi G, Balode A, Dumpis U, Stammet P, Arag I, Esteves F, Muzlovic I, Tomic V, Mart AT, Lawrence C, Salomon J, Paul M, Lerman Y, Rossini A, Salvia A, Samso JV, Fierro J. Survey of metallo-β-lactamase-producing Enterobacteriaceae colonizing patients in European ICUs and rehabilitation units, 2008–11. J Antimicrob Chemother 2015; 70:1981-8. [DOI: 10.1093/jac/dkv055] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/07/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
- C. C. Papagiannitsis
- National Medicines Institute, Warsaw, Poland
- Faculty of Medicine in Plzeň, Charles University in Prague, Plzeň, Czech Republic
| | - R. Izdebski
- National Medicines Institute, Warsaw, Poland
| | - A. Baraniak
- National Medicines Institute, Warsaw, Poland
| | - J. Fiett
- National Medicines Institute, Warsaw, Poland
| | - M. Herda
- National Medicines Institute, Warsaw, Poland
| | - J. Hrabák
- Faculty of Medicine in Plzeň, Charles University in Prague, Plzeň, Czech Republic
| | - L. P. G. Derde
- University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Y. Carmeli
- Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
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14
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Harmer CJ, Hall RM. pRMH760, a Precursor of A/C2 Plasmids Carrying blaCMY and blaNDM Genes. Microb Drug Resist 2014; 20:416-23. [DOI: 10.1089/mdr.2014.0012] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Ruth M. Hall
- School of Molecular Bioscience, The University of Sydney, Sydney, Australia
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15
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Abstract
Plasmids represent one of the most difficult challenge for counteracting the dissemination of antimicrobial resistance. They contribute to the spread of relevant resistance determinants, promoting horizontal gene transfer among unrelated bacteria. Undistinguishable plasmids were identified in unrelated bacterial strains isolated at huge geographically distant area, with no apparent epidemiological links. These plasmids belong to families that are largely prevalent in naturally occurring bacteria, usually carry multiple physically linked genetic determinants, conferring resistance to different classes of antibiotics simultaneously. Plasmids also harbour virulence factors and addiction systems, promoting their stability and maintenance in the bacterial host, in different environmental conditions. The characteristics of the most successful plasmids that were at the origin of the spread of carbapenemase, expanded-spectrum β-lactamase, and plasmid-mediated quinolone resistance genes are discussed in this review.
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Affiliation(s)
- Alessandra Carattoli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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Carbapenemases in Klebsiella pneumoniae and other Enterobacteriaceae: an evolving crisis of global dimensions. Clin Microbiol Rev 2013; 25:682-707. [PMID: 23034326 DOI: 10.1128/cmr.05035-11] [Citation(s) in RCA: 834] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
SUMMARY The spread of Enterobacteriaceae, primarily Klebsiella pneumoniae, producing KPC, VIM, IMP, and NDM carbapenemases, is causing an unprecedented public health crisis. Carbapenemase-producing enterobacteria (CPE) infect mainly hospitalized patients but also have been spreading in long-term care facilities. Given their multidrug resistance, therapeutic options are limited and, as discussed here, should be reevaluated and optimized. Based on susceptibility data, colistin and tigecycline are commonly used to treat CPE infections. Nevertheless, a review of the literature revealed high failure rates in cases of monotherapy with these drugs, whilst monotherapy with either a carbapenem or an aminoglycoside appeared to be more effective. Combination therapies not including carbapenems were comparable to aminoglycoside and carbapenem monotherapies. Higher success rates have been achieved with carbapenem-containing combinations. Pharmacodynamic simulations and experimental infections indicate that modification of the current patterns of carbapenem use against CPE warrants further attention. Epidemiological data, though fragmentary in many countries, indicate CPE foci and transmission routes, to some extent, whilst also underlining the lack of international collaborative systems that could react promptly and effectively. Fortunately, there are sound studies showing successful containment of CPE by bundles of measures, among which the most important are active surveillance cultures, separation of carriers, and assignment of dedicated nursing staff.
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Sonnevend Á, Ghazawi A, Yahfoufi N, Al-Baloushi A, Hashmey R, Mathew M, Tariq WZ, Pál T. VIM-4 carbapenemase-producing Enterobacter cloacae in the United Arab Emirates. Clin Microbiol Infect 2012; 18:E494-6. [PMID: 23078093 DOI: 10.1111/1469-0691.12051] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Screening 34 carbapenem non-susceptible Enterobacteriaceae recovered in Abu Dhabi hospitals identified an Enterobacter cloacae strain carrying bla(VIM-4) , bla(CMY-4) and bla(CTX-M-15) . It was isolated from the urine of an Egyptian patient repeatedly hospitalized and treated with broad-spectrum antibiotics, including carbapenems, in the United Arab Emirates. The bla(VIM-4) coding class I integron, highly similar to In416, was carried on a 175-kilobase non-conjugative incA/C type plasmid also hybridizing with the bla(CMY-4) probe. This is the first detailed report on the isolation of a Verona integron-encoded metallo-β-lactamase (VIM) -producing enteric bacterium in the Arabian Peninsula with characteristics suggestive of spreading from the Mediterranean region.
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Affiliation(s)
- Á Sonnevend
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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18
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Shevchenko OV, Mudrak DY, Skleenova EY, Kozyreva VK, Ilina EN, Ikryannikova LN, Alexandrova IA, Sidorenko SV, Edelstein MV. First detection of VIM-4 metallo-β-lactamase-producing Escherichia coli in Russia. Clin Microbiol Infect 2012; 18:E214-7. [PMID: 22487052 DOI: 10.1111/j.1469-0691.2012.03827.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An Escherichia coli isolate co-producing VIM-4 metallo-β-lactamase and CTX-M-15 extended spectrum β-lactamase was recovered from the urine of a patient with head trauma in Moscow, Russia. The bla(VIM-4) and bla(CTX-M-15) genes were carried, respectively, by transmissible plasmids of IncW and IncI1 groups. The nucleotide sequence of the VIM-4-encoding integron was nearly identical to that of In416, which represent a large group of structurally related integrons previously found in Enterobacteriaceae all around the Mediterranean basin. This is the first report of a metallo-β-lactamase-producing E. coli in Russia.
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Affiliation(s)
- O V Shevchenko
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical Academy, Smolensk, Russia
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19
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Carattoli A, Villa L, Poirel L, Bonnin RA, Nordmann P. Evolution of IncA/C blaCMY-₂-carrying plasmids by acquisition of the blaNDM-₁ carbapenemase gene. Antimicrob Agents Chemother 2012; 56:783-6. [PMID: 22123704 PMCID: PMC3264282 DOI: 10.1128/aac.05116-11] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 11/20/2011] [Indexed: 01/09/2023] Open
Abstract
The bla(NDM-1) gene has been reported to be often located on broad-host-range plasmids of the IncA/C type in clinical but also environmental bacteria recovered from the New Delhi, India, area. IncA/C-type plasmids are the main vehicles for the spread of the cephalosporinase gene bla(CMY-2), frequently identified in the United States, Canada, and Europe. In this study, we completed the sequence of IncA/C plasmid pNDM-KN carrying the bla(NDM-1) gene, recovered from a Klebsiella pneumoniae isolate from Kenya. This sequence was compared with those of three IncA/C-type reference plasmids from Escherichia coli, Yersinia ruckeri, and Photobacterium damselae. Comparative analysis showed that the bla(NDM-1) gene was located on a widely diffused plasmid scaffold known to be responsible for the spread of bla(CMY-2)-like genes and consequently for resistance to broad-spectrum cephalosporins. Considering that IncA/C plasmids possess a broad host range, this scaffold might support a large-scale diffusion of the bla(NDM-1) gene among Gram-negative rods.
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Affiliation(s)
- Alessandra Carattoli
- Department of Infectious, Parasitic, and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Laura Villa
- Department of Infectious, Parasitic, and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Laurent Poirel
- Service de Bactériologie-Virologie, INSERM U914 Emerging Resistance to Antibiotics, Hôpital de Bicêtre, Faculté de Médecine et Université Paris-Sud, K.-Bicêtre, France
| | - Rémy A. Bonnin
- Service de Bactériologie-Virologie, INSERM U914 Emerging Resistance to Antibiotics, Hôpital de Bicêtre, Faculté de Médecine et Université Paris-Sud, K.-Bicêtre, France
| | - Patrice Nordmann
- Service de Bactériologie-Virologie, INSERM U914 Emerging Resistance to Antibiotics, Hôpital de Bicêtre, Faculté de Médecine et Université Paris-Sud, K.-Bicêtre, France
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20
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Antibiotic and metal resistance among hospital and outdoor strains of Pseudomonas aeruginosa. Res Microbiol 2011; 162:689-700. [DOI: 10.1016/j.resmic.2011.06.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Accepted: 05/10/2011] [Indexed: 11/24/2022]
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21
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Ktari S, Mnif B, Louati F, Rekik S, Mezghani S, Mahjoubi F, Hammami A. Spread of Klebsiella pneumoniae isolates producing OXA-48 -lactamase in a Tunisian university hospital. J Antimicrob Chemother 2011; 66:1644-6. [DOI: 10.1093/jac/dkr181] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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22
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Evolution and spread of a multidrug-resistant Proteus mirabilis clone with chromosomal AmpC-type cephalosporinases in Europe. Antimicrob Agents Chemother 2011; 55:2735-42. [PMID: 21402851 DOI: 10.1128/aac.01736-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteus mirabilis isolates obtained in 1999 to 2008 from three European countries were analyzed; all carried chromosomal AmpC-type cephalosporinase bla(CMY) genes from a Citrobacter freundii origin (bla(CMY-2)-like genes). Isolates from Poland harbored several bla(CMY) genes (bla(CMY-4), bla(CMY-12), bla(CMY-14), bla(CMY-15), and bla(CMY-38) and the new gene bla(CMY-45)), while isolates from Italy and Greece harbored bla(CMY-16) only. Earlier isolates with bla(CMY-4) or bla(CMY-12), recovered in France from Greek and Algerian patients, were also studied. All isolates showed striking similarities. Their bla(CMY) genes resided within ISEcp1 transposition modules, named Tn6093, characterized by a 110-bp distance between ISEcp1 and bla(CMY), and identical fragments of both C. freundii DNA and a ColE1-type plasmid backbone. Moreover, these modules were inserted into the same chromosomal site, within the pepQ gene. Since ColE1 plasmids carrying ISEcp1 with similar C. freundii DNA fragments (Tn6114) had been identified earlier, it is likely that a similar molecule had mediated at some stage this DNA transfer between C. freundii and P. mirabilis. In addition, isolates with bla(CMY-12), bla(CMY-15), and bla(CMY-38) genes harbored a second bla(CMY) copy within a shorter ISEcp1 module (Tn6113), always inserted downstream of the ppiD gene. Sequence analysis of all mobile bla(CMY-2)-like genes indicated that those integrated in the P. mirabilis chromosome form a distinct cluster that may have evolved by the stepwise accumulation of mutations. All of these observations, coupled to strain typing data, suggest that the bla(CMY) genes studied here may have originated from a single ISEcp1-mediated mobilization-transfer-integration process, followed by the spread and evolution of a P. mirabilis clone over time and a large geographic area.
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Colinon C, Jocktane D, Brothier E, Rossolini GM, Cournoyer B, Nazaret S. Genetic analyses ofPseudomonas aeruginosaisolated from healthy captive snakes: evidence of high inter- and intrasite dissemination and occurrence of antibiotic resistance genes. Environ Microbiol 2010; 12:716-29. [DOI: 10.1111/j.1462-2920.2009.02115.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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International spread and persistence of TEM-24 is caused by the confluence of highly penetrating enterobacteriaceae clones and an IncA/C2 plasmid containing Tn1696::Tn1 and IS5075-Tn21. Antimicrob Agents Chemother 2009; 54:825-34. [PMID: 19995930 DOI: 10.1128/aac.00959-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
TEM-24 remains one of the most widespread TEM-type extended-spectrum beta-lactamases (ESBLs) among Enterobacteriaceae. To analyze the reasons influencing its spread and persistence, a multilevel population genetics study was carried out on 28 representative TEM-24 producers from Belgium, France, Portugal, and Spain (13 Enterobacter aerogenes isolates, 6 Escherichia coli isolates, 6 Klebsiella pneumoniae isolates, 2 Proteus mirabilis isolates, and 1 Klebsiella oxytoca isolate, from 1998 to 2004). Clonal relatedness (XbaI pulsed-field gel electrophoresis [PFGE] and E. coli phylogroups) and antibiotic susceptibility were determined by standard procedures. Plasmid analysis included determination of the incompatibility group (by PCR, hybridization, and/or sequencing) and comparison of restriction fragment length polymorphism (RFLP) patterns. Characterization of genetic elements conferring antibiotic resistance included integrons (classes 1, 2, and 3) and transposons (Tn3, Tn21, and Tn402). Similar PFGE patterns were identified among E. aerogenes, K. pneumoniae, and P. mirabilis isolates, while E. coli strains were diverse (phylogenetic groups A, B2, and D). Highly related 180-kb IncA/C2 plasmids conferring resistance to kanamycin, tobramycin, chloramphenicol, trimethoprim, and sulfonamides were identified. Each plasmid contained defective In0-Tn402 (dfrA1-aadA1, aacA4, or aacA4-aacC1-orfE-aadA2-cmlA1) and In4-Tn402 (aacA4 or dfrA1-aadA1) variants. These integrons were located within Tn21, Tn1696, or hybrids of these transposons, with IS5075 interrupting their IRtnp and IRmer. In all cases, blaTEM-24 was part of an IS5075-DeltaTn1 transposon within tnp1696, mimicking other genetic elements containing blaTEM-2 and blaTEM-3 variants. The international dissemination of TEM-24 is fuelled by an IncA/C2 plasmid acquired by different enterobacterial clones which seem to evolve by gaining diverse genetic elements. This work highlights the risks of a confluence between highly penetrating clones and highly promiscuous plasmids in the spread of antibiotic resistance, and it contributes to the elucidation of the origin and evolution of TEM-2 ESBL derivatives.
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Dispersal of carbapenemase blaVIM-1 gene associated with different Tn402 variants, mercury transposons, and conjugative plasmids in Enterobacteriaceae and Pseudomonas aeruginosa. Antimicrob Agents Chemother 2009; 54:320-7. [PMID: 19901094 DOI: 10.1128/aac.00783-09] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of bla(VIM-1) within four different genetic platforms from distinct Enterobacteriaceae and Pseudomonas aeruginosa isolates in an area with a low prevalence of metallo-beta-lactamase producers is reported. Forty-three VIM-1-producing isolates (including 19 Enterobacter cloacae, 2 Escherichia coli, and 2 P. aeruginosa isolates, 18 Klebsiella pneumoniae isolate, and 2 Klebsiella oxytoca isolate) recovered from 2005 to 2007 and corresponding to 15 pulsed-field gel electrophoresis types were studied. The Enterobacteriaceae isolates corresponded to a hospital outbreak, and the P. aeruginosa isolates were sporadically recovered. The genetic context of the integrons carrying bla(VIM-1) (arbitrarily designated types A, B, C, and D) was characterized by PCR mapping based on known Tn402 and mercury transposons and further sequencing. Among Enterobacteriaceae isolates, bla(VIM-1) was part of integrons located either in an In2-Tn402 element linked to Tn21 (type A; In110-bla(VIM-1)-aacA4-aadA1) or in a Tn402 transposon lacking the whole tni module [type B; In113-bla(VIM-1)-aacA4-dhfrII (also called dfrB1)-aadA1-catB2] and the transposon was associated with an IncHI2 or IncI1 plasmid, respectively. Among P. aeruginosa isolates, bla(VIM-1) was part of a new gene cassette array located in a defective Tn402 transposon carrying either tniBDelta3 and tniA (type C; bla(VIM-1)-aadA1) or tniC and DeltatniQ (type D; bla(VIM-1)-aadB), and both Tn402 variants were associated with conjugative plasmids of 30 kb. The dissemination of bla(VIM-1) was associated with different genetic structures and bacterial hosts, depicting a complex emergence and evolutionary network scenario in our facility, Ramón y Cajal University Hospital, Madrid, Spain. Knowledge of the complex epidemiology of bla(VIM-1) is necessary to control this emerging threat.
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26
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Unusual class 1 integron-associated gene cassette configuration found in IncA/C plasmids from Salmonella enterica. Antimicrob Agents Chemother 2009; 53:2640-2. [PMID: 19307357 DOI: 10.1128/aac.00233-09] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
IncA/C plasmids carrying an unusual cassette configuration in a class 1 integron and five further shared resistance genes, aacC4, aphA1, hph, sul2, and tetA(D) were found in Salmonella enterica serovars Senftenberg and Ohio. A deletion formed using a short region of homology in the 5' conserved segment and the orfF cassette created an array with only part of orfF followed by the aadA2 cassette. The IncA/C plasmids were not recoverable by conjugation, but additional conjugative resistance plasmids were present in some strains.
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Post V, Hall RM. Insertion sequences in the IS1111 family that target the attC recombination sites of integron-associated gene cassettes. FEMS Microbiol Lett 2008; 290:182-7. [PMID: 19025573 DOI: 10.1111/j.1574-6968.2008.01412.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Members of the recently identified IS1111 family differ from the majority of insertion sequences (IS) in that they target specific sites in an orientation-specific manner. However, the way in which target selection is achieved is not known. ISKpn4 is representative of a new subgroup of the IS1111 family whose members are found in the attC sites (59-be) of the gene cassettes associated with integrons. The transposases of this subgroup are closely related (over 75% identity), confirming that closely related IS usually share a common target. However, among more distant relatives encoding a transposase <45% identical to those of the ISKpn4 group, one IS, ISPa25, was found that also targets attC sites. It appears that the targeting determinant of the ISKpn4 group has become associated with a transposase gene from a different group, and this allowed us to localize the region that is likely to be required for target selection to a long noncoding region found downstream of the transposase gene in all IS1111 family members. This region may determine an RNA used to guide the IS to its specific target.
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Affiliation(s)
- Virginia Post
- School of Molecular and Microbial Biosciences, Biochemistry and Microbiology, The University of Sydney, NSW, Australia
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29
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Relative strengths of the class 1 integron promoter hybrid 2 and the combinations of strong and hybrid 1 with an active p2 promoter. Antimicrob Agents Chemother 2008; 53:277-80. [PMID: 19001114 DOI: 10.1128/aac.00912-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The relative strengths of the uncommon promoters hybrid 2, hybrid 1 with an active P2 promoter (hybrid 1+P2), and strong+P2, which drive transcription of resistance genes in class 1 integrons, were evaluated using bla(GES-1) as a reporter gene cassette. Hybrid 2 was stronger than hybrid 1. Coupling P2 with the strong promoter and with hybrid 1 caused a measurable increase in GES-1 expression.
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