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Di Pilato V, Pollini S, Miriagou V, Rossolini GM, D'Andrea MM. Carbapenem-resistant Klebsiella pneumoniae: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge. Expert Rev Anti Infect Ther 2024; 22:25-43. [PMID: 38236906 DOI: 10.1080/14787210.2024.2305854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Klebsiella pneumoniae is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in K. pneumoniae has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant K. pneumoniae (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids. AREAS COVERED Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in K. pneumoniae. EXPERT OPINION CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.
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Affiliation(s)
- Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Vivi Miriagou
- Laboratory of Bacteriology, Hellenic Pasteur Institute, Athens, Greece
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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Wang P, Li C, Yin Z, Jiang X, Li X, Mu X, Wu N, Chen F, Zhou D. Genomic epidemiology and heterogeneity of Providencia and their blaNDM-1-carrying plasmids. Emerg Microbes Infect 2023; 12:2275596. [PMID: 37874004 PMCID: PMC10796120 DOI: 10.1080/22221751.2023.2275596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Providencia as an opportunistic pathogen can cause serious infection, and moreover the emergence of multi-drug-resistant Providencia strains poses a potentially life-threatening risk to public health. However, a comprehensive genomic study to reveal the population structure and dissemination of Providencia is still lacking. In this study, we conducted a genomic epidemiology analysis on the 580 global sequenced Providencia isolates, including 257 ones sequenced in this study (42 ones were fully sequenced). We established a genome sequence-based species classification scheme for Providencia, redefining the conventional 11 Providencia species into seven genocomplexes that were further divided into 18 genospecies, providing an extensively updated reference for Providencia species discrimination based on the largest Providencia genome dataset to date. We then dissected the profile of antimicrobial resistance genes and the prevalence of multi-drug-resistant Providencia strains among these genocomplexes/genospecies, disclosing the presence of diverse and abundant antimicrobial resistance genes and high resistance ratios against multiple classes of drugs in Providencia. We further dissected the genetic basis for the spread of blaNDM-1 in Providencia. blaNDM-1 genes were mainly carried by five incompatible (Inc) groups of plasmids: IncC, IncW, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001, and the last three were newly designated in this study. By tracking the spread of blaNDM-1-carrying plasmids, IncC, IncpPROV114-NR, IncpCHS4.1-3, and IncpPrY2001 plasmids were found to be highly involved in parallel horizontal transfer or vertical clonal expansion of blaNDM-1 among Providencia. Overall, our study provided a comprehensive genomic view of species differentiation, antimicrobial resistance prevalence, and plasmid-mediated blaNDM-1 dissemination in Providencia.
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Affiliation(s)
- Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Cuidan Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, People’s Republic of China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiaoyuan Jiang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, People’s Republic of China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Nier Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, People’s Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
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De Belder D, Martino F, Tijet N, Melano RG, Faccone D, De Mendieta JM, Rapoport M, Albornoz E, Petroni A, Tuduri E, Derdoy L, Cogut S, Errecalde L, Pasteran F, Corso A, Gomez SA. Co-integrate Col3m bla NDM-1-harboring plasmids in clinical Providencia rettgeri isolates from Argentina. Microbiol Spectr 2023; 11:e0165123. [PMID: 37732774 PMCID: PMC10581215 DOI: 10.1128/spectrum.01651-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/01/2023] [Indexed: 09/22/2023] Open
Abstract
The first cases of bla NDM in Argentina were detected in three Providencia rettgeri (Pre) recovered from two hospitals in Buenos Aires city in 2013. The isolates were genetically related, but the plasmid profile was different. Here, we characterized the bla NDM-1-harboring plasmids of the first three cases detected in Argentina. Hybrid assembly obtained from short- and long-read sequencing rendered bla NDM-1 in Col3M plasmids of ca. 320 kb (p15268A_320) in isolate PreM15268, 210 kb (p15758B_210) in PreM15758, and 225 kb (p15973A_225) in PreM15973. In addition, PreM15758 harbored a 98-kb circular plasmid (p15758C_98) flanked by a putative recombination site (hin-TnAs2), with 100% nucleotide ID and coverage with p15628A_320. Analysis of PFGE/S1-nuclease gel, Southern hybridization with bla NDM-1 probe, hybrid assembly of short and long reads suggests that pM15758C_98 can integrate by homologous recombination. The three bla NDM-1-plasmids were non-conjugative in vitro. Moreover, tra genes were incomplete, and oriT was not found in the three bla NDM-1-plasmids. In two isolates, blaNDM-1 was embedded in a partially conserved structure flanked by two ISKox2. In addition, all plasmids harbored aph(3')-Ia, aph(3')-VI, and qnrD1 genes and aac(6´)Ib-cr, bla OXA-1, catB3, and arr3 as part of a class 1 integron. Also, p15268A_320 and p15973A_225 harbored bla PER-2. To the best of our knowledge, this is the first report of clinical P. rettgeri harboring blaNDM-1 in an atypical genetic environment and located in unusual chimeric Col3M plasmids. The study and continuous surveillance of these pathogens are crucial to tracking the evolution of these resistant plasmids and finding solutions to tackle their dissemination. IMPORTANCE Infections caused by carbapenem hydrolyzing enzymes like NDM (New Delhi metallo-beta-lactamase) represent a serious problem worldwide because they restrict available treatment options and increase morbidity and mortality, and treatment failure prolongs hospital stays. The first three cases of NDM in Argentina were caused by genetically related P. rettgeri recovered in two hospitals. In this work, we studied the genetic structure of the plasmids encoding bla NDM in those index cases and revealed the enormous plasticity of these genetic elements. In particular, we found a small plasmid that was also found inserted in the larger plasmids by homologous recombination as a co-integrate element. We also found that the bla NDM plasmids were not able to transfer or move to other hosts, suggesting their role as reservoir elements for the acquisition of resistance genes. It is necessary to unravel the dissemination strategies and the evolution of these resistant plasmids to find solutions to tackle their spread.
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Affiliation(s)
- Denise De Belder
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
- National Council on Scientific and Technical Research (CONICET), Buenos Aires, Argentina
| | - Florencia Martino
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Nathalie Tijet
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Roberto G. Melano
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Diego Faccone
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
- National Council on Scientific and Technical Research (CONICET), Buenos Aires, Argentina
| | - Juan Manuel De Mendieta
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Melina Rapoport
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Ezequiel Albornoz
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Alejandro Petroni
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Ezequiel Tuduri
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Laura Derdoy
- Hospital General de Agudos José María Ramos Mejía, Buenos Aires, Argentina
| | - Sandra Cogut
- Hospital General de Agudos Dr. Juan A. Fernández, Buenos Aires, Argentina
| | - Laura Errecalde
- Hospital General de Agudos Dr. Juan A. Fernández, Buenos Aires, Argentina
| | - Fernando Pasteran
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Alejandra Corso
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Sonia A. Gomez
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance (NRRLAR), National Institute of Infectious Diseases–ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
- National Council on Scientific and Technical Research (CONICET), Buenos Aires, Argentina
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Peng J, Xia Z, Zhang T, Zhao X, Chi L, Liu X, Zhao Y, Li R, Li Y, Qin S. Identification of tmexC3-tmexD3-toprJ1b in an XDR Providencia rettgeri clinical isolate co-producing NDM-1 and OXA-10 carbapenemases. J Glob Antimicrob Resist 2023; 34:229-233. [PMID: 37536658 DOI: 10.1016/j.jgar.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023] Open
Abstract
OBJECTIVES Emergence of carbapenemase and tigecycline resistance genes in pathogens threatens the efficacy of last-resort antibiotics. High attention should be paid to the spread and convergence of such resistance genes. This study reports an extensively drug-resistant (XDR) Providencia rettgeri clinical strain co-harbouring carbapenemase genes blaNDM-1, blaOXA-10 and the tmexCD3-toprJ1b gene cluster. METHODS The phenotype and genotype of P. rettgeri Pre20-95 were investigated by antimicrobial susceptibility testing, conjugation assay, stability testing and whole genome sequencing. Bioinformatics tools were used to uncover the genetic structures of its multidrug-resistant (MDR) plasmid pPre20-95-1 and SXT/R391 integrative and conjugative element ICEPreChn20-95. RESULTS P. rettgeri strain Pre20-95 was isolated from a human clinical infection and displayed an extensively drug-resistant (XDR) phenotype. Whole genome sequencing (WGS) analysis identified a pPrY2001-like MDR plasmid, namely pPre20-95-1, co-harbouring blaNDM-1 and blaOXA-10 genes in Pre20-95. The multidrug resistance region of pPre20-95-1 was composed of a Tn6625-derived module and a ∆Tn1696 structure, and blaNDM-1 and blaOXA-10 were located in a composite Tn structure consisting of insertion sequences ISCR1 and ISAba125 and an In125-like class 1 integron, respectively. Furthermore, the novel RND efflux pump gene cluster tmexCD3-toprJ1b was identified on the SXT/R391 ICE ICEPreChn20-95 of its chromosome, and reverse PCR showed that it could form a circular intermediate for transmission. CONCLUSION Our findings highlight further dissemination of the tmexCD3-toprJ1b gene cluster into a clinical isolate of P. rettgeri and convergence with multiple carbapenemase genes, which increases the risk of the emergence of XDR strains and threatens the treatment of Enterobacterales bacterial infections.
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Affiliation(s)
- Junke Peng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Ziwei Xia
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Tingting Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Xiaoyu Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Leizi Chi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China
| | - Xu Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Ya Zhao
- The First Affiliated Hospital of Henan University of Chinese Medicine, Henan Zhengzhou, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yonghong Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China.
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, China.
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Wu T, Zou H, Xia H, Zhou Z, Zhao L, Meng M, Li Q, Guan Y, Li X. Genomic insight into transmission mechanisms of carbapenem-producing Citrobacter spp. isolates between the WWTP and connecting rivers. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115150. [PMID: 37336090 DOI: 10.1016/j.ecoenv.2023.115150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/01/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) poses major health risks worldwide. Most studies have focused on carbapenem resistance in Klebsiella pneumoniae and Escherichia coli; however, the occurrence and transmission of carbapenem-resistant Citrobacter spp. (CRCS) are poorly understood. In this study, we investigated the occurrence and potential transmission patterns of CRCS in different functional areas of an urban wastewater treatment plant (WWTP) and connecting rivers during one-year monitoring in Shandong Province, China. In total, 14 CRCS were detected in 376 environmental samples, including those from the WWTP inlet (n = 7), WWTP anaerobic tank (n = 2), and rivers (n = 5). Citrobacter braakii (n = 6) was the dominant subtype among 14 CRCS isolates, followed by Citrobacter freundii (n = 5), Citrobacter sedlakii (n = 2), and Citrobacter werkmanii (n = 1). All CRCS were resistant to imipenem, meropenem, ampicillin, amoxicillin/clavulanic acid, cefotaxime, ceftazidime, trimethoprim/sulfamethoxazole, and ciprofloxacin. Plasmid analysis showed that the blaKPC-2 gene was located on IncN and IncFII (Yp) plasmids, whereas the blaNDM gene was located on IncX3 and IncN2 plasmids. Clonal transmission of CRCS harboring carbapenem genes occurred between the WWTP and connecting rivers on a temporal or spatial scale. High genomic relatedness of NDM-5-producing C. sedlakii was identified between river water and WWTP aerosol, suggesting a potential exposure risk of CRCS for workers and surrounding residents near the WWTP. Furthermore, NDM-5-producing C. sedlakii isolated from rivers was related to C. sedlakii isolated from soil and well water in different regions of China, indicating that NDM-5-producing C. sedlakii may be widespread in China. These findings indicate that rare healthcare-associated pathogens such as CRCS can contribute to widespread carbapenem production in the environment; thus, CRCS should be continuously monitored.
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Affiliation(s)
- Tianle Wu
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiyun Zou
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiyu Xia
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ziyu Zhou
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ling Zhao
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Min Meng
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Qi Li
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yanyu Guan
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuewen Li
- Department of environment and health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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Cahill N, Hooban B, Fitzhenry K, Joyce A, O'Connor L, Miliotis G, McDonagh F, Burke L, Chueiri A, Farrell ML, Bray JE, Delappe N, Brennan W, Prendergast D, Gutierrez M, Burgess C, Cormican M, Morris D. First reported detection of the mobile colistin resistance genes, mcr-8 and mcr-9, in the Irish environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162649. [PMID: 36906027 DOI: 10.1016/j.scitotenv.2023.162649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/01/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collected were assessed for the presence of antimicrobial resistant bacteria using Brilliance ESBL, Brilliance CRE, mSuperCARBA and McConkey agar containing a ciprofloxacin disc. All water and integrated constructed wetland influent and effluent samples were filtered and enriched in buffered peptone water prior to culture, while wastewater samples were cultured directly. Isolates collected were identified via MALDI-TOF, were tested for susceptibility to 16 antimicrobials, including colistin, and subsequently underwent whole genome sequencing. Overall, eight mcr positive Enterobacterales (one mcr-8 and seven mcr-9) were recovered from six samples (freshwater (n = 2), healthcare facility wastewater (n = 2), wastewater treatment plant influent (n = 1) and integrated constructed wetland influent (piggery farm waste) (n = 1)). While the mcr-8 positive K. pneumoniae displayed resistance to colistin, all seven mcr-9 harbouring Enterobacterales remained susceptible. All isolates demonstrated multi-drug resistance and through whole genome sequencing analysis, were found to harbour a wide variety of antimicrobial resistance genes i.e., 30 ± 4.1 (10-61), including the carbapenemases, blaOXA-48 (n = 2) and blaNDM-1 (n = 1), which were harboured by three of the isolates. The mcr genes were located on IncHI2, IncFIIK and IncI1-like plasmids. The findings of this study highlight potential sources and reservoirs of mcr genes in the environment and illustrate the need for further research to gain a better understanding of the role the environment plays in the persistence and dissemination of antimicrobial resistance.
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Affiliation(s)
- Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland.
| | - Brigid Hooban
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Kelly Fitzhenry
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Aoife Joyce
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Liam Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Maeve Louise Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - James E Bray
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Niall Delappe
- National Carbapenemase-Producing Enterobacterales Reference Laboratory, National Salmonella, Shigella and Listeria Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Wendy Brennan
- National Carbapenemase-Producing Enterobacterales Reference Laboratory, National Salmonella, Shigella and Listeria Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Deirdre Prendergast
- Department of Agriculture, Food and the Marine, Celbridge, Co. Kildare, Ireland
| | | | - Catherine Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland; National Carbapenemase-Producing Enterobacterales Reference Laboratory, National Salmonella, Shigella and Listeria Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
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Xu J, Wang Y, Liu F, Duan G, Yang H. Genome mining reveals the prevalence and extensive diversity of toxin-antitoxin systems in Staphylococcus aureus. Front Microbiol 2023; 14:1165981. [PMID: 37293231 PMCID: PMC10244574 DOI: 10.3389/fmicb.2023.1165981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/28/2023] [Indexed: 06/10/2023] Open
Abstract
Introduction Staphylococcus aureus (S. aureus) is a highly pathogenic and adaptable Gram-positive bacterium that exhibits persistence in various environments. The toxin-antitoxin (TA) system plays a crucial role in the defense mechanism of bacterial pathogens, allowing them to survive in stressful conditions. While TA systems in clinical pathogens have been extensively studied, there is limited knowledge regarding the diversity and evolutionary complexities of TA systems in S. aureus. Methods We conducted a comprehensive in silico survey using 621 publicly available S. aureus isolates. We employed bioinformatic search and prediction tools, including SLING, TADB2.0, and TASmania, to identify TA systems within the genomes of S. aureus. Results Our analysis revealed a median of seven TA systems per genome, with three type II TA groups (HD, HD_3, and YoeB) being present in over 80% of the strains. Additionally, we observed that TA genes were predominantly encoded in the chromosomal DNA, with some TA systems also found within the Staphylococcal Cassette Chromosomal mec (SCCmec) genomic islands. Discussion This study provides a comprehensive overview of the diversity and prevalence of TA systems in S. aureus. The findings enhance our understanding of these putative TA genes and their potential implications in S. aureus ecology and disease management. Moreover, this knowledge could guide the development of novel antimicrobial strategies.
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Liu X, Li R, Chan EWC, Chen S. Complete Genetic Analysis of Plasmids Carrying Multiple Resistance, Virulence, and Phage-Like Genes in Foodborne Escherichia coli Isolate. Microbiol Spectr 2023; 11:e0282022. [PMID: 36943060 PMCID: PMC10101111 DOI: 10.1128/spectrum.02820-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Bacterial antimicrobial resistance, especially phenotypic resistance to multiple drugs (MDR), has posed a serious threat to public health worldwide. To clarify the mechanism of transmission of multidrug resistance encoding plasmids in Enterobacterales, all seven plasmids of an Escherichia coli (E. coli) strain 1108 obtained from a chicken meat sample were extracted and sequenced by Illumina Nextseq 500 and MinION platforms. Plasmids in strain 1108 possessed 16 known antimicrobial resistance genes, with p1108-NDM (~97K) being the most variable plasmid. The multidrug resistance region of p1108-NDM was punctuated by eight IS26 insertion sequences; thus, four MDR regions were found in the backbone of this plasmid. The plasmid p1108-MCR (~65K) was found to lack the ISApl1 element and harbor the blaCTX-M-64-ISEcp1 transposition unit. Moreover, the ISEcp1-blaCMY-2 transposition unit was found in plasmid p1108-CMY2 (~98K), whereas plasmid p1108-emrB (~102K) was associated with resistance to erythromycin (emrB) and streptomycin (aadA22). p1108-IncY (96K) was a phage P1-like plasmid, while p1108-IncFIB (~194K) was found to harbor a virulence region similar to ColV plasmids, and they were found to encode a conserved conjugative transfer protein but harbor no resistance genes. Finally, no mobile element and resistant genes were found in p1108-ColV (~2K). Carriage of mcr-1-encoding elements in carbapenemase-producing Escherichia coli will potentially render all antimicrobial treatment regimens ineffective. Enhanced surveillance and effective intervention strategies are urgently needed to control the transmission of such multidrug resistance plasmids. IMPORTANCE Antimicrobial resistance (AMR) has been increasingly prevalent in agricultural and clinical fields. Understanding the genetic environment involved in AMR genes is important for preventing transmission and developing mitigation strategies. In this study, we investigated the genetic features of an E. coli strain (1108) isolated from food product and harboring 16 AMR genes, including blaNDM-1 and mcr-1 genes encoding resistance to last line antibiotics, meropenem, and colistin. Moreover, this strain also carried virulence genes such as iroBCDEN, iucABCD, and iutA. Our findings confirmed that multiple conjugative plasmids that were formed through active recombination and translocation events were associated with transmission of AMR determinants. Our data warrant the continuous monitoring of emergence and further transmission of these important MDR pathogens.
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Affiliation(s)
- Xiaobo Liu
- National Engineering Laboratory for Deep Process of Rice and By-Products, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ruichao Li
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People’s Republic of China
| | - Edward Wai-Chi Chan
- The State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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9
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Wu C, Zhou Y, Ai W, Guo Y, Wu X, Wang B, Zhao H, Rao L, Wang X, Zhang J, Yu F, Wang L. Co-occurrence of OXA-232, RmtF-encoding plasmids, and pLVPK-like virulence plasmid contributed to the generation of ST15-KL112 hypervirulent multidrug-resistant Klebsiella pneumoniae. Front Microbiol 2023; 14:1133590. [PMID: 36925476 PMCID: PMC10011171 DOI: 10.3389/fmicb.2023.1133590] [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: 12/29/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains and restricted therapeutic options pose a global threat to public health. Aminoglycosides are a wise choice, which can effectively reduce the mortality rate when combined with β-lactam drugs. However, in this study, we identified a ST15-KL112 CRKP FK3006 which not only exhibited resistance to carbapenems, but also exhibited high level resistance to aminoglycosides. In addition to the multidrug resistant phenotype, FK3006 also owned typical pathogenic characteristic, including hypermucoviscosity and hypervirulence phenotypes. According to the whole-genome sequencing, one pLVPK-like virulence plasmid, and three key resistant plasmids (bla OXA-232, bla CTX-M-15, and rmtF) were observed in FK3006. Compared to other typical ST15 CRKP, the presence of pLVPK-like virulence plasmid (p3006-2) endowed the FK3006 with high virulence features. High siderophore production, more cell invasive and more resistant to serum killing was observed in FK3006. The Galleria mellonella infection model also further confirmed the hypervirulent phenotype of FK3006 in vivo. Moreover, according to the conjugation assay, p3006-2 virulence plasmid also could be induced transfer with the help of conjugative IncFIIK p3006-11 plasmid (bla CTX-M-15). In addition to the transmissible plasmid, several insertion sequences and transposons were found around bla CTX-M-15, and rmtF to generate the mobile antimicrobial resistance island (ARI), which also make a significant contribution to the dissemination of resistant determinants. Overall, we reported the uncommon co-existence of bla OXA-232, rmtF-encoding plasmids, and pLVPK-like virulence plasmid in ST15-KL112 K. pneumoniae. The dissemination threatens of these high-risk elements in K. pneumoniae indicated that future studies are necessary to evaluate the prevalence of such isolates.
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Affiliation(s)
- Chunyang Wu
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ying Zhou
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenxiu Ai
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Yinjuan Guo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaocui Wu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bingjie Wang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huilin Zhao
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lulin Rao
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xinyi Wang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiao Zhang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liangxing Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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10
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Caméléna F, Poncin T, Magnan M, Jacquier H, Merimèche M, Berçot B. Detection of Klebsiella pneumoniae isolates coproducing the plasmid-encoded 16S rRNA methyltransferase RmtF and carbapenemase in Paris, France. Int J Antimicrob Agents 2022; 60:106634. [PMID: 35830946 DOI: 10.1016/j.ijantimicag.2022.106634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 11/05/2022]
Affiliation(s)
- François Caméléna
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; Université de Paris, INSERM 1137, IAME, Paris, France
| | - Thibaut Poncin
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; Université de Paris, INSERM 1137, IAME, Paris, France
| | | | - Hervé Jacquier
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; Université de Paris, INSERM 1137, IAME, Paris, France
| | - Manel Merimèche
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; Université de Paris, INSERM 1137, IAME, Paris, France
| | - Béatrice Berçot
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; Université de Paris, INSERM 1137, IAME, Paris, France.
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11
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Rajni E, Jain A, Garg VK, Sharma R, Vohra R, Jain SS. Providencia Causing UTIs: Are We Reaching a Dead End!!! Indian J Crit Care Med 2022; 26:446-451. [PMID: 35656046 PMCID: PMC9067475 DOI: 10.5005/jp-journals-10071-24163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Materials and methods Results Conclusion How to cite this article
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Affiliation(s)
- Ekadashi Rajni
- Department of Microbiology, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
- Ekadashi Rajni, Department of Microbiology, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India, Phone: +91 9680544426, e-mail:
| | - Ashish Jain
- Department of Respiratory Medicine, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
| | - Vishnu K Garg
- Department of Anaesthesiology, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
| | - Richa Sharma
- Department of Microbiology, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
| | - Rajat Vohra
- Department of PSM, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
| | - Srishti S Jain
- Department of Critical Care, Mahatma Gandhi Medical College and Hospital, Jaipur, Rajasthan, India
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12
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Dissemination Routes of Carbapenem and Pan-Aminoglycoside Resistance Mechanisms in Hospital and Urban Wastewater Canalizations of Ghana. mSystems 2022; 7:e0101921. [PMID: 35103490 PMCID: PMC8805638 DOI: 10.1128/msystems.01019-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Wastewater has a major role in antimicrobial resistance (AMR) dynamics and public health. The impact on AMR of wastewater flux at the community-hospital interface in low- and middle-income countries (LMICs) is poorly understood. Therefore, the present study analyzed the epidemiological scenario of resistance genes, mobile genetic elements (MGEs), and bacterial populations in wastewater around the Tamale metropolitan area (Ghana). Wastewater samples were collected from the drainage and canalizations before and after three hospitals and one urban waste treatment plant (UWTP). From all carbapenem/pan-aminoglycoside-resistant bacteria, 36 isolates were selected to determine bacterial species and phenotypical resistance profiles. Nanopore sequencing was used to screen resistance genes and plasmids, whereas, sequence types, resistome and plasmidome contents, pan-genome structures, and resistance gene variants were analyzed with Illumina sequencing. The combination of these sequencing data allowed for the resolution of the resistance gene-carrying platforms. Hospitals and the UWTP collected genetic and bacterial elements from community wastewater and amplified successful resistance gene-bacterium associations, which reached the community canalizations. Uncommon carbapenemase/β-lactamase gene variants, like blaDIM-1, and novel variants, including blaVIM-71, blaCARB-53, and blaCMY-172, were identified and seem to spread via clonal expansion of environmental Pseudomonas spp. However, blaNDM-1, blaCTX-M-15, and armA genes, among others, were associated with MGEs that allowed for their dissemination between environmental and clinical bacterial hosts. In conclusion, untreated hospital wastewater in Ghana is a hot spot for the emergence and spread of genes and gene-plasmid-bacterium associations that accelerate AMR, including to last-resort antibiotics. Urgent actions must be taken in wastewater management in LMICs in order to delay AMR expansion. IMPORTANCE Antimicrobial resistance (AMR) is one the major threats to public health today, especially resistance to last-resort compounds for the treatment of critical infections, such as carbapenems and aminoglycosides. Innumerable works have focused on the clinical ambit of AMR, but studies addressing the impact of wastewater cycles on the emergence and dissemination of resistant bacteria are still limited. The lack of knowledge is even greater when referring to low- and middle-income countries, where there is an absence of accurate sanitary systems. Furthermore, the combination of short- and long-read sequencing has surpassed former technical limitations, allowing the complete characterization of resistance genes, mobile genetic platforms, plasmids, and bacteria. The present study deciphered the multiple elements and routes involved in AMR dynamics in wastewater canalizations and, therefore, in the local population of Tamale, providing the basis to adopt accurate control measures to preserve and promote public health.
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13
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Shen S, Huang X, Shi Q, Guo Y, Yang Y, Yin D, Zhou X, Ding L, Han R, Yu H, Hu F. Occurrence of NDM-1, VIM-1, and OXA-10 Co-Producing Providencia rettgeri Clinical Isolate in China. Front Cell Infect Microbiol 2022; 11:789646. [PMID: 35047418 PMCID: PMC8761753 DOI: 10.3389/fcimb.2021.789646] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections related to hospital-acquired Infections. In recent years, P. rettgeri clinical strains producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamase which reduce the efficiency of antimicrobial therapy have been reported. However, there are few reports of P. rettgeri co-producing two metallo-β-lactamases in one isolate. Here, we first reported a P. rettgeri strain (P138) co-harboring blaNDM-1, blaVIM-1, and blaOXA-10. The specie were identified using MALDI-TOF MS. The results of antimicrobial susceptibility testing by broth microdilution method indicated that P. rettgeri P138 was resistant to meropenem (MIC = 64μg/ml), imipenem (MIC = 64μg/ml), and aztreonam (MIC = 32μg/ml). Conjugation experiments revealed that the blaNDM-1-carrying plasmid was transferrable. The carbapenemase genes were detected using PCR and confirmed by PCR-based sequencing. The complete genomic sequence of the P. rettgeri was identified using Illumina (Illumina, San Diego, CA, USA) short-read sequencing (150bp paired-end reads), and many common resistance genes had been identified, including blaNDM-1, blaVIM-1, blaOXA-10, aac(6’)-Il, aadA5, ant(2’’)-Ia, aadA1, aac(6’)-Ib3, aadA1, aph(3’)-Ia, aac(6’)-Ib-cr, qnrD1, qnrA1, and catA2. The blaNDM-1 gene was characterized by the following structure: IS110–TnpA–IntI1–aadB–IS91–GroEL–GroES–DsbD–PAI–ble–blaNDM-1–IS91–QnrS1–IS110. Blast comparison revealed that the blaNDM-1 gene structure shared >99% similarity with plasmid p5_SCLZS62 (99% nucleotide identity and query coverage). In summary, we isolated a P. rettgeri strain coproducing blaNDM-1, blaVIM-1, and blaOXA-10. To the best of our acknowledge, this was first reported in the world. The occurrence of the strain needs to be closely monitored.
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Affiliation(s)
- Siquan Shen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Xiangning Huang
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Qingyu Shi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Yan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Yang Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Xun Zhou
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Hua Yu
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
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Martin C, Stebbins B, Ajmani A, Comendul A, Hamner S, Hasan NA, Colwell R, Ford T. Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1572-1585. [PMID: 33459951 DOI: 10.1007/s10646-020-02342-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
In-depth studies of the microbiome and mobile resistome profile of different environments is central to understanding the role of the environment in antimicrobial resistance (AMR), which is one of the urgent threats to global public health. In this study, we demonstrated the use of a rapid (and easily portable) sequencing approach coupled with user-friendly bioinformatics tools, the MinION (Oxford Nanopore Technologies), on the evaluation of the microbial as well as mobile metal and antibiotic resistome profile of semi-rural wastewater. A total of 20 unique phyla, 43 classes, 227 genera, and 469 species were identified in samples collected from the Amherst Wastewater Treatment Plant, both from primary and secondary treated wastewater. Alpha diversity indices indicated that primary samples were significantly richer and more microbially diverse than secondary samples. A total of 1041 ARGs, 68 MRGs, and 17 MGEs were detected in this study. There were more classes of AMR genes in primary than secondary wastewater, but in both cases multidrug, beta-lactam and peptide AMR predominated. Of note, OXA β-lactamases, some of which are also carbapenemases, were enriched in secondary samples. Metal resistance genes against arsenic, copper, zinc and molybdenum were the dominant MRGs in the majority of the samples. A larger proportion of resistome genes were located in chromosome-derived sequences except for mobilome genes, which were predominantly located in plasmid-derived sequences. Genetic elements related to transposase were the most common MGEs in all samples. Mobile or MGE/plasmid-associated resistome genes that confer resistance to last resort antimicrobials such as carbapenems and colistin were detected in most samples. Worryingly, several of these potentially transferable genes were found to be carried by clinically-relevant hosts including pathogenic bacterial species in the orders Aeromonadales, Clostridiales, Enterobacterales and Pseudomonadales. This study demonstrated that the MinION can be used as a metagenomics approach to evaluate the microbiome, resistome, and mobilome profile of primary and secondary wastewater.
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Affiliation(s)
| | | | - Asha Ajmani
- University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | | | | | - Nur A Hasan
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Rita Colwell
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Timothy Ford
- University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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Zheng XR, Sun YH, Zhu JH, Wu SL, Ping C, Fang LX, Jiang HX. Two novel bla NDM-1-harbouring transposons on pPrY2001-like plasmids coexisting with a novel cfr-encoding plasmid in food animal source Enterobacteriaceae. J Glob Antimicrob Resist 2021; 26:222-226. [PMID: 34245899 DOI: 10.1016/j.jgar.2021.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 06/13/2021] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES This study reports identification of the carbapenemase-encoding gene from carbapenem-resistant Enterobacterales from food animals. METHODS A total of 40 bacterial isolates recovered from 475 faecal swabs obtained on one farm were tested for the presence of the blaNDM-1 gene by PCR. Species identification of three blaNDM-1-positive strains was conducted by MALDI-TOF/MS. Antimicrobial susceptibility testing was performed by broth microdilution. Transferability of the blaNDM-1 and cfr genes was determined by filter mating. The genetic environment of blaNDM-1 and cfr was analysed by whole-genome sequencing. RESULTS Two Proteus mirabilis (JPM24 and YPM35) and one Providencia rettgeri (YPR25) carried blaNDM-1. The blaNDM-1 genes were located on conjugable pPrY2001-like plasmids often reported to carry important antimicrobial resistance genes (ARGs). YPR25 and YPM35 shared two almost identical conjugable plasmids, one carrying blaNDM-1 and the other cfr. The blaNDM-1 gene in YPR25 (same as YPM35) and JPM24 was located in two novel transposons, designated Tn6922 and Tn6923, respectively. Tn6922 and Tn6923 carried 14 and 7 ARGs, respectively, and both contained multiple copies of IS26 in the same direction, with a high degree of similarity. Additionally, cfr was located on a plasmid with an unreported high frequency of conjugative transfer in YPR25 (same as YPM35). CONCLUSION We identified two novel blaNDM-1-containing transposons (Tn6922 and Tn6923) present on pPrY2001-like plasmids. The pPrY2001-like blaNDM-1 plasmids coexisted with a novel cfr plasmid, and both could transfer at high frequency, highlighting the importance of continuous surveillance of multiresistant Enterobacterales of animal origin that can serve as a reservoir for ARGs.
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Affiliation(s)
- Xing-Run Zheng
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yin-Huan Sun
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Jia-Hang Zhu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Si-Li Wu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Cai Ping
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Liang-Xing Fang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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16
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Pérez-Vázquez M, Sola Campoy PJ, Ortega A, Bautista V, Monzón S, Ruiz-Carrascoso G, Mingorance J, González-Barberá EM, Gimeno C, Aracil B, Sáez D, Lara N, Fernández S, González-López JJ, Campos J, Kingsley RA, Dougan G, Oteo-Iglesias J. Emergence of NDM-producing Klebsiella pneumoniae and Escherichia coli in Spain: phylogeny, resistome, virulence and plasmids encoding blaNDM-like genes as determined by WGS. J Antimicrob Chemother 2020; 74:3489-3496. [PMID: 31504589 DOI: 10.1093/jac/dkz366] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/18/2019] [Accepted: 07/24/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES NDM carbapenemases have spread worldwide. However, little information exists about the impact of NDM-producing Enterobacteriaceae in Spain. By WGS, we sought to elucidate the population structure of NDM-like-producing Klebsiella pneumoniae and Escherichia coli in Spain and to determine the plasmids harbouring blaNDM-like genes. METHODS High-resolution SNP typing, core-genome MLST and plasmid reconstruction (PlasmidID) were performed on 59 NDM-like-producing K. pneumoniae and 8 NDM-like-producing E. coli isolated over an 8 year period in Spain. RESULTS Five major epidemic clones of NDM-producing K. pneumoniae caused five important nationwide outbreaks: ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1; in contrast, the spread of NDM-producing E. coli was polyclonal. Three blaNDM types were identified: blaNDM-1, 61.2%; blaNDM-7, 32.8%; and blaNDM-5, 6%. Five K. pneumoniae isolates co-produced other carbapenemases (three blaOXA-48 and two blaVIM-1). The average number of acquired resistance genes was higher in K. pneumoniae than in E. coli. The plasmids encoding blaNDM-like genes belonged to IncFII, IncFIB, IncX3, IncR, IncN and IncC types, of which IncF, IncR and IncC were associated with MDR. The genetic surroundings of blaNDM-like genes showed a highly variable region upstream of ISAba125. CONCLUSIONS In recent years NDM-producing K. pneumoniae and E. coli have emerged in Spain; the spread of a few high-risk K. pneumoniae clones such as ST437/NDM-7, ST437/NDM-1, ST147/NDM-1, ST11/NDM-1 and ST101/NDM-1 have caused several interregional outbreaks. In contrast, the spread of NDM-producing E. coli has been polyclonal. Plasmid types IncFII, IncFIB, IncX3, IncR, IncN and IncC carried blaNDM, and the same IncX3 plasmid was detected in K. pneumoniae and E. coli.
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Affiliation(s)
- María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro J Sola Campoy
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Adriana Ortega
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Monzón
- Unidad de Bioinformátia (BU-ISCIII), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Guillermo Ruiz-Carrascoso
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Microbiología, Hospital Universitario La Paz-idiPAZ, Madrid, Spain
| | - Jesus Mingorance
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Servicio de Microbiología, Hospital Universitario La Paz-idiPAZ, Madrid, Spain
| | | | - Concepción Gimeno
- Servicio de Microbiología, Hospital General Universitario de Valencia, Valencia, Spain
| | - Belén Aracil
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - David Sáez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Noelia Lara
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Fernández
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan José González-López
- Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain.,Clinical Microbiology Department, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - José Campos
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
| | - Robert A Kingsley
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Quadram Institute Bioscience, Colney, Norwich, UK
| | - Gordon Dougan
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI RD12/0015 and REIPI RD16/0016), Instituto de Salud Carlos III, Madrid, Spain
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17
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Li P, Zhu T, Zhou D, Lu W, Liu H, Sun Z, Ying J, Lu J, Lin X, Li K, Ying J, Bao Q, Xu T. Analysis of Resistance to Florfenicol and the Related Mechanism of Dissemination in Different Animal-Derived Bacteria. Front Cell Infect Microbiol 2020; 10:369. [PMID: 32903722 PMCID: PMC7438884 DOI: 10.3389/fcimb.2020.00369] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Bacterial resistance to antibiotics has become an important concern for public health. This study was aimed to investigate the characteristics and the distribution of the florfenicol-related resistance genes in bacteria isolated from four farms. A total of 106 florfenicol-resistant Gram-negative bacilli were examined for florfenicol-related resistance genes, and the positive isolates were further characterized. The antimicrobial sensitivity results showed that most of them (100, 94.33%) belonged to multidrug resistance Enterobacteriaceae. About 91.51% of the strains carried floR gene, while 4.72% carried cfr gene. According to the pulsed-field gel electrophoresis results, 34 Escherichia coli were subdivided into 22 profiles, the genetic similarity coefficient of which ranged from 80.3 to 98.0%. The multilocus sequence typing (MLST) results revealed 17 sequence types (STs), with ST10 being the most prevalent. The genome sequencing result showed that the Proteus vulgaris G32 genome consists of a 4.06-Mb chromosome, a 177,911-bp plasmid (pG32-177), and a 51,686-bp plasmid (pG32-51). A floR located in a drug-resistant region on the chromosome of P. vulgaris G32 was with IS91 family transposase, and the other floR gene on the plasmid pG32-177 was with an ISCR2 insertion sequence. The cfr gene was located on the pG32-51 flanked by IS26 element and TnpA26. This study suggested that the mobile genetic elements played an important role in the replication of resistance genes and the horizontal resistance gene transfer.
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Affiliation(s)
- Peizhen Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Tingyuan Zhu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jun Ying
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Jianchao Ying
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
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18
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Aris P, Boroumand MA, Douraghi M. Amikacin resistance due to the aphA6 gene in multi-antibiotic resistant Acinetobacter baumannii isolates belonging to global clone 1 from Iran. BMC Microbiol 2019; 19:221. [PMID: 31533627 PMCID: PMC6751817 DOI: 10.1186/s12866-019-1592-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 09/09/2019] [Indexed: 02/08/2023] Open
Abstract
Background TnaphA6-carrying repAci6 plasmids have been detected in Acinetobacter baumannii isolates belonging to global clones, GC1 and GC2, worldwide. Here, we examined whether RepAci6 plasmids family play a role in the dissemination of the aphA6 in GC1 A. baumannii isolates from Iran. Results We found that 22 isolates carried the repAci6 gene, suggesting that they contain a RepAci6 plasmid family. Using the primers linking the aphA6 gene to the backbone of repAci6 plasmid, it was revealed that 16 isolates from different hospitals harbored TnaphA6 on a repAci6 plasmid. Conclusions This study provides evidence for the dissemination of TnaphA6 on the plasmids encoding RepAci6 in Iranian A. baumannii isolates. Furthermore, it seems that TnaphA6 might be acquired by distinct plasmids separately as it was found to be located on the variants of repAci6 plasmids.
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Affiliation(s)
- Parisa Aris
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, PO Box: 14155-6446, Tehran, Iran
| | - Mohammad Ali Boroumand
- Department of Pathology, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, PO Box: 14155-6446, Tehran, Iran. .,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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19
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Dong D, Li M, Liu Z, Feng J, Jia N, Zhao H, Zhao B, Zhou T, Zhang X, Tong Y, Zhu Y. Characterization of a NDM-1- Encoding Plasmid pHFK418-NDM From a Clinical Proteus mirabilis Isolate Harboring Two Novel Transposons, Tn 6624 and Tn 6625. Front Microbiol 2019; 10:2030. [PMID: 31551967 PMCID: PMC6737455 DOI: 10.3389/fmicb.2019.02030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 08/19/2019] [Indexed: 11/13/2022] Open
Abstract
Acquisition of the blaNDM–1 gene by Proteus mirabilis is a concern because it already has intrinsic resistance to polymyxin E and tigecycline antibiotics. Here, we describe a P. mirabilis isolate that carries a pPrY2001-like plasmid (pHFK418-NDM) containing a blaNDM–1 gene. The pPrY2001-like plasmid, pHFK418-NDM, was first reported in China. The pHFK418-NDM plasmid was sequenced using a hybrid approach based on Illumina and MinION platforms. The sequence of pHFK418-NDM was compared with those of the six other pPrY2001-like plasmids deposited in GenBank. We found that the multidrug-resistance encoding region of pHFK418-NDM contains ΔTn10 and a novel transposon Tn6625. Tn6625 consists of ΔTn1696, Tn6260, In251, ΔTn125 (carrying blaNDM–1), ΔTn2670, and a novel mph(E)-harboring transposon Tn6624. In251 was first identified in a clinical isolate, suggesting that it has been transferred efficiently from environmental organisms to clinical isolates. Genomic comparisons of all these pPrY2001-like plasmids showed that their relatively conserved backbones could integrate the numerous and various accessory modules carrying multifarious antibiotic resistance genes. Our results provide a greater depth of insight into the horizontal transfer of resistance genes and add interpretive value to the genomic diversity and evolution of pPrY2001-like plasmids.
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Affiliation(s)
- Dandan Dong
- Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Laboratory Diagnostics, The Medical Faculty of Qingdao University, Qingdao, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Manli Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Zhenzhen Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Laboratory Diagnostics, The Medical Faculty of Qingdao University, Qingdao, China
| | - Jiantao Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Laboratory Diagnostics, The Medical Faculty of Qingdao University, Qingdao, China
| | - Nan Jia
- Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hui Zhao
- Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Tingting Zhou
- Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yuanqi Zhu
- Department of Laboratory Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Laboratory Diagnostics, The Medical Faculty of Qingdao University, Qingdao, China
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20
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Arango-Argoty GA, Dai D, Pruden A, Vikesland P, Heath LS, Zhang L. NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes. MICROBIOME 2019; 7:88. [PMID: 31174603 PMCID: PMC6555988 DOI: 10.1186/s40168-019-0703-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/28/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. Therefore, effective environmental monitoring tools should ideally capture not only antibiotic resistance genes (ARGs), but also mobile genetic elements (MGEs) and indicators of co-selective forces, such as metal resistance genes (MRGs). A major challenge towards characterizing the potential human health risk of antibiotic resistance is the ability to identify ARG-carrying microorganisms, of which human pathogens are arguably of greatest risk. Historically, short reads produced by next-generation sequencing technologies have hampered confidence in assemblies for achieving these purposes. RESULTS Here, we introduce NanoARG, an online computational resource that takes advantage of the long reads produced by nanopore sequencing technology. Specifically, long nanopore reads enable identification of ARGs in the context of relevant neighboring genes, thus providing valuable insight into mobility, co-selection, and pathogenicity. NanoARG was applied to study a variety of nanopore sequencing data to demonstrate its functionality. NanoARG was further validated through characterizing its ability to correctly identify ARGs in sequences of varying lengths and a range of sequencing error rates. CONCLUSIONS NanoARG allows users to upload sequence data online and provides various means to analyze and visualize the data, including quantitative and simultaneous profiling of ARGs, MRGs, MGEs, and putative pathogens. A user-friendly interface allows users the analysis of long DNA sequences (including assembled contigs), facilitating data processing, analysis, and visualization. NanoARG is publicly available and freely accessible at https://bench.cs.vt.edu/nanoarg .
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Affiliation(s)
| | - D. Dai
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - A. Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - P. Vikesland
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - L. S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA USA
| | - L. Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, VA USA
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21
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Abdallah M, Balshi A. First literature review of carbapenem-resistant Providencia. New Microbes New Infect 2018; 25:16-23. [PMID: 29983987 PMCID: PMC6031241 DOI: 10.1016/j.nmni.2018.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/22/2018] [Accepted: 05/29/2018] [Indexed: 01/22/2023] Open
Abstract
Providencia species are Gram-negative bacteria that belong to the Enterobacteriaceae family. They have intrinsic resistance to colistin and tigecycline, which makes treatment of the multidrug-resistant strains of Providencia challenging. Carbapenem-resistant Providencia species are increasingly reported. In this review, patients' characteristics, resistance mechanisms, treatment and infection control measures of carbapenem-resistant Providencia species in the literature are described.
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Affiliation(s)
- M Abdallah
- Pharmaceutical Care Services, Riyadh, Saudi Arabia
| | - A Balshi
- Intensive Care Unit, King Saud Medical City, Riyadh, Saudi Arabia
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22
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Shin S, Jeong SH, Lee H, Hong JS, Park MJ, Song W. Emergence of multidrug-resistant Providencia rettgeri isolates co-producing NDM-1 carbapenemase and PER-1 extended-spectrum β-lactamase causing a first outbreak in Korea. Ann Clin Microbiol Antimicrob 2018; 17:20. [PMID: 29728111 PMCID: PMC5935979 DOI: 10.1186/s12941-018-0272-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/28/2018] [Indexed: 01/22/2023] Open
Abstract
Background Nosocomial outbreak due to carbapenem-resistant Enterobacteriaceae has become serious challenge to patient treatment and infection control. We describe an outbreak due to a multidrug-resistant Providencia rettgeri from January 2016 to January 2017 at a University Hospital in Seoul, Korea. Methods A total of eight non-duplicate P. rettgeri isolates were discovered from urine samples from eight patients having a urinary catheter and admitted in a surgical intensive care unit. The β-lactamase genes were identified using polymerase chain reaction and direct sequencing, and strain typing was done with pulsed-field gel electrophoresis (PFGE). Results All isolates showed high-level resistance to extended-spectrum cephalosporins, aztreonam, meropenem, ertapenem, ciprofloxacin, and amikacin. They harbored the blaNDM-1 carbapenemase and the blaPER-1 type extended-spectrum β-lactamases genes. PFGE revealed that all isolates from eight patients were closely related strains. Conclusions The 13-month outbreak ended following reinforcement of infection control measures, including contact isolation precautions and environmental disinfection. This is the first report of an outbreak of a P. rettgeri clinical isolates co-producing NDM-1 and PER-1 β-lactamase.
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Affiliation(s)
- Saeam Shin
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute for Antimicrobial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute for Antimicrobial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Jun Sung Hong
- Department of Laboratory Medicine and Research Institute for Antimicrobial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Min-Jeong Park
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, South Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Seoul, South Korea.
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23
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Marquez-Ortiz RA, Haggerty L, Olarte N, Duarte C, Garza-Ramos U, Silva-Sanchez J, Castro BE, Sim EM, Beltran M, Moncada MV, Valderrama A, Castellanos JE, Charles IG, Vanegas N, Escobar-Perez J, Petty NK. Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance. Genome Biol Evol 2018; 9:1725-1741. [PMID: 28854628 PMCID: PMC5554438 DOI: 10.1093/gbe/evx115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/21/2022] Open
Abstract
Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.
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Affiliation(s)
- Ricaurte Alejandro Marquez-Ortiz
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia.,The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Leanne Haggerty
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | | | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), CISEI, Cuernavaca, Morelos, México
| | - Jesus Silva-Sanchez
- Instituto Nacional de Salud Pública (INSP), CISEI, Cuernavaca, Morelos, México
| | - Betsy E Castro
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | - Eby M Sim
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Mauricio Beltran
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - María V Moncada
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | | | - Jaime E Castellanos
- Grupo de Patogénesis Infecciosa, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Ian G Charles
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Natasha Vanegas
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia.,The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Javier Escobar-Perez
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | - Nicola K Petty
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
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24
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Characterization of the Complete Nucleotide Sequences of IMP-4-Encoding Plasmids, Belonging to Diverse Inc Families, Recovered from Enterobacteriaceae Isolates of Wildlife Origin. Antimicrob Agents Chemother 2018; 62:AAC.02434-17. [PMID: 29483121 DOI: 10.1128/aac.02434-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/29/2018] [Indexed: 11/20/2022] Open
Abstract
The complete nucleotide sequences of six IMP-4-encoding plasmids recovered from Enterobacteriaceae isolates of wildlife origin were characterized. Sequencing data showed that plasmids of different incompatibility groups (IncM, IncI1, IncF, and nontypeable [including an IncX5_2 and two pPrY2001-like]) carried the blaIMP-4-carrying integrons In809 or In1460. Most of the plasmids carried an mph(A) region, and chrA-like, aac(3)-IId, and blaTEM-1b genes. Finally, plasmid analysis revealed the involvement of two different IS26- and Tn1696-associated mechanisms in the mobilization of IMP-4-encoding integrons.
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25
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Potter RF, Wallace MA, McMullen AR, Prusa J, Stallings CL, Burnham CAD, Dantas G. bla IMP-27 on transferable plasmids in Proteus mirabilis and Providencia rettgeri. Clin Microbiol Infect 2018; 24:1019.e5-1019.e8. [PMID: 29496594 DOI: 10.1016/j.cmi.2018.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 02/02/2018] [Accepted: 02/10/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVES A carbapenem-resistant Providencia rettgeri (PR1) isolate was recovered from a wound infection in Missouri, USA. This isolate possessed an EDTA-inhibitable carbapenemase that was unidentified using the Xpert CARBA-R assay. Our objective was to elucidate the molecular determinant of carbapenem resistance in this isolate. We then sought to test the transmissibility of blaIMP-27 loci in clinical P. rettgeri and Proteus mirabilis isolates. METHODS In October 2016 the novel ambler Class B carbapenemase blaIMP-27, was reported in two different Proteus mirabilis (PM185 and PM187) isolates. Broth mating assays for transfer of carbapenemase activity were performed for the three clinical isolates with recipient sodium azide-resistant Escherichia coli J53. Antibiotic susceptibility testing and phenotypic carbapenemase activity testing were performed on the clinical isolates, J53 and transconjugants using the Kirby-Bauer disc diffusion method according to CLSI guidelines. Plasmid DNA from PM187, PR1 and their transconjugants were used as input for Nextera Illumina sequencing libraries and sequenced on a NextSeq platform. RESULTS PR1 was resistant to both imipenem and meropenem. PM187 and PR1 could transfer resistance to E. coli through plasmid conjugation (pPM187 and pPR1). pPM187 had a virB/virD4 type IV secretion system whereas pPR1 had a traB/traD type IV secretion system. CONCLUSION Two of three blaIMP-27-bearing clinical isolates tested could conjugate resistance into E. coli. The resulting transconjugants became positive for phenotypic carbapenemase production but did not pass clinical resistance breakpoints. blaIMP-27 can be transmitted on different plasmid replicon types that rely on distinct classes of type IV secretion system for horizontal transfer.
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Affiliation(s)
- R F Potter
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - M A Wallace
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - A R McMullen
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - J Prusa
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - C L Stallings
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - C A D Burnham
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Department of Pediatrics, St Louis Children's Hospital, St Louis, MO, USA.
| | - G Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Department of Molecular Microbiology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
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Baron S, Leulmi Z, Villard C, Olaitan AO, Telke AA, Rolain JM. Inactivation of the arn operon and loss of aminoarabinose on lipopolysaccharide as the cause of susceptibility to colistin in an atypical clinical isolate of proteus vulgaris. Int J Antimicrob Agents 2017; 51:450-457. [PMID: 29203405 DOI: 10.1016/j.ijantimicag.2017.11.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/15/2017] [Accepted: 11/24/2017] [Indexed: 12/27/2022]
Abstract
Colistin has become a last-line antibiotic for the treatment of multidrug-resistant bacterial infections; however, resistance to colistin has emerged in recent years. Some bacteria, such as Proteus and Serratia spp., are intrinsically resistant to colistin although the exact mechanism of resistance is unknown. Here we identified the molecular support for intrinsic colistin resistance in Proteus spp. by comparative genomic, transcriptomic and proteomic analyses of colistin-susceptible (CSUR P1868_S) and colistin-resistant (CSUR P1867_R) strains of an atypical Proteus vulgaris. A significant difference in outer membrane glycoside structures in both strains that was corroborated by MALDI-TOF/MS analysis was found, which showed an absence of 4-amino-4-deoxy-l-arabinose (L-Ara4N) in the outer membrane lipid A moiety of the susceptible strain. Comparative genomic analysis with other resistant strains of P. vulgaris available in a local database found a mutation in the arnBCADTEF operon of the susceptible strain. Transcriptomic analysis of genes belonging to the arnBCADTEF operon showed a significant decrease in mRNA expression level of these genes in the susceptible strain, supporting addition of L-Ara4N in the outer membrane lipid A moiety as an explanation for colistin resistance. Insertion of the arnD gene that was suggested to be altered in the susceptible strain by in silico analysis led to a 16-fold increase of colistin MIC in the susceptible strain, confirming its role in colistin resistance in this species. Here we show that constitutive activation of the arn operon and addition of L-Ara4N is the main molecular mechanism of colistin resistance in P. vulgaris.
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Affiliation(s)
- Sophie Baron
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Facultés de Médecine et de Pharmacie, 19-21 bd Jean Moulin, Marseille, France
| | - Zineb Leulmi
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Facultés de Médecine et de Pharmacie, 19-21 bd Jean Moulin, Marseille, France
| | - Claude Villard
- Aix-Marseille Université, Plateforme Protéomique et Innovation Technologique, Faculté de Pharmacie, 27 boulevard Jean Moulin, Marseille 13385 CEDEX 05, France
| | - Abiola Olumuyiwa Olaitan
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Facultés de Médecine et de Pharmacie, 19-21 bd Jean Moulin, Marseille, France
| | - Amar A Telke
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Facultés de Médecine et de Pharmacie, 19-21 bd Jean Moulin, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Facultés de Médecine et de Pharmacie, 19-21 bd Jean Moulin, Marseille, France.
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Doi Y, Wachino JI, Arakawa Y. Aminoglycoside Resistance: The Emergence of Acquired 16S Ribosomal RNA Methyltransferases. Infect Dis Clin North Am 2017; 30:523-537. [PMID: 27208771 DOI: 10.1016/j.idc.2016.02.011] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Aminoglycoside-producing Actinobacteria are known to protect themselves from their own aminoglycoside metabolites by producing 16S ribosomal RNA methyltransferase (16S-RMTase), which prevents them from binding to the 16S rRNA targets. Ten acquired 16S-RMTases have been reported from gram-negative pathogens. Most of them posttranscriptionally methylate residue G1405 of 16S rRNA resulting in high-level resistance to gentamicin, tobramycin, amikacin, and plazomicin. Strains that produce 16S-RMTase are frequently multidrug-resistant or even extensively drug-resistant. Although the direct clinical impact of high-level aminoglycoside resistance resulting from production of 16S-RMTase is yet to be determined, ongoing spread of this mechanism will further limit treatment options for multidrug-resistant and extensively drug-resistant gram-negative infections.
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Affiliation(s)
- Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, S829 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA.
| | - Jun-Ichi Wachino
- Department of Bacteriology, Nagoya University School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
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Characterization of pHeBE7, an IncFII-type virulence-resistance plasmid carrying bla CTX-M-98b , bla TEM-1, and rmtB genes, detected in Escherichia coli from a chicken isolate in China. Plasmid 2017; 92:37-42. [DOI: 10.1016/j.plasmid.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/02/2017] [Accepted: 07/05/2017] [Indexed: 11/20/2022]
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IncFII Conjugative Plasmid-Mediated Transmission of blaNDM-1 Elements among Animal-Borne Escherichia coli Strains. Antimicrob Agents Chemother 2016; 61:AAC.02285-16. [PMID: 27821455 DOI: 10.1128/aac.02285-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 11/01/2016] [Indexed: 01/06/2023] Open
Abstract
This study aims to investigate the prevalence and transmission dynamics of the blaNDM-1 gene in animal Escherichia coli strains. Two IncFII blaNDM-1-encoding plasmids with only minor structural variation in the MDR region, pHNEC46-NDM and pHNEC55-NDM, were found to be responsible for the transmission of blaNDM-1 in these strains. The blaNDM-1 gene can be incorporated into plasmids and stably inherited in animal-borne E. coli strains that can be maintained in animal gut microflora even without carbapenem selection pressure.
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Shen P, Zhang Y, Li G, Jiang X. Characterization of the genetic environment of the blaKPC-2 gene among Klebsiella pneumoniae isolates from a Chinese Hospital. Braz J Infect Dis 2016; 20:384-8. [PMID: 27183358 PMCID: PMC9427567 DOI: 10.1016/j.bjid.2016.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/19/2016] [Accepted: 04/19/2016] [Indexed: 11/07/2022] Open
Abstract
Infection caused by carbapenem-resistant Klebsiella pneumoniae has become a major healthcare threat and KPC-2 enzyme is a dominant factor mediating carbapenems resistance in K. pneumoniae. This study was designed to determine the genetic environment of blaKPC-2, which prevailed in clinical K. pneumoniae isolates recovered in Huashan Hospital, Shanghai, China. Forty-two clinical isolates were included in this study by blaKPC-2 screening. After multilocus sequence typing and plasmid analyses of PCR-based replicon typing (PBRT), junction PCR, mapping PCR and crossing PCR assays, primer walking, and amplicon sequencing were used to analyze the genetic environment of the blaKPC-2 gene. ST423, ST65, ST977, and ST11 were all detected in KPC-2-producing K. pneumoniae. Two types of blaKPC-2-bearing genetic structure were found: Tn1721-blaKPC-2-Tn3 and Tn1721-blaKPC-2-ΔTn3-IS26; and were carried in IncX and IncFII plasmids, respectively. In conclusion, the genetic environment of the blaKPC-2 gene was diverse and Tn1721-blaKPC-2-ΔTn3-IS26 was dominant in clinical K. pneumoniae isolates in Huashan Hospital. This study sheds some light on the genetic environment and should foster further studies about the mechanism of the blaKPC-2 dissemination.
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Affiliation(s)
- Pinghua Shen
- Fudan University, Shanghai Medical College, Huashan Hospital, Department of Laboratory Medicine, Shanghai, China
| | - Ying Zhang
- Fudan University, Shanghai Medical College, Huashan Hospital, Department of Laboratory Medicine, Shanghai, China; Hospital of Fudan University, Department of Laboratory Medicine, Obstetrics and Gynecology, Shanghai, China
| | - Gang Li
- Fudan University, Shanghai Medical College, Huashan Hospital, Department of Laboratory Medicine, Shanghai, China; Fudan University, Shanghai Medical College, Jinshan Hospital, Department of Laboratory Medicine, Shanghai, China
| | - Xiaofei Jiang
- Fudan University, Shanghai Medical College, Huashan Hospital, Department of Laboratory Medicine, Shanghai, China.
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Abstract
Transposons of the Tn3 family form a widespread and remarkably homogeneous group of bacterial transposable elements in terms of transposition functions and an extremely versatile system for mediating gene reassortment and genomic plasticity owing to their modular organization. They have made major contributions to antimicrobial drug resistance dissemination or to endowing environmental bacteria with novel catabolic capacities. Here, we discuss the dynamic aspects inherent to the diversity and mosaic structure of Tn3-family transposons and their derivatives. We also provide an overview of current knowledge of the replicative transposition mechanism of the family, emphasizing most recent work aimed at understanding this mechanism at the biochemical level. Previous and recent data are put in perspective with those obtained for other transposable elements to build up a tentative model linking the activities of the Tn3-family transposase protein with the cellular process of DNA replication, suggesting new lines for further investigation. Finally, we summarize our current view of the DNA site-specific recombination mechanisms responsible for converting replicative transposition intermediates into final products, comparing paradigm systems using a serine recombinase with more recently characterized systems that use a tyrosine recombinase.
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Tada T, Miyoshi-Akiyama T, Shimada K, Nga TTT, Thu LTA, Son NT, Ohmagari N, Kirikae T. Dissemination of clonal complex 2 Acinetobacter baumannii strains co-producing carbapenemases and 16S rRNA methylase ArmA in Vietnam. BMC Infect Dis 2015; 15:433. [PMID: 26471294 PMCID: PMC4608321 DOI: 10.1186/s12879-015-1171-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 10/01/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii strains co-producing carbapenemase and 16S rRNA methylase are highly resistant to carbapenems and aminoglycosides. METHODS Ninety-three isolates of multidrug-resistant A. baumannii were obtained from an intensive care unit in a hospital in Vietnam. Antimicrobial susceptibility tests and whole genome sequencing were performed. Multilocus sequence typing and the presence of drug resistant genes were determined and a maximum-likelihood phylogenetic tree was constructed by SNP alignment of whole genome sequencing data. RESULTS The majority of isolates belonged to clonal complex 2 (ST2, ST570 and ST571), and carried carbapenemase encoding genes bla OXA-23 and bla OXA-66. Two isolates encoded carbapenemase genes bla NDM-1 and bla OXA-58 and the 16S rRNA methylase encoding gene armA and did not belong to clonal complex 2 (ST16). CONCLUSION A. baumannii isolates producing 16S rRNA methylase ArmA and belonging to clonal complex 2 are widespread, and isolates co-producing NDM-1 and ArmA are emerging, in medical settings in Vietnam.
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Affiliation(s)
- Tatsuya Tada
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan.
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan.
| | - Kayo Shimada
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan.
| | | | | | | | - Norio Ohmagari
- Disease Control and Prevention Center, Division of Infectious Diseases, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo, 162-8655, Japan.
| | - Teruo Kirikae
- Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan.
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Unprecedented Silver Resistance in Clinically Isolated Enterobacteriaceae: Major Implications for Burn and Wound Management. Antimicrob Agents Chemother 2015; 59:4734-41. [PMID: 26014954 DOI: 10.1128/aac.00026-15] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/22/2015] [Indexed: 11/20/2022] Open
Abstract
Increased utilization of inorganic silver as an adjunctive to many medical devices has raised concerns of emergent silver resistance in clinical bacteria. Although the molecular basis for silver resistance has been previously characterized, to date, significant phenotypic expression of these genes in clinical settings is yet to be observed. Here, we identified the first strains of clinical bacteria expressing silver resistance at a level that could significantly impact wound care and the use of silver-based dressings. Screening of 859 clinical isolates confirmed 31 harbored at least 1 silver resistance gene. Despite the presence of these genes, MIC testing revealed most of the bacteria displayed little or no increase in resistance to ionic silver (200 to 300 μM Ag(+)). However, 2 isolates (Klebsiella pneumonia and Enterobacter cloacae) were capable of robust growth at exceedingly high silver concentrations, with MIC values reaching 5,500 μM Ag(+). DNA sequencing of these two strains revealed the presence of genes homologous to known genetic determinants of heavy metal resistance. Darkening of the bacteria's pigment was observed after exposure to high silver concentrations. Scanning electron microscopy images showed the presence of silver nanoparticles embedded in the extracellular polymeric substance of both isolates. This finding suggested that the isolates may neutralize ionic silver via reduction to elemental silver. Antimicrobial testing revealed both organisms to be completely resistant to many commercially available silver-impregnated burn and wound dressings. Taken together, these findings provide the first evidence of clinical bacteria capable of expressing silver resistance at levels that could significantly impact wound management.
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Sun F, Yin Z, Feng J, Qiu Y, Zhang D, Luo W, Yang H, Yang W, Wang J, Chen W, Xia P, Zhou D. Production of plasmid-encoding NDM-1 in clinical Raoultella ornithinolytica and Leclercia adecarboxylata from China. Front Microbiol 2015; 6:458. [PMID: 26052314 PMCID: PMC4439573 DOI: 10.3389/fmicb.2015.00458] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/27/2015] [Indexed: 12/17/2022] Open
Abstract
Raoultella ornithinolytica YNKP001 and Leclercia adecarboxylata P10164, which harbor conjugative plasmids pYNKP001-NDM and pP10164-NDM, respectively, were isolated from two different Chinese patients, and their complete nucleotide sequences were determined. Production of NDM-1 enzyme by these plasmids accounts for the carbapenem resistance of these two strains. This is the first report of bla NDM in L. adecarboxylata and third report of this gene in R. ornithinolytica. pYNKP001-NDM is very similar to the IncN2 NDM-1-encoding plasmids pTR3, pNDM-ECS01, and p271A, whereas pP10164-NDM is similar to the IncFIIY bla NDM-1-carrying plasmid pKOX_NDM1. The bla NDM-1 genes of pYNKP001-NDM and pP10164-NDM are embedded in Tn125-like elements, which represent two distinct truncated versions of the NDM-1-encoding Tn125 prototype observed in pNDM-BJ01. Flanking of these two Tn125-like elements by miniature inverted repeat element (MITE) or its remnant indicates that MITE facilitates transposition and mobilization of bla NDM-1 gene contexts.
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Affiliation(s)
- Fengjun Sun
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University Chongqing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China ; Laboratory Animal Center, Academy of Military Medical Sciences Beijing, China
| | - Yefeng Qiu
- Laboratory Animal Center, Academy of Military Medical Sciences Beijing, China
| | - Defu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Wenbo Luo
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University Chongqing, China ; State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Jie Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, The Third Military Medical University Chongqing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
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Chen Z, Li H, Feng J, Li Y, Chen X, Guo X, Chen W, Wang L, Lin L, Yang H, Yang W, Wang J, Zhou D, Liu C, Yin Z. NDM-1 encoded by a pNDM-BJ01-like plasmid p3SP-NDM in clinical Enterobacter aerogenes. Front Microbiol 2015; 6:294. [PMID: 25926823 PMCID: PMC4396501 DOI: 10.3389/fmicb.2015.00294] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/25/2015] [Indexed: 11/13/2022] Open
Abstract
A carbapenem-nonsusceptible Enterobacter aerogenes strain named 3-SP was isolated from a human case of pneumonia in a Chinese teaching hospital. NDM-1 carbapenemase is produced by a pNDM-BJ01-like conjugative plasmid designated p3SP-NDM to account for carbapenem resistance of 3-SP. p3SP-NDM was fully sequenced and compared with all publically available pNDM-BJ01-like plasmids. The genetic differences between p3SP-NDM and pNDM-BJ01 include only 18 single nucleotide polymorphisms, a 1 bp deletion and a 706 bp deletion. p3SP-NDM and pNDM-BJ01 harbor an identical Tn125 element organized as ISAba125, blaNDM−1, bleMBL, ΔtrpF, dsbC, cutA, ΔgroES, groEL, ISCR27, and ISAba125. The blaNDM−1 surrounding regions in these pNDM-BJ01-like plasmids have a conserved linear organization ISAba14-aphA6-Tn125-unknown IS, with considerable genetic differences identified within or immediately downstream of Tn125. All reported pNDM-BJ01-like plasmids are exclusively found in Acinetobacter, whereas this is the first report of identification of a pNDM-BJ01-like plasmid in Enterobacteriaceae.
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Affiliation(s)
- Zhenhong Chen
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Hongxia Li
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Jiao Feng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Yuxue Li
- The First Hospital of Shijiazhuang City Shijiazhuang, China
| | - Xin Chen
- Zhongshan School of Medicine, Sun Yat-Sen University Guangzhou, China
| | - Xuemin Guo
- Zhongshan School of Medicine, Sun Yat-Sen University Guangzhou, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Li Wang
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Lei Lin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Jie Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
| | - Changting Liu
- Nanlou Respiratory Diseases Department, Chinese People's Liberation Army General Hospital Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology Beijing, China
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Löhr IH, Hülter N, Bernhoff E, Johnsen PJ, Sundsfjord A, Naseer U. Persistence of a pKPN3-like CTX-M-15-encoding IncFIIK plasmid in a Klebsiella pneumonia ST17 host during two years of intestinal colonization. PLoS One 2015; 10:e0116516. [PMID: 25738592 PMCID: PMC4349654 DOI: 10.1371/journal.pone.0116516] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/10/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES To characterize the CTX-M-15-encoding plasmid in a Klebsiella pneumoniae ST17 strain, responsible for an outbreak at a Norwegian neonatal intensive care unit and subsequent colonization of affected children for up to two years. To identify plasmid-mediated features relevant for the outbreak dynamics, and to investigate the plasmids capability of horizontal transfer, its segregational stability and plasmid-mediated fitness costs. METHODS Plasmid profiling was performed by S1-nuclease PFGE, PCR-based replicon typing and Southern blot-hybridization. The complete sequence of the CTX-M-15-encoding plasmid was obtained by 454 sequencing. Plasmid self-transferability was investigated by broth- and filter mating, segregational stability was explored by serial passage, and plasmid-conferred fitness costs were examined in pairwise head-to-head competitions and by growth rate comparisons. RESULTS CTX-M-15 was encoded by a ~180 kb IncFIIK plasmid in K. pneumoniae ST17. S1-nuclease PFGE profiles of the first and the last CTX-M-15-producing K. pneumoniae isolates, recovered from the four children colonized the longest, suggested that the plasmid was stably maintained during intestinal carriage of up to two years. The DNA sequence of the pKPN3-like plasmid, pKp848CTX, uncovered a Tn3-like antibiotic resistance region and multiple heavy metal- and thermoresistance determinants. Plasmid pKp848CTX could not be transferred to Escherichia coli in vitro and we found no evidence to support horizontal plasmid transfer in vivo. Segregational plasmid loss ranging from 0.83% to 17.5% was demonstrated in evolved populations in vitro, but only minor fitness costs were associated with plasmid-carriage. CONCLUSIONS Plasmid pKp848CTX encodes phenotypic traits, which may have had an impact on the fitness and survival of the K. pneumoniae ST17 strain in the outbreak setting. The antibiotic resistance plasmid pKp848CTX was stably maintained during two years of intestinal colonization, conferring negligible fitness cost to its host, and thus seem well adapted to its K. pneumoniae host.
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Affiliation(s)
- Iren Høyland Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- * E-mail:
| | - Nils Hülter
- Department of Pharmacy, UiT the Arctic University of Norway, Tromsø, Norway
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Pål Jarle Johnsen
- Department of Pharmacy, UiT the Arctic University of Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, UiT the Arctic University of Norway, Tromsø, Norway
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Umaer Naseer
- Department of Medical Biology, UiT the Arctic University of Norway, Tromsø, Norway
- Department of Food-borne Infections, Norwegian Institute of Public Health, Oslo, Norway
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Molecular characterization of blaNDM-5 carried on an IncFII plasmid in an Escherichia coli isolate from a nontraveler patient in Spain. Antimicrob Agents Chemother 2014; 59:659-62. [PMID: 25313215 DOI: 10.1128/aac.04040-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A carbapenem-resistant Escherichia coli isolate (sequence type 448 [ST448]) was recovered from a urine culture of a female patient with no recent record of traveling. PCR screening identified the presence of bla(NDM-5), bla(TEM-1), bla(OXA-1), bla(CMY-42), and rmtB. bla(NDM-5) was carried in a conjugative IncFII-type plasmid (90 kb) together with bla(TEM-1) and rmtB. The genetic environment of bla(NDM-5) showed a structure similar to those of pMC-NDM and pGUE-NDM, identified in Poland and France in E. coli of African and Indian origin, respectively.
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Rodrigues C, Machado E, Ramos H, Peixe L, Novais Â. Expansion of ESBL-producing Klebsiella pneumoniae in hospitalized patients: a successful story of international clones (ST15, ST147, ST336) and epidemic plasmids (IncR, IncFIIK). Int J Med Microbiol 2014; 304:1100-8. [PMID: 25190354 DOI: 10.1016/j.ijmm.2014.08.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/31/2014] [Accepted: 08/04/2014] [Indexed: 10/24/2022] Open
Abstract
The aim of this study was to characterize by a multi-level approach extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae isolates other than E. coli from Portuguese hospitals. Eighty-eight ESBL-producing clinical isolates (69 Klebsiella pneumoniae, 13 Enterobacter cloacae complex, 3 Klebsiella oxytoca, 1 Enterobacter asburiae, 1 Proteus mirabilis and 1 Serratia marcescens) recovered from hospitals located in the North (A) or Centre (B, C) regions during two time periods (2006-7 and 2010) were analyzed. Standard methods were used for bacterial identification, antibiotic susceptibility testing, ESBL characterization, clonal (PFGE, MLST) and plasmid (S1-PFGE, I-CeuI-PFGE, replicon typing, hybridization) analysis. Isolates produced mostly CTX-M-15 (47%) or SHV-12 (30%), and less frequently other SHV- (15%; SHV-2, -5, -28, -55, -106) or TEM- (9%; TEM-10, -24, -199)-types, with marked local and temporal variations. The increase of CTX-M-15 and diverse SHV ESBL-types observed in Hospital A was associated with the amplification of multidrug-resistant (MDR) K. pneumoniae epidemic clones (ST15, ST147, ST336). SHV-12 and TEM-type ESBLs were mostly identified in diverse isolates of different Enterobacteriaceae species in Hospitals B and C in 2006-7. Particular plasmid types were linked to blaCTX-M-15 (IncR or non-typeable plasmids), blaSHV-12 (IncR or IncHI2), blaSHV-28/-55/-106 (IncFIIK1 or IncFIIK5), blaTEM-10 (IncL/M) or blaTEM-24 (IncA/C), mostly in epidemic clones. In our country, the amplification of CTX-M-15 and diverse SHV-type ESBL among non-E. coli Enterobacteriaceae is linked to international MDR K. pneumoniae clones (ST15, ST147, ST336) and plasmid types (IncR, IncFIIK). Furthermore, we highlight the potential of IncFIIK plasmids (here firstly associated with blaSHV-2/-28/-55/-106) to disseminate as antibiotic resistance plasmids.
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Affiliation(s)
- Carla Rodrigues
- REQUIMTE, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; CEBIMED/FP-ENAS, Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, 4249-004 Porto, Portugal
| | - Elisabete Machado
- REQUIMTE, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal; CEBIMED/FP-ENAS, Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, 4249-004 Porto, Portugal
| | - Helena Ramos
- Centro Hospitalar do Porto - Hospital Geral de Santo António, 4099-001 Porto, Portugal
| | - Luísa Peixe
- REQUIMTE, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ângela Novais
- REQUIMTE, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal.
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