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Zhang Z, Kuang D, Xu X, Zhan Z, Ren H, Shi C. Dissemination of IncC plasmids in Salmonella enterica serovar Thompson recovered from seafood and human diarrheic patients in China. Int J Food Microbiol 2024; 417:110708. [PMID: 38653121 DOI: 10.1016/j.ijfoodmicro.2024.110708] [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: 12/18/2023] [Revised: 03/26/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024]
Abstract
Salmonella Thompson is a prevalent foodborne pathogen and a major threat to food safety and public health. This study aims to reveal the dissemination mechanism of S. Thompson with co-resistance to ceftriaxone and ciprofloxacin. In this study, 181 S. Thompson isolates were obtained from a retrospective screening on 2118 serotyped Salmonella isolates from foods and patients, which were disseminated in 12 of 16 districts in Shanghai, China. A total of 10 (5.5 %) S. Thompson isolates exhibited resistance to ceftriaxone (MIC ranging from 8 to 32 μg/mL) and ciprofloxacin (MIC ranging from 2 to 8 μg/mL). The AmpC β-lactamase gene blaCMY-2 and plasmid-mediated quinolone resistance (PMQR) genes of qnrS and qepA were identified in the 9 isolates. Conjugation results showed that the co-transfer of blaCMY-2, qnrS, and qepA occurred on the IncC plasmids with sizes of ∼150 (n = 8) or ∼138 (n = 1) kbp. Three typical modules of ISEcp1-blaCMY-2-blc-sugE, IS26-IS15DIV-qnrS-ISKpn19, and ISCR3-qepA-intl1 were identified in an ST3 IncC plasmid pSH11G0791. Phylogenetic analysis indicated that IncC plasmids evolved into Lineages 1, 2, and 3. IncC plasmids from China including pSH11G0791 in this study fell into Lineage 1 with those from the USA, suggesting their close genotype relationship. In conclusion, to our knowledge, it is the first report of the co-existence of blaCMY-2, qnrS, and qepA in IncC plasmids, and the conjugational transfer contributed to their dissemination in S. Thompson. These findings underline further challenges for the prevention and treatment of Enterobacteriaceae infections posed by IncC plasmids bearing blaCMY-2, qnrS, and qepA.
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Affiliation(s)
- Zengfeng Zhang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dai Kuang
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; National Health Commission (NHC) Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, China
| | - Xuebin Xu
- Laboratory of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200050, China
| | - Zeqiang Zhan
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Ren
- Xianyang Center for Food and Drug Control, Shaanxi, China
| | - Chunlei Shi
- MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
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Tomeh R, Nemati A, Hashemi Tabar G, Tozzoli R, Badouei MA. Antimicrobial resistance, β-lactamase genotypes, and plasmid replicon types of Shiga toxin-producing Escherichia coli isolated from different animal hosts. J Appl Microbiol 2024; 135:lxae059. [PMID: 38467395 DOI: 10.1093/jambio/lxae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/11/2024] [Accepted: 03/10/2024] [Indexed: 03/13/2024]
Abstract
AIMS The primary objective of this study was to analyze antimicrobial resistance (AMR), with a particular focus on β-lactamase genotypes and plasmid replicon types of Shiga toxin-producing Escherichia coli (STEC) strains originating from various animal hosts. METHODS AND RESULTS A total of 84 STEC strains were isolated from cattle (n = 32), sheep/goats (n = 26), pigeons (n = 20), and wild animals (n = 6) between 2010 and 2018 in various regions of Iran. The Kirby-Bauer susceptibility test and multiple polymerase chain reaction (PCR) panels were employed to elucidate the correlation between AMR and plasmid replicon types in STEC isolates. The predominant replicon types were IncFIC and IncFIB in cattle (46.8%), IncFIC in sheep/goats (46.1%), IncA/C in pigeons (90%), and IncP in wild animals (50%). STEC of serogroups O113, O26, and O111 harbored the IncFIB (100%), IncI1 (80%), and IncFIC + IncA/C (100%) plasmids, respectively. A remarkable AMR association was found between ciprofloxacin (100%), neomycin (68.7%), and tetracycline (61.7%) resistance with IncFIC; amoxicillin + clavulanic acid (88.8%) and tetracycline (61.7%) with IncA/C; ciprofloxacin (100%) with IncFIB; fosfomycin (85.7%) and sulfamethoxazole + trimethoprim (80%) with IncI1. IncI1 appeared in 83.3%, 50%, and 100% of the isolates harboring blaCTX-M, blaTEM, and blaOXA β-lactamase genes, respectively. CONCLUSIONS The emergence of O26/IncI1/blaCTX-M STEC in cattle farms poses a potential risk to public health.
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Affiliation(s)
- Rwida Tomeh
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Ali Nemati
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Gholamreza Hashemi Tabar
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Rosangela Tozzoli
- European Union Reference Laboratory for Escherichia coli, Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Mahdi Askari Badouei
- Department of Pathobiology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
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Piccirilli A, Di Marcantonio S, Costantino V, Simonetti O, Busetti M, Luzzati R, Principe L, Di Domenico M, Rinaldi A, Cammà C, Perilli M. Identification of IncA Plasmid, Harboring blaVIM-1 Gene, in S. enterica Goldcoast ST358 and C. freundii ST62 Isolated in a Hospitalized Patient. Antibiotics (Basel) 2023; 12:1659. [PMID: 38136693 PMCID: PMC10741216 DOI: 10.3390/antibiotics12121659] [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: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In the present study, we analyzed the genome of two S. enterica strains TS1 and TS2 from stool and blood cultures, respectively, and one strain of C. freundii TS3, isolated from a single hospitalized patient with acute myeloid leukemia. The S. enterica Goldcoast ST358 (O:8 (C2-C3) serogroup), sequenced by the MiSeq Illumina system, showed the presence of β-lactamase genes (blaVIM-1, blaSHV-12 and blaOXA-10), aadA1, ant(2″)-Ia, aac(6')-Iaa, aac(6')-Ib3, aac(6')-Ib-cr, qnrVC6, parC(T57S), and several incompatibility plasmids. A wide variety of insertion sequences (ISs) and transposon elements were identified. In C. freundii TS3, these were the blaVIM-1, blaCMY-150, and blaSHV-12, aadA1, aac(6')-Ib3, aac(6')-Ib-cr, mph(A), sul1, dfrA14, ARR-2, qnrVC6, and qnrB38. IncA plasmid isolated from E.coli/K12 transconjugant and C. freundii exhibited a sequence identity >99.9%. The transfer of IncA plasmid was evaluated by conjugation experiments.
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Affiliation(s)
- Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
| | - Sascia Di Marcantonio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
| | - Venera Costantino
- Microbiology Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (V.C.); (M.B.)
| | - Omar Simonetti
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (O.S.); (R.L.)
| | - Marina Busetti
- Microbiology Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (V.C.); (M.B.)
| | - Roberto Luzzati
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (O.S.); (R.L.)
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, “S. Giovanni di Dio” Hospital, 88900 Crotone, Italy;
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Antonio Rinaldi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
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Sheng H, Wu S, Xue Y, Zhao W, Caplan AB, Hovde CJ, Minnich SA. Engineering conjugative CRISPR-Cas9 systems for the targeted control of enteric pathogens and antibiotic resistance. PLoS One 2023; 18:e0291520. [PMID: 37699034 PMCID: PMC10497133 DOI: 10.1371/journal.pone.0291520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Pathogenic Escherichia coli and Salmonella enterica pose serious public health threats due to their ability to cause severe gastroenteritis and life-threatening sequela, particularly in young children. Moreover, the emergence and dissemination of antibiotic resistance in these bacteria have complicated control of infections. Alternative strategies that effectively target these enteric pathogens and negate or reduce the need of antibiotics are urgently needed. Such an alternative is the CRISPR-Cas9 system because it can generate sequence-specific lethal double stranded DNA breaks. In this study, two self-transmissible broad host range conjugative plasmids, pRK24 and pBP136, were engineered to deliver multiplexed CRSIPR-Cas9 systems that specifically target Enterohemorrhagic and Enteropathogenic strains of E. coli (EHEC and EPEC), S. enterica, and blaCMY-2 antibiotic resistance plasmids. Using in vitro mating assays, we show that the conjugative delivery of pRK24-CRISPR-Cas9 carrying guide RNAs to the EPEC/EHEC eae (intimin) gene can selectively kill enterohemorrhagic E. coli O157 eae+ cells (3 log kill at 6 h) but does not kill the isogenic Δeae mutant (P<0.001). Similar results were also obtained with a pBP136 derivative, pTF16, carrying multiplexed guide RNAs targeting E. coli eae and the S. enterica ssaN gene coding for the type III secretion ATPase. Another pBP136 derivative, TF18, carries guide RNAs targeting S. enterica ssaN and the antibiotic resistance gene, blaCMY-2, carried on the multi-drug resistant pAR06302. Introduction of pTF18 into bacteria harboring pAR06302 showed plasmids were cured at an efficiency of 53% (P<0.05). Using a murine neonate EPEC infection model, pTF16 was delivered by a murine derived E. coli strain to EPEC infected mice and showed significant reductions of intestinal EPEC (P<0.05). These results suggest that establishing conjugative CRISPR-Cas9 antimicrobials in the intestinal microbiome may provide protection from enteric pathogens and reduce antibiotic resistance without disrupting the normal microbiota.
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Affiliation(s)
- Haiqing Sheng
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Sarah Wu
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, Idaho, United States of America
| | - Yansong Xue
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Wei Zhao
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Allan B. Caplan
- Department of Plant Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Carolyn J. Hovde
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
| | - Scott A. Minnich
- Animal, Veterinary and Food Science, University of Idaho, Moscow, Idaho, United States of America
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Algarni S, Ricke SC, Foley SL, Han J. The Dynamics of the Antimicrobial Resistance Mobilome of Salmonella enterica and Related Enteric Bacteria. Front Microbiol 2022; 13:859854. [PMID: 35432284 PMCID: PMC9008345 DOI: 10.3389/fmicb.2022.859854] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
The foodborne pathogen Salmonella enterica is considered a global public health risk. Salmonella enterica isolates can develop resistance to several antimicrobial drugs due to the rapid spread of antimicrobial resistance (AMR) genes, thus increasing the impact on hospitalization and treatment costs, as well as the healthcare system. Mobile genetic elements (MGEs) play key roles in the dissemination of AMR genes in S. enterica isolates. Multiple phenotypic and molecular techniques have been utilized to better understand the biology and epidemiology of plasmids including DNA sequence analyses, whole genome sequencing (WGS), incompatibility typing, and conjugation studies of plasmids from S. enterica and related species. Focusing on the dynamics of AMR genes is critical for identification and verification of emerging multidrug resistance. The aim of this review is to highlight the updated knowledge of AMR genes in the mobilome of Salmonella and related enteric bacteria. The mobilome is a term defined as all MGEs, including plasmids, transposons, insertion sequences (ISs), gene cassettes, integrons, and resistance islands, that contribute to the potential spread of genes in an organism, including S. enterica isolates and related species, which are the focus of this review.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Steven L. Foley
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- Cellular and Molecular Biology Graduate Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, FDA National Center for Toxicological Research, Jefferson, AR, United States
- *Correspondence: Jing Han,
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6
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Liu J, Lin X, Soteyome T, Ye Y, Chen D, Yang L, Xu Z. A strategy design based on antibiotic‑resistance and plasmid replicons genes of clinical Escherichia coli strains. Bioengineered 2022; 13:7500-7514. [PMID: 35259054 PMCID: PMC9208507 DOI: 10.1080/21655979.2022.2047543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Since antimicrobial resistance, especially β-lactam resistance genes were common in clinical Escherichia coli strains, this study had designed and developed multiplex amplification platform for rapid and accurate detection of such resistance genes in 542 clinical E. coli isolates. The obtained specimens were subjected to bacteriological examination, antimicrobial susceptibility testing, and detection of β-lactamase genes and plasmid replicons. The major virulence genes were detected by 7 groups of multiplex PCR and eight groups of multiplex PCR were designed to detect 8 different plasmid replicons including parA-parB, iteron, repA, and RNAI. It was found that most MDR isolates were co-resistant to penicillins (AMP) and fluoroquindones (LVX, CIP) and distribution of LVX and CIP resistance was significantly higher among female than male gender. RNAI (AY234375) showed the highest detection rate, followed by the iteron (J01724) and repA (M26308), indicating the relatively higher carriage rate of corresponding plasmids. BlaOXA acquired the highest carriage rate, followed by group 2 blaCTX-M and blaSHV-1, indicating their prevalence among clinical E. coli. Among the β-lactamase genes, blaOXA acquired the highest carriage rate, followed by group 2 blaCTX-M and blaSHV-1, indicating their prevalence among clinical E. coli. The RNAI (AY234375) showed the highest detection rate, followed by the iteron (J01724) and repA (M26308), indicating the relatively higher carriage rate of the corresponding plasmids by clinical E. coli isolates. It is shown that the developed multiplex amplification methodology is applicable to AMR detection, and such identification of plasmid replicons and β-lactamase genes may aid in the understanding of clinical E. coli isolate epidemiology.
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Affiliation(s)
- Junyan Liu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, Guangdong, China.,Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA.,College of Light Industry and Food Sciences, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Innovation Research Institute of Modern Agricultural Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.,Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Xin Lin
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, Guangdong, China
| | - Thanapop Soteyome
- Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand
| | - Yanrui Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Dingqiang Chen
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou University, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, Guangdong, China.,Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, USA.,Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand.,Research Institute for Food Nutrition and Human Health, Guangzhou, Guangdong, China
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7
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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8
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Beukers AG, John MA, Davis R, Lee A, van Hal SJ. Hospital outbreak of New Delhi metallo-β-lactamase type-1 (NDM-1) in Salmonella enterica with inter-species plasmid transmission. J Hosp Infect 2021; 117:23-27. [PMID: 34428503 DOI: 10.1016/j.jhin.2021.08.014] [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: 05/14/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
New Delhi metallo-β-lactamase (NDM) gene confers high-level resistance to an array of β-lactams including carbapenems. Short- and long-read sequencing was used to investigate outbreaks of NDM-positive Enterobacterales including a potential horizontal gene transfer (HGT) event of an NDM-positive plasmid between Salmonella enterica and Klebsiella pneumoniae. Genomic analysis demonstrated a high degree of similarity between NDM-carrying plasmids from patient 1 in K. pneumoniae and patient 2 with S. enterica, K. pneumoniae and Klebsiella oxytoca, confirming an inter-species HGT event. The utility of whole-genome sequencing was demonstrated for in-hospital outbreaks, previously undetected using traditional infection-control surveillance.
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Affiliation(s)
- A G Beukers
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
| | - M A John
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - R Davis
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - A Lee
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NSW, Australia
| | - S J van Hal
- Department of Microbiology and Infectious Diseases, Royal Prince Alfred Hospital, Sydney, NSW, Australia; University of Sydney, Sydney, NSW, Australia
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9
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Yu Y, Andrey DO, Yang RS, Sands K, Tansawai U, Li M, Portal E, Gales AC, Niumsup PR, Sun J, Liao X, Liu YH, Walsh TR. A Klebsiella pneumoniae strain co-harbouring mcr-1 and mcr-3 from a human in Thailand. J Antimicrob Chemother 2021; 75:2372-2374. [PMID: 32294160 DOI: 10.1093/jac/dkaa133] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Yang Yu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Diego O Andrey
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK.,Service of Infectious Diseases, Geneva University Hospitals and Faculty of Medicine, 1211 Geneva, Switzerland
| | - Run-Shi Yang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Uttapoln Tansawai
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK.,Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Mei Li
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Edward Portal
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
| | - Ana C Gales
- Federal University of Sao Paulo - UNIFESP, Infectious Diseases Department, Escola Paulista de Medicina, São Paulo, Brazil
| | - Pannika R Niumsup
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xiaoping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, Cardiff University, Cardiff CF14 4XN, UK
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10
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Abstract
A putative type II toxin-antitoxin (TA) module almost exclusively associated with conjugative IncC plasmids is homologous to the higBA family of TA systems found in chromosomes and plasmids of several species of bacteria. Despite the clinical significance and strong association with high-profile antimicrobial resistance (AMR) genes, the TA system of IncC plasmids remains largely uncharacterized. In this study, we present evidence that IncC plasmids encode a bona fide HigB-like toxin that strongly inhibits bacterial growth and results in cell elongation in Escherichia coli. IncC HigB toxin acts as a ribosome-dependent endoribonuclease that significantly reduces the transcript abundance of a subset of adenine-rich mRNA transcripts. A glycine residue at amino acid position 64 is highly conserved in HigB toxins from different bacterial species, and its replacement with valine (G64V) abolishes the toxicity and the mRNA cleavage activity of the IncC HigB toxin. The IncC plasmid higBA TA system functions as an effective addiction module that maintains plasmid stability in an antibiotic-free environment. This higBA addiction module is the only TA system that we identified in the IncC backbone and appears essential for the stable maintenance of IncC plasmids. We also observed that exposure to subinhibitory concentrations of ciprofloxacin, a DNA-damaging fluoroquinolone antibiotic, results in elevated higBA expression, which raises interesting questions about its regulatory mechanisms. A better understanding of this higBA-type TA module potentially allows for its subversion as part of an AMR eradication strategy. IMPORTANCE Toxin-antitoxin (TA) systems play vital roles in maintaining plasmids in bacteria. Plasmids with incompatibility group C are large plasmids that disseminate via conjugation and carry high-profile antibiotic resistance genes. We present experimental evidence that IncC plasmids carry a TA system that functions as an effective addiction module and maintains plasmid stability in an antibiotic-free environment. The toxin of IncC plasmids acts as an endoribonuclease that targets a subset of mRNA transcripts. Overexpressing the IncC toxin gene strongly inhibits bacterial growth and results in cell elongation in Escherichia coli hosts. We also identify a conserved amino acid residue in the toxin protein that is essential for its toxicity and show that the expression of this TA system is activated by a DNA-damaging antibiotic, ciprofloxacin. This mobile TA system may contribute to managing bacterial stress associated with DNA-damaging antibiotics.
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11
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Huang WC, Wong MY, Wang SH, Hashimoto M, Lin MH, Lee MF, Wu JJ, Wang MC, Lin WH, Jeng SL, Wang JL, Chen YL, Teng CH. The Ferric Citrate Uptake System Encoded in a Novel bla CTX-M-3- and bla TEM-1-Harboring Conjugative Plasmid Contributes to the Virulence of Escherichia coli. Front Microbiol 2021; 12:667782. [PMID: 34122381 PMCID: PMC8187952 DOI: 10.3389/fmicb.2021.667782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 04/23/2021] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli is one major cause of bacterial infections and can horizontally acquire antimicrobial resistance and virulence genes through conjugation. Because conjugative plasmids can rapidly spread among bacteria of different species, the plasmids carrying both antimicrobial resistance and virulence genes may pose a significant threat to public health. Therefore, the identification and characterization of these plasmids may facilitate a better understanding of E. coli pathogenesis and the development of new strategies against E. coli infections. Because iron uptake ability is a potential virulence trait of bacteria, we screened for E. coli conjugative plasmids able to confer both iron uptake ability and ampicillin resistance. The plasmid pEC41, which was derived from the bacteremia clinical isolate EC41, was identified. EC41, which carried the fimH27 allele, belonged to sequence type (ST) 405 and phylogroup D. According to the sequencing analyses, pEC41 was 86 kb in size, and its backbone structure was almost identical to that of another highly conjugative plasmid, pCTX-M3, in which the extended-spectrum β-lactamase gene blaCTX–M–3 was originally identified. pEC41 carried blaCTX–M–3 and blaTEM–1. The ferric citrate uptake (fec) system was identified in pEC41 and was responsible for conferring iron uptake ability. The fec system contributes to the pathogenesis of EC41 in systemic infections but not in urinary tract infections (UTIs). However, this system promoted competitive fitness of a cystitis-associated clinical isolate to colonize urinary tracts. Additionally, the distribution of the fec system was related to E. coli isolates associated with human bacteremia and UTIs. In summary, the present study identified a novel conjugative plasmid, pEC41, which conferred both antimicrobial resistance and an extra iron uptake ability to E. coli. The iron uptake ability was encoded in the fec system and contributed to E. coli pathogenesis. This study is the first to show that the fec system is a virulence factor in E. coli.
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Affiliation(s)
- Wen-Chun Huang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Min-Yi Wong
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ssu-Han Wang
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Masayuki Hashimoto
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Meng-He Lin
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Mei-Feng Lee
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Jiunn-Jong Wu
- Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shuen-Lin Jeng
- Department of Statistics, Institute of Data Science, Center for Innovative FinTech Business Models, National Cheng Kung University, Tainan, Taiwan
| | - Jiun-Ling Wang
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan.,Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Lei Chen
- Department of Biotechnology, National Kaohsiung Normal University, Kaohsiung, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.,Center of Allergy and Clinical Immunology Research (ACIR), National Cheng Kung University, Tainan, Taiwan
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12
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Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance. Microbiol Mol Biol Rev 2021; 85:85/2/e00031-20. [PMID: 33910982 DOI: 10.1128/mmbr.00031-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
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13
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Johnson TJ. Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9:eESP-0013-2020. [PMID: 33634776 PMCID: PMC11163845 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/12/2021] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
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Affiliation(s)
- Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108
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14
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He DD, Cui MM, Zhang TL, Hu GZ, Liu JH, Pan YS. Characterization of bla CMY-2-carrying IncC and rmtB-carrying IncI1/ST136 plasmids in an avian Escherichia coli ST224 strain. Plasmid 2021; 114:102555. [PMID: 33472047 DOI: 10.1016/j.plasmid.2021.102555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022]
Abstract
To analyze characteristics and underlying evolutionary processes of IncC and IncI1 plasmids in a multidrug-resistant avian E. coli strain, antibiotic susceptibility testing, PCR, conjugation assays, and next-generation sequencing were performed. The type 1 IncC plasmid pEC009.1 harbored three antimicrobial resistance regions including ISEcp1-blaCMY-2-blc-sugE, ARI-B resistance island, and ARI-A island that was a mosaic multidrug resistance region (MRR) comprised of a class 1 integron with cassette array |aac(6')-II(aacA7)|qacE∆1|sul1|, IS26-mphR(A)-mrx-mph(A)-IS26, IS26-fosA3-IS26, and mercury resistance cluster merRTPABDE. It is the first report of three different size circular forms derived from IS26-mphR(A)-mrx-mph(A)-IS26-fosA3-IS26 in ARI-A of type 1 IncC plasmid. In IncI1/ST136 pEC009.2, the truncated transposon Tn1722 carrying blaTEM-1b, rmtB, aac(3)-IId(aacC2d), and a class 1 integron with cassette array |dfrA12|orfF|aadA2|, inserted into the plasmid backbone generating 5-bp direct repeats (DRs, TATAA) at the boundaries of the region, which was highly similar to that of other IncI1 plasmids, and differed by the arrangements of resistance determinants. Comparison among two epidemic plasmid lineages showed complex MRRs respectively located in the specific position in type 1 IncC and IncI1/ST136 plasmids with conserved backbones, and these have evolved via multiple events involved in mobile elements-mediated loss and gain of resistance genes and accessory genes. Strains harboring these plasmids may serve as a reservoir for antibiotic resistance genes, thereby contributing to the rapid spread of resistance genes and posing a public health threat.
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Affiliation(s)
- Dan-Dan He
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Meng-Mei Cui
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Teng-Li Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Gong-Zheng Hu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Jian-Hua Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yu-Shan Pan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
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15
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Kongsanan P, Angkititrakul S, Kiddee A, Tribuddharat C. Spread of Antimicrobial-Resistant Salmonella from Poultry to Humans in Thailand. Jpn J Infect Dis 2020; 74:220-227. [PMID: 33250489 DOI: 10.7883/yoken.jjid.2020.548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Food animal production is important for every country. Several antibiotic agents are used in poultry farming to reduce the economic losses arising from mostly untested infectious diseases. This continued study was performed to determine the prevalence of antibiotic-resistant Salmonella in broiler chickens, poultry farmers, and Salmonella bacteremia patients. A total of 121 Salmonella isolates were collected from the Thai provinces of Khon Kaen (65 isolates), Ratchaburi (43 isolates), and Phayao (13 isolates). Salmonella from chicken showed a high rate of resistance to nalidixic acid and tetracycline. Sixty-four percent of Salmonella isolates carried class 1 integrons (intI1 gene-positive). Among the 121 Salmonella isolates, there were 15 serotypes, with S. Enteritidis being the most common. A clonal relationship between the chicken and human isolates was demonstrated by 3 molecular typing methods: enterobacterial repetitive intergenic consensus polymerase chain reaction; pulsed-field gel electrophoresis; and high-throughput multilocus sequence typing. A spread of the sequence type 11 clone was found between chickens and humans. This study revealed a large-scale Salmonella outbreak in Thailand, a link between resistant bacteria from poultry farms and vertical transmission through the food chain, and horizontal transmission of resistance genes. These results can be used for future surveillance and monitoring.
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Affiliation(s)
- Paweena Kongsanan
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Thailand.,Medical Technology and Reference Laboratory for Infectious Diseases, Bamrasnaradura Infectious Diseases Institute, Ministry of Public Health, Thailand
| | - Sunpetch Angkititrakul
- Research Group for Animal Health Technology, Faculty of Veterinary Medicine, Khon Kaen University, Thailand
| | - Anong Kiddee
- Department of Microbiology and Parasitology, School of Medical Sciences, University of Phayao, Thailand
| | - Chanwit Tribuddharat
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Thailand
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16
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Vincent AT, Hosseini N, Charette SJ. The Aeromonas salmonicida plasmidome: a model of modular evolution and genetic diversity. Ann N Y Acad Sci 2020; 1488:16-32. [PMID: 33040386 DOI: 10.1111/nyas.14503] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/30/2020] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
High-throughput genomic sequencing has helped to reveal the plasmidome of Aeromonas salmonicida. This literature review provides an overview of A. salmonicida's rich plasmidome by presenting all the plasmids identified so far, addressing their biological importance and the functional links between them. The plasmids of A. salmonicida, especially those bearing antibiotic resistance genes, can provide clues about interactions of this species with other pathogens (animals and humans), as is the case for pRAS3-3432 and Chlamydia suis or pSN254b and Salmonella enterica. In addition to antibiotic resistance, plasmids play an important role in the virulence of A. salmonicida, particularly for the subspecies salmonicida and the plasmid pAsa5, which carries genes for the type-three secretion system, a virulence factor essential for the bacterium. The A. salmonicida plasmidome also has many cryptic plasmids with no known biological function, but which can be used for the acquisition of new genetic elements. Striking examples are pAsa7 and pAsaXII that provide, respectively, resistance to chloramphenicol and formaldehyde and are derivatives of cryptic pAsa2.
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Affiliation(s)
- Antony T Vincent
- Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Quebec, Canada
| | - Nava Hosseini
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (Hôpital Laval), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, Quebec City, Quebec, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (Hôpital Laval), Quebec City, Quebec, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada
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17
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Pan Y, Fang Y, Feng Y, Lyu N, Chen L, Li J, Xu X, Zhu B, Hu Y. Discovery of mcr-3.1 gene carried by a prophage located in a conjugative IncA/C2 plasmid from a Salmonella Choleraesuis clinical isolate. J Infect 2020; 82:414-451. [PMID: 33007341 DOI: 10.1016/j.jinf.2020.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/10/2020] [Accepted: 09/12/2020] [Indexed: 02/02/2023]
Affiliation(s)
- Yuanlong Pan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Yuan Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Na Lyu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Luping Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China
| | - Xuebin Xu
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; Beijing Key Laboratory of Microbial Drug Resistance and Resistome, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China; Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan Province, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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18
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Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy. Microorganisms 2020; 8:microorganisms8081232. [PMID: 32806766 PMCID: PMC7466171 DOI: 10.3390/microorganisms8081232] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 11/21/2022] Open
Abstract
Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using “Microbial Assembly”. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6′)-Ib4, ant(3″)-Ia, aph(3″)-Ib, aph(3′)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.
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Deciphering the Structural Diversity and Classification of the Mobile Tigecycline Resistance Gene tet(X)-Bearing Plasmidome among Bacteria. mSystems 2020; 5:5/2/e00134-20. [PMID: 32345737 PMCID: PMC7190383 DOI: 10.1128/msystems.00134-20] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tigecycline is an expanded-spectrum tetracycline used as a last-resort antimicrobial for treating infections caused by superbugs such as carbapenemase-producing or colistin-resistant pathogens. Emergence of the plasmid-mediated mobile tigecycline resistance gene tet(X4) created a great public health concern. However, the diversity of tet(X4)-bearing plasmids and bacteria remains largely uninvestigated. To cover this knowledge gap, we comprehensively identified and characterized the tet(X)-bearing plasmidome in different sources using advanced sequencing technologies for the first time. The huge diversity of tet(X4)-bearing mobile elements demonstrates the high level of transmissibility of the tet(X4) gene among bacteria. It is crucial to enhance stringent surveillance of tet(X) genes in animal and human pathogens globally. The emergence of novel plasmid-mediated resistance genes constitutes a great public concern. Recently, mobile tet(X) variants were reported in diverse pathogens from different sources. However, the diversity of tet(X)-bearing plasmids remains largely unknown. In this study, the phenotypes and genotypes of all the tet(X)-positive tigecycline-resistant strains isolated from a slaughterhouse in China were characterized by antimicrobial susceptibility testing, conjugation, pulsed-field gel electrophoresis with S1 nuclease (S1-PFGE), and PCR. The diversity and polymorphism of tet(X)-harboring strains and plasmidomes were investigated by whole-genome sequencing (WGS) and single-plasmid-molecule analysis. Seventy-four tet(X4)-harboring Escherichia coli strains and one tet(X6)-bearing Providencia rettgeri strain were identified. The tet(X4)-bearing elements in 27 strains could be transferred to the recipient strain via plasmids. All tet(X4)-bearing plasmids isolated in this study and 15 tet(X4)-bearing plasmids reported online were analyzed. tet(X4)-bearing plasmids ranged from 9 to 294 kb and were categorized as ColE2-like, IncQ, IncX1, IncA/C2, IncFII, IncFIB, and hybrid plasmids with different replicons. The core tet(X4)-bearing genetic contexts were divided into four major groups: ISCR2-tet(X4)-abh, △ISCR2-abh-tet(X4)-ISCR2, ISCR2-abh-tet(X4)-ISCR2-virD2-floR, and abh-tet(X4)-ISCR2-yheS-cat-zitR-ISCR2-virD2-floR. Tandem repeats of tet(X4) were universally mediated by ISCR2. Different tet(X)-bearing strains existed in the same microbiota. Reorganization of tet(X4)-bearing multidrug resistance plasmids was found to be mediated by IS26 and other homologous regions. Finally, single-plasmid-molecule analysis captured the heterogenous state of tet(X4)-bearing plasmids. These findings significantly expand our knowledge of the tet(X)-bearing plasmidome among microbiotas, which establishes a baseline for investigating the structure and diversity of human, animal, and environmental tigecycline resistomes. Characterization of tet(X) genes among different microbiotas should be performed systematically to understand the evolution and ecology. IMPORTANCE Tigecycline is an expanded-spectrum tetracycline used as a last-resort antimicrobial for treating infections caused by superbugs such as carbapenemase-producing or colistin-resistant pathogens. Emergence of the plasmid-mediated mobile tigecycline resistance gene tet(X4) created a great public health concern. However, the diversity of tet(X4)-bearing plasmids and bacteria remains largely uninvestigated. To cover this knowledge gap, we comprehensively identified and characterized the tet(X)-bearing plasmidome in different sources using advanced sequencing technologies for the first time. The huge diversity of tet(X4)-bearing mobile elements demonstrates the high level of transmissibility of the tet(X4) gene among bacteria. It is crucial to enhance stringent surveillance of tet(X) genes in animal and human pathogens globally.
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20
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Zheng Z, Cheng Q, Chan EWC, Chen S. Genetic and Biochemical Characterization of VMB-1, a Novel Metallo-β-Lactamase Encoded by a Conjugative, Broad-Host Range IncC Plasmid from Vibrio spp. ACTA ACUST UNITED AC 2020; 4:e1900221. [PMID: 32293144 DOI: 10.1002/adbi.201900221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/21/2019] [Indexed: 11/12/2022]
Abstract
The increasing incidence of phenotypic resistance to carbapenems in recent years is mainly attributed to acquisition of mobile carbapenemase-encoding genetic elements by major bacterial pathogens. Here, a novel carbapenemase known as Vibrio metallo-β-lactamase 1 (VMB-1), which is encoded by a gene (blaVMB-1 ) located in an integron-bearing, highly transmissible IncC type plasmid, namely pVB1796, is identified and characterized, both genetically and functionally. Recovered from a foodborne Vibrio alginolyticus strain that exhibits resistance to all known β-lactam antibiotics, pVB1796 is found to possess a hybrid backbone that exhibits unique features of both type 1 and type 2 IncC elements. VMB-1 exhibits 94% sequence homology with several recently reported but poorly characterized metallo-β-lactamases (MBLs) produced by the marine organisms Alteromonadaceae, Glaciecola, and Thalassomonas actiniarum. Sequence alignment analysis shows that VMB-1 shares a structurally identical active site with subclass B1 MBLs. Importantly, pVB1796 is found to be efficiently transferred from Vibrio to other Gram-negative bacterial pathogens, including Salmonella typhimurium, Klebsiella pneumoniae, and Acinetobacter baumanni, via conjugation. These findings suggest that blaVMB-1 -bearing plasmids have the potential to be disseminated to other Gram-negative bacterial pathogens in the near future and render carbapenems useless in treatment of multidrug resistant infections.
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Affiliation(s)
- Zhiwei Zheng
- Shenzhen Key Laboratory for Food Biological Safety Control, Food Safety and Technology Research Centre, The Hong Kong PolyU Shenzhen Research Institute, Shenzhen, 518052, P. R. China.,Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong
| | - Qipeng Cheng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong.,State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, 999077, Hong Kong
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, 999077, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, 999077, Hong Kong
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Stalder T, Press MO, Sullivan S, Liachko I, Top EM. Linking the resistome and plasmidome to the microbiome. THE ISME JOURNAL 2019; 13:2437-2446. [PMID: 31147603 PMCID: PMC6776055 DOI: 10.1038/s41396-019-0446-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/02/2019] [Accepted: 05/10/2019] [Indexed: 01/08/2023]
Abstract
The rapid spread of antibiotic resistance among bacterial pathogens is a serious human health threat. While a range of environments have been identified as reservoirs of antibiotic resistance genes (ARGs), we lack understanding of the origins of these ARGs and their spread from environment to clinic. This is partly due to our inability to identify the natural bacterial hosts of ARGs and the mobile genetic elements that mediate this spread, such as plasmids and integrons. Here we demonstrate that the in vivo proximity-ligation method Hi-C can reconstruct a known plasmid-host association from a wastewater community, and identify the in situ host range of ARGs, plasmids, and integrons by physically linking them to their host chromosomes. Hi-C detected both previously known and novel associations between ARGs, mobile genetic elements and host genomes, thus validating this method. We showed that IncQ plasmids and class 1 integrons had the broadest host range in this wastewater, and identified bacteria belonging to Moraxellaceae, Bacteroides, and Prevotella, and especially Aeromonadaceae as the most likely reservoirs of ARGs in this community. A better identification of the natural carriers of ARGs will aid the development of strategies to limit resistance spread to pathogens.
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Affiliation(s)
- Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA.
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.
| | | | | | | | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA.
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.
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Advantage of the F2:A1:B- IncF Pandemic Plasmid over IncC Plasmids in In Vitro Acquisition and Evolution of bla CTX-M Gene-Bearing Plasmids in Escherichia coli. Antimicrob Agents Chemother 2019; 63:AAC.01130-19. [PMID: 31332067 PMCID: PMC6761558 DOI: 10.1128/aac.01130-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022] Open
Abstract
Despite a fitness cost imposed on bacterial hosts, large conjugative plasmids play a key role in the diffusion of resistance determinants, such as CTX-M extended-spectrum β-lactamases. Among the large conjugative plasmids, IncF plasmids are the most predominant group, and an F2:A1:B- IncF-type plasmid encoding a CTX-M-15 variant was recently described as being strongly associated with the emerging worldwide Escherichia coli sequence type 131 (ST131)-O25b:H4 H30Rx/C2 sublineage. Despite a fitness cost imposed on bacterial hosts, large conjugative plasmids play a key role in the diffusion of resistance determinants, such as CTX-M extended-spectrum β-lactamases. Among the large conjugative plasmids, IncF plasmids are the most predominant group, and an F2:A1:B- IncF-type plasmid encoding a CTX-M-15 variant was recently described as being strongly associated with the emerging worldwide Escherichia coli sequence type 131 (ST131)-O25b:H4 H30Rx/C2 sublineage. In this context, we investigated the fitness cost of narrow-range F-type plasmids, including the F2:A1:B- IncF-type CTX-M-15 plasmid, and of broad-range C-type plasmids in the K-12-like J53-2 E. coli strain. Although all plasmids imposed a significant fitness cost to the bacterial host immediately after conjugation, we show, using an experimental-evolution approach, that a negative impact on the fitness of the host strain was maintained throughout 1,120 generations with the IncC-IncR plasmid, regardless of the presence or absence of cefotaxime, in contrast to the F2:A1:B- IncF plasmid, whose cost was alleviated. Many chromosomal and plasmid rearrangements were detected after conjugation in transconjugants carrying the IncC plasmids but not in transconjugants carrying the F2:A1:B- IncF plasmid, except for insertion sequence (IS) mobilization from the fliM gene leading to the restoration of motility of the recipient strains. Only a few mutations occurred on the chromosome of each transconjugant throughout the experimental-evolution assay. Our findings indicate that the F2:A1:B- IncF CTX-M-15 plasmid is well adapted to the E. coli strain studied, contrary to the IncC-IncR CTX-M-15 plasmid, and that such plasmid-host adaptation could participate in the evolutionary success of the CTX-M-15-producing pandemic E. coli ST131-O25b:H4 lineage.
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Cheng P, Li F, Liu R, Yang Y, Xiao T, Ishfaq M, Xu G, Zhang X. Prevalence and molecular epidemiology characteristics of carbapenem-resistant Escherichia coli in Heilongjiang Province, China. Infect Drug Resist 2019; 12:2505-2518. [PMID: 31496764 PMCID: PMC6697665 DOI: 10.2147/idr.s208122] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 07/23/2019] [Indexed: 11/30/2022] Open
Abstract
Objective This retrospective study was conducted to determine the prevalence and molecular epidemiology characteristics of carbapenem-resistant Escherichia coli (CRE). Methods A total of 593 Escherichia coli (E. coli) isolates were recovered from pigs and urban river from 2009 to 2014 in Heilongjiang Province of China. Forty CRE including 22 strains isolated from fecal samples of pigs and 18 strains isolated from water samples were selected. PCR detection of resistance determinants, multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and phylogenetic groups were performed to characterize CRE isolates. Conjugation experiments, plasmid stability testing, PCR-based replicon typing (PBRT), and PCR mapping were conducted to analyze blaNDM-carrying plasmids. In vitro time–growth studies and competition experiments were carried out to assess the fitness impact of NDM carriage. Results Five NDM-1-positive E. coli isolates were identified from water samples. Genetic environment analysis revealed that a cluster of genes (ISAba125-blaNDM-1-bleMBL-ΔtrpF) was detected in all of the NDM-1-positive isolates. Conjugation assays showed that blaNDM-1 could be successfully transferred to E. coli J53 from 5 donor strains at frequencies of 4.6×10−5 to 2.6×10−2. The plasmids from all transconjugants belonged to different plasmid replicon types including IncA/C (n=2), IncFII (n=1) and IncX3 (n=2). In vitro time–growth studies revealed that blaNDM-1 did not have a significant impact on cell proliferation. Meanwhile, competition experiments showed that the acquisition of blaNDM-1 can place an energy burden on the bacterial host and incur fitness cost. However, plasmid stability testing showed that blaNDM-1-carrying plasmid remained stable in the hosts after seven passages without antimicrobial selection. Conclusion The study revealed the early molecular epidemiology and dissemination characteristics of CRE. In addition, the overall antimicrobial resistance in E. coli recovered from water samples is higher than the strains isolated from fecal samples of pigs. Furthermore, we isolated and identified five NDM-1-producing E. coli strains from water samples.
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Affiliation(s)
- Ping Cheng
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Fulei Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Ruimeng Liu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Yuqi Yang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Tianshi Xiao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Muhammad Ishfaq
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Guofeng Xu
- First Department of Respiratory Disease, Inflammation and Allergic Diseases Research Unit, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, People's Republic of China
| | - Xiuying Zhang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Faculty of Basic Veterinary Science, College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
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24
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Fenske GJ, Thachil A, McDonough PL, Glaser A, Scaria J. Geography Shapes the Population Genomics of Salmonella enterica Dublin. Genome Biol Evol 2019; 11:2220-2231. [PMID: 31329231 PMCID: PMC6703130 DOI: 10.1093/gbe/evz158] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 01/11/2023] Open
Abstract
Salmonella enterica serotype Dublin (S. Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated data set comprising of 880 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin in the UK are genomically distinct from US, Brazilian, and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and are mediated by an IncA/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in the serotype. Comparison of S. Dublin to a closely related serotype, S. enterica serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not found in S. Enteritidis. Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.
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Affiliation(s)
- Gavin J Fenske
- Department of Veterinary and Biomedical Sciences, South Dakota State University
| | - Anil Thachil
- Department of Population Medicine and Diagnostic Sciences, Cornell University
| | - Patrick L McDonough
- Department of Population Medicine and Diagnostic Sciences, Cornell University
| | - Amy Glaser
- Department of Population Medicine and Diagnostic Sciences, Cornell University
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University
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25
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Wrobel A, Ottoni C, Leo JC, Linke D. pYR4 From a Norwegian Isolate of Yersinia ruckeri Is a Putative Virulence Plasmid Encoding Both a Type IV Pilus and a Type IV Secretion System. Front Cell Infect Microbiol 2018; 8:373. [PMID: 30460204 PMCID: PMC6232867 DOI: 10.3389/fcimb.2018.00373] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/04/2018] [Indexed: 01/14/2023] Open
Abstract
Enteric redmouth disease caused by the pathogen Yersinia ruckeri is a significant problem for fish farming around the world. Despite its importance, only a few virulence factors of Y. ruckeri have been identified and studied in detail. Here, we report and analyze the complete DNA sequence of pYR4, a plasmid from a highly pathogenic Norwegian Y. ruckeri isolate, sequenced using PacBio SMRT technology. Like the well-known pYV plasmid of human pathogenic Yersiniae, pYR4 is a member of the IncFII family. Thirty-one percent of the pYR4 sequence is unique compared to other Y. ruckeri plasmids. The unique regions contain, among others genes, a large number of mobile genetic elements and two partitioning systems. The G+C content of pYR4 is higher than that of the Y. ruckeri NVH_3758 genome, indicating its relatively recent horizontal acquisition. pYR4, as well as the related plasmid pYR3, comprises operons that encode for type IV pili and for a conjugation system (tra). In contrast to other Yersinia plasmids, pYR4 cannot be cured at elevated temperatures. Our study highlights the power of PacBio sequencing technology for identifying mis-assembled segments of genomic sequences. Comparative analysis of pYR4 and other Y. ruckeri plasmids and genomes, which were sequenced by second and the third generation sequencing technologies, showed errors in second generation sequencing assemblies. Specifically, in the Y. ruckeri 150 and Y. ruckeri ATCC29473 genome assemblies, we mapped the entire pYR3 plasmid sequence. Placing plasmid sequences on the chromosome can result in erroneous biological conclusions. Thus, PacBio sequencing or similar long-read methods should always be preferred for de novo genome sequencing. As the tra operons of pYR3, although misplaced on the chromosome during the genome assembly process, were demonstrated to have an effect on virulence, and type IV pili are virulence factors in many bacteria, we suggest that pYR4 directly contributes to Y. ruckeri virulence.
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Affiliation(s)
| | - Claudio Ottoni
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Jack C Leo
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Department of Biosciences, University of Oslo, Oslo, Norway
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26
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Unlu O, Aktas Z, Tugrul HM. Analysis of Virulence Factors and Antimicrobial Resistance in Salmonella Using Molecular Techniques and Identification of Clonal Relationships Among the Strains. Microb Drug Resist 2018; 24:1475-1482. [PMID: 29920160 DOI: 10.1089/mdr.2018.0042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A total of 50 Salmonella enterica strains were isolated from clinical samples from 2009 to 2012 and analyzed for the presence of virulence genes found in SPI-1, SPI-2, and plasmids. The distribution and frequency of the antimicrobial resistance genes and plasmids were revealed, and pulsed-field gel electrophoresis (PFGE) patterns were investigated. Five genes were identified from the seven strains with resistance or intermediate resistance to ampicillin: blaSHV-1 (present in six strains), qnrS1 (present in five strains), blaTEM-1 (present in three strains), blaCTX-M-1 (present in one strain), and qnrB1 (present in one strain). One trimethoprim-sulfamethoxazole-resistant strain was positive for sulI but negative for sulII. In addition, we detected TEM-1 and qnrS1 in one strain; SHV-1 and qnrS1 in two strains; TEM-1, SHV-1, CTX-M-1, and qnrS1 in one strain; TEM-1, SHV-1, and qnrB1 in one strain; and SHV-1 and sulI genes in one strain together. Plasmid-based replicon typing assay revealed that all 50 strains carried FIIS, 13 carried I1, 1 carried I2, 4 carried P, 1 carried A/C, and 4 carried X1 replicon. PFGE was used to type 46 of the 50 strains and classify them into 22 major groups, 33 pulsotypes, and 8 major clusters. All strains carried all the virulence genes of interest on both Salmonella Pathogenicity Islands 1 and 2 and plasmids suggested high potential for pathogenicity. All antimicrobial-resistant strains contained at least one of the resistance genes of interest, confirming a phenotype-genotype association in antimicrobial resistance.
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Affiliation(s)
- Ozge Unlu
- Department of Medical Microbiology, Faculty of Medicine, Beykent University, Istanbul, Turkey
| | - Zerrin Aktas
- Department of Medical Microbiology, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Hamdi Murat Tugrul
- Department of Medical Microbiology, Faculty of Medicine, Trakya University, Edirne, Turkey
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27
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Nonaka L, Yamamoto T, Maruyama F, Hirose Y, Onishi Y, Kobayashi T, Suzuki S, Nomura N, Masuda M, Yano H. Interplay of a non-conjugative integrative element and a conjugative plasmid in the spread of antibiotic resistance via suicidal plasmid transfer from an aquaculture Vibrio isolate. PLoS One 2018; 13:e0198613. [PMID: 29879198 PMCID: PMC5991714 DOI: 10.1371/journal.pone.0198613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 05/22/2018] [Indexed: 12/01/2022] Open
Abstract
The capture of antimicrobial resistance genes (ARGs) by mobile genetic elements (MGEs) plays a critical role in resistance acquisition for human-associated bacteria. Although aquaculture environments are recognized as important reservoirs of ARGs, intra- and intercellular mobility of MGEs discovered in marine organisms is poorly characterized. Here, we show a new pattern of interspecies ARGs transfer involving a 'non-conjugative' integrative element. To identify active MGEs in a Vibrio ponticus isolate, we conducted whole-genome sequencing of a transconjugant obtained by mating between Escherichia coli and Vibrio ponticus. This revealed integration of a plasmid (designated pSEA1) into the chromosome, consisting of a self-transmissible plasmid backbone of the MOBH group, ARGs, and a 13.8-kb integrative element Tn6283. Molecular genetics analysis suggested a two-step gene transfer model. First, Tn6283 integrates into the recipient chromosome during suicidal plasmid transfer, followed by homologous recombination between the Tn6283 copy in the chromosome and that in the newly transferred pSEA1. Tn6283 is unusual among integrative elements in that it apparently does not encode transfer function and its excision barely generates unoccupied donor sites. Thus, its movement is analogous to the transposition of insertion sequences rather than to that of canonical integrative and conjugative elements. Overall, this study reveals the presence of a previously unrecognized type of MGE in a marine organism, highlighting diversity in the mode of interspecies gene transfer.
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Affiliation(s)
- Lisa Nonaka
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
| | - Tatsuya Yamamoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
| | | | - Yuu Hirose
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Tempaku, Toyohashi, Aichi, Japan
| | - Yuki Onishi
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | | | - Satoru Suzuki
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Ehime, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
| | - Michiaki Masuda
- Department of Microbiology, Dokkyo Medical University School of Medicine, Mibu, Tochigi, Japan
| | - Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Japan
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28
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Complete Sequence of the IncA/C 1 Plasmid pCf587 Carrying blaPER-2 from Citrobacter freundii. Antimicrob Agents Chemother 2018; 62:AAC.00006-18. [PMID: 29463531 DOI: 10.1128/aac.00006-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/13/2018] [Indexed: 12/29/2022] Open
Abstract
The blaPER-2-harboring plasmid pCf587 (191,541 bp) belongs to lineage IncA/C1 and is closely related to pRA1. It contains a large resistance island including the blaPER-2 gene between two copies of ISKox2-like elements, the toxin-antitoxin module pemK-pemI, several other resistance genes inserted within a Tn2 transposon, a Tn21-like structure, and a class 1 integron. pCf587 belongs to sequence type 13 (ST13), a new plasmid multilocus sequence typing (pMLST) ST.
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29
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Impact of co-carriage of IncA/C plasmids with additional plasmids on the transfer of antimicrobial resistance in Salmonella enterica isolates. Int J Food Microbiol 2018; 271:77-84. [DOI: 10.1016/j.ijfoodmicro.2018.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/22/2017] [Accepted: 01/19/2018] [Indexed: 11/22/2022]
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30
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Ma L, Yin Z, Zhang D, Zhan Z, Wang Q, Duan X, Gao H, Liang Q, Zhao Y, Feng J, Zhao Y, Tong Y, Dai E, Zhou D. Comparative genomics of type 1 IncC plasmids from China. Future Microbiol 2017; 12:1511-1522. [PMID: 29140102 DOI: 10.2217/fmb-2017-0072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study dealt with genomic characterization of type 1 IncC resistance plasmids, capable of spreading across taxonomic borders, from China. Materials & methods: p112298-tetA was sequenced and compared with type 1 IncC reference plasmid pR148 and two available sequenced type 1 IncC plasmids pHS36-NDM and pVAS3-1 from China. Results: These plasmids contained one or more exogenous resistance islands, which included the ARI-A islands, the ARI-B islands, the ISEcp1-blaCMY units and the bla KPC-2 region and were inserted at various sites in the IncC backbone and thus represented three distinct lineages. Conclusion: Complex rearrangement and homologous recombination events have occurred during evolution of p112298-tetA, making it significantly differ modularly from the other three plasmids with respect to both plasmid backbone and exogenous resistance regions.
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Affiliation(s)
- Lizhi Ma
- Department of Emergency Medicine, General Hospital of Chinese People's Armed Police Forces, Beijing 100039, China
| | - Zhe Yin
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Defu Zhang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Zhe Zhan
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Qian Wang
- Department of Emergency Medicine, General Hospital of Chinese People's Armed Police Forces, Beijing 100039, China
| | - Xiongbo Duan
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Huixia Gao
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Quanhui Liang
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yuzong Zhao
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
- College of Food Science & Project Engineering, Bohai University, Jinzhou 121013, China
| | - Jiao Feng
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yachao Zhao
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
| | - Erhei Dai
- Department of Laboratory Medicine, The Fifth Hospital of Shijiazhuang, Hebei Medical University, Shijiazhuang, Hebei 050021, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen & Biosecurity, Beijing Institute of Microbiology & Epidemiology, Beijing 100071, China
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31
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Highly Tigecycline-Resistant Klebsiella pneumoniae Sequence Type 11 (ST11) and ST147 Isolates from Companion Animals. Antimicrob Agents Chemother 2017; 61:AAC.02640-16. [PMID: 28396550 DOI: 10.1128/aac.02640-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
In this study, we characterized two tigecycline-resistant Klebsiella pneumoniae isolates from dog urine samples. The isolates were genetically unrelated, belonging to sequence type 11 (ST11) and ST147, both classically related to human isolates. To the best of our knowledge, this is the first identification of tigecycline-resistant isolates from animals. We unveil here the worrisome circulation among animals of bacterial clones resistant to this last-resort antibiotic.
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32
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Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device. Antimicrob Agents Chemother 2016; 60:6780-6786. [PMID: 27600047 DOI: 10.1128/aac.01121-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/22/2016] [Indexed: 01/13/2023] Open
Abstract
Two A/C incompatibility group (IncA/C family) plasmids from the 1960s have been sequenced and classified into the A/C2 type 1 group. R16a and IP40a contain novel antibiotic resistance islands and a complete GIsul2 genomic island not previously found in the family. In the 173.1-kb R16a, the 29.9-kb antibiotic resistance island (ARI) is located in a unique backbone position not utilized by ARIs. ARIR16a consists of Tn1, Tn6020, and Tn6333, harboring the resistance genes blaTEM-1D and aphA1b and a mer module, respectively; a truncated Tn5393 copy; and a gene cluster with unknown function. Plasmid IP40a is 170.4 kb in size and contains a 5.6-kb ARI inserted into the kfrA gene. ARIIP40a carrying blaTEM-1D and aphA1b genes is composed of Tn1 with a Tn6023 insertion. Additionally, IP40a harbors single IS2, IS186, and Tn1000 insertions scattered in the backbone; an IS150 copy in GIsul2; and a complete Tn6333 carrying a mer module at the position of ARIR16a Loss of resistance markers in R16a, IP40a, and R55 was observed during stability tests. Every phenotypic change proved to be the result of recombination events involving mobile elements. Intramolecular transposition of IS copies that generated IP40a derivatives lacking large parts of the backbone could account for the formation of other family members, too. The MinION platform proved to be a valuable tool in bacterial genome sequencing since it generates long reads that span repetitive elements and facilitates full-length plasmid or chromosome assembly. Nanopore technology enables rapid characterization of large, low-copy-number plasmids and their rearrangement products.
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Trudel MV, Vincent AT, Attéré SA, Labbé M, Derome N, Culley AI, Charette SJ. Diversity of antibiotic-resistance genes in Canadian isolates of Aeromonas salmonicida subsp. salmonicida: dominance of pSN254b and discovery of pAsa8. Sci Rep 2016; 6:35617. [PMID: 27752114 PMCID: PMC5067588 DOI: 10.1038/srep35617] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/26/2016] [Indexed: 12/26/2022] Open
Abstract
The bacterium Aeromonas salmonicida subsp. salmonicida is a common pathogen in fish farms worldwide. Since the antibiotic resistance of this bacterial species is on the increase, it is important to have a broader view on this issue. In the present study, we tested the presence of known plasmids conferring multi-drug resistance as well as antibiotic resistance genes by a PCR approach in 100 Canadian A. salmonicida subsp. salmonicida isolates. Our study highlighted the dominance of the conjugative pSN254b plasmid, which confers multi-drug resistance. We also identified a new multi-drug plasmid named pAsa8, which has been characterized by a combination of sequencing technologies (Illumina and Oxford nanopore). This new plasmid harbors a complex class 1 integron similar to the one of the Salmonella genomic island 1 (SGI1) found in Salmonella enterica and Proteus mirabilis. Consequently, in addition to providing an update on the A. salmonicida subsp. salmonicida isolates that are resistant to antibiotics, our data suggest that this bacterium is potentially an important reservoir of drug resistance genes and should consequently be monitored more extensively. In addition, we describe a screening method that has the potential to become a diagnostic tool that is complementary to other methods currently in use.
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Affiliation(s)
- Mélanie V Trudel
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Antony T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Sabrina A Attéré
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
| | - Myriam Labbé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biologie, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Alexander I Culley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
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Oneko M, Kariuki S, Muturi-Kioi V, Otieno K, Otieno VO, Williamson JM, Folster J, Parsons MB, Slutsker L, Mahon BE, Hamel MJ. Emergence of Community-Acquired, Multidrug-Resistant Invasive Nontyphoidal Salmonella Disease in Rural Western Kenya, 2009-2013. Clin Infect Dis 2016; 61 Suppl 4:S310-6. [PMID: 26449946 DOI: 10.1093/cid/civ674] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Nontyphoidal Salmonella (NTS), mainly serotypes Typhimurium and Enteritidis, cause invasive infections with high mortality in children in sub-Saharan Africa. Multidrug resistance is common, and resistance to third-generation cephalosporins has emerged. METHODS We reviewed clinical features, outcomes, and antimicrobial resistance patterns in invasive NTS infections among children aged 6 weeks to 5 years participating in malaria vaccine studies in an area of high malaria and human immunodeficiency virus (HIV) transmission in Siaya, western Kenya. Blood culture was performed in hospitalized children and pediatric outpatients with prolonged fever. RESULTS From July 2009 to December 2013, 1696 children aged 6 weeks to 17 months were enrolled into vaccine trials and followed for up to 53 months. We obtained 1692 blood cultures from 847 children. Of 134 bacterial pathogens isolated, 102 (76.1%) were Salmonella serogroup B or D. Invasive NTS disease occurred in 94 (5.5%) children, with an incidence of 1870, 4134, and 6510 episodes per 100 000 person-years overall, in infants, and in HIV-infected children, respectively. Malaria infection within the past 2 weeks occurred in 18.8% (3/16) of invasive NTS episodes in HIV-infected and 66.2% (53/80) in HIV-uninfected children. Case fatality rate was 3.1%. Salmonella group B resistant to ceftriaxone emerged in 2009 and 2010 (6.2% [2/32 isolates]), rising to 56.5% (13/23 isolates) in 2012 and 2013. CONCLUSIONS Incidence of invasive NTS disease was high in this area of high malaria and HIV transmission, especially in HIV-infected children. Rapidly emerging resistance against ceftriaxone requires urgent reevaluation of antibiotic recommendations and primary prevention of exposure to Salmonella.
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Affiliation(s)
- Martina Oneko
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu
| | - Simon Kariuki
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu
| | | | - Kephas Otieno
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu
| | - Vincent O Otieno
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu
| | | | - Jason Folster
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Barbara E Mahon
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Mary J Hamel
- Centers for Disease Control and Prevention, Atlanta, Georgia
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35
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Kempf AJ, Hulsebus HJ, Akbar S. Multiple Plasmids Contribute to Antibiotic Resistance and Macrophage Survival In Vitro in CMY2-Bearing Salmonella enterica. Foodborne Pathog Dis 2016; 13:398-404. [PMID: 27070176 DOI: 10.1089/fpd.2015.2067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Multiple drug resistance (MDR) in bacteria represents a notable problem but if carried on plasmid their spread could become a significant threat to public health. Plasmids in members of the Enterobacteriaceae family and in particular Salmonella and Escherichia coli strains have been implicated in the spread of antibiotic resistance genes. However, the mechanisms involved in the transfer of plasmid-borne resistance genes are not fully understood. Here, we analyzed the ability of Salmonella enterica clinical isolates to transfer plasmid-borne MDR to E. coli. We also determined whether possession of an Inc A/C plasmid by a S. enterica isolate would confer increased fitness compared to an isolate not carrying the plasmid. Sixteen human and animal isolates of S. enterica were screened using a three-panel multiplex PCR assay, and simplex PCR for the blaCMY-2 gene. Using these data we selected a suitable strain as a plasmid donor for the construction of a new Salmonella strain with an Inc A/C plasmid. This allowed us to compare isogenic strains with and without the Inc A/C plasmid in multiple growth, fitness, and invasion assays. The results showed that possession of Inc A/C plasmid confers significant fitness advantage when tested in J774 macrophages as opposed to HEp-2 cells where no significant difference was found. In addition, stress assays performed in vitro showed that the possession of this large plasmid by Salmonella strains tested here does not appear to incur a significant fitness cost. Gaining a better understanding of molecular mechanisms of plasmid transfer between pathogenic bacteria will allow us to characterize the role of MDR in pathogenicity of bacteria and to identify methods to reduce the frequency of dissemination of multiple antibiotic resistance genes.
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Affiliation(s)
- Allen J Kempf
- 1 Department of Microbiology and Immunology, Des Moines University , Des Moines, Iowa
| | - Holly J Hulsebus
- 1 Department of Microbiology and Immunology, Des Moines University , Des Moines, Iowa
| | - Samina Akbar
- 1 Department of Microbiology and Immunology, Des Moines University , Des Moines, Iowa.,2 College of Osteopathic Medicine, Marian University , Indianapolis, Indiana
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36
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Lyimo B, Buza J, Subbiah M, Temba S, Kipasika H, Smith W, Call DR. IncF Plasmids Are Commonly Carried by Antibiotic Resistant Escherichia coli Isolated from Drinking Water Sources in Northern Tanzania. Int J Microbiol 2016; 2016:3103672. [PMID: 27110245 PMCID: PMC4823495 DOI: 10.1155/2016/3103672] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/29/2016] [Indexed: 01/06/2023] Open
Abstract
The aim of this study was to identify the replicon types of plasmids, conjugation efficiencies, and the complement of antibiotic resistance genes for a panel of multidrug resistant E. coli isolates from surface waters in northern Tanzania. Standard membrane filtration was used to isolate and uidA PCR was used to confirm the identity of strains as E. coli. Antibiotic susceptibility was determined by breakpoint assay and plasmid conjugation was determined by filter-mating experiments. PCR and sequencing were used to identify resistance genes and PCR-based replicon typing was used to determine plasmid types. Filter mating experiments indicated conjugation efficiencies ranged from 10(-1) to 10(-7). Over 80% of the donor cells successfully passed their resistance traits and eleven different replicon types were detected (IncI1, FIC, P, FIIA, A/C, FIB, FIA, H12, K/B B/O, and N). IncF plasmids were most commonly detected (49% of isolates), followed by types IncI1 and IncA/C. Detection of these public health-relevant conjugative plasmids and antibiotic resistant traits in Tanzanian water suggests the possible pollution of these water sources from human, livestock, and wild animal wastes and also shows the potential of these water sources in the maintenance and transmission of these resistance traits between environments, animals, and people.
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Affiliation(s)
- Beatus Lyimo
- Nelson Mandela African Institution of Science and Technology, 447 Arusha, Tanzania
| | - Joram Buza
- Nelson Mandela African Institution of Science and Technology, 447 Arusha, Tanzania
| | - Murugan Subbiah
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA
| | - Sylivester Temba
- Nelson Mandela African Institution of Science and Technology, 447 Arusha, Tanzania
| | - Honest Kipasika
- Nelson Mandela African Institution of Science and Technology, 447 Arusha, Tanzania
| | - Woutrina Smith
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Douglas R. Call
- Nelson Mandela African Institution of Science and Technology, 447 Arusha, Tanzania
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA
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37
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Bien TLT, Sato-Takabe Y, Ogo M, Usui M, Suzuki S. Persistence of Multi-Drug Resistance Plasmids in Sterile Water under Very Low Concentrations of Tetracycline. Microbes Environ 2015; 30:339-43. [PMID: 26639579 PMCID: PMC4676558 DOI: 10.1264/jsme2.me15122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The persistence of the multi-drug resistance plasmids pAQU1 and IncFIB was examined in bacterial populations under very low selective pressure. We herein demonstrated that these plasmids stably remained not only in the original host, but also in a transconjugant, even after being in a non-culturable state. In seawater microcosms containing Photobacterium damselae 04Ya311 possessing pAQU1, no significant loss of pAQU1 was observed during a 30-d starvation period. The copy numbers of pAQU1 and IncFIB in E. coli were constant. The results of the present study suggest that these plasmids have the ability to remain among various bacteria under oligotrophic conditions with low antibiotic selection pressure.
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38
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Epidemiologic and Genotypic Review of Carbapenemase-Producing Organisms in British Columbia, Canada, between 2008 and 2014. J Clin Microbiol 2015; 54:317-27. [PMID: 26607987 DOI: 10.1128/jcm.02289-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022] Open
Abstract
Carbapenemase-producing organisms (CPOs) are a serious emerging problem for health care facilities worldwide. Owing to their resistance to most antimicrobial therapies, CPOs are difficult to treat and pose a challenge for infection prevention and control. Since 2010, lab-based surveillance for CPOs and PCR-based testing were implemented in British Columbia (BC), Canada. A review of CPOs in BC from 2008 to March 2014 was done to characterize the resistance mechanisms and possible clonal strain transmission and to compare pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and plasmid restriction fragment length polymorphism (RFLP) as molecular typing tools. During this study period, a total of 177 CPO cases were identified. Patient demographics and travel history were reviewed, and a descriptive analysis was carried out. PFGE profiles, MLST, and plasmid RFLP analysis for a subset of Escherichia coli, Klebsiella pneumoniae, and Enterobacter species isolates were obtained and analyzed. Our findings demonstrate that CPOs have been increasing in number in BC over time, from 1 isolate/year retrospectively identified in 2008 and 2009 to 82 isolates in 2013 and 30 isolates in the first quarter of 2014. Overall, K. pneumoniae isolates lack clonality, although some seemingly related clusters have been found. Plasmid analysis showed evidence of the spread of plasmids carrying carbapenemase-encoding genes between the examined isolates. Analysis of Enterobacter cloacae isolates revealed a more clonal nature of these CPOs in BC. The presence of related clusters provides evidence of interpatient organism transmission both within and between institutions. Although in our study, NDM-harboring E. cloacae isolates appeared to spread clonally, the spread of carbapenem resistance in K. pneumoniae seems to be plasmid mediated.
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39
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LaPara TM, Madson M, Borchardt S, Lang KS, Johnson TJ. Multiple Discharges of Treated Municipal Wastewater Have a Small Effect on the Quantities of Numerous Antibiotic Resistance Determinants in the Upper Mississippi River. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:11509-11515. [PMID: 26325533 DOI: 10.1021/acs.est.5b02803] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This study evaluated multiple discharges of treated wastewater on the quantities of antibiotic resistance genes (ARGs) in the Upper Mississippi River. Surface water and treated wastewater samples were collected along the Mississippi River during three different periods of 4 days during the summer of 2012, and quantitative real-time PCR (qPCR) was used to enumerate several ARGs and related targets. Even though the wastewater effluents contained 75- to 831-fold higher levels of ARGs than the river water, the quantities of ARGs in the Mississippi River did not increase with downstream distance. Plasmids from the incompatibility group A/C were detected at low levels in the wastewater effluents but not in the river water; synthetic DNA containing an ampicillin resistance gene (bla) from cloning vectors was not detected in either the wastewater effluent or river samples. A simple 1D model suggested that the primary reason for the small impact of the wastewater discharges on ARG levels was the large flow rate of the Mississippi River compared to that of the wastewater discharges. Furthermore, this model generally overpredicted the ARG levels in the Mississippi River, suggesting that substantial loss mechanisms (e.g., decay or deposition) were occurring in the river.
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Affiliation(s)
- Timothy M LaPara
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Matthew Madson
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Spencer Borchardt
- Department of Civil, Environmental, and Geo- Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
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40
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Kiss J, Papp PP, Szabó M, Farkas T, Murányi G, Szakállas E, Olasz F. The master regulator of IncA/C plasmids is recognized by the Salmonella Genomic island SGI1 as a signal for excision and conjugal transfer. Nucleic Acids Res 2015. [PMID: 26209134 PMCID: PMC4605294 DOI: 10.1093/nar/gkv758] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The genomic island SGI1 and its variants, the important vehicles of multi-resistance in Salmonella strains, are integrative elements mobilized exclusively by the conjugative IncA/C plasmids. Integration and excision of the island are carried out by the SGI1-encoded site-specific recombinase Int and the recombination directionality factor Xis. Chromosomal integration ensures the stable maintenance and vertical transmission of SGI1, while excision is the initial step of horizontal transfer, followed by conjugation and integration into the recipient. We report here that SGI1 not only exploits the conjugal apparatus of the IncA/C plasmids but also utilizes the regulatory mechanisms of the conjugation system for the exact timing and activation of excision to ensure efficient horizontal transfer. This study demonstrates that the FlhDC-family activator AcaCD, which regulates the conjugation machinery of the IncA/C plasmids, serves as a signal of helper entry through binding to SGI1 xis promoter and activating SGI1 excision. Promoters of int and xis genes have been identified and the binding site of the activator has been located by footprinting and deletion analyses. We prove that expression of xis is activator-dependent while int is constitutively expressed, and this regulatory mechanism is presumably responsible for the efficient transfer and stable maintenance of SGI1.
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Affiliation(s)
- János Kiss
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Péter Pál Papp
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Mónika Szabó
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Tibor Farkas
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Gábor Murányi
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Erik Szakállas
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
| | - Ferenc Olasz
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő H2100, Hungary
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41
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Harmer CJ, Hall RM. The A to Z of A/C plasmids. Plasmid 2015; 80:63-82. [DOI: 10.1016/j.plasmid.2015.04.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 04/03/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
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42
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Lang KS, Johnson TJ. Transcriptome modulations due to A/C2 plasmid acquisition. Plasmid 2015; 80:83-9. [DOI: 10.1016/j.plasmid.2015.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 10/23/2022]
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43
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Flach CF, Johnning A, Nilsson I, Smalla K, Kristiansson E, Larsson DGJ. Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake. J Antimicrob Chemother 2015; 70:2709-17. [PMID: 26124213 DOI: 10.1093/jac/dkv167] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/26/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Antibiotic-polluted environments may function as reservoirs for novel resistance plasmids not yet encountered in pathogens. The aims of this study were to assess the potential of resistance transfer between bacteria from such environments and Escherichia coli, and to characterize the conjugative elements involved. METHODS Sediment samples from Kazipally lake and Asanikunta tank, two Indian lakes with a history of severe pollution with fluoroquinolones, were investigated. Proportions of resistant bacteria were determined by selective cultivation, while horizontal gene transfer was studied using a GFP-tagged E. coli as recipient. Retrieved transconjugants were tested for susceptibility by Etest(®) and captured conjugative resistance elements were characterized by WGS. RESULTS The polluted lakes harboured considerably higher proportions of ciprofloxacin-resistant and sulfamethoxazole-resistant bacteria than did other Indian and Swedish lakes included for comparison (52% versus 2% and 60% versus 7%, respectively). Resistance plasmids were captured from Kazipally lake, but not from any of the other lakes; in the case of Asanikunta tank because of high sediment toxicity. Eight unique IncA/C and IncN resistance plasmids were identified among 11 sequenced transconjugants. Five plasmids were fully assembled, and four of these carried the quinolone resistance gene qnrVC1, which has previously only been found on chromosomes. Acquired resistance genes, in the majority of cases associated with class 1 integrons, could be linked to decreased susceptibility to several different classes of antibiotics. CONCLUSIONS Our study shows that environments heavily polluted with antibiotics contain novel multiresistance plasmids transferrable to E. coli.
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Affiliation(s)
- Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Johnning
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Ida Nilsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Kornelia Smalla
- Julius Kühn-Institut-Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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44
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Carraro N, Poulin D, Burrus V. Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner. PLoS Genet 2015; 11:e1005298. [PMID: 26061412 PMCID: PMC4489591 DOI: 10.1371/journal.pgen.1005298] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/23/2015] [Indexed: 02/07/2023] Open
Abstract
Integrative and Conjugative Elements (ICEs) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae. SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation. Conjugative transfer of SXT/R391 ICEs involves a transient extrachromosomal circular plasmid-like form that is thought to be the substrate for single-stranded DNA translocation to the recipient cell through the mating pore. This plasmid-like form is thought to be non-replicative and is consequently expected to be highly unstable. We report here that the ICE R391 of Providencia rettgeri is impervious to loss upon cell division. We have investigated the genetic determinants contributing to R391 stability. First, we found that a hipAB-like toxin/antitoxin system improves R391 stability as its deletion resulted in a tenfold increase of R391 loss. Because hipAB is not a conserved feature of SXT/R391 ICEs, we sought for alternative and conserved stabilization mechanisms. We found that conjugation itself does not stabilize R391 as deletion of traG, which abolishes conjugative transfer, did not influence the frequency of loss. However, deletion of either the relaxase-encoding gene traI or the origin of transfer (oriT) led to a dramatic increase of R391 loss correlated with a copy number decrease of its plasmid-like form. This observation suggests that replication initiated at oriT by TraI is essential not only for conjugative transfer but also for stabilization of SXT/R391 ICEs. Finally, we uncovered srpMRC, a conserved locus coding for two proteins distantly related to the type II (actin-type ATPase) parMRC partitioning system of plasmid R1. R391 and plasmid stabilization assays demonstrate that srpMRC is active and contributes to reducing R391 loss. While partitioning systems usually stabilizes low-copy plasmids, srpMRC is the first to be reported that stabilizes a family of ICEs.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Poulin
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Laboratory of bacterial molecular genetics, Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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45
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Carraro N, Matteau D, Burrus V, Rodrigue S. Unraveling the regulatory network of IncA/C plasmid mobilization: When genomic islands hijack conjugative elements. Mob Genet Elements 2015; 5:1-5. [PMID: 26442183 PMCID: PMC4588540 DOI: 10.1080/2159256x.2015.1045116] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 04/09/2015] [Accepted: 04/21/2015] [Indexed: 12/12/2022] Open
Abstract
Conjugative plasmids of the A/C incompatibility group (IncA/C) have become substantial players in the dissemination of multidrug resistance. These large conjugative plasmids are characterized by their broad host-range, extended spectrum of antimicrobials resistance, and prevalence in enteric bacteria recovered from both environmental and clinical settings. Until recently, relatively little was known about the basic biology of IncA/C plasmids, mostly because of the hindrance of multidrug resistance for molecular biology experiments. To circumvent this issue, we previously developed pVCR94ΔX, a convenient prototype that codes for a reduced set of antibiotic resistances. Using pVCR94ΔX, we then characterized the regulatory pathway governing IncA/C plasmid dissemination. We found that the expression of roughly 2 thirds of the genes encoded by this plasmid, including large operons involved in the conjugation process, depends on an FlhCD-like master activator called AcaCD. Beyond the mobility of IncA/C plasmids, AcaCD was also shown to play a key role in the mobilization of different classes of genomic islands (GIs) identified in various pathogenic bacteria. By doing so, IncA/C plasmids can have a considerable impact on bacterial genomes plasticity and evolution.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of Bacterial Molecular Genetics; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
| | - Dominick Matteau
- Laboratory of Microbial Systems and Synthetic Biology; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
| | - Vincent Burrus
- Laboratory of Bacterial Molecular Genetics; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
| | - Sébastien Rodrigue
- Laboratory of Microbial Systems and Synthetic Biology; Département de Biologie; Université de Sherbrooke ; Sherbrooke, Canada
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46
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Vinuesa P, Contreras-Moreira B. Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: a case study of pIncA/C plasmids. Methods Mol Biol 2015; 1231:203-232. [PMID: 25343868 DOI: 10.1007/978-1-4939-1720-4_14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
GET_HOMOLOGUES is an open-source software package written in Perl and R to define robust core- and pan-genomes by computing consensus clusters of orthologous gene families from whole-genome sequences using the bidirectional best-hit, COGtriangles, and OrthoMCL clustering algorithms. The granularity of the clusters can be fine-tuned by a user-configurable filtering strategy based on a combination of blastp pairwise alignment parameters, hmmscan-based scanning of Pfam domain composition of the proteins in each cluster, and a partial synteny criterion. We present detailed protocols to fit exponential and binomial mixture models to estimate core- and pan-genome sizes, compute pan-genome trees from the pan-genome matrix using a parsimony criterion, analyze and graphically represent the pan-genome structure, and identify lineage-specific gene families for the 12 complete pIncA/C plasmids currently available in NCBI's RefSeq. The software package, license, and detailed user manual can be downloaded for free for academic use from two mirrors: http://www.eead.csic.es/compbio/soft/gethoms.php and http://maya.ccg.unam.mx/soft/gethoms.php.
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Affiliation(s)
- Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca, Morelos, Mexico,
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47
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Wasyl D, Kern-Zdanowicz I, Domańska-Blicharz K, Zając M, Hoszowski A. High-level fluoroquinolone resistant Salmonella enterica serovar Kentucky ST198 epidemic clone with IncA/C conjugative plasmid carrying blaCTX-M-25 gene. Vet Microbiol 2015; 175:85-91. [DOI: 10.1016/j.vetmic.2014.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F. Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences. PLoS Genet 2014; 10:e1004766. [PMID: 25522143 PMCID: PMC4270462 DOI: 10.1371/journal.pgen.1004766] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 09/19/2014] [Indexed: 11/19/2022] Open
Abstract
Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ–proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages. Plasmids are difficult to analyze in WGS datasets, due to the fragmented nature of the obtained sequences. We developed a method, called PLACNET, which greatly facilitates this analysis. As an example, we analyzed the plasmidome of E. coli ST131, an ExPEC clonal group involved in human urinary tract infections and septicemia. Relevant variation within this clone (e.g., antibiotic resistance and virulence) is frequently caused by the acquisition and loss of plasmids and other mobile genetic elements. Nevertheless, our knowledge of the ST131 plasmidome is limited to a few antibiotic resistance plasmids and to identification of replicons from known plasmid groups. PLACNET analysis extends the number of sequenced plasmids in ST131, which can be used for comparative genomics, from 11 to 50. The ST131 plasmidome is seemingly huge, encompassing roughly 50% of the main plasmid groups of γ–proteobacteria. MOBF12/IncF plasmids are apparently the most active players in the dissemination of relevant genetic information.
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Affiliation(s)
- Val F. Lanza
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
| | - María de Toro
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
| | - M. Pilar Garcillán-Barcia
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de E. coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Teresa M. Coque
- Departamento de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública, (CIBER-ESP), Madrid, Spain
| | - Fernando de la Cruz
- Departamento de Biología Molecular (Universidad de Cantabria) and Instituto de Biomedicina y Biotecnología de Cantabria IBBTEC (UC-SODERCAN-CSIC), Santander, Spain
- * E-mail:
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Wei DD, Wan LG, Yu Y, Xu QF, Deng Q, Cao XW, Liu Y. Characterization of extended-spectrum beta-lactamase, carbapenemase, and plasmid quinolone determinants in Klebsiella pneumoniae isolates carrying distinct types of 16S rRNA methylase genes, and their association with mobile genetic elements. Microb Drug Resist 2014; 21:186-93. [PMID: 25469905 DOI: 10.1089/mdr.2014.0073] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Eighty-four multidrug-resistant Klebsiella pneumoniae (MDR-KP) isolates from a Chinese hospital from January to October 2012 were evaluated to characterize the coexistence of 16S rRNA methylase, extended-spectrum β-lactamase, carbapenemase, and plasmid-mediated quinolone resistance determinants and their association with mobile genetic elements. Among the 84 MDR-KP isolates studied, 19 isolates exhibited high-level resistance to amikacin mediated by the production of the 16S rRNA methylase. They carried 19 armA genes (22.9%) and three rmtB genes (3.6%). CTX-M genes were found in all of the isolates. Among these armA- or rmtB/CTX-M-producing K. pneumoniae isolates, 31.6% carried the carbapenemase genes (blaKPC-2 [26.3%], blaIMP-4 [10.5%], and blaNDM-1 [5.3%]), which made them resistant to imipenem (minimum inhibitory concentration [MIC] ≥16 mg/L). All positive strains possessed qnr-like genes (16 qnrA1, 10 qnrS1, and 7 qnrB4 genes) and 18 harbored an aac(6')-Ib-cr gene. Mobile elements ISEcp1, IS26, ISCR1, ISAba125, and sul-1 integrons were detected in 19/19 (100%), 16/19 (84.2%), 18/19 (94.7%), 9/19 (47.4%), and 18/19 (94.7%) isolates, respectively. The mobilizing elements occurred in different combinations in the study isolates. Majority of armA and qnr genes were in MDR-KP strains carrying integrons containing the ISCR1. Close to 80% of blaTEM-1 and blaSHV-12 were linked to IS26 while ≥90% of blaCTX-Ms and blaCMYs were linked to ISEcp1. ISAba125 was located upstream of blaNDM-1 and some blaCMY-2 genes. In addition, seven transconjugants were available for further analysis, and armA, qnrS1, acc(6')-Ib-cr, blaCTX-M-15, blaTEM-1, and blaNDM-1 were cotransferred. This study points to the dissemination of 16S rRNA methylase genes and the prevalence of selected elements implicated in evolution of resistance determinants in collection of clinical K. pneumoniae in China.
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Affiliation(s)
- Dan-Dan Wei
- 1 Department of Bacteriology, First Affiliated Hospital of Nanchang University, Nanchang University , Nanchang, People's Republic of China
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50
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Carraro N, Matteau D, Luo P, Rodrigue S, Burrus V. The master activator of IncA/C conjugative plasmids stimulates genomic islands and multidrug resistance dissemination. PLoS Genet 2014; 10:e1004714. [PMID: 25340549 PMCID: PMC4207636 DOI: 10.1371/journal.pgen.1004714] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/27/2014] [Indexed: 01/22/2023] Open
Abstract
Dissemination of antibiotic resistance genes occurs mostly by conjugation, which mediates DNA transfer between cells in direct contact. Conjugative plasmids of the IncA/C incompatibility group have become a substantial threat due to their broad host-range, the extended spectrum of antimicrobial resistance they confer, their prevalence in enteric bacteria and their very efficient spread by conjugation. However, their biology remains largely unexplored. Using the IncA/C conjugative plasmid pVCR94ΔX as a prototype, we have investigated the regulatory circuitry that governs IncA/C plasmids dissemination and found that the transcriptional activator complex AcaCD is essential for the expression of plasmid transfer genes. Using chromatin immunoprecipitation coupled with exonuclease digestion (ChIP-exo) and RNA sequencing (RNA-seq) approaches, we have identified the sequences recognized by AcaCD and characterized the AcaCD regulon. Data mining using the DNA motif recognized by AcaCD revealed potential AcaCD-binding sites upstream of genes involved in the intracellular mobility functions (recombination directionality factor and mobilization genes) in two widespread classes of genomic islands (GIs) phylogenetically unrelated to IncA/C plasmids. The first class, SGI1, confers and propagates multidrug resistance in Salmonella enterica and Proteus mirabilis, whereas MGIVmi1 in Vibrio mimicus belongs to a previously uncharacterized class of GIs. We have demonstrated that through expression of AcaCD, IncA/C plasmids specifically trigger the excision and mobilization of the GIs at high frequencies. This study provides new evidence of the considerable impact of IncA/C plasmids on bacterial genome plasticity through their own mobility and the mobilization of genomic islands. Multidrug resistance is a major health concern that complicates treatments of even the most common infections caused by bacteria. In recent years, IncA/C plasmids have emerged and spread in bacteria infecting humans, food-producing animals and food products, driving at the same time the dissemination of a broad spectrum of antibiotic resistance genes in environmental and in clinical settings. In this study, we have characterized the regulatory pathway that governs IncA/C plasmid dissemination. We have found that AcaCD, the master activator complex encoded by these plasmids, is not only essential for the dissemination of IncA/C plasmids but also activates unrelated mobile genetic elements in bacterial genomes, thereby further promoting the interspecies propagation of multidrug resistance and other adaptive traits at a very high frequency.
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Affiliation(s)
- Nicolas Carraro
- Laboratory of bacterial molecular genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Dominick Matteau
- Laboratory of microbial systems and synthetic biology, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Peng Luo
- Laboratory of bacterial molecular genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada; CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Sébastien Rodrigue
- Laboratory of microbial systems and synthetic biology, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
| | - Vincent Burrus
- Laboratory of bacterial molecular genetics, Département de biologie, Université de Sherbrooke, Sherbrooke, Canada
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