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Song H, Zou S, Huang Y, Jian C, Liu W, Tian L, Gong L, Chen Z, Sun Z, Wang Y. Salmonella Typhimurium with Eight Tandem Copies of blaNDM-1 on a HI2 Plasmid. Microorganisms 2023; 12:20. [PMID: 38257847 PMCID: PMC10819877 DOI: 10.3390/microorganisms12010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Carbapenem-resistant Salmonella has recently aroused increasing attention. In this study, a total of four sequence type 36 Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) isolates were consecutively isolated from an 11-month-old female patient with a gastrointestinal infection, of which one was sensitive to carbapenems and three were resistant to carbapenems. Via antibiotic susceptibility testing, a carbapenemases screening test, plasmid conjugation experiments, Illumina short-reads, and PacBio HiFi sequencing, we found that all four S. Typhimurium isolates contained a blaCTX-M-14-positive IncI1 plasmid. One carbapenem-sensitive S. Typhimurium isolate then obtained an IncHI2 plasmid carrying blaNDM-1 and an IncP plasmid without any resistance genes during the disease progression. The blaNDM-1 gene was located on a new 30 kb multiple drug resistance region, which is flanked by IS26 and TnAs2, respectively. In addition, the ST_F0903R isolate contained eight tandem copies of the ISCR1 unit (ISCR1-dsbD-trpF-ble-blaNDM-1-ISAba125Δ1), but an increase in MICs to carbapenems was not observed. Our work further provided evidence of the rapid spread and amplification of blaNDM-1 through plasmid. Prompting the recognition of carbapenem-resistant Enterobacterales and the initiation of appropriate infection control measures are essential to avoid the spread of these organisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.S.); (S.Z.); (Y.H.); (C.J.); (W.L.); (L.T.); (L.G.); (Z.C.); (Y.W.)
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2
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Occurrence of Serratia marcescens Carrying blaIMP-26 and mcr-9 in Southern China: New Insights in the Evolution of Megaplasmid IMP-26. Antibiotics (Basel) 2022; 11:antibiotics11070869. [PMID: 35884123 PMCID: PMC9312351 DOI: 10.3390/antibiotics11070869] [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: 05/26/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 12/10/2022] Open
Abstract
The spread of multidrug-resistant enterobacteria strains has posed a significant concern in public health, especially when the strain harbors metallo-beta-lactamase (MBL)-encoding and mobilized colistin resistance (mcr) genes as such genetic components potentially mediate multidrug resistance. Here we report an IncHI2/2A plasmid carrying blaIMP-26 and mcr-9 in multidrug-resistant Serratia marcescens human isolates YL4. Antimicrobial susceptibility testing was performed by the broth microdilution method. According to the results, S. marcescens YL4 was resistant to several antimicrobials, including β-lactams, fluorquinolones, sulfanilamide, glycylcycline, and aminoglycosides, except for amikacin. To investigate the plasmid further, we conducted whole-genome sequencing and sequence analysis. As shown, S. marcescens YL4 possessed a circular chromosome with 5,171,477 bp length and two plasmids, pYL4.1 (321,744 bp) and pYL4.2 (46,771 bp). Importantly, sharing high similarity with plasmids pZHZJ1 and pIMP-26, pYL4.1 has an IncHI2/2A backbone holding a variable region containing blaIMP-26, mcr-9, and two copies of blaTEM-1B. After comprehensively comparing relevant plasmids, we proposed an evolutionary pathway originating from ancestor pZHZJ1. Then, via an acquisition of the mcr-9 element and a few recombination events, this plasmid eventually evolved into pYL4.1 and pIMP-26 through two different pathways. In addition, the phage-like plasmid pYL4.2 also carried a blaTEM-1B gene. Remarkably, this study first identified a multidrug-resistant S. marcescens strain co-harboring blaIMP-26 and mcr-9 on a megaplasmid pYL4.1 and also included a proposed evolutionary pathway of epidemic megaplasmids carrying blaIMP-26.
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3
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Kaze M, Brooks L, Sistrom M. Antimicrobial resistance in Bacillus-based biopesticide products. MICROBIOLOGY-SGM 2021; 167. [PMID: 34351257 DOI: 10.1099/mic.0.001074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The crisis of antimicrobial resistant bacterial infections is one of the most pressing public health issues. Common agricultural practices have been implicated in the generation of antimicrobial resistant bacteria. Biopesticides, live bacteria used for pest control, are non-pathogenic and considered safe for consumption. Application of bacteria-based pesticides to crops in high concentrations raises the possibility of unintentional contributions to the movement and generation of antimicrobial resistance genes in the environment. However, the presence of clinically relevant antimicrobial resistance genes and their resistance phenotypes are currently unknown. Here we use a combination of multiple bioinformatic and microbiological techniques to define resistomes of widely used biopesticides and determine how the presence of suspected antimicrobial resistance genes translates to observable resistance phenotypes in several biopesticide products. Our results demonstrate that biopesticide products are reservoirs of clinically relevant antimicrobial resistance genes and bear resistance to multiple drug classes.
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Affiliation(s)
- Mo Kaze
- Department of Quantitative and Systems Biology, School of Natural Sciences, University of California Merced, Merced, USA
| | - Lauren Brooks
- Department of Biology, Utah Valley University, Orem, USA
| | - Mark Sistrom
- Department of Quantitative and Systems Biology, School of Natural Sciences, University of California Merced, Merced, USA
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4
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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A framework for identifying the recent origins of mobile antibiotic resistance genes. Commun Biol 2021; 4:8. [PMID: 33398069 PMCID: PMC7782503 DOI: 10.1038/s42003-020-01545-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome. Ebmeyer and colleagues developed a genomic framework for identification and scrutiny of the origins of antibiotic resistance genes. Using data scoured from the literature and publicly available genomes, their results indicate that only 81% of previously reported origins are valid, and that the majority of resistance genes of which the origin is known to date emerged in taxa that have been associated with infection in humans and domesticated animals.
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Characterization of an IncR Plasmid with Two Copies of IS CR-Linked qnrB6 from ST 968 Klebsiella pneumoniae. Int J Genomics 2020; 2020:3484328. [PMID: 33299848 PMCID: PMC7707992 DOI: 10.1155/2020/3484328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/19/2020] [Indexed: 11/21/2022] Open
Abstract
To characterize the molecular structure of IncR plasmid-related sequences, comparative genomic analysis was conducted using 261 IncR plasmid backbone-related sequences. Among the sequences, 257 were IncR plasmids including the multidrug-resistance IncR plasmid pR50-74 from Klebsiella pneumoniae strain R50 of this work, and the other four were from bacterial chromosomes. The IncR plasmids were derived from different bacterial genera or species, mainly Klebsiella pneumoniae (70.82%, 182/257), Escherichia coli (11.28%, 29/257), Enterobacter cloacae (7.00%, 18/257), and Citrobacter freundii (3.50%, 9/257). The bacterial chromosomes carrying IncR plasmid backbone sequences were derived from Proteus mirabilis AOUC-001 and Klebsiella pneumoniae KPN1344, among others. The IncR backbone sequence of P. mirabilis AOUC-001 chromosome shows the highest identity with that of pR50-74. Complex class 1 integrons carrying various copies of ISCR1-sdr-qnrB6-△qacE/sul1 (ISCR1-linked qnrB6 unit) were identified in IncR plasmids. In addition to two consecutive copies of qnrB6-qacE-sul1, the other resistance genes encoded on pR50-74 are all related to mobile genetic elements, such as IS1006, IS26, and the class 1 integron. This study provides a clear understanding of the mobility and plasticity of the IncR plasmid backbone sequence and emphasizes the important role of ISCR in the recruitment of multicopy resistance genes.
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Prevalence of Aminoglycoside Resistance Genes and Molecular Characterization of a Novel Gene, aac(3)-IIg, among Clinical Isolates of the Enterobacter cloacae Complex from a Chinese Teaching Hospital. Antimicrob Agents Chemother 2020; 64:AAC.00852-20. [PMID: 32571822 DOI: 10.1128/aac.00852-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022] Open
Abstract
Members of the Enterobacter cloacae complex are important opportunistic human pathogens capable of causing a wide variety of infections. During recent decades, aminoglycoside-resistant E. cloacae complex isolates have increasingly been reported and have become a major concern. Here, we employed high-throughput sequencing in combination with specific PCR assays to investigate the prevalence of aminoglycoside resistance genes among 170 isolates of the E. cloacae complex collected from a teaching hospital in Wenzhou, China. A total of 12 known genes [aphA-1, strA, strB, aac(6')-IIc, aadA2, aac(3)-IId, aadB, aadA1, rmtB, armA, aadA5, and aac(6')-Ie-aph(2'')-Ia] and 1 novel gene [aac(3)-IIg] were identified, with aphA-1 (71.18%), strA (55.29%), and strB (52.35%) being the most prevalent, and aac(3)-IIg was detected with a positive rate of 21.76% (37/170). The aac(3)-IIg gene was 810 bp in length and encoded a protein that shared 72 to 78% identities with previously known AAC(3)-II aminoglycoside 3-N-acetyltransferases. The MICs of gentamicin and tobramycin were 512 μg/ml and 64 μg/ml, respectively, when aac(3)-IIg was cloned into Escherichia coli DH5α. All aac(3)-IIg-positive isolates exerted broad aminoglycoside resistance profiles, mediated by the coexistence of multiple resistance genes. Moreover, aminoglycoside resistance and resistance genes were found to be transferable in most strains (24/37). Nevertheless, pulsed-field gel electrophoresis (PFGE) and dendrogram analysis showed clonal diversity among these isolates. S1 nuclease PFGE, Southern hybridization, and whole-genome sequencing indicated that aac(3)-IIg was located on transferable as well as nontransferable plasmids of various sizes. The analysis of the genetic environment suggested that aac(3)-IIg is embedded within a class 1 integron, with IS26 playing an important role in its mobility.
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Lin M, Yang Y, Yang Y, Chen G, He R, Wu Y, Zhong LL, El-Sayed Ahmed MAEG, Feng S, Shen C, Wen X, Huang J, Li H, Zheng X, Tian GB. Co-Occurrence of mcr-9 and bla NDM-1 in Enterobacter cloacae Isolated from a Patient with Bloodstream Infection. Infect Drug Resist 2020; 13:1397-1402. [PMID: 32494170 PMCID: PMC7229791 DOI: 10.2147/idr.s248342] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/16/2020] [Indexed: 01/22/2023] Open
Abstract
Background Bloodstream infection (BSI) caused by carbapenem-resistant Enterobacteriaceae are potentially life-threatening related to poorer outcomes. Colistin is considered one of the last-resort treatments against human infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Therefore, emergence of strains from the blood that co-harboring mcr and carbapenem resistance genes were considered as a serious problem. Purpose In this study, two mcr-9-harboring MDR Enterobacter cloacae isolates BSI034 and BSI072 recovered from BSI patients were identified, one of which co-harbored mcr-9 and blaNDM-1. The genetic characteristics of the MDR plasmid needed to be clarified. Methods S1-PFGE and Southern blotting were conducted to determine the location of mcr-9. Whole-genome sequencing was performed to obtain the complete genome and plasmid sequences. The resistome and virulence genes of the strains, accompanied by the genetic characteristics of mcr-9- and blaNDM-1-harboring plasmids, were analyzed. Results Whole-genome sequencing showed that BSI034 harbored mcr-9-carrying IncHI2-type pBSI034-MCR9 and blaNDM-1-carrying IncX3-type pBSI034-NDM1. The 278,517 bp pBSI034-MCR9 carried mcr-9 along with the other 19 resistance genes. mcr-9 was flanked by IS903B (1057 bp) and IS26 (820 bp) in the same orientation. In addition to resistance genes, strain BSI034 also carried a chromosome-located Yersinia high-pathogenicity island, which harbored genes of yersiniabactin biosynthesis operon ybtSXQPAUTE, irp1/2, and fyuA. Conclusion We described the complete genome and mcr-9/blaNDM-1-co-harboring plasmid of E. cloacae from a BSI patient. Notable differences were observed within mosaic modules between pBSI034-MCR9 and other mcr-9-harboring plasmids due to extensive recombination via horizontal gene transfer.
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Affiliation(s)
- Minmin Lin
- Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Yongqiang Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510006, People's Republic of China
| | - Yanxian Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
| | - Guanping Chen
- Sun Yat-sen University School of Medicine, Guangzhou 510006, People's Republic of China
| | - Ruowen He
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
| | - Yiping Wu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
| | - Lan-Lan Zhong
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
| | - Mohamed Abd El-Gawad El-Sayed Ahmed
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology (MUST), Cairo, 6th of October City, Egypt
| | - Siyuan Feng
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
| | - Cong Shen
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
| | - Xin Wen
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
| | - Jin Huang
- Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Hongyu Li
- Department of Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, People's Republic of China
| | - Xiaobin Zheng
- Department of Respiratory Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, People's Republic of China
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, People's Republic of China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, People's Republic of China
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Adelowo OO, Ikhimiukor OO, Knecht C, Vollmers J, Bhatia M, Kaster AK, Müller JA. A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance. PLoS One 2020; 15:e0229451. [PMID: 32130234 PMCID: PMC7055906 DOI: 10.1371/journal.pone.0229451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/06/2020] [Indexed: 01/30/2023] Open
Abstract
In many countries, emission of insufficiently treated wastewater into water bodies appears to be an important factor in spreading clinically relevant antimicrobial resistant bacteria. In this study, we looked for the presence of Enterobacteriaceae strains with resistance to 3rd generation cephalosporin antibiotics in four urban wetlands in southwestern Nigeria by isolation, whole genome sequencing and qPCR enumeration of marker genes. Genome analysis of multi-drug resistant and potentially pathogenic Escherichia coli isolates (members of the widely distributed ST10 complex) revealed the presence of the extended spectrum beta-lactamase gene blaCTX-M-15 on self-transmissible IncF plasmids. The gene was also present together with a blaTEM-1B gene on self-transmissible IncH plasmids in multi-drug resistant Enterobacter cloacae isolates. A Citrobacter freundii isolate carried blaTEM-1B on an IncR-type plasmid without discernable conjugation apparatus. All strains were isolated from a wetland for which previous qPCR enumeration of marker genes, in particular the ratio of intI1 to 16S rRNA gene copy numbers, had indicated a strong anthropogenic impact. Consistent with the isolation origin, qPCR analysis in this study showed that the blaCTX-M gene was present at an abundance of 1x10-4 relative to bacterial 16S rRNA gene copy numbers. The results indicate that contamination of these urban aquatic ecosystems with clinically relevant antibiotic resistant bacteria is substantial in some areas. Measures should therefore be put in place to mitigate the propagation of clinically relevant antimicrobial resistance within the Nigerian aquatic ecosystems.
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Affiliation(s)
- Olawale Olufemi Adelowo
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
- * E-mail: , (OOA); (JAM)
| | - Odion Osebhahiemen Ikhimiukor
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Environmental Microbiology and Biotechnology Laboratory, Department of Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Camila Knecht
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- Otto-von-Guericke-Universität Magdeburg—Institute of Apparatus and Environmental Technology, Magdeburg, Germany
| | - John Vollmers
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Mudit Bhatia
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
| | - Anne-Kirstin Kaster
- Institute for Biological Interfaces (IBG5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Jochen A. Müller
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research—UFZ, Leipzig, Germany
- * E-mail: , (OOA); (JAM)
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10
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Li R, Chen K, Chan EWC, Chen S. Resolution of dynamic MDR structures among the plasmidome of Salmonella using MinION single-molecule, long-read sequencing. J Antimicrob Chemother 2019; 73:2691-2695. [PMID: 29992309 DOI: 10.1093/jac/dky243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 05/27/2018] [Indexed: 11/12/2022] Open
Abstract
Background ISCR1 is an important mobile genetic element mediating the transfer of antibiotic resistance genes. Genetic diversity regarding distribution and copy numbers of ISCR1 within a bacterial population derived from an ancestral strain, which may reflect the degree of genetic plasticity conferred by such an element, has not been studied. Objectives To investigate the plasmid heterogeneity in Salmonella conferred by ISCR1. Methods Nanopore long-read and other sequencing technologies were used to resolve the structures harbouring different copies of ISCR1-qnrB6 from the perspective of single molecules. Results Salmonella London Sa128 was positive for ISCR1-qnrB6 and harboured an MDR-encoding conjugative IncF plasmid, pSa128, containing a complex class 1 integron. The plasmid pSa128T from the transconjugant was larger compared with the original plasmid pSa128, presumably due to amplification of ISCR1-qnrB6. Single-molecule, long-read analysis indicated that both plasmids in the donor and transconjugant strains were in a heterogeneous state that contains variable numbers of ISCR1-qnrB6, with four and eight copies in single plasmids being the dominant types. This type of plasmid heterogeneity in populations of one strain can be regarded as an atypical plasmidome. Conclusions This study highlights the importance of investigation of a single plasmid structure based on long-read sequencing technologies, with a focus on analysing the complex structures of the MDR region, which is expected to exhibit genetic polymorphism or plasmid heterogeneity in various MDR-encoding elements even among members of the same strain. The availability of a single-molecule sequencing technique represents a paradigm shift in the capability of performing population genetic analysis of antibiotic-resistant organisms.
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Affiliation(s)
- Ruichao Li
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China.,State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, P. R. China
| | - Kaichao Chen
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China.,State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China.,State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Sheng Chen
- Shenzhen Key Lab for Food Biological Safety Control, Food Safety and Technology Research Center, Hong Kong PolyU Shen Zhen Research Institute, Shenzhen, P. R. China.,State Key Lab of Chirosciences, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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11
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Wang S, Zhou K, Xiao S, Xie L, Gu F, Li X, Ni Y, Sun J, Han L. A Multidrug Resistance Plasmid pIMP26, Carrying bla IMP-26, fosA5, bla DHA-1, and qnrB4 in Enterobacter cloacae. Sci Rep 2019; 9:10212. [PMID: 31308469 PMCID: PMC6629617 DOI: 10.1038/s41598-019-46777-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/04/2019] [Indexed: 11/20/2022] Open
Abstract
IMP-26 was a rare IMP variant with more carbapenem-hydrolyzing activities, which was increasingly reported now in China. This study characterized a transferable multidrug resistance plasmid harboring blaIMP-26 from one Enterobacter cloacae bloodstream isolate in Shanghai and investigated the genetic environment of resistance genes. The isolate was subjected to antimicrobial susceptibility testing and multilocus sequence typing using broth microdilution method, Etest and PCR. The plasmid was analyzed through conjugation experiments, S1-nuclease pulsed-field gel electrophoresis and hybridization. Whole genome sequencing and sequence analysis was conducted for further investigation of the plasmid. E. cloacae RJ702, belonging to ST528 and carrying blaIMP-26, blaDHA-1, qnrB4 and fosA5, was resistant to almost all β-lactams, but susceptible to quinolones and tigecycline. The transconjugant inherited the multidrug resistance. The resistance genes were located on a 329,420-bp IncHI2 conjugative plasmid pIMP26 (ST1 subtype), which contained trhK/trhV, tra, parA and stbA family operon. The blaIMP-26 was arranged following intI1. The blaDHA-1 and qnrB4 cluster was the downstream of ISCR1, same as that in p505108-MDR. The fosA5 cassette was mediated by IS4. This was the first report on complete nucleotide of a blaIMP-26-carrying plasmid in E. cloacae in China. Plasmid pIMP26 hosted high phylogenetic mosaicism, transferability and plasticity.
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Affiliation(s)
- Su Wang
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kaixin Zhou
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuzhen Xiao
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lianyan Xie
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Feifei Gu
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinxin Li
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuxing Ni
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Lizhong Han
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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12
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Roy Chowdhury P, Fourment M, DeMaere MZ, Monahan L, Merlino J, Gottlieb T, Darling AE, Djordjevic SP. Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids. Plasmid 2019; 102:56-61. [PMID: 30885788 DOI: 10.1016/j.plasmid.2019.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/13/2019] [Indexed: 11/17/2022]
Abstract
IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critically important antibiotics and heavy metals. Here we present the identification and analysis of IncHI2-ST1 plasmid pSPRC-Echo1, isolated from an Enterobacter hormaechei strain from a Sydney hospital, which predates other multi-drug resistant IncHI2-ST1 plasmids reported from Australia. Our time-resolved phylogeny analysis indicates pSPRC-Echo1 represents a new lineage of IncHI2-ST1 plasmids and show how their diversification relates to the era of antibiotics.
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Affiliation(s)
- Piklu Roy Chowdhury
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney, Australia.
| | - Mathieu Fourment
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Matthew Z DeMaere
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Leigh Monahan
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia; Faculty of Medicine, University of Sydney, NSW, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital, NSW Health Pathology, Hospital Road, Concord 2139, NSW, Australia; Faculty of Medicine, University of Sydney, NSW, Australia
| | - Aaron E Darling
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
| | - Steven P Djordjevic
- The Ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia
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13
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Characteristics of Carbapenemase-Producing Enterobacteriaceae in Wastewater Revealed by Genomic Analysis. Antimicrob Agents Chemother 2018; 62:AAC.02501-17. [PMID: 29483120 DOI: 10.1128/aac.02501-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/22/2018] [Indexed: 12/19/2022] Open
Abstract
Wastewater is considered a major source of antibiotic-resistant bacteria released into the environment. Here, we characterized carbapenemase-producing Enterobacteriaceae (CPE) in wastewater by whole-genome analysis. Wastewater samples (n = 40) were collected from municipal wastewater treatment plants and hospital wastewater in Japan and Taiwan. Samples were screened for CPE using selective media, and the obtained isolates were sequenced using an Illumina MiSeq. The isolates (n = 45) included the following microorganisms: Klebsiella quasipneumoniae (n = 12), Escherichia coli (n = 10), Enterobacter cloacae complex (n = 10), Klebsiella pneumoniae (n = 8), Klebsiella variicola (n = 2), Raoultella ornithinolytica (n = 1), Citrobacter freundii (n = 1), and Citrobacter amalonaticus (n = 1). Among the 45 isolates, 38 harbored at least one carbapenemase-encoding gene. Of these, the blaGES (blaGES-5, blaGES-6, and blaGES-24) genes were found in 29 isolates. The genes were situated in novel class 1 integrons, but the integron structures were different between the Japanese (In1439 with blaGES-24 and In1440 with blaGES-5) and Taiwanese (In1441 with blaGES-5 and In1442 with blaGES-6) isolates. Other carbapenemase-encoding genes (blaVIM-1, blaNDM-5, blaIMP-8, blaIMP-19, and blaKPC-2) were found in one to three isolates. Notably, class 1 integrons previously reported among clinical isolates obtained in the same regions as the present study, namely, In477 with blaIMP-19 and In73 with blaIMP-8, were found among the Japanese and Taiwanese isolates, respectively. The results indicate that CPE with various carbapenemase-encoding genes in different genetic contexts were present in biologically treated wastewater, highlighting the need to monitor for antibiotic resistance in wastewater.
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14
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Molecular Characterization of IMP-1-Producing Enterobacter cloacae Complex Isolates in Tokyo. Antimicrob Agents Chemother 2018; 62:AAC.02091-17. [PMID: 29311089 DOI: 10.1128/aac.02091-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 11/29/2017] [Indexed: 12/21/2022] Open
Abstract
Although KPC enzymes are most common among carbapenemases produced by Enterobacter cloacae complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here, we carried out a molecular epidemiological study and plasmid analysis of IMP-1-producing E. cloacae complex isolates collected from three hospitals in central Tokyo using whole-genome sequencing. Seventy-one isolates were classified into several sequence types (STs), and 49 isolates were identified as Enterobacter hormaechei ST78. Isolates of ST78 were divided into three clades by core-genome single nucleotide polymorphism (SNP)-based phylogenetic analysis. Whereas isolates of clade 3 were isolated from only one hospital, isolates of clade 1 and 2 were identified from multiple hospitals. Ten of 12 clade 1 isolates and 1 of 4 clade 2 isolates carried blaIMP-1 on IncHI2 plasmids, with high similarity of genetic structures. In addition, these plasmids shared backbone structures with IncHI2 plasmids carrying blaIMP reported from other countries of the Asia-Pacific region. All isolates of clade 3 except one carried blaIMP-1 in In1426 on IncW plasmids. An isolate of clade 3, which lacked IncW plasmids, carried blaIMP-1 in In1426 on an IncFIB plasmid. These observations suggest that IMP-producing E. cloacae complex isolates with a diversity of host genomic backgrounds have spread in central Tokyo, and they indicate the possible contribution of IncHI2 plasmids toward this phenomenon.
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15
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Tomova A, Ivanova L, Buschmann AH, Godfrey HP, Cabello FC. Plasmid-Mediated Quinolone Resistance (PMQR) Genes and Class 1 Integrons in Quinolone-Resistant Marine Bacteria and Clinical Isolates of Escherichia coli from an Aquacultural Area. MICROBIAL ECOLOGY 2018. [PMID: 28642992 DOI: 10.1007/s00248-017-1016-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Antimicrobial usage in aquaculture selects for antimicrobial-resistant microorganisms in the marine environment. The relevance of this selection to terrestrial animal and human health is unclear. Quinolone-resistance genes qnrA, qnrB, and qnrS were chromosomally located in four randomly chosen quinolone-resistant marine bacteria isolated from an aquacultural area with heavy quinolone usage. In quinolone-resistant uropathogenic clinical isolates of Escherichia coli from a coastal area bordering the same aquacultural region, qnrA was chromosomally located in two E. coli isolates, while qnrB and qnrS were located in small molecular weight plasmids in two other E. coli isolates. Three quinolone-resistant marine bacteria and three quinolone-resistant E. coli contained class 1 integrons but without physical association with PMQR genes. In both marine bacteria and uropathogenic E. coli, class 1 integrons had similar co-linear structures, identical gene cassettes, and similarities in their flanking regions. In a Marinobacter sp. marine isolate and in one E. coli clinical isolate, sequences immediately upstream of the qnrS gene were homologous to comparable sequences of numerous plasmid-located qnrS genes while downstream sequences were different. The observed commonality of quinolone resistance genes and integrons suggests that aquacultural use of antimicrobials might facilitate horizontal gene transfer between bacteria in diverse ecological locations.
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Affiliation(s)
- Alexandra Tomova
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | - Larisa Ivanova
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA
| | | | - Henry P Godfrey
- Department of Pathology, New York Medical College, Valhalla, NY, USA
| | - Felipe C Cabello
- Department of Microbiology and Immunology, New York Medical College, Valhalla, NY, USA.
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16
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Dissemination and Characteristics of a Novel Plasmid-Encoded Carbapenem-Hydrolyzing Class D β-Lactamase, OXA-436, Found in Isolates from Four Patients at Six Different Hospitals in Denmark. Antimicrob Agents Chemother 2017; 62:AAC.01260-17. [PMID: 29061750 DOI: 10.1128/aac.01260-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/13/2017] [Indexed: 12/31/2022] Open
Abstract
The diversity of OXA-48-like carbapenemases is continually expanding. In this study, we describe the dissemination and characteristics of a novel carbapenem-hydrolyzing class D β-lactamase (CHDL) named OXA-436. In total, six OXA-436-producing Enterobacteriaceae isolates, including Enterobacter asburiae (n = 3), Citrobacter freundii (n = 2), and Klebsiella pneumoniae (n = 1), were identified in four patients in the period between September 2013 and April 2015. All three species of OXA-436-producing Enterobacteriaceae were found in one patient. The amino acid sequence of OXA-436 showed 90.4 to 92.8% identity to the amino acid sequences of other acquired OXA-48-like variants. Expression of OXA-436 in Escherichia coli and kinetic analysis of purified OXA-436 revealed an activity profile similar to that of OXA-48 and OXA-181, with activity against penicillins, including temocillin; limited or no activity against extended-spectrum cephalosporins; and activity against carbapenems. The blaOXA-436 gene was located on a conjugative ∼314-kb IncHI2/IncHI2A plasmid belonging to plasmid multilocus sequence typing sequence type 1 in a region surrounded by chromosomal genes previously identified to be adjacent to blaOXA genes in Shewanella spp. In conclusion, OXA-436 is a novel CHDL with functional properties similar to those of OXA-48-like CHDLs. The described geographical spread among different Enterobacteriaceae and the plasmid location of blaOXA-436 illustrate its potential for further dissemination.
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17
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Ludden C, Reuter S, Judge K, Gouliouris T, Blane B, Coll F, Naydenova P, Hunt M, Tracey A, Hopkins KL, Brown NM, Woodford N, Parkhill J, Peacock SJ. Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing. Microb Genom 2017; 3:e000114. [PMID: 29026655 PMCID: PMC5605956 DOI: 10.1099/mgen.0.000114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
Abstract
Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by mobile genetic elements. We hypothesized that wastewater contributes to the dissemination of carbapenemase-producing Enterobacteriaceae (CPE), and studied this through a cross-sectional observational study of wastewater in the East of England. We isolated clinically relevant species of CPE in untreated and treated wastewater, confirming that waste treatment does not prevent release of CPE into the environment. We observed that CPE-positive plants were restricted to those in direct receipt of hospital waste, suggesting that hospital effluent may play a role in disseminating carbapenem resistance. We postulated that plasmids carrying carbapenemase genes were exchanged between bacterial hosts in sewage, and used short-read (Illumina) and long-read (MinION) technologies to characterize plasmids encoding resistance to antimicrobials and heavy metals. We demonstrated that different CPE species (Enterobacter kobei and Raoultella ornithinolytica) isolated from wastewater from the same treatment plant shared two plasmids of 63 and 280 kb. The former plasmid conferred resistance to carbapenems (blaOXA-48), and the latter to numerous drug classes and heavy metals. We also report the complete genome sequence for Enterobacter kobei. Small, portable sequencing instruments such as the MinION have the potential to improve the quality of information gathered on antimicrobial resistance in the environment.
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Affiliation(s)
- Catherine Ludden
- 1London School of Hygiene and Tropical Medicine, London, UK.,2Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sandra Reuter
- 3Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kim Judge
- 2Wellcome Trust Sanger Institute, Cambridge, UK.,3Department of Medicine, University of Cambridge, Cambridge, UK
| | - Theodore Gouliouris
- 3Department of Medicine, University of Cambridge, Cambridge, UK.,4Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Beth Blane
- 3Department of Medicine, University of Cambridge, Cambridge, UK
| | - Francesc Coll
- 1London School of Hygiene and Tropical Medicine, London, UK.,2Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Martin Hunt
- 2Wellcome Trust Sanger Institute, Cambridge, UK
| | - Alan Tracey
- 2Wellcome Trust Sanger Institute, Cambridge, UK
| | - Katie L Hopkins
- 5Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Nicholas M Brown
- 4Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Neil Woodford
- 5Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
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18
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Bereza-Malcolm L, Aracic S, Franks AE. Development and Application of a Synthetically-Derived Lead Biosensor Construct for Use in Gram-Negative Bacteria. SENSORS (BASEL, SWITZERLAND) 2016; 16:E2174. [PMID: 27999352 PMCID: PMC5191153 DOI: 10.3390/s16122174] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023]
Abstract
The use of lead in manufacturing has decreased significantly over the last few decades. However, previous widespread use of lead-containing products and their incorrect disposal has resulted in environmental contamination. Accumulation of harmful quantities of lead pose a threat to all living organisms, through inhalation, ingestion, or direct contact, resulting in lead poisoning. This study utilized synthetic biology principles to develop plasmid-based whole-cell bacterial biosensors for detection of lead. The genetic element of the lead biosensor construct consists of pbrR, which encodes the regulatory protein, together with its divergent promoter region and a promoterless gfp. GFP expression is controlled by PbrR in response to the presence of lead. The lead biosensor genetic element was cloned onto a low-copy number broad host range plasmid, which can stably exist in a range of laboratory and environmental isolates, including Pseudomonas, Shewanella, and Enterobacter. The biosensors constructed were found to be sensitive, rapid, and specific and could, as such, serve as monitoring tools for lead-contaminated water.
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Affiliation(s)
- Lara Bereza-Malcolm
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Sanja Aracic
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Ashley E Franks
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia.
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19
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Dubert J, Osorio CR, Prado S, Barja JL. Persistence of Antibiotic Resistant Vibrio spp. in Shellfish Hatchery Environment. MICROBIAL ECOLOGY 2016; 72:851-860. [PMID: 26552396 DOI: 10.1007/s00248-015-0705-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
The characterization of antibiotic-resistant vibrios isolated from shellfish aquaculture is necessary to elucidate the potential transfer of resistance and to establish effective strategies against vibriosis. With this aim, we analyzed a collection of bacterial isolates obtained from 15 failed hatchery larval cultures that, for the most part, had been treated experimentally with chloramphenicol to prevent vibriosis. Isolates were obtained during a 2-year study from experimental cultures of five different clam species. Among a total of 121 Vibrio isolates studied, 28 were found to be chloramphenicol resistant, suggesting that the shellfish hatchery had been using a sublethal concentration of the antibiotic. Interestingly, chloramphenicol-resistant vibrios showed also resistance to tetracycline and amoxicillin (group A; n = 19) or to streptomycin (group B; n = 9). Chloramphenicol-resistant vibrios were subjected to a PCR amplification and DNA sequencing of the chloramphenicol acetyltransferase genes (cat), and the same approach was followed to study the tetracycline resistance markers (tet). 16S ribosomal RNA (rRNA) gene sequencing revealed that chloramphenicol-resistant vibrios pertained mostly to the Splendidus clade. Conjugation assays demonstrated that various R-plasmids which harbored the cat II/tet(D) genes and cat III gene in groups A and B respectively, were transferred to E. coli and bivalve pathogenic vibrios. Most interestingly, transconjugants exhibited the antibiotic resistance patterns of the donors, despite having been selected only on the basis of chloramphenicol resistance. This is the first report carried out in a bivalve hatchery elucidating the persistence of resistant vibrios, the mechanisms of antibiotic resistance, and the transfer of different R-plasmids.
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Affiliation(s)
- Javier Dubert
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology and Aquaculture Institute, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain.
| | - Carlos R Osorio
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology and Aquaculture Institute, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Susana Prado
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology and Aquaculture Institute, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Juan L Barja
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology and Aquaculture Institute, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
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20
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Abraham S, O'Dea M, Trott DJ, Abraham RJ, Hughes D, Pang S, McKew G, Cheong EYL, Merlino J, Saputra S, Malik R, Gottlieb T. Isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from cats. Sci Rep 2016; 6:35527. [PMID: 27767038 PMCID: PMC5073282 DOI: 10.1038/srep35527] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/26/2016] [Indexed: 12/13/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are a pressing public health issue due to limited therapeutic options to treat such infections. CREs have been predominantly isolated from humans and environmental samples and they are rarely reported among companion animals. In this study we report on the isolation and plasmid characterization of carbapenemase (IMP-4) producing Salmonella enterica Typhimurium from a companion animal. Carbapenemase-producing S. enterica Typhimurium carrying blaIMP-4 was identified from a systemically unwell (index) cat and three additional cats at an animal shelter. All isolates were identical and belonged to ST19. Genome sequencing revealed the acquisition of a multidrug-resistant IncHI2 plasmid (pIMP4-SEM1) that encoded resistance to nine antimicrobial classes including carbapenems and carried the blaIMP-4-qacG-aacA4-catB3 cassette array. The plasmid also encoded resistance to arsenic (MIC-150 mM). Comparative analysis revealed that the plasmid pIMP4-SEM1 showed greatest similarity to two blaIMP-8 carrying IncHI2 plasmids from Enterobacter spp. isolated from humans in China. This is the first report of CRE carrying a blaIMP-4 gene causing a clinical infection in a companion animal, with presumed nosocomial spread. This study illustrates the broader community risk entailed in escalating CRE transmission within a zoonotic species such as Salmonella, and in a cycle that encompasses humans, animals and the environment.
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Affiliation(s)
- Sam Abraham
- School of Veterinary and Life Sciences, Murdoch University, WA, Australia
| | - Mark O'Dea
- School of Veterinary and Life Sciences, Murdoch University, WA, Australia
| | - Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, SA, Australia
| | - Rebecca J Abraham
- School of Veterinary and Life Sciences, Murdoch University, WA, Australia.,Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, SA, Australia
| | - David Hughes
- Concord Veterinary Hospital, North Strathfield NSW, Australia
| | - Stanley Pang
- School of Veterinary and Life Sciences, Murdoch University, WA, Australia
| | - Genevieve McKew
- Department of Microbiology &Infectious Diseases, Concord Hospital, NSW and The University of Sydney, NSW, Australia
| | - Elaine Y L Cheong
- Department of Microbiology &Infectious Diseases, Concord Hospital, NSW and The University of Sydney, NSW, Australia
| | - John Merlino
- Department of Microbiology &Infectious Diseases, Concord Hospital, NSW and The University of Sydney, NSW, Australia
| | - Sugiyono Saputra
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, SA, Australia
| | - Richard Malik
- Centre for Veterinary Education, University of Sydney, NSW, Australia
| | - Thomas Gottlieb
- Department of Microbiology &Infectious Diseases, Concord Hospital, NSW and The University of Sydney, NSW, Australia
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21
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Fyfe C, Grossman TH, Kerstein K, Sutcliffe J. Resistance to Macrolide Antibiotics in Public Health Pathogens. Cold Spring Harb Perspect Med 2016; 6:a025395. [PMID: 27527699 PMCID: PMC5046686 DOI: 10.1101/cshperspect.a025395] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Macrolide resistance mechanisms can be target-based with a change in a 23S ribosomal RNA (rRNA) residue or a mutation in ribosomal protein L4 or L22 affecting the ribosome's interaction with the antibiotic. Alternatively, mono- or dimethylation of A2058 in domain V of the 23S rRNA by an acquired rRNA methyltransferase, the product of an erm (erythromycin ribosome methylation) gene, can interfere with antibiotic binding. Acquired genes encoding efflux pumps, most predominantly mef(A) + msr(D) in pneumococci/streptococci and msr(A/B) in staphylococci, also mediate resistance. Drug-inactivating mechanisms include phosphorylation of the 2'-hydroxyl of the amino sugar found at position C5 by phosphotransferases and hydrolysis of the macrocyclic lactone by esterases. These acquired genes are regulated by either translation or transcription attenuation, largely because cells are less fit when these genes, especially the rRNA methyltransferases, are highly induced or constitutively expressed. The induction of gene expression is cleverly tied to the mechanism of action of macrolides, relying on antibiotic-bound ribosomes stalled at specific sequences of nascent polypeptides to promote transcription or translation of downstream sequences.
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Affiliation(s)
- Corey Fyfe
- Tetraphase Pharmaceuticals, Watertown, Massachusetts 02472
| | | | - Kathy Kerstein
- Tetraphase Pharmaceuticals, Watertown, Massachusetts 02472
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22
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Chen CM, Yu WL, Huang M, Liu JJ, Chen IC, Chen HF, Wu LT. Characterization of IS26-composite transposons and multidrug resistance in conjugative plasmids from Enterobacter cloacae. Microbiol Immunol 2016. [PMID: 26223152 DOI: 10.1111/1348-0421.12289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SHV-12 is the most widespread resistance determinant of Enterobacter cloacae in Taiwan; however, blaSHV-12 has rarely been mobilized. Six multidrug-resistant E. cloacae isolates were collected. After conjugal transfer, plasmid profiling and analysis of incompatibility groups was performed to characterize the genetic context of blaSHV-12 -containing fragments. The presence of mobile genetic elements was demonstrated by PCR, cloning, sequencing and bioinformatics analyses. Four different β-lactamase genes (blaTEM-1 , blaSHV-12 , blaCTX-M-3 and/or blaCTX-M-14 ) were observed in the conjugative plasmids belonging to the IncHI2 (n = 4), IncI1 or IncP incompatibility groups. The IS26-blaSHV-12 -IS26 locus was located in five different genetic environments. A novel structural organization of a class 1 integron with the aac(6')-IIc cassette truncated by IS26 was identified in one isolate. Thus, blaSHV-12 was obtained from different plasmids through IS26-mediated homologous recombination. IS26 plays a vital role in the distribution of mobile resistance elements between different plasmids found in multidrug-resistant E. cloacae isolates.
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Affiliation(s)
- Chih-Ming Chen
- Division of Infectious Disease, Department of Internal Medicine, Tungs' Taichung Metro Harbor Hospital, Taichung
| | - Wen-Liang Yu
- Departments of Medical Research.,Intensive Care Medicine, Chi-Mei Medical Center, Yungkang City, Tainan.,Department of Medicine, Taipei Medical University, Taipei
| | - Mei Huang
- Division of Infectious Disease, Chang Bing Show Chwan Memorial Hospital, Changhua County
| | - Jau-Jin Liu
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
| | - I-Chien Chen
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
| | - Huei-Fen Chen
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
| | - Lii-Tzu Wu
- Institute of Medical Science and Department of Microbiology, China Medical University and Hospital, Taichung, Taiwan
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Abstract
Three mechanisms for plasmid-mediated quinolone resistance (PMQR) have been discovered since 1998. Plasmid genes qnrA, qnrB, qnrC, qnrD, qnrS, and qnrVC code for proteins of the pentapeptide repeat family that protects DNA gyrase and topoisomerase IV from quinolone inhibition. The qnr genes appear to have been acquired from chromosomal genes in aquatic bacteria, are usually associated with mobilizing or transposable elements on plasmids, and are often incorporated into sul1-type integrons. The second plasmid-mediated mechanism involves acetylation of quinolones with an appropriate amino nitrogen target by a variant of the common aminoglycoside acetyltransferase AAC(6')-Ib. The third mechanism is enhanced efflux produced by plasmid genes for pumps QepAB and OqxAB. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. The plasmid-mediated mechanisms provide only low-level resistance that by itself does not exceed the clinical breakpoint for susceptibility but nonetheless facilitates selection of higher-level resistance and makes infection by pathogens containing PMQR harder to treat.
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Complete Sequence of a Novel IncR-F33:A-:B- Plasmid, pKP1034, Harboring fosA3, blaKPC-2, blaCTX-M-65, blaSHV-12, and rmtB from an Epidemic Klebsiella pneumoniae Sequence Type 11 Strain in China. Antimicrob Agents Chemother 2015; 60:1343-8. [PMID: 26666939 DOI: 10.1128/aac.01488-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/05/2015] [Indexed: 12/17/2022] Open
Abstract
A high fosfomycin resistance rate was observed in Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) in our previous study, but little is known about its mechanisms. In this study, we explored the prevalence of plasmid-mediated fosfomycin resistance determinants among fosfomycin-resistant KPC-KP strains from a Chinese university hospital and determined the complete sequence of a novel fosA3-carrying plasmid isolated from an epidemic K. pneumoniae sequence type (ST) 11 strain. A total of 97 KPC-KP strains were studied, of which 57 (58.8%) were resistant to fosfomycin, including 44 (45.4%) harboring fosA3 and 1 harboring fosA. All fosA3-positive strains belonged to the dominant ST11-pulse type (PT) A clone according to multilocus sequence typing and pulsed-field gel electrophoresis, suggesting clonal dissemination. The fosA-positive isolate belonged to ST11-PTE. The fosA3-carrying plasmid pKP1034 is 136,848 bp in length and is not self-transmissible. It is a multireplicon plasmid belonging to IncR-F33:A-: B-. Besides fosA3, a variety of other resistance determinants, including blaKPC-2, rmtB, blaCTX-M-65, and blaSHV-12, are identified in pKP1034, which would allow for coselection of fosA3 by most β-lactams and/or aminoglycosides and facilitate its dissemination despite limited use of fosfomycin in China. Detailed comparisons with related plasmids revealed that pKP1034 is highly mosaic and might have evolved from alarming recombination of the blaKPC-2-carrying plasmid pKPC-LK30 from Taiwan and the epidemic fosA3-carrying plasmid pHN7A8 from mainland China.
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Complete nucleotide sequence of a conjugative plasmid carrying bla(PER-1). Antimicrob Agents Chemother 2015; 59:3582-4. [PMID: 25779581 DOI: 10.1128/aac.00518-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
The nucleotide sequence of a self-transmissible plasmid pVPH1 harboring bla(PER-1) from Vibrio parahaemolyticus was determined. pVPH1 was 183,730 bp in size and shared a backbone similar to pAQU1 and pAQU2, differing mainly in an ∼40-kb multidrug resistance (MDR) region. A complex class 1 integron was identified together with ISCR1 and bla(PER-1) (ISCR1-bla(PER-1)-gst-abct-qacEΔ1-sul1), which was shown to form a circular intermediate playing an important role in the dissemination of bla(PER-1).
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Closely related NDM-1-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. PLoS One 2014; 9:e104899. [PMID: 25144712 PMCID: PMC4140731 DOI: 10.1371/journal.pone.0104899] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/16/2014] [Indexed: 12/01/2022] Open
Abstract
Objective Two plasmids carrying blaNDM-1 isolated from carbapenem-resistant Klebsiella pneumoniae (CR-KP) and carbapenem-resistant Escherichia coli (CR-EC) were sequenced. CR-KP and CR-EC were isolated from two Taiwanese patients without travel histories. Methods Complete sequencing of the plasmids (pLK75 and pLK78) was conducted using a shotgun approach. Annotation of the contigs was performed using the RAST Server, followed by manual inspection and correction. Results These similar plasmids were obtained from two patients with overlapping stays at the same hospital. The pLK75 and pLK78 plasmids were 56,489-bp and 56,072-bp in length, respectively. Plasmid annotation revealed a common backbone similar to the IncN plasmid pR46. The regions flanking the blaNDM-1 genes in these plasmids were very similar to plasmid pNDM-HU01 in Japan, which contains a complex class 1 integron located next to an ISCR1 element. The ISCR1 element has been suggested to provide a powerful mechanism for mobilising antibiotic resistance genes. Conclusion Two indigenous NDM-1-producing Enterobacteriaceae cases were identified for the first time in Taiwan, highlighting the alarming introduction of NDM-1-producing Enterobacteriaceae in this region.
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Interspecies transfer of blaIMP-4 in a patient with prolonged colonization by IMP-4-producing Enterobacteriaceae. J Clin Microbiol 2014; 52:3816-8. [PMID: 25056334 DOI: 10.1128/jcm.01491-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A patient was colonized by IMP-4-producing Enterobacter cloacae and Escherichia coli strains for 7 months. IMP-4-producing E. cloacae strains were first and last isolated at day 33 and at 8 months after admission, respectively. IMP-4-producing E. coli strains were first and last isolated at days 88 and 181 after admission, respectively. The E. cloacae and E. coli isolates shared identical genetic features in terms of blaIMP-4, blaTEM-1, qnrB2, aacA4, HI2 plasmids, and ISCR1. This study shows the first prolonged colonization with in vivo interspecies transfer of blaIMP-4.
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Li J, Lan R, Xiong Y, Ye C, Yuan M, Liu X, Chen X, Yu D, Liu B, Lin W, Bai X, Wang Y, Sun Q, Wang Y, Zhao H, Meng Q, Chen Q, Zhao A, Xu J. Sequential isolation in a patient of Raoultella planticola and Escherichia coli bearing a novel ISCR1 element carrying blaNDM-1. PLoS One 2014; 9:e89893. [PMID: 24594606 PMCID: PMC3940617 DOI: 10.1371/journal.pone.0089893] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 01/23/2014] [Indexed: 11/30/2022] Open
Abstract
Background The gene for New Delhi metallo-β-lactamase 1 (NDM-1) has been reported to be transmitted via plasmids which are easily transferable and capable of wide distribution. We report the isolation of two NDM-1 producing strains and possible in vivo transfer of blaNDM-1 in a patient. Methods Clinical samples were collected for bacterial culture and antibiotic susceptibility testing from a patient during a 34-day hospitalization. The presence of blaNDM-1 was detected by PCR and sequencing. Plasmids of interest were sequenced. Medical records were reviewed for evidence of association between the administration of antibiotics and the acquisition of the NDM-1 resistance. Results A NDM-1 positive Raoultella planticola was isolated from blood on the ninth day of hospitalization without administration of any carbapenem antibiotics and a NDM-1 positive Escherichia coli was isolated from feces on the 29th day of hospitalization and eight days after imipenem administration. The blaNDM-1 was carried by a 280 kb plasmid pRpNDM1-1 in R. planticola and a 58 kb plasmid pEcNDM1-4 in E. coli. The two plasmids shared a 4812 bp NDM-1-ISCR1 element which was found to be excisable from the plasmid as a free form and transferrable in vitro to a NDM-1 negative plasmid from E. coli. Conclusion blaNDM-1 was embedded in an ISCR1 complex class 1 integron as a novel 4812 bp NDM-1-ISCR1 element. The element was found to be able to self excise to become a free form, which may provide a new vehicle for NDM-1 dissemination. This mechanism could greatly accelerate the spread of NDM-1 mediated broad spectrum β-lactam resistance.
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Affiliation(s)
- Juan Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Yanwen Xiong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Min Yuan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Xinfeng Liu
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, Gansu Province, China
| | - Xia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Deshan Yu
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, Gansu Province, China
| | - Bin Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Wenchao Lin
- College of Life Sciences, Nankai University, Tianjin, China
| | - Xuemei Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Yan Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Qiangzheng Sun
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Yiting Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Hongqing Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Qiong Meng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Qiang Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Ailan Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, China CDC, Changping, Beijing, China
- * E-mail:
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Jones-Dias D, Manageiro V, Francisco A, Martins A, Domingues G, Louro D, Ferreira E, Caniça M. Assessing the molecular basis of transferable quinolone resistance in Escherichia coli and Salmonella spp. from food-producing animals and food products. Vet Microbiol 2013; 167:523-31. [DOI: 10.1016/j.vetmic.2013.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 08/08/2013] [Accepted: 08/10/2013] [Indexed: 10/26/2022]
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Quiroga MP, Arduino SM, Merkier AK, Quiroga C, Petroni A, Roy PH, Centrón D. “Distribution and functional identification of complex class 1 integrons”. INFECTION GENETICS AND EVOLUTION 2013; 19:88-96. [DOI: 10.1016/j.meegid.2013.06.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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Association of Transferable Quinolone Resistance Determinant qnrB19 with Extended-Spectrum β -Lactamases in Salmonella Give and Salmonella Heidelberg in Venezuela. Int J Microbiol 2013; 2013:628185. [PMID: 24187555 PMCID: PMC3800642 DOI: 10.1155/2013/628185] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 08/13/2013] [Accepted: 08/29/2013] [Indexed: 11/18/2022] Open
Abstract
Four nontyphoidal Salmonella strains with resistance to extended-spectrum cephalosporins and nonclassical quinolone resistance phenotype were studied. Two S. Give were isolated from pediatric patients with acute gastroenteritis, and two S. Heidelberg were recovered from raw chicken meat. Phenotypic characterization included antimicrobial susceptibility testing and detection of extended-spectrum β-lactamases (ESBLs) by the double-disc synergy method. The detection of quinolone resistance-determining regions (QRDR) of gyrA, gyrB, and gyrC genes, blaESBLs genes, and plasmid-mediated quinolone resistance (PMQR) determinants was carried out by molecular methods. Plasmid analysis included Southern blot and restriction patterns. Transferability of resistance genes was examined by transformation. blaTEM-1 + blaSHV-12 genes were detected in S. Give SG9611 and blaTEM-1 + blaCTX-M-2 in the other three strains: S. Give SG9811, S. Heidelberg SH7511, and SH7911. Regardless of origin and serovars, the qnrB19 gene was detected in the 4 strains studied. All determinants of resistance were localized in plasmids and successfully transferred by transformation. This study highlights the circulation of qnrB19 associated with blaTEM-1, blaSHV-12, and blaCTX-M-2 in S. Give and S. Heidelberg in Venezuela. The recognition of factors associated with increasing resistance and the study of the molecular mechanisms involved can lead to a more focused use of antimicrobial agents.
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Xia R, Ren Y, Xu H. Identification of plasmid-mediated quinolone resistance qnr genes in multidrug-resistant Gram-negative bacteria from hospital wastewaters and receiving waters in the Jinan area, China. Microb Drug Resist 2013; 19:446-56. [PMID: 23844849 DOI: 10.1089/mdr.2012.0210] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) qnr genes by the polymerase chain reaction (PCR) in antibiotic-resistant bacteria isolates collected from aquatic environments in Jinan during 2 years (2008.3-2009.11). Genes were identified to variant level by PCR restriction fragment length polymorphism analysis or sequencing. qnrA1, qnrB2, qnrB4, qnrB6, qnrB9, qnrS1, and the new qnrB variant qnrB26 were detected in 31 strains from six genera (Klebsiella spp., Escherichia coli, Enterobacter spp., Proteus spp., Shigella spp., and Citrobacter spp.), four of which contained double qnr genes. Other PMQR genes, aac(6')-Ib-cr and qepA, were found in 12 (38.7%) and 5 (16.1%) of 31 isolates, respectively; while qepA was found in Shigella spp. for the first time. Eight types of β-lactamase genes and eight other types of resistance genes were also present in the 31 qnr-positive isolates. The detection rate for five β-lactamase genes (blaTEM, blaCTX, ampR, blaDHA, and blaSHV) was >45%. Class 1 integrons and complex class 1 integrons were prevalent in these strains, which contained 15 different gene cassette arrays and 5 different insertion sequence common region 1 (ISCR1)-mediated downstream structures. qnrA1, qnrB2, and qnrB6 were present in three ISCR1-mediated downstream structures: qnrA1-ampR, sapA-like-qnrB2, and sdr-qnrB6. We also analyzed the horizontal transferability of PMQR genes and other resistance determinants. The qnr genes and some integrons and resistance genes from 18 (58.1%) of the 31 qnr-positive strains could be transferred to E. coli J53 Azi(R) or E. coli DH5α recipient strains using conjugation or transformation methods. The results showed that a high number of qnr genes were associated with other resistance genes in aquatic environments in Jinan. This suggests that we should avoid over-using antibiotics and monitor aquatic environments to control the spread of antibiotic resistance genes.
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Affiliation(s)
- Ruirui Xia
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University , Jinan, China
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Characterization of a new blaOXA-48-carrying plasmid in Enterobacteriaceae. Antimicrob Agents Chemother 2013; 57:4064-7. [PMID: 23733457 DOI: 10.1128/aac.02550-12] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work, we characterized a new, 160-kb, blaOXA-48-harboring IncL/M-type plasmid isolated from a Klebsiella pneumoniae strain from France. Moreover, we report the transfer of a 60-kb OXA-48-encoding plasmid from Klebsiella pneumoniae to other Enterobacteriaceae in two patients.
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Diversity of integron- and culture-associated antibiotic resistance genes in freshwater floc. Appl Environ Microbiol 2012; 78:4367-72. [PMID: 22467502 DOI: 10.1128/aem.00405-12] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinically important antibiotic resistance genes were detected in culturable bacteria and class 1 integron gene cassettes recovered from suspended floc, a significant aquatic repository for microorganisms and trace elements, across freshwater systems variably impacted by anthropogenic activities. Antibiotic resistance gene cassettes in floc total community DNA differed appreciably in number and type from genes detected in bacteria cultured from floc. The number of floc antibiotic resistance gene cassette types detected across sites was positively correlated with total (the sum of Ag, As, Cu, and Pb) trace element concentrations in aqueous solution and in a component of floc readily accessible to bacteria. In particular, concentrations of Cu and Pb in the floc component were positively correlated with floc resistance gene cassette diversity. Collectively, these results identify suspended floc as an important reservoir, distinct from bulk water and bed sediment, for antibiotic resistance in aquatic environments ranging from heavily impacted urban sites to remote areas of nature reserves and indicate that trace elements, particularly Cu and Pb, are geochemical markers of resistance diversity in this environmental reservoir. The increase in contamination of global water supplies suggests that aquatic environments will become an even more important reservoir of clinically important antibiotic resistance in the future.
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Cain AK, Hall RM. Evolution of IncHI2 plasmids via acquisition of transposons carrying antibiotic resistance determinants. J Antimicrob Chemother 2012; 67:1121-7. [DOI: 10.1093/jac/dks004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Comparative genomics of Klebsiella pneumoniae strains with different antibiotic resistance profiles. Antimicrob Agents Chemother 2011; 55:4267-76. [PMID: 21746949 DOI: 10.1128/aac.00052-11] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is a global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology of K. pneumoniae strains and occurrences of specific antibiotic resistance genes, such as plasmid-borne extended-spectrum β-lactamases (ESBLs), have been extensively studied, only four complete genomes of K. pneumoniae are available. To better understand the multidrug resistance factors in K. pneumoniae, we determined by pyrosequencing the nearly complete genome DNA sequences of two strains with disparate antibiotic resistance profiles, broadly drug-susceptible strain JH1 and strain 1162281, which is resistant to multiple clinically used antibiotics, including extended-spectrum β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, and sulfamethoxazoles. Comparative genomic analysis of JH1, 1162281, and other published K. pneumoniae genomes revealed a core set of 3,631 conserved orthologous proteins, which were used for reconstruction of whole-genome phylogenetic trees. The close evolutionary relationship between JH1 and 1162281 relative to other K. pneumoniae strains suggests that a large component of the genetic and phenotypic diversity of clinical isolates is due to horizontal gene transfer. Using curated lists of over 400 antibiotic resistance genes, we identified all of the elements that differentiated the antibiotic profile of MDR strain 1162281 from that of susceptible strain JH1, such as the presence of additional efflux pumps, ESBLs, and multiple mechanisms of fluoroquinolone resistance. Our study adds new and significant DNA sequence data on K. pneumoniae strains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates.
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Naseer U, Sundsfjord A. The CTX-M Conundrum: Dissemination of Plasmids andEscherichia coliClones. Microb Drug Resist 2011; 17:83-97. [DOI: 10.1089/mdr.2010.0132] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Umaer Naseer
- Research Group for Host-Microbe Interactions, Department of Medical Biology, University of Tromsø, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Research Group for Host-Microbe Interactions, Department of Medical Biology, University of Tromsø, Tromsø, Norway
- Reference Centre for Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
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Abstract
Aminoglycosides have been an essential component of the armamentarium in the treatment of life-threatening infections. Unfortunately, their efficacy has been reduced by the surge and dissemination of resistance. In some cases the levels of resistance reached the point that rendered them virtually useless. Among many known mechanisms of resistance to aminoglycosides, enzymatic modification is the most prevalent in the clinical setting. Aminoglycoside modifying enzymes catalyze the modification at different -OH or -NH₂ groups of the 2-deoxystreptamine nucleus or the sugar moieties and can be nucleotidyltransferases, phosphotransferases, or acetyltransferases. The number of aminoglycoside modifying enzymes identified to date as well as the genetic environments where the coding genes are located is impressive and there is virtually no bacteria that is unable to support enzymatic resistance to aminoglycosides. Aside from the development of new aminoglycosides refractory to as many as possible modifying enzymes there are currently two main strategies being pursued to overcome the action of aminoglycoside modifying enzymes. Their successful development would extend the useful life of existing antibiotics that have proven effective in the treatment of infections. These strategies consist of the development of inhibitors of the enzymatic action or of the expression of the modifying enzymes.
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Krauland M, Harrison L, Paterson D, Marsh J. Novel integron gene cassette arrays identified in a global collection of multi-drug resistant non-typhoidal Salmonella enterica. Curr Microbiol 2010; 60:217-23. [PMID: 19921331 DOI: 10.1007/s00284-009-9527-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Accepted: 10/19/2009] [Indexed: 10/20/2022]
Abstract
Investigation of integron carriage in a global collection of multi-drug resistant Salmonella enterica identified 3 unique class 1 integron gene cassette arrays not previously reported in this species. The present study used PCR and DNA sequence analysis to characterize the structure of these gene cassette arrays. A approximately 4.0 kb integron containing the gene cassette array arr2/cmlA5/bla (OXA10) /aadA1 was found in isolates belonging to serovars Isangi and Typhimurium from South Africa. A approximately 6.0 kb integron containing the gene cassettes aac(6')IIc/ereA2/IS1247/aac/arr/ereA2 was found in isolates belonging to serovar Heidelberg from the Philippines. In this gene cassette array, the insertion sequence, IS1247, and two putative resistance genes, disrupt the erythromycin resistance gene cassette. Finally, a approximately 6.0 kb integron containing the gene cassette qacH/dfrA32/ereA1/aadA2/cmlA/aadA1 was found in serovar Stanley isolates from Taiwan. This integron, which has not been previously reported in any bacterial species, contains a new dihydrofolate reductase gene cassette sequence designated dfrA32, with only 90% sequence similarity to previously reported dfrA cassettes. The S. enterica integrons described in the present study represent novel collections of resistance genes which confer multi-drug resistance and have the potential to be widely disseminated among S. enterica as well as other bacterial species.
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Affiliation(s)
- Mary Krauland
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, USA
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Richter SN, Frasson I, Bergo C, Manganelli R, Cavallaro A, Palù G. Characterisation of qnr plasmid-mediated quinolone resistance in Enterobacteriaceae from Italy: association of the qnrB19 allele with the integron element ISCR1 in Escherichia coli. Int J Antimicrob Agents 2010; 35:578-83. [PMID: 20356715 DOI: 10.1016/j.ijantimicag.2010.02.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 02/03/2010] [Accepted: 02/10/2010] [Indexed: 11/30/2022]
Abstract
The spread of plasmid-mediated quinolone resistance determinants (qnr-like determinants) was evaluated in a collection of 232 ciprofloxacin-resistant or extended-spectrum beta-lactamase (ESBL)-producing enterobacterial isolates recovered between November 2007 and May 2008 at Padua University Hospital, Italy. qnr genes were mainly found in Klebsiella pneumoniae (68%) and to a lesser extent in Escherichia coli (5.1%). Among the qnrA1, qnrS1 and qnrB19 alleles found, the latter was by far the most frequent. Genetic environment analysis revealed that one qnrB19 gene in E. coli was embedded in an ISCR1 complex class 1 integron. All other qnrB19 genes were flanked by an ISEcp1C region as part of the Tn2012 transposon. qnrA1- and qnrS1-containing strains were not clonally related. Both topoisomerase II mutations and ESBL (mainly SHV-12, TEM-1 and TEM-150 types) were present in most of the qnr-positive strains. qnrB19 is extremely frequent in K. pneumoniae isolates from Italy. In addition, association of qnrB19 with the ISCR1 mobile element in E. coli suggests a broad distribution of this resistance gene in the near future.
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Affiliation(s)
- Sara N Richter
- Department of Histology, Microbiology and Medical Biotechnologies, University of Padua, via Gabelli 63, 35121 Padua, Italy.
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Fortini D, García-Fernández A, Veldman K, Mevius D, Carattoli A. Novel genetic environment of plasmid-mediated quinolone resistance gene qnrB2 in Salmonella Bredeney from poultry. J Antimicrob Chemother 2009; 64:1332-4. [PMID: 19808233 DOI: 10.1093/jac/dkp356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniela Fortini
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
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Gutierrez B, Herrera-Leon S, Escudero JA, Hidalgo L, Gonzalez-Sanz R, Arroyo M, San Millan Á, Echeita MA, Gonzalez-Zorn B. Novel genetic environment of qnrB2 associated with TEM-1 and SHV-12 on pB1004, an IncHI2 plasmid, in Salmonella Bredeney BB1047 from Spain. J Antimicrob Chemother 2009; 64:1334-6. [DOI: 10.1093/jac/dkp340] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Turner MS, Andersson P, Bell JM, Turnidge JD, Harris T, Giffard PM. Plasmid-borne blaSHV genes in Klebsiella pneumoniae are associated with strong promoters. J Antimicrob Chemother 2009; 64:960-4. [PMID: 19749204 DOI: 10.1093/jac/dkp338] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Extended-spectrum beta-lactamases (ESBLs) belonging to the SHV family remain a major cause of ESBL-positive phenotypes in Klebsiella pneumoniae. The bla(SHV) gene is a normal constituent of the K. pneumoniae chromosome. However, most ESBL-encoding bla(SHV) genes found in K. pneumoniae are plasmid borne. The objective was to determine the contribution of promoter variants to the expression of plasmid-borne bla(SHV) genes. METHODS K. pneumoniae clinical isolates were analysed for the presence of IS26 insertions characteristic of plasmid-borne bla(SHV), and differences in their bla(SHV) promoter sequences and expression levels. A high resolution melting (HRM)-based method for rapid promoter analysis was developed. RESULTS An IS26 insertion characteristic of the plasmid-borne bla(SHV-1)/bla(SHV-2)/bla(SHV-5) family was 100% linked to a promoter mutated in the -10 region, a mutation previously only found on the chromosome. The mutation was shown by real-time reverse transcriptase PCR to be associated with increased bla(SHV) expression. CONCLUSIONS Plasmid-borne bla(SHV) is associated with strong promoters. It is likely that an SHV-dependent ESBL-positive phenotype requires both a strong promoter and a coding sequence mutation. An HRM assay can indicate bla(SHV) expression.
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Affiliation(s)
- Mark S Turner
- Institute of Heath and Biomedical Innovation, Queensland University of Technology, Musk Ave., Kelvin Grove, QLD 4059, Australia
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