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Negeri AA, Mamo H, Gahlot DK, Gurung JM, Seyoum ET, Francis MS. Characterization of plasmids carrying bla CTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia. Sci Rep 2023; 13:8595. [PMID: 37237011 DOI: 10.1038/s41598-023-35402-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.
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Affiliation(s)
- Abebe Aseffa Negeri
- National Clinical Bacteriology and Mycology Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Dharmender K Gahlot
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Jyoti M Gurung
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Eyasu Tigabu Seyoum
- Global One Health Initiative of the Ohio State University, East African Regional Office, Addis Ababa, Ethiopia
| | - Matthew S Francis
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.
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Girlich D, Bonnin RA, Proust A, Naas T, Dortet L. Undetectable Production of the VIM-1 Carbapenemase in an Atlantibacter hermannii Clinical Isolate. Front Microbiol 2021; 12:741972. [PMID: 34987484 PMCID: PMC8721206 DOI: 10.3389/fmicb.2021.741972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
The differential expression of VIM-1 in Atlantibacter hermannii WEB-2 and Enterobacter hormaechei ssp. hoffmannii WEB-1 clinical isolates from a rectal swab of a hospitalized patient in France was investigated. A. hermannii WEB-2 was resistant to all β-lactams except carbapenems. It produced ESBL SHV-12, but the Carba NP test failed to detect any carbapenemase activity despite the production of VIM-1. Conversely, E. hormaechei WEB-1, previously recovered from the same patient, was positive for the detection of carbapenemase activity. The blaVIM–1 gene was located on a plasmid and embedded within class 1 integron. Both plasmids were of the same IncA incompatibility group and conferred the same resistance pattern when electroporated in Escherichia coli TOP10 or Enterobacter cloacae CIP7933. Quantitative RT-PCR experiments indicated a weaker replication of pWEB-2 in A. hermannii as compared to E. hormaechei. An isogenic mutant of A. hermannii WEB-2 selected after sequential passages with increased concentrations of imipenem possessed higher MICs for carbapenems and cephalosporins including cefiderocol, higher levels of the blaVIM–1 gene transcripts, and detectable carbapenemase activity using the Carba NP test. Assessment of read coverage demonstrated that a duplication of the region surrounding blaVIM–1 gene occurred in the A. hermannii mutant with detectable carbapenemase activity. The lack of detection of the VIM-1 carbapenemase activity in A. hermannii WEB-2 isolate was likely due to a weak replication of the IncA plasmid harboring the blaVIM–1 gene. Imipenem as selective pressure led to a duplication of this gene on the plasmid and to the restoration of a significant carbapenem-hydrolyzing phenotype.
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Affiliation(s)
- Delphine Girlich
- LabEx Lermit, Faculty of Medicine, INSERM UMR 1184—Team RESIST, Université Paris-Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Rémy A. Bonnin
- LabEx Lermit, Faculty of Medicine, INSERM UMR 1184—Team RESIST, Université Paris-Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Alexis Proust
- Department of Hormonal Biochemistry, Hôpital de Bicêtre, Assistance Publique—Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- LabEx Lermit, Faculty of Medicine, INSERM UMR 1184—Team RESIST, Université Paris-Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- LabEx Lermit, Faculty of Medicine, INSERM UMR 1184—Team RESIST, Université Paris-Sud, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique - Hôpitaux de Paris, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- *Correspondence: Laurent Dortet,
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Abstract
A putative type II toxin-antitoxin (TA) module almost exclusively associated with conjugative IncC plasmids is homologous to the higBA family of TA systems found in chromosomes and plasmids of several species of bacteria. Despite the clinical significance and strong association with high-profile antimicrobial resistance (AMR) genes, the TA system of IncC plasmids remains largely uncharacterized. In this study, we present evidence that IncC plasmids encode a bona fide HigB-like toxin that strongly inhibits bacterial growth and results in cell elongation in Escherichia coli. IncC HigB toxin acts as a ribosome-dependent endoribonuclease that significantly reduces the transcript abundance of a subset of adenine-rich mRNA transcripts. A glycine residue at amino acid position 64 is highly conserved in HigB toxins from different bacterial species, and its replacement with valine (G64V) abolishes the toxicity and the mRNA cleavage activity of the IncC HigB toxin. The IncC plasmid higBA TA system functions as an effective addiction module that maintains plasmid stability in an antibiotic-free environment. This higBA addiction module is the only TA system that we identified in the IncC backbone and appears essential for the stable maintenance of IncC plasmids. We also observed that exposure to subinhibitory concentrations of ciprofloxacin, a DNA-damaging fluoroquinolone antibiotic, results in elevated higBA expression, which raises interesting questions about its regulatory mechanisms. A better understanding of this higBA-type TA module potentially allows for its subversion as part of an AMR eradication strategy. IMPORTANCE Toxin-antitoxin (TA) systems play vital roles in maintaining plasmids in bacteria. Plasmids with incompatibility group C are large plasmids that disseminate via conjugation and carry high-profile antibiotic resistance genes. We present experimental evidence that IncC plasmids carry a TA system that functions as an effective addiction module and maintains plasmid stability in an antibiotic-free environment. The toxin of IncC plasmids acts as an endoribonuclease that targets a subset of mRNA transcripts. Overexpressing the IncC toxin gene strongly inhibits bacterial growth and results in cell elongation in Escherichia coli hosts. We also identify a conserved amino acid residue in the toxin protein that is essential for its toxicity and show that the expression of this TA system is activated by a DNA-damaging antibiotic, ciprofloxacin. This mobile TA system may contribute to managing bacterial stress associated with DNA-damaging antibiotics.
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Kurittu P, Khakipoor B, Brouwer MS, Heikinheimo A. Plasmids conferring resistance to extended-spectrum beta-lactamases including a rare IncN+IncR multireplicon carrying blaCTX-M-1 in Escherichia coli recovered from migrating barnacle geese ( Branta leucopsis). OPEN RESEARCH EUROPE 2021; 1:46. [PMID: 37645149 PMCID: PMC10446048 DOI: 10.12688/openreseurope.13529.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 08/31/2023]
Abstract
Background: Increasing antimicrobial resistance (AMR) is a global threat and wild migratory birds may act as mediators of resistant bacteria across country borders. Our objective was to study extended-spectrum beta-lactamase (ESBL) and plasmid-encoded AmpC (pAmpC) producing Escherichia coli in barnacle geese using whole genome sequencing (WGS) and to identify plasmids harboring bla genes. Methods: Barnacle geese feces (n=200) were collected during fall 2017 and spring 2018 from an urban area in Helsinki, Finland. ESBL/AmpC-producing E. coli were recovered from nine samples (4.5%) and isolates were subjected to WGS on both short- and long-read sequencers, enabling hybrid assembly and determination of the genomic location of bla genes. Results: A rare multireplicon IncN+IncR was recovered from one isolate carrying bla CTX-M-1 in addition to aadA2b, lnu(F), and qnrS1. Moreover, rarely detected IncY plasmids in two isolates were found to harbor multiple resistance genes in addition to the human-associated bla CTX-M-15. Poultry-associated bla CMY-2 was identified from the widely distributed IncI1 and IncK plasmids from four different isolates. One isolate harbored an IncI1 plasmid with bla CTX-M-1 and flor. A chromosomal point mutation in the AmpC promoter was identified in one of the isolates. WGS analysis showed isolates carried multiple resistance and virulence genes and harbored multiple different plasmid replicons in addition to bla-carrying plasmids. Conclusions: Our findings suggest that wild migratory birds serve as a limited source of ESBL/AmpC-producing E. coli and may act as disseminators of the epidemic plasmid types IncI1 and IncK but also rarely detected plasmid types carrying multidrug resistance. Human and livestock-associated ESBL enzyme types were recovered from samples, suggesting a potential for interspecies transmission. WGS offers a thorough method for studying AMR from different sources and should be implemented more widely in the future for AMR surveillance and detection. Understanding plasmid epidemiology is vital for efforts to mitigate global AMR spread.
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Affiliation(s)
- Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Banafsheh Khakipoor
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- Laboratory and Research Division, Microbiology Unit, Finnish Food Authority, Seinäjoki, Finland
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Identification of a blaVIM-1-Carrying IncA/C 2 Multiresistance Plasmid in an Escherichia coli Isolate Recovered from the German Food Chain. Microorganisms 2020; 9:microorganisms9010029. [PMID: 33374123 PMCID: PMC7824508 DOI: 10.3390/microorganisms9010029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/13/2020] [Accepted: 12/21/2020] [Indexed: 11/17/2022] Open
Abstract
Within the German national monitoring of zoonotic agents, antimicrobial resistance determination also targets carbapenemase-producing (CP) Escherichia coli by selective isolation from food and livestock. In this monitoring in 2019, the CP E. coli 19-AB01133 was recovered from pork shoulder. The isolate was assigned to the phylogenetic group B1 and exhibited the multi-locus sequence-type ST5869. Molecular investigations, including whole genome sequencing, of 19-AB01133 revealed that the isolate carried the resistance genes blaVIM-1, blaSHV-5 and blaCMY-13 on a self-transmissible IncA/C2 plasmid. The plasmid was closely related to the previously described VIM-1-encoding plasmid S15FP06257_p from E. coli of pork origin in Belgium. Our results indicate an occasional spread of the blaVIM-1 gene in Enterobacteriaceae of the European pig population. Moreover, the blaVIM-1 located on an IncA/C2 plasmid supports the presumption of a new, probably human source of carbapenemase-producing Enterobacteriaceae (CPE) entering the livestock and food chain sector.
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Emergence of Carbapenem-Resistant Providencia rettgeri and Providencia stuartii Producing IMP-Type Metallo-β-Lactamase in Japan. Antimicrob Agents Chemother 2020; 64:AAC.00382-20. [PMID: 32816727 PMCID: PMC7577129 DOI: 10.1128/aac.00382-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/08/2020] [Indexed: 12/31/2022] Open
Abstract
Four Providencia rettgeri isolates and one Providencia stuartii isolate were obtained from urine samples of five patients in 2018 in Japan. All of the isolates were resistant to imipenem and meropenem, and three were highly resistant to both carbapenems, with MICs of 512 μg/ml. The three highly carbapenem-resistant isolates harbored blaIMP-70, encoding a variant of IMP-1 metallo-β-lactamase with two amino acid substitutions (Val67Phe and Phe87Val), and the other two harbored blaIMP-1 and blaIMP-11, respectively. Whole-genome sequencing revealed that an isolate harbored two copies of blaIMP-1 on the chromosome and that the other four harbored a copy of blaIMP-11 or blaIMP-70 in a plasmid. Expression of blaIMP-70 conferred carbapenem resistance in Escherichia coli Recombinant IMP-70 and an IMP-1 variant with Val67Phe but without Phe87Val had significant higher hydrolytic activities against meropenem than recombinant IMP-1, indicating that an amino acid substitution of Val67Phe affects increased activities against meropenem in IMP-70. These results suggest that Providencia spp. become more highly resistant to carbapenems by acquisition of two copies of blaIMP-1 or by mutation of blaIMP genes with amino acid substitutions, such as blaIMP-70.
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Nafplioti K, Souli M, Adamou P, Moraitou E, Giannopoulou P, Chra P, Damala M, Vogiatzakis E, Trikka-Graphakos E, Baka V, Prifti E, Antoniadou A, Galani I. Characterization of 16S rRNA methylase genes in Enterobacterales and Pseudomonas aeruginosa in Athens Metropolitan area, 2015-2016. Eur J Clin Microbiol Infect Dis 2020; 40:111-121. [PMID: 32794063 DOI: 10.1007/s10096-020-04006-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
The aim of this study was to characterize the 16S rRNA methylase (RMT) genes in aminoglycoside-resistant Enterobacterales and Pseudomonas aeruginosa isolates in 2015-2016 in hospitals in Athens, Greece. Single-patient, Gram-negative clinical isolates resistant to both amikacin and gentamicin (n = 292) were consecutively collected during a two-year period (2015-2016) in five tertiary care hospitals in Athens. RMT genes were detected by PCR. In all RMT-producing isolates, ESBL and carbapenemase production was confirmed by PCR, and the clonal relatedness and the plasmid contents were also characterized. None of the 138 P. aeruginosa isolates harbored any of the RMT genes surveyed although some were highly resistant to aminoglycosides (MICs > = 512 mg/L). Among 154 Enterobacterales, 31 Providencia stuartii (93.9%), 42 Klebsiella pneumoniae (37.8%), six Proteus mirabilis (75%), and two Escherichia coli (100%) isolates were confirmed as highly resistant to amikacin, gentamicin, and tobramycin with MICs ≥ 512 mg/L, harboring mainly the rmtB (98.8%). All were carbapenemase producers. P. stuartii, P. mirabilis, and E. coli produced VIM-type carbapenemases. K. pneumoniae produced KPC- (n = 34, 81.0%), OXA-48 (n = 4, 9.5%), KPC- and VIM- (n = 3, 7.1%), or only VIM-type (n = 1, 2.4%) enzymes. Two groups of similar IncC plasmids were detected one harboring rmtB1, blaVEB-1, blaOXA-10, and blaTEM-1, and the other additionally blaVIM-1 and blaSHV-5. Among RMT-producing Enterobacterales, rmtB1 predominated and was associated with carbapenemase-encoding gene(s). Similar IncC plasmids carrying a multiresistant region, including ESBL genes, and in the case of VIM-producing isolates, the blaVIM-1, were responsible for this dissemination. The co-dissemination of these genes poses a public health threat.
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Affiliation(s)
- Konstantina Nafplioti
- 4th Department of Internal Medicine, Infectious Diseases Laboratory, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Maria Souli
- 4th Department of Internal Medicine, Infectious Diseases Laboratory, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Panagiota Adamou
- 4th Department of Internal Medicine, Infectious Diseases Laboratory, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Eleni Moraitou
- Department of Clinical Microbiology, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | | | - Paraskevi Chra
- Microbiology Department, Korgialenio Benakio Hellenic Red Cross Hospital, Athens, Greece
| | - Maria Damala
- Microbiology Department, "Alexandra" General Hospital of Athens, Athens, Greece
| | - Evangelos Vogiatzakis
- Department of Clinical Microbiology, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | | | - Vasiliki Baka
- Microbiology Department, Korgialenio Benakio Hellenic Red Cross Hospital, Athens, Greece
| | - Eleni Prifti
- Microbiology Department, "Alexandra" General Hospital of Athens, Athens, Greece
| | - Anastasia Antoniadou
- 4th Department of Internal Medicine, Infectious Diseases Laboratory, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece
| | - Irene Galani
- 4th Department of Internal Medicine, Infectious Diseases Laboratory, National and Kapodistrian University of Athens, School of Medicine, Athens, Greece. .,University General Hospital "ATTIKON", Rimini 1, 124 62, Chaidari, Greece.
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Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy. Microorganisms 2020; 8:microorganisms8081232. [PMID: 32806766 PMCID: PMC7466171 DOI: 10.3390/microorganisms8081232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 11/21/2022] Open
Abstract
Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using “Microbial Assembly”. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6′)-Ib4, ant(3″)-Ia, aph(3″)-Ib, aph(3′)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.
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Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, Mevius DJ, Hordijk J. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 2019; 73:1121-1137. [PMID: 29370371 DOI: 10.1093/jac/dkx488] [Citation(s) in RCA: 495] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.
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Affiliation(s)
- M Rozwandowicz
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M S M Brouwer
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - B Gonzalez-Zorn
- Department of Animal Health and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - B Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - D J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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10
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Ambrose SJ, Harmer CJ, Hall RM. Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria. Plasmid 2018; 99:40-55. [PMID: 30081066 DOI: 10.1016/j.plasmid.2018.08.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/12/2018] [Accepted: 08/02/2018] [Indexed: 01/14/2023]
Abstract
The large, broad host range IncC plasmids are important contributors to the spread of key antibiotic resistance genes and over 200 complete sequences of IncC plasmids have been reported. To track the spread of these plasmids accurate typing to identify the closest relatives is needed. However, typing can be complicated by the high variability in resistance gene content and various typing methods that rely on features of the conserved backbone have been developed. Plasmids can be broadly typed into two groups, type 1 and type 2, using four features that differentiate the otherwise closely related backbones. These types are found in many different countries in bacteria from humans and animals. However, hybrids of type 1 and type 2 are also occasionally seen, and two further types, each represented by a single plasmid, were distinguished. Generally, the antibiotic resistance genes are located within a small number of resistance islands, only one of which, ARI-B, is found in both type 1 and type 2. The introduction of each resistance island generates a new lineage and, though they are continuously evolving via the loss of resistance genes or introduction of new ones, the island positions serve as valuable lineage-specific markers. A current type 2 lineage of plasmids is derived from an early type 2 plasmid but the sequences of early type 1 plasmids include features not seen in more recent type 1 plasmids, indicating a shared ancestor rather than a direct lineal relationship. Some features, including ones essential for maintenance or for conjugation, have been examined experimentally.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Botts RT, Apffel BA, Walters CJ, Davidson KE, Echols RS, Geiger MR, Guzman VL, Haase VS, Montana MA, La Chat CA, Mielke JA, Mullen KL, Virtue CC, Brown CJ, Top EM, Cummings DE. Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland. Front Microbiol 2017; 8:1922. [PMID: 29067005 PMCID: PMC5641379 DOI: 10.3389/fmicb.2017.01922] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
Self-transmissible and mobilizable plasmids contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance. The objective of this study was to capture and characterize self-transmissible and mobilizable resistance plasmids from a coastal wetland impacted by urban stormwater runoff and human wastewater during the rainy season. Four plasmids were captured, two self-transmissible and two mobilizable, using both mating and enrichment approaches. Plasmid genomes, sequenced with either Illumina or PacBio platforms, revealed representatives of incompatibility groups IncP-6, IncR, IncN3, and IncF. The plasmids ranged in size from 36 to 144 kb and encoded known resistance genes for most of the major classes of antibiotics used to treat Gram-negative infections (tetracyclines, sulfonamides, β-lactams, fluoroquinolones, aminoglycosides, and amphenicols). The mobilizable IncP-6 plasmid pLNU-11 was discovered in a strain of Citrobacter freundii enriched from the wetland sediments with tetracycline and nalidixic acid, and encodes a novel AmpC-like β-lactamase (blaWDC-1), which shares less than 62% amino acid sequence identity with the PDC class of β-lactamases found in Pseudomonas aeruginosa. Although the IncR plasmid pTRE-1611 was captured by mating wetland bacteria with P. putida KT2440 as recipient, it was found to be mobilizable rather than self-transmissible. Two self-transmissible multidrug-resistance plasmids were also captured: the small (48 kb) IncN3 plasmid pTRE-131 was captured by mating wetland bacteria with Escherichia coli HY842 where it is seemed to be maintained at nearly 240 copies per cell, while the large (144 kb) IncF plasmid pTRE-2011, which was isolated from a cefotaxime-resistant environmental strain of E. coli ST744, exists at just a single copy per cell. Furthermore, pTRE-2011 bears the globally epidemic blaCTX-M-55 extended-spectrum β-lactamase downstream of ISEcp1. Our results indicate that urban coastal wetlands are reservoirs of diverse self-transmissible and mobilizable plasmids of relevance to human health.
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Affiliation(s)
- Ryan T Botts
- Department of Mathematical, Information and Computer Sciences, Point Loma Nazarene University, San Diego, CA, United States
| | - Brooke A Apffel
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - C J Walters
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Kelly E Davidson
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Ryan S Echols
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Michael R Geiger
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Victoria L Guzman
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Victoria S Haase
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Michal A Montana
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Chip A La Chat
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Jenna A Mielke
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Kelly L Mullen
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Cierra C Virtue
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
| | - Celeste J Brown
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - Eva M Top
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, United States
| | - David E Cummings
- Department of Biology, Point Loma Nazarene University, San Diego, CA, United States
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12
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Di Luca MC, Sørum V, Starikova I, Kloos J, Hülter N, Naseer U, Johnsen PJ, Samuelsen Ø. Low biological cost of carbapenemase-encoding plasmids following transfer from Klebsiella pneumoniae to Escherichia coli. J Antimicrob Chemother 2016; 72:85-89. [PMID: 27591293 DOI: 10.1093/jac/dkw350] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 06/20/2016] [Accepted: 07/27/2016] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVES The objective of this study was to determine the biological cost, stability and sequence of two carbapenemase-encoding plasmids containing blaKPC-2 (pG12-KPC-2) and blaVIM-1 (pG06-VIM-1) isolated from Klebsiella pneumoniae when newly acquired by uropathogenic Escherichia coli clinical isolates of different genetic backgrounds. METHODS The two plasmids were transferred into plasmid-free E. coli clinical isolates by transformation. The fitness effect of newly acquired plasmids on the host cell was assessed in head-to-head competitions with the corresponding isogenic strain. Plasmid stability was estimated by propagating monocultures for ∼312 generations. Plasmid nucleotide sequences were determined using next-generation sequencing technology. Assembly, gap closure, annotation and comparative analyses were performed. RESULTS Both plasmids were stably maintained in three of four E. coli backgrounds and resulted in low to moderate reductions in host fitness ranging from 1.1% to 3.6%. A difference in fitness cost was observed for pG12-KPC-2 between two different genetic backgrounds, while no difference was detected for pG06-VIM-1 between three different genetic backgrounds. In addition, a difference was observed between pG12-KPC-2 and pG06-VIM-1 in the same genetic background. In general, the magnitude of biological cost of plasmid carriage was both host and plasmid dependent. The sequences of the two plasmids showed high backbone similarity to previously circulating plasmids in K. pneumoniae. CONCLUSIONS The low to modest fitness cost of newly acquired and stably maintained carbapenemase-encoding plasmids in E. coli indicates a potential for establishment and further dissemination into other Enterobacteriaceae species. We also show that the fitness cost is both plasmid and host specific.
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Affiliation(s)
- Maria Chiara Di Luca
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Vidar Sørum
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Irina Starikova
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Julia Kloos
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nils Hülter
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Umaer Naseer
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway .,Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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13
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Oikonomou O, Liakopoulos A, Phee LM, Betts J, Mevius D, Wareham DW. Providencia stuartii Isolates from Greece: Co-Carriage of Cephalosporin (blaSHV-5, blaVEB-1), Carbapenem (blaVIM-1), and Aminoglycoside (rmtB) Resistance Determinants by a Multidrug-Resistant Outbreak Clone. Microb Drug Resist 2016; 22:379-86. [PMID: 27380549 DOI: 10.1089/mdr.2015.0215] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Providencia stuartii has emerged as an important nosocomial pathogen. We describe an outbreak due to a multidrug-resistant strain over a 4-month period in a critical care unit in Athens. Molecular typing revealed each of the isolates to be clonally related with coresistance to cephalosporins, carbapenems, aminoglycosides, and quinolones. Each isolate contained a 220-kb multi-replicon (IncA/C and IncR) conjugative plasmid encoding TEM-1, SHV-5, VEB-1, and VIM-1 β-lactamases and the 16S rDNA methylase RmtB. Antimicrobial therapy was unsuccessful in 3 of 6 cases, and resistance was readily transmissible to susceptible strains of Escherichia coli by transformation and conjugation. This highlights the clinical importance of P. stuartii and its ability to disseminate critical resistance determinants to other bacterial pathogens.
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Affiliation(s)
- Olga Oikonomou
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
| | - Apostolos Liakopoulos
- 2 Department of Bacteriology and TSEs, Central Veterinary Institute, Wageningen University , Lelystad, the Netherlands
| | - Lynette M Phee
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
| | - Jonathan Betts
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
| | - Dik Mevius
- 2 Department of Bacteriology and TSEs, Central Veterinary Institute, Wageningen University , Lelystad, the Netherlands
| | - David W Wareham
- 1 Antimicrobial Research Group, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London , London, United Kingdom
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14
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Kocsis E, Gužvinec M, Butić I, Krešić S, Crnek SŠ, Tambić A, Cornaglia G, Mazzariol A. blaNDM-1 Carriage on IncR Plasmid in Enterobacteriaceae Strains. Microb Drug Resist 2015; 22:123-8. [PMID: 26484384 DOI: 10.1089/mdr.2015.0083] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Four NDM-1-producing Enterobacteriaceae strains (three Klebsiella pneumoniae and one Citrobacter koseri) were isolated between 2009 and 2011 through a nationwide surveillance for carbapenem-resistant Enterobacteriaceae in Croatia to study the molecular genetic background of blaNDM and the responsible plasmid types. Phenotypically, the clinical strains proved to be multidrug resistant. All strains remained susceptible to tigecycline and colistin. The clinical strains harbored variable antibiotic resistance determinants, notably, blaNDM-1, blaTEM-1, blaSHV-1, blaSHV-12, blaOXA-1, blaOXA-9, blaCTX-M-15, blaCMY-4, qnrB1, and aac(6')Ib-cr in different combinations. Two K. pneumoniae belonged to sequence type ST15 and one strain to ST16. As for the plasmid types, C. koseri and one of the ST15 K. pneumoniae carried IncR, and the second ST15 K. pneumoniae carried IncR and colE. The K. pneumoniae ST16 strain hosted A/C and colE plasmids. The blaNDM-1 gene was detected on conjugative high-molecular-weight plasmids, namely, A/C and IncR types. It is noteworthy that this is the first description of K. pneumoniae ST16 expressing NDM-1 in Europe. Remarkably, our study underscores the importance of the IncR plasmid as a reservoir of multidrug resistance. To the best of our knowledge, the IncR plasmid carrying blaNDM-1 in C. koseri is reported for the first time.
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Affiliation(s)
- Erika Kocsis
- 1 Department of Diagnostics and Public Health, University of Verona , Verona, Italy .,2 Institute of Medical Microbiology, Semmelweis University , Budapest, Hungary
| | - Marija Gužvinec
- 3 Department of Clinical Microbiology, University Hospital for Infectious Diseases , Zagreb, Croatia
| | - Iva Butić
- 3 Department of Clinical Microbiology, University Hospital for Infectious Diseases , Zagreb, Croatia
| | - Sanja Krešić
- 4 Institute of Public Health , Bjelovar, Croatia
| | - Sandra Šestan Crnek
- 5 Department of Clinical Microbiology and Hospital Infections, University Hospital Dubrava , Zagreb, Croatia
| | - Arjana Tambić
- 3 Department of Clinical Microbiology, University Hospital for Infectious Diseases , Zagreb, Croatia
| | - Giuseppe Cornaglia
- 1 Department of Diagnostics and Public Health, University of Verona , Verona, Italy
| | - Annarita Mazzariol
- 1 Department of Diagnostics and Public Health, University of Verona , Verona, Italy
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15
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Chen YT, Siu LK, Tsai YK, Lin FM, Koh TH, Chen JH. A Common Flanking Region in Promiscuous Plasmids Encoding blaNDM-1 in Klebsiella pneumoniae Isolated in Singapore. Microb Drug Resist 2015; 22:109-14. [PMID: 26308279 DOI: 10.1089/mdr.2015.0132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacteria encoding the New Delhi metallo-β-lactamase gene (blaNDM-1) are regarded as superbugs for their resistance to multiple antibiotics. Plasmids encoding blaNDM-1 have been observed to be spreading among gram-negative bacteria around the world. Previous studies have demonstrated that multiple modifications of blaNDM-1-harboring plasmids might contribute to the spread of the gene. In this study, we analyzed blaNDM-1-encoding plasmids from two Klebsiella pneumoniae isolates, DU7433 and DU1301, found to be unrelated by pulsed field gel electrophoresis and multilocus sequencing typing (DU7433: ST14 and DU1301: ST11), and compared them with previously published plasmids. Although strains DU1301, DU7433, and previously published strain DU43320 carried unrelated plasmids, their transconjugants exhibited similar antimicrobial resistance profiles. Transconjugants lacked the resistance to aztreonam, ciprofloxacin, gentamicin, tetracycline, and trimethoprim/sulfamethoxazole when compared with the corresponding clinical isolates. Plasmids pTR1 from DU1301 and pTR2 from DU7433 had completely different plasmid backbones except a short conserved region of blaNDM-1 and ble flanked with truncated or nontruncated ISAba125 and trpF. The presence of this common region among known blaNDM-1-carrying plasmids implies that the dissemination of blaNDM-1 may be facilitated by mobilization of this conserved immediate region among different plasmids. Control measures should be strictly enforced whenever increasing incidences of epidemiological unrelated strains were identified.
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Affiliation(s)
- Ying-Tsong Chen
- 1 Institute of Molecular and Genomic Medicine, National Health Research Institutes , Zhunan, Taiwan .,2 Institute of Genomics and Bioinformatics, National Chung Hsing University , Taichung, Taiwan .,3 Biotechnology Center, National Chung Hsing University , Taichung, Taiwan
| | - L Kristopher Siu
- 4 National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes , Zhunan, Taiwan .,5 PhD Program for Aging, College of Medicine, China Medical University , Taichung, Taiwan
| | - Yu-Kuo Tsai
- 4 National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes , Zhunan, Taiwan
| | - Fu-Mei Lin
- 4 National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes , Zhunan, Taiwan
| | - Tse Hsien Koh
- 6 Department of Pathology, Singapore General Hospital , Singapore , Singapore
| | - Jiun-Han Chen
- 7 Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology , Hsinchu, Taiwan
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16
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Zurfluh K, Glier M, Hächler H, Stephan R. Replicon typing of plasmids carrying blaCTX-M-15 among Enterobacteriaceae isolated at the environment, livestock and human interface. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 521-522:75-78. [PMID: 25828415 DOI: 10.1016/j.scitotenv.2015.03.079] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/19/2015] [Accepted: 03/19/2015] [Indexed: 06/04/2023]
Abstract
One of the currently most important antibiotic resistance mechanisms in Enterobacteriaceae is based on the production of ESBL enzymes that inactivate β-lactam antibiotics including cephalosporins and monobactams by hydrolyzing their β-lactam ring. In humans, the most prevalent ESBL enzyme type is encoded by blaCTX-M-15. CTX-M-15 producing enterobacterial strains were also frequently isolated from environmental samples including surface water and freshwater fish. Plasmids, which can be grouped in different plasmid incompatibility types, play a key role in the horizontal spread of these multidrug resistance genes. The purpose of this study was to investigate the diversity of plasmids that carry blaCTX-M-15 genes among Enterobacteriaceae isolated at the environment, livestock and human interface. In total, 81 blaCTX-M-15-harboring isolates collected between 2009 and 2014 were tested for its ability to transfer blaCTX-M-15 by conjugation. These plasmids were further typed. Transfer of a single blaCTX-M-15-harboring plasmid was observed in 32 (39.5%) of the isolates. The most frequent replicon types detected among these plasmids are IncF-type plasmids (n=12) (mostly multi replicon plasmids with a combination of following replicons: IncFII, IncFIA and IncFIB), followed by IncI1 (n=8), IncK (n=3) and IncR (n=1). A noticeable number of plasmids (n=8) could not be assigned to any of the tested replicon types. Knowledge about the plasmid types circulating in bacterial populations is indispensable for understanding epidemiological dynamics and for establishing intervention strategies to stop further dissemination of particular plasmids.
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Affiliation(s)
- Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Zurich, Switzerland
| | - Melinda Glier
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Zurich, Switzerland
| | - Herbert Hächler
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Zurich, Switzerland.
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17
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Harmer CJ, Hall RM. The A to Z of A/C plasmids. Plasmid 2015; 80:63-82. [DOI: 10.1016/j.plasmid.2015.04.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 04/03/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
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18
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Giakkoupi P, Tryfinopoulou K, Polemis M, Pappa O, Miriagou V, Vatopoulos A. Circulation of a multiresistant, conjugative, IncA/C plasmid within the nosocomial Providencia stuartii population in the Athens area. Diagn Microbiol Infect Dis 2015; 82:62-4. [DOI: 10.1016/j.diagmicrobio.2015.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 02/12/2015] [Accepted: 02/17/2015] [Indexed: 10/24/2022]
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19
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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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20
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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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21
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Complete sequence of a conjugative incn plasmid harboring blaKPC-2, blaSHV-12, and qnrS1 from an Escherichia coli sequence type 648 strain. Antimicrob Agents Chemother 2014; 58:6974-7. [PMID: 25182636 DOI: 10.1128/aac.03632-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We sequenced a novel conjugative blaKPC-2-harboring IncN plasmid, pYD626E, from an Escherichia coli sequence type 648 strain previously identified in Pittsburgh, Pennsylvania. pYD626E was 72,800 bp long and carried four β-lactamase genes, blaKPC-2, blaSHV-12, blaLAP-1, and blaTEM-1. In addition, it harbored qnrS1 (fluoroquinolone resistance) and dfrA14 (trimethoprim resistance). The plasmid profile and clinical history supported the in vivo transfer of this plasmid between Klebsiella pneumoniae and Escherichia coli.
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22
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Comparative genomics of an IncA/C multidrug resistance plasmid from Escherichia coli and Klebsiella isolates from intensive care unit patients and the utility of whole-genome sequencing in health care settings. Antimicrob Agents Chemother 2014; 58:4814-25. [PMID: 24914121 DOI: 10.1128/aac.02573-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The IncA/C plasmids have been implicated for their role in the dissemination of β-lactamases, including gene variants that confer resistance to expanded-spectrum cephalosporins, which are often the treatment of last resort against multidrug-resistant, hospital-associated pathogens. A bla(FOX-5) gene was detected in 14 Escherichia coli and 16 Klebsiella isolates that were cultured from perianal swabs of patients admitted to an intensive care unit (ICU) of the University of Maryland Medical Center (UMMC) in Baltimore, MD, over a span of 3 years. Four of the FOX-encoding isolates were obtained from subsequent samples of patients that were initially negative for an AmpC β-lactamase upon admission to the ICU, suggesting that the AmpC β-lactamase-encoding plasmid was acquired while the patient was in the ICU. The genomes of five E. coli isolates and six Klebsiella isolates containing bla(FOX-5) were selected for sequencing based on their plasmid profiles. An ∼ 167-kb IncA/C plasmid encoding the FOX-5 β-lactamase, a CARB-2 β-lactamase, additional antimicrobial resistance genes, and heavy metal resistance genes was identified. Another FOX-5-encoding IncA/C plasmid that was nearly identical except for a variable region associated with the resistance genes was also identified. To our knowledge, these plasmids represent the first FOX-5-encoding plasmids sequenced. We used comparative genomics to describe the genetic diversity of a plasmid encoding a FOX-5 β-lactamase relative to the whole-genome diversity of 11 E. coli and Klebsiella isolates that carry this plasmid. Our findings demonstrate the utility of whole-genome sequencing for tracking of plasmid and antibiotic resistance gene distribution in health care settings.
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23
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Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae. Antimicrob Agents Chemother 2014; 58:4207-10. [PMID: 24752259 DOI: 10.1128/aac.02773-13] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report here the complete nucleotide sequence of two IncR replicons encoding multidrug resistance determinants, including β-lactam (blaDHA-1, blaSHV-12), aminoglycoside (aphA1, strA, strB), and fluoroquinolone (qnrB4, aac6'-1b-cr) resistance genes. The plasmids have backbones that are similar to each other, including the replication and stability systems, and contain a wide variety of transposable elements carrying known antibiotic resistance genes. This study confirms the increasing clinical importance of IncR replicons as resistance gene carriers.
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24
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Premkumar L, Kurth F, Neyer S, Schembri MA, Martin JL. The multidrug resistance IncA/C transferable plasmid encodes a novel domain-swapped dimeric protein-disulfide isomerase. J Biol Chem 2013; 289:2563-76. [PMID: 24311786 DOI: 10.1074/jbc.m113.516898] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The multidrug resistance-encoding IncA/C conjugative plasmids disseminate antibiotic resistance genes among clinically relevant enteric bacteria. A plasmid-encoded disulfide isomerase is associated with conjugation. Sequence analysis of several IncA/C plasmids and IncA/C-related integrative and conjugative elements (ICE) from commensal and pathogenic bacteria identified a conserved DsbC/DsbG homolog (DsbP). The crystal structure of DsbP reveals an N-terminal domain, a linker region, and a C-terminal catalytic domain. A DsbP homodimer is formed through domain swapping of two DsbP N-terminal domains. The catalytic domain incorporates a thioredoxin-fold with characteristic CXXC and cis-Pro motifs. Overall, the structure and redox properties of DsbP diverge from the Escherichia coli DsbC and DsbG disulfide isomerases. Specifically, the V-shaped dimer of DsbP is inverted compared with EcDsbC and EcDsbG. In addition, the redox potential of DsbP (-161 mV) is more reducing than EcDsbC (-130 mV) and EcDsbG (-126 mV). Other catalytic properties of DsbP more closely resemble those of EcDsbG than EcDsbC. These catalytic differences are in part a consequence of the unusual active site motif of DsbP (CAVC); substitution to the EcDsbC-like (CGYC) motif converts the catalytic properties to those of EcDsbC. Structural comparison of the 12 independent subunit structures of DsbP that we determined revealed that conformational changes in the linker region contribute to mobility of the catalytic domain, providing mechanistic insight into DsbP function. In summary, our data reveal that the conserved plasmid-encoded DsbP protein is a bona fide disulfide isomerase and suggest that a dedicated oxidative folding enzyme is important for conjugative plasmid transfer.
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Affiliation(s)
- Lakshmanane Premkumar
- From the Institute for Molecular Bioscience, Division of Chemistry and Structural Biology and
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25
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Nosocomial dissemination of Providencia stuartii isolates producing extended-spectrum β-lactamases VEB-1 and SHV-5, metallo-β-lactamase VIM-1, and RNA methylase RmtB. J Glob Antimicrob Resist 2013; 1:115-116. [DOI: 10.1016/j.jgar.2013.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 03/20/2013] [Accepted: 03/22/2013] [Indexed: 11/15/2022] Open
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Papagiannitsis CC, Miriagou V, Giakkoupi P, Tzouvelekis LS, Vatopoulos AC. Characterization of pKP1780, a novel IncR plasmid from the emerging Klebsiella pneumoniae ST147, encoding the VIM-1 metallo-β-lactamase. J Antimicrob Chemother 2013; 68:2259-62. [PMID: 23711894 DOI: 10.1093/jac/dkt196] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES To determine the complete nucleotide sequence of the VIM-1-encoding plasmid pKP1780 from Klebsiella pneumoniae ST147 representing a distinct group of IncR replicons. METHODS The plasmid pKP1780 was from a K. pneumoniae clinical strain (KP-1780) isolated in Greece in 2009. Plasmid DNA was extracted from an Escherichia coli DH5α transformant and sequenced using the 454 Genome Sequencer GS FLX procedure on a standard fragment DNA library. Contig gaps were filled by sequencing of PCR-produced fragments. Annotation and comparative analysis were performed using software available on the Internet. RESULTS Plasmid pKP1780 (49 770 bp) consisted of an IncR-related sequence (12 083 bp) including replication and stability systems, and a multidrug resistance (MDR) mosaic region (37 687 bp). blaVIM-1 along with the aacA7, dfrA1 and aadA1 cassettes comprised the variable region of an integron similar to In-e541 from pNL194. The mosaic structure also included the strA, strB, aphA1 and mphA resistance genes as well as intact (n = 10) or defective (n = 3) insertion sequences and fragments of various transposons. CONCLUSIONS The mosaic structure of pKP1780 exhibited high similarity with the acquired region of the IncN plasmid pNL194, indicating the acquisition of the VIM-1-encoding MDR region from pNL194 by an IncR-type plasmid.
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Affiliation(s)
- C C Papagiannitsis
- Department of Microbiology, National School of Public Health, Athens, Greece
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Characterization of pKP1433, a novel KPC-2-encoding plasmid from Klebsiella pneumoniae sequence type 340. Antimicrob Agents Chemother 2013; 57:3427-9. [PMID: 23629721 DOI: 10.1128/aac.00054-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of pKP1433 (55,417 bp), a blaKPC-2-carrying plasmid from Klebsiella pneumoniae sequence type 340, was determined. pKP1433 displayed extensive sequence and structural similarities with the IncN plasmids possessing the KPC-2-encoding Tn4401b isoform. However, the replication, partitioning, and stability of pKP1433 were determined by sequences related to diverse non-IncN plasmids.
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Bush K. Carbapenemases: Partners in crime. J Glob Antimicrob Resist 2013; 1:7-16. [PMID: 27873609 DOI: 10.1016/j.jgar.2013.01.005] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 01/23/2013] [Indexed: 10/27/2022] Open
Abstract
Carbapenemases, β-lactamases that inactivate carbapenems and most β-lactam antibiotics, are most widely known for their ability to confer resistance to β-lactams. They include serine carbapenemases, such as the widespread KPC family of enzymes, and the metallo-β-lactamases that contain the IMP, NDM and VIM enzyme families acquired by Gram-negative bacteria on transferable elements. These enzymes are almost always produced by organisms that encode at least one other β-lactamase, with as many as eight different β-lactamase genes detected in a single isolate. This consortium of β-lactamases includes a full spectrum of molecular and biochemical characteristics, providing the producing organism with a range of catalytic activities. In addition to the variety of β-lactamases found in carbapenemase-producing Gram-negative pathogens are multiple other resistance factors, especially aminoglycoside-modifying enzymes and 16S rRNA methylases that confer resistance to aminoglycosides. Other acquired genes encode fluoroquinolone, trimethoprim, sulfonamide, rifampicin and chloramphenicol resistance determinants on mobile elements that travel together with β-lactamase genes. Thus, the recent proliferation of transferable carbapenemases serves to magnify resistance to virtually all antibiotic classes. Judicial use of current antibiotics and a quest for novel antibacterial agents are necessary, as multidrug-resistant bacteria continue to multiply.
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Affiliation(s)
- Karen Bush
- Department of Molecular and Cellular Biochemistry, Jordan Hall A311, Indiana University, 1001 E. Third Street, Bloomington, IN 47405, USA.
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