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Yao Y, Falgenhauer L, Rezazadeh Y, Falgenhauer J, Imirzalioglu C, Chakraborty T. Predominant transmission of KPC-2 carbapenemase in Germany by a unique IncN plasmid variant harboring a novel non-transposable element (NTE KPC -Y). Microbiol Spectr 2024; 12:e0256423. [PMID: 38084979 PMCID: PMC10790570 DOI: 10.1128/spectrum.02564-23] [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: 06/23/2023] [Accepted: 10/30/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Current infection control protocols assume that the spread of KPC-2 carbapenemase-producing Enterobacterales (KPC2-CPE) by detected carriers to other in-house patients is through clonal transmission and can be restricted by implementing containment measures. We examined the presence of the bla KPC-2 gene in different genera and species of Enterobacterales isolated from humans at different hospitals and surface waters between 2013 and 2019 in Germany. We found that a single IncN[pMLST15] plasmid carrying the bla KPC-2 gene on a novel non-Tn4401-element (NTEKPC-Y), flanked by an adjacent region encoding 12 other antibiotic resistance genes, was uniquely present in multiple species of KPC2-CPE isolates. These findings demonstrate the selective impact of specific IncN plasmids as major drivers of carbapenemase dissemination and suggest "plasmid-based endemicity" for KPC2-CPE. Studies on the dynamics of plasmid-based KPC2-CPE transmission and its presence in persistent reservoirs need to be urgently considered to implement effective surveillance and prevention measures in healthcare institutions.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Yalda Rezazadeh
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - the IncN Study GroupHauriAnja M.1HeinmüllerPetra1DomannEugen2GhoshHiren2GoesmannAlexander2JanssenStefan2GatermannSören3KaaseMartin3PfennigwerthNiels3ExnerMartin4OvermannJörg5BunkBoyke5SpröerCathrin5Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen - HLPUG, Dillenburg, GermanyJustus Liebig University Giessen, Giessen, GermanyGerman National Reference Centre for Multidrug-Resistant Gram-negative Bacteria, Ruhr-University Bochum, Bochum, GermanyUniversity of Bonn, Bonn, GermanyLeibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
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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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Ramkisson T, Rip D. Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context. AIMS Microbiol 2023; 9:668-691. [PMID: 38173973 PMCID: PMC10758576 DOI: 10.3934/microbiol.2023034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 01/05/2024] Open
Abstract
Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.
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Affiliation(s)
- Taish Ramkisson
- Department of Food Science, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Diane Rip
- Department of Food Science, Stellenbosch University, Stellenbosch, 7600, South Africa
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Harding-Crooks R, Smith D, Fanning S, Fox EM. Dissemination of carbapenemase-producing Enterobacteriaceae and associated resistance determinants through global food systems. Compr Rev Food Sci Food Saf 2023; 22:2706-2727. [PMID: 37083194 DOI: 10.1111/1541-4337.13159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
Antimicrobial agents are a critical component of modern healthcare systems, fulfilling a core function in patient care and improving individual patient outcomes and consequently overall public health. However, the efficacy of antimicrobial interventions is being consistently eroded by the emergence and dissemination of various antimicrobial resistance (AMR) mechanisms. One highly valued class of antimicrobial compounds is carbapenems, which retain efficacy in treating most multidrug-resistant infections and are considered "last line" agents. Therefore, recent trends in proliferation of carbapenem resistance (CR) via dissemination of carbapenemase-encoding genes among members of the Enterobacteriaceae family pose a significant threat to public health. While much of the focus relating to this has been on nosocomial environments, community-acquired carbapenemase-producing Enterobacteriaceae (CPE) infections and their associated transmission routes are less well studied. Among these community-associated vectors, the role of food chains and contaminated foods is important, since Enterobacteriaceae occupy niches within these settings. This review examines foodborne CPE transmission by exploring how interactions within and between food, the food chain, and agriculture not only promote and disseminate CPE, but also create reservoirs of mobile genetic elements that may lead to further carbapenemase gene proliferation both within and between microbial communities. Additionally, recent developments regarding the global occurrence and molecular epidemiology of CPEs in food chains will be reviewed.
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Affiliation(s)
| | - Darren Smith
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
- Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Edward M Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
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Li C, Zong G, Chen X, Tan M, Gao W, Fu J, Zhang P, Wang B, Cao G. Bifunctional protein ArsR M contributes to arsenite methylation and resistance in Brevundimonas sp. M20. BMC Microbiol 2023; 23:134. [PMID: 37193944 PMCID: PMC10190100 DOI: 10.1186/s12866-023-02876-z] [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: 02/21/2023] [Accepted: 04/30/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Arsenic (As) with various chemical forms, including inorganic arsenic and organic arsenic, is the most prevalent water and environmental toxin. This metalloid occurs worldwide and many of its forms, especially arsenite [As(III)], cause various diseases including cancer. Organification of arsenite is an effective way for organisms to cope with arsenic toxicity. Microbial communities are vital contributors to the global arsenic biocycle and represent a promising way to reduce arsenite toxicity. METHODS Brevundimonas sp. M20 with arsenite and roxarsone resistance was isolated from aquaculture sewage. The arsHRNBC cluster and the metRFHH operon of M20 were identified by sequencing. The gene encoding ArsR/methyltransferase fusion protein, arsRM, was amplified and expressed in Escherichia coli BL21 (DE3), and this strain showed resistance to arsenic in the present of 0.25-6 mM As(III), aresenate, or pentavalent roxarsone. The methylation activity and regulatory action of ArsRM were analyzed using Discovery Studio 2.0, and its functions were confirmed by methyltransferase activity analysis and electrophoretic mobility shift assays. RESULTS The minimum inhibitory concentration of the roxarsone resistant strain Brevundimonas sp. M20 to arsenite was 4.5 mM. A 3,011-bp arsenite resistance ars cluster arsHRNBC and a 5649-bp methionine biosynthesis met operon were found on the 3.315-Mb chromosome. Functional prediction analyses suggested that ArsRM is a difunctional protein with transcriptional regulation and methyltransferase activities. Expression of ArsRM in E. coli increased its arsenite resistance to 1.5 mM. The arsenite methylation activity of ArsRM and its ability to bind to its own gene promoter were confirmed. The As(III)-binding site (ABS) and S-adenosylmethionine-binding motif are responsible for the difunctional characteristic of ArsRM. CONCLUSIONS We conclude that ArsRM promotes arsenite methylation and is able to bind to its own promoter region to regulate transcription. This difunctional characteristic directly connects methionine and arsenic metabolism. Our findings contribute important new knowledge about microbial arsenic resistance and detoxification. Future work should further explore how ArsRM regulates the met operon and the ars cluster.
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Affiliation(s)
- Congcong Li
- Shandong Quancheng Test & Technology Limited Company, Ji'nan, 250101, China
| | - Gongli Zong
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Ji'nan, 250117, Shandong, China
| | - Xi Chen
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Ji'nan, 250117, Shandong, China
| | - Meixia Tan
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Ji'nan, 250117, Shandong, China
| | - Wenhui Gao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Ji'nan, 250117, Shandong, China
| | - Jiafang Fu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Ji'nan, 250117, Shandong, China
| | - Peipei Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, China
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Ji'nan, 250117, Shandong, China
| | - Bing Wang
- Shandong Quancheng Test & Technology Limited Company, Ji'nan, 250101, China.
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250062, China.
- NHC Key Laboratory of Biotechnology Drugs, Shandong Academy of Medical Sciences, Ji'nan, 250117, Shandong, China.
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Snaith AE, Dunn SJ, Moran RA, Newton PN, Dance DAB, Davong V, Kuenzli E, Kantele A, Corander J, McNally A. The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microb Genom 2023; 9:mgen001000. [PMID: 37171860 PMCID: PMC10272864 DOI: 10.1099/mgen.0.001000] [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: 08/24/2022] [Accepted: 02/24/2023] [Indexed: 05/13/2023] Open
Abstract
Increased colonization by antimicrobial-resistant organisms is closely associated with international travel. This study investigated the diversity of mobile genetic elements involved with antimicrobial resistance (AMR) gene carriage in extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli that colonized travellers to Laos. Long-read sequencing was used to reconstruct complete plasmid sequences from 48 isolates obtained from the daily stool samples of 23 travellers over a 3 week period. This method revealed a collection of 105 distinct plasmids, 38.1 % (n=40) of which carried AMR genes. The plasmids in this population were diverse, mostly unreported and included 38 replicon types, with F-type plasmids (n=23) the most prevalent amongst those carrying AMR genes. Fine-scale analysis of all plasmids identified numerous AMR gene contexts and emphasized the importance of IS elements, specifically members of the IS6/IS26 family, in the evolution of complex multidrug resistance regions. We found a concerning convergence of ESBL and colistin resistance determinants, with three plasmids from two different F-type lineages carrying bla CTX-M and mcr genes. The extensive diversity seen here highlights the worrying probability that stable new vehicles for AMR will evolve in E. coli populations that can disseminate internationally through travel networks.
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Affiliation(s)
- Ann E. Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Steven J. Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert A. Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Paul N. Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Laos
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - David A. B. Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Laos
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Viengmon Davong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Rue Mahosot, Vientiane, Laos
| | - Esther Kuenzli
- Department of Medicine, Swiss Tropical and Public Health Institute of Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Anu Kantele
- Meilahti Infectious Diseases and Vaccine Research Center, MeVac, Biomedicum 1, Haartmaninkatu 8, Helsinki University Hospital and University of Helsinki, Helsinki 00290, Finland
- Multidisciplinary Center of Excellence in Antimicrobial Resistance Research, University of Helsinki, Helsinki, Finland
- Human Microbiome Research Program, Faculty of Medicine, Haartmaninkatu 4, 00014 University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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Antimicrobial Resistance of Salmonella Strains Isolated from Human, Wild Boar, and Environmental Samples in 2018-2020 in the Northwest of Italy. Pathogens 2022; 11:pathogens11121446. [PMID: 36558780 PMCID: PMC9787983 DOI: 10.3390/pathogens11121446] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/26/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance is one of the most challenging public health problems worldwide, and integrated surveillance is a key aspect in a One Health control strategy. Additionally, Salmonella is the second most common zoonosis in Europe. We aimed to investigate the circulation of Salmonella strains and their related antimicrobial resistance in human, environmental, and wild boar samples from the northwest of Italy, from 2018 to 2020, to obtain a more comprehensive epidemiological picture. Salmonella Typhimurium 1,4,[5],12:i:-, S. Veneziana and S. Newport were the most common serotypes occurring in humans, the environment, and wild boar, respectively. Antimicrobial resistance was rather common in Salmonella isolates, with those from human displaying the highest degree of resistance against sulfadiazine−sulfamerazine−sulfamethazine (>90% of resistance). Moreover, resistance against azithromycin were exclusively observed in environmental samples, while only 7.7% (95% CI = 1.6−20.8) of wild boar isolates experienced resistance against trimethoprim−sulfamethoxazole. Multidrug resistance concurrently involved up to seven antimicrobial classes in human isolates, including third-generation cephalosporins and fluoroquinolones. Salmonella Typhimurium in humans and serotypes Goldcoast and Rissen from environmental sources showed the highest levels of resistance. This study shows diverse antimicrobial resistance patterns in Salmonella strains isolated from different sources and gives a broad picture of antimicrobial resistance spread in wild animals, humans, and the environment.
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Farooq M, Smoglica C, Ruffini F, Soldati L, Marsilio F, Di Francesco CE. Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy. Animals (Basel) 2022; 12:ani12182310. [PMID: 36139170 PMCID: PMC9495165 DOI: 10.3390/ani12182310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance is a complex and widespread problem threatening human and animal health. In poultry farms, a wide distribution of resistant bacteria and their relative genes is described worldwide, including in Italy. In this paper, a comparison of resistance gene distribution in litter samples, recovered from four conventional and four antibiotic-free broiler flocks, was performed to highlight any influence of farming systems on the spreading and maintenance of resistance determinants. Conventional PCR tests, targeting the resistance genes related to the most used antibiotics in poultry farming, along with some critically important antibiotics for human medicine, were applied. In conventional farms, n. 10 out of n. 30 investigated genes were present in at least one sample, the most abundant fragments being the tet genes specific for tetracyclines, followed by those for aminoglycosides and chloramphenicol. All conventional samples resulted negative for colistin, carbapenems, and vancomycin resistance genes. A similar trend was observed for antibiotic-free herds, with n. 13 out of n. 30 amplified genes, while a positivity for the mcr-1 gene, specific for colistin, was observed in one antibiotic-free flock. The statistical analysis revealed a significant difference for the tetM gene, which was found more frequently in the antibiotic-free category. The analysis carried out in this study allowed us to obtain new data about the distribution of resistance patterns in the poultry industry in relation to farming types. The PCR test is a quick and non-expensive laboratory tool for the environmental monitoring of resistance determinants identifying potential indicators of AMR dissemination.
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Affiliation(s)
- Muhammad Farooq
- Faculty of Veterinary Medicine, University of Teramo, Loc. Piano D’Accio, 64100 Teramo, Italy
| | - Camilla Smoglica
- Faculty of Veterinary Medicine, University of Teramo, Loc. Piano D’Accio, 64100 Teramo, Italy
| | | | - Lidia Soldati
- Faculty of Veterinary Medicine, University of Teramo, Loc. Piano D’Accio, 64100 Teramo, Italy
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, University of Teramo, Loc. Piano D’Accio, 64100 Teramo, Italy
| | - Cristina E. Di Francesco
- Faculty of Veterinary Medicine, University of Teramo, Loc. Piano D’Accio, 64100 Teramo, Italy
- Correspondence: ; Tel.: +39-0861-266869
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Dankittipong N, Fischer EAJ, Swanenburg M, Wagenaar JA, Stegeman AJ, de Vos CJ. Quantitative Risk Assessment for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms. Antibiotics (Basel) 2022; 11:antibiotics11020281. [PMID: 35203883 PMCID: PMC8868399 DOI: 10.3390/antibiotics11020281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/10/2022] Open
Abstract
Early detection of emerging carbapenem-resistant Enterobacteriaceae (CPE) in food-producing animals is essential to control the spread of CPE. We assessed the risk of CPE introduction from imported livestock, livestock feed, companion animals, hospital patients, and returning travelers into livestock farms in The Netherlands, including (1) broiler, (2) broiler breeder, (3) fattening pig, (4) breeding pig, (5) farrow-to-finish pig, and (6) veal calf farms. The expected annual number of introductions was calculated from the number of farms exposed to each CPE source and the probability that at least one animal in an exposed farm is colonized. The total number of farms with CPE colonization was estimated to be the highest for fattening pig farms, whereas the probability of introduction for an individual farm was the highest for broiler farms. Livestock feed and imported livestock are the most likely sources of CPE introduction into Dutch livestock farms. Sensitivity analysis indicated that the number of fattening pig farms determined the number of high introductions in fattening pigs from feed, and that uncertainty on CPE prevalence impacted the absolute risk estimate for all farm types. The results of this study can be used to inform risk-based surveillance for CPE in livestock farms.
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Affiliation(s)
- Natcha Dankittipong
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
- Correspondence:
| | - Egil A. J. Fischer
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
| | - Manon Swanenburg
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (M.S.); (C.J.d.V.)
| | - Jaap A. Wagenaar
- Department Biomolecular Health Science, Infectious Diseases & Immunology, Utrecht University, Androclusgebouw, Yalelaan 1, 3584 CL Utrecht, The Netherlands;
| | - Arjan J. Stegeman
- Department Population Health Sciences, Farm Animal Health, Utrecht University, Martinus G. de Bruingebouw, Yalelaan 7, 3584 CL Utrecht, The Netherlands; (E.A.J.F.); (A.J.S.)
| | - Clazien J. de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; (M.S.); (C.J.d.V.)
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Bombaywala S, Purohit HJ, Dafale NA. Mobility of antibiotic resistance and its co-occurrence with metal resistance in pathogens under oxidative stress. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 297:113315. [PMID: 34298350 DOI: 10.1016/j.jenvman.2021.113315] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
The bacterial communities are challenged with oxidative stress during their exposure to bactericidal antibiotics, metals, and different levels of dissolved oxygen (DO) encountered in diverse environmental habitats. The frequency of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) co-selection is increased by selective pressure posed by oxidative stress. Hence, study of resistance acquisition is important from an evolutionary perspective. To understand the dependence of oxidative stress on the dissemination of ARGs and MRGs through a pathogenic bacterial population, 12 metagenomes belonging to gut, water and soil habitats were evaluated. The metagenome-wide analysis showed the chicken gut to pose the most diverse pool of ARGs (30.4 ppm) and pathogenic bacteria (Simpson diversity = 0.98). The most common types of resistances found in all the environmental samples were efflux pumps (13.22 ppm) and genes conferring resistance to vancomycin (12.4 ppm), tetracycline (12.1 ppm), or beta-lactam (9.4 ppm) antibiotics. Additionally, limiting DO level in soil was observed to increase the abundance of excision nucleases (uvrA and uvrB), DNA polymerase (polA), catalases (katG), and other oxidative stress response genes (OSGs). This was further evident from major variations occurred in antibiotic efflux genes due to the effect of DO concentration on two human pathogens, namely Salmonella enterica and Shigella sonnei found in all the selected habitats. In conclusion, the microbial community, when challenged with oxidative stress caused by environmental variations in oxygen level, tends to accumulate higher amounts of ARGs with increased dissemination potential through triggering non-lethal mutagenesis. Furthermore, the genetic linkage or co-occurrence of ARGs and MRGs provides evidence for selecting ARGs under high concentrations of heavy metals.
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Affiliation(s)
- Sakina Bombaywala
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hemant J Purohit
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India
| | - Nishant A Dafale
- Environmental Biotechnology & Genomics Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur, 4400 20, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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11
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Exploring the Global Spread of Klebsiella grimontii Isolates Possessing blaVIM-1 and mcr-9. Antimicrob Agents Chemother 2021; 65:e0072421. [PMID: 34181480 DOI: 10.1128/aac.00724-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The spread of plasmid-mediated carbapenemases within Klebsiella oxytoca is well-documented. In contrast, data concerning the closely related species Klebsiella grimontii are scarce. In fact, despite the recent report of the first blaKPC-2-producing K. grimontii, nothing is known about its clonality and antibiotic resistance patterns. In a retrospective search in our collection, we identified 2 blaVIM-positive K. oxytoca strains. Whole-genome sequencing with both Illumina and Nanopore indicated that our strains actually belonged to K. grimontii and were of sequence type 172 (ST172) and ST189. Moreover, the two strains were associated with 297-kb IncHI2/HI2A-pST1 and 90.6-kb IncFII(Yp) plasmids carrying blaVIM-1 together with mcr-9 and blaVIM-1, respectively. In the IncHI2/HI2A plasmid, blaVIM-1 was located in a class 1 integron (In110), while mcr-9 was associated with the qseC-qseB-like regulatory elements. Overall, this plasmid was shown to be very similar to those carried by other Enterobacterales isolated from food and animal sources (e.g., Salmonella and Enterobacter spp. detected in Germany and Egypt). The IncFII(Yp) plasmid was unique, and its blaVIM-1 region was associated with a rare integron (In1373). Mapping of In1373 indicated a possible origin in Austria from an Enterobacter hormaechei carrying a highly similar plasmid. Core-genome phylogenies indicated that the ST172 K. grimontii belonged to a clone of identical Swedish and Swiss strains (≤15 single nucleotide variants [SNVs] to each other), whereas the ST189 strain was sporadic. Surveillance of carbapenemase-producing K. oxytoca strains should be reinforced to detect and prevent the dissemination of new species belonging to the Klebsiella genus.
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Abstract
Brevundimonas sp. is a bacteria able to grow in metal(loid) contaminated soil from Puchuncaví Valley, central Chile. This study has isolated a bacterial strain capable of growth under high doses of arsenic (As) (6000 mg L−1), and a draft genome sequence was generated. Additionally, real-time PCR was performed to examine the effect of As on some genes related to As resistance. Results demonstrated a total of 3275 predicted annotated genes with several genes related to the ars operon, metal(loid) resistance-related genes, metal efflux pumps, and detoxifying enzymes. Real-time PCR showed that the arsB involved in the efflux of As was down-regulated, whereas arsR, arsH, and ACR3 did not show differences with the addition of As. Our study provides novel evidence of diverse As regulating systems in tolerant bacteria that will lead to a better understanding of how microorganisms overcome toxic elements and colonize As contaminated soils and to the possible use of their specific properties in bioremediation.
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Diaconu EL, Alba P, Feltrin F, Di Matteo P, Iurescia M, Chelli E, Donati V, Marani I, Giacomi A, Franco A, Carfora V. Emergence of IncHI2 Plasmids With Mobilized Colistin Resistance ( mcr)- 9 Gene in ESBL-Producing, Multidrug-Resistant Salmonella Typhimurium and Its Monophasic Variant ST34 From Food-Producing Animals in Italy. Front Microbiol 2021; 12:705230. [PMID: 34335538 PMCID: PMC8322855 DOI: 10.3389/fmicb.2021.705230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/14/2021] [Indexed: 12/18/2022] Open
Abstract
A collection of 177 genomes of Salmonella Typhimurium and its monophasic variant isolated in 2014-2019 from Italian poultry/livestock (n = 165) and foodstuff (n = 12), previously screened for antimicrobial susceptibility and assigned to ST34 and single-locus variants, were studied in-depth to check the presence of the novel mcr-9 gene and to investigate their genetic relatedness by whole genome sequencing (WGS). The study of accessory resistance genes revealed the presence of mcr-9.1 in 11 ST34 isolates, displaying elevated colistin minimum inhibitory concentration values up to 2 mg/L and also a multidrug-resistant (MDR) profile toward up to seven antimicrobial classes. Five of them were also extended-spectrum beta-lactamases producers (bla SHV - 12 type), mediated by the corresponding antimicrobial resistance (AMR) accessory genes. All mcr-9-positive isolates harbored IncHI2-ST1 plasmids. From the results of the Mash analysis performed on all 177 genomes, the 11 mcr-9-positive isolates fell together in the same subcluster and were all closely related. This subcluster included also two mcr-9-negative isolates, and other eight mcr-9-negative ST34 isolates were present within the same parental branch. All the 21 isolates within this branch presented an IncHI2/2A plasmid and a similar MDR gene pattern. In three representative mcr-9-positive isolates, mcr-9 was demonstrated to be located on different IncHI2/IncHI2A large-size (∼277-297 kb) plasmids, using a combined Illumina-Oxford Nanopore WGS approach. These plasmids were also compared by BLAST analysis with publicly available IncHI2 plasmid sequences harboring mcr-9. In our plasmids, mcr-9 was located in a ∼30-kb region lacking different genetic elements of the typical core structure of mcr-9 cassettes. In this region were also identified different genes involved in heavy metal metabolism. Our results underline how genomics and WGS-based surveillance are increasingly indispensable to achieve better insights into the genetic environment and features of plasmid-mediated AMR, as in the case of such IncHI2 plasmids harboring other MDR genes beside mcr-9, that can be transferred horizontally also to other major Salmonella serovars spreading along the food chain.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Virginia Carfora
- National Reference Laboratory for Antimicrobial Resistance, General Diagnostics Department, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,”Rome, Italy
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Analysis of 56,348 Genomes Identifies the Relationship between Antibiotic and Metal Resistance and the Spread of Multidrug-Resistant Non-Typhoidal Salmonella. Microorganisms 2021; 9:microorganisms9071468. [PMID: 34361911 PMCID: PMC8306355 DOI: 10.3390/microorganisms9071468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 01/14/2023] Open
Abstract
Salmonella enterica is common foodborne pathogen that generates both enteric and systemic infections in hosts. Antibiotic resistance is common is certain serovars of the pathogen and of great concern to public health. Recent reports have documented the co-occurrence of metal resistance with antibiotic resistance in one serovar of S. enterica. Therefore, we sought to identify possible co-occurrence in a large genomic dataset. Genome assemblies of 56,348 strains of S. enterica comprising 20 major serovars were downloaded from NCBI. The downloaded assemblies were quality controlled and in silico serotyped to ensure consistency and avoid improper annotation from public databases. Metal and antibiotic resistance genes were identified in the genomes as well as plasmid replicons. Co-occurrent genes were identified by constructing a co-occurrence matrix and grouping said matrix using k-means clustering. Three groups of co-occurrent genes were identified using k-means clustering. Group 1 was comprised of the pco and sil operons that confer resistance to copper and silver, respectively. Group 1 was distributed across four serovars. Group 2 contained the majority of the genes and little to no co-occurrence was observed. Metal and antibiotic co-occurrence was identified in group 3 that contained genes conferring resistance to: arsenic, mercury, beta-lactams, sulfonamides, and tetracyclines. Group 3 genes were also associated with an IncQ1 class plasmid replicon. Metal and antibiotic co-occurrence from group 3 genes is mostly isolated to one clade of S. enterica I 4,[5],12:i:-.
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15
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Pauly N, Hammerl JA, Schwarz S, Grobbel M, Meemken D, Malorny B, Tenhagen BA, Käsbohrer A, Irrgang A. Co-occurrence of the blaVIM-1 and blaSHV-12 genes on an IncHI2 plasmid of an Escherichia coli isolate recovered from German livestock. J Antimicrob Chemother 2021; 76:531-533. [PMID: 33175149 PMCID: PMC7816165 DOI: 10.1093/jac/dkaa436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- N Pauly
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - J A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - S Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - M Grobbel
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - D Meemken
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
| | - B Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - B-A Tenhagen
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - A Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Vienna, Austria
| | - A Irrgang
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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16
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Heiden SE, Sydow K, Schaefer S, Klempien I, Balau V, Bauer P, Hübner NO, Schaufler K. Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany. Microorganisms 2021; 9:microorganisms9071345. [PMID: 34206177 PMCID: PMC8305640 DOI: 10.3390/microorganisms9071345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae limits therapeutic options and presents a major public health problem. Resistances to carbapenems are mostly conveyed by metallo-beta-lactamases (MBL) including VIM, which are often encoded on resistance plasmids. We characterized four VIM-positive isolates that were obtained as part of a routine diagnostic screening from two laboratories in north-eastern Germany between June and August 2020. Whole-genome sequencing was performed to address (a) phylogenetic properties, (b) plasmid content, and (c) resistance gene carriage. In addition, we performed phenotypic antibiotic and mercury resistance analyses. The genomic analysis revealed three different bacterial species including C. freundii, E. coli and K. oxytoca with four different sequence types. All isolates were geno- and phenotypically multidrug-resistant (MDR) and the phenotypic profile was explained by the underlying resistance gene content. Three isolates of four carried nearly identical VIM-1-resistance plasmids, which in addition encoded a mercury resistance operon and showed some similarity to two publicly available plasmid sequences from sources other than the two laboratories above. Our results highlight the circulation of a nearly identical IncN-type VIM-1-resistance plasmid in different Enterobacteriaceae in north-eastern Germany.
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Affiliation(s)
- Stefan E. Heiden
- Pharmaceutical Microbiology, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Katharina Sydow
- Pharmaceutical Microbiology, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
| | - Stephan Schaefer
- MVZ Laboratory Limbach Vorpommern-Rügen, 18435 Stralsund, Germany;
| | - Ingo Klempien
- Klinische Hygiene und Infektiologie, Helios Hanseklinikum, 18435 Stralsund, Germany;
| | - Veronika Balau
- IMD Laboratory Greifswald, Institute of Medical Diagnostics, 17493 Greifswald, Germany;
| | | | - Nils-Olaf Hübner
- Central Unit for Infection Prevention and Control, University Medicine Greifswald, 17475 Greifswald, Germany;
| | - Katharina Schaufler
- Pharmaceutical Microbiology, University of Greifswald, 17489 Greifswald, Germany; (S.E.H.); (K.S.)
- Correspondence: ; Tel.: +49-38344204869
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17
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First IncHI2 Plasmid Carrying mcr-9.1, blaVIM-1, and Double Copies of blaKPC-3 in a Multidrug-Resistant Escherichia coli Human Isolate. mSphere 2021; 6:e0030221. [PMID: 34047653 PMCID: PMC8265643 DOI: 10.1128/msphere.00302-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report a novel IncHI2 plasmid coharboring blaVIM-1, two copies of blaKPC-3, and mcr-9.1 resistance genes in a human Escherichia coli isolate of the new serogroup O188. The blaVIM-1 gene was included in a class 1 integron, mcr-9.1 in a cassette bracketed by IS903 and ΔIS1R, and blaKPC-3 in two copies within a new composite Tn4401-like transposon. The emergence of carbapenem and colistin resistance genes in a single plasmid is of great concern for upcoming clinical therapies.
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18
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de Man TJB, Yaffee AQ, Zhu W, Batra D, Alyanak E, Rowe LA, McAllister G, Moulton-Meissner H, Boyd S, Flinchum A, Slayton RB, Hancock S, Spalding Walters M, Laufer Halpin A, Rasheed JK, Noble-Wang J, Kallen AJ, Limbago BM. Multispecies Outbreak of Verona Integron-Encoded Metallo-ß-Lactamase-Producing Multidrug Resistant Bacteria Driven by a Promiscuous Incompatibility Group A/C2 Plasmid. Clin Infect Dis 2021; 72:414-420. [PMID: 32255490 DOI: 10.1093/cid/ciaa049] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/17/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Antibiotic resistance is often spread through bacterial populations via conjugative plasmids. However, plasmid transfer is not well recognized in clinical settings because of technical limitations, and health care-associated infections are usually caused by clonal transmission of a single pathogen. In 2015, multiple species of carbapenem-resistant Enterobacteriaceae (CRE), all producing a rare carbapenemase, were identified among patients in an intensive care unit. This observation suggested a large, previously unrecognized plasmid transmission chain and prompted our investigation. METHODS Electronic medical record reviews, infection control observations, and environmental sampling completed the epidemiologic outbreak investigation. A laboratory analysis, conducted on patient and environmental isolates, included long-read whole-genome sequencing to fully elucidate plasmid DNA structures. Bioinformatics analyses were applied to infer plasmid transmission chains and results were subsequently confirmed using plasmid conjugation experiments. RESULTS We identified 14 Verona integron-encoded metallo-ß-lactamase (VIM)-producing CRE in 12 patients, and 1 additional isolate was obtained from a patient room sink drain. Whole-genome sequencing identified the horizontal transfer of blaVIM-1, a rare carbapenem resistance mechanism in the United States, via a promiscuous incompatibility group A/C2 plasmid that spread among 5 bacterial species isolated from patients and the environment. CONCLUSIONS This investigation represents the largest known outbreak of VIM-producing CRE in the United States to date, which comprises numerous bacterial species and strains. We present evidence of in-hospital plasmid transmission, as well as environmental contamination. Our findings demonstrate the potential for 2 types of hospital-acquired infection outbreaks: those due to clonal expansion and those due to the spread of conjugative plasmids encoding antibiotic resistance across species.
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Affiliation(s)
- Tom J B de Man
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anna Q Yaffee
- Epidemic Intelligence Service, Division of Scientific Education and Professional Development, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,Kentucky Department for Public Health, Frankfort, Kentucky, USA
| | - Wenming Zhu
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dhwani Batra
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Efe Alyanak
- Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lori A Rowe
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Moulton-Meissner
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sandra Boyd
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Andrea Flinchum
- Kentucky Department for Public Health, Frankfort, Kentucky, USA
| | - Rachel B Slayton
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Steven Hancock
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.,Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Australia
| | - Maroya Spalding Walters
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - James Kamile Rasheed
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Judith Noble-Wang
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alexander J Kallen
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brandi M Limbago
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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19
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Ejikeugwu C, Nworie O, Saki M, Al-Dahmoshi HOM, Al-Khafaji NSK, Ezeador C, Nwakaeze E, Eze P, Oni E, Obi C, Iroha I, Esimone C, Adikwu MU. Metallo-β-lactamase and AmpC genes in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates from abattoir and poultry origin in Nigeria. BMC Microbiol 2021; 21:124. [PMID: 33882823 PMCID: PMC8059301 DOI: 10.1186/s12866-021-02179-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
Background Gram-negative bacteria (GNB) including Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae represent the most relevant reservoir of resistance genes such as metallo-β-lactamase (MBL) and AmpC genes that give them the undue advantage to resist antimicrobial onslaught. This study aimed to investigate the occurrence of MBL (blaIMP-1, blaIMP-2, blaVIM-1, blaVIM-2) and AmpC (blaFOX, blaDHA, blaCMY, blaACC) resistance genes in aforementioned GNB collected from abattoir and poultry sources in Nigeria. Results In total, 370 isolates were collected from abattoir tables (n = 130), anal region of cows (n = 120), and the cloacae of poultry birds (n = 120). The test isolates showed high rate of resistance to cephalosporins and carbapenems. The MBLs were phenotypically detected in 22 E. coli, 22 P. aeruginosa, and 18 K. pneumoniae isolates using combined disc test (CDT). However, only 11 E. coli, 24 P. aeruginosa, and 18 Klebsiella pneumoniae isolates were phenotypically confirmed to be AmpC producers using cefoxitin-cloxacillin double disk synergy test (CC-DDST). MBL encoding genes (particularly the blaIMP-1 genes and blaIMP-2 genes) were detected by polymerase chain reaction (PCR) in 12 (54.6%) E. coli, 15 (83.3%) K. pneumoniae, and 16 (72.7%) P. aeruginosa isolates. AmpC genes (particularly the blaCMY genes and blaFOX genes) were found in a total of 5 (29.4%) E. coli isolates, 5 (27.8%) isolates of K. pneumoniae, and 10 (41.7%) isolates of P. aeruginosa. Conclusions Our study showed the circulation of MBL and AmpC genes in GNB from abattoir and poultry origin in Nigeria. Adoption of regular control policies is necessary to reduce the spread of these species as soon as possible, especially in poultry and slaughterhouses.
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Affiliation(s)
- Chika Ejikeugwu
- Department of Applied Microbiology, Ebonyi State University, Abakaliki, Nigeria
| | - Okoro Nworie
- Department of Biological Sciences, Alex Ekwueme Federal University, Ndufu-Alike Ikwo, Ikwo, Nigeria
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Hussein O M Al-Dahmoshi
- Biology Department, College of Science, University of Babylon, Hilla City, Babylon Province, Iraq
| | - Noor S K Al-Khafaji
- Biology Department, College of Science, University of Babylon, Hilla City, Babylon Province, Iraq
| | - Chika Ezeador
- Department of Medical Microbiology & Parasitology, Nnamdi Azikiwe University, Awka, Nigeria
| | - Emmanuel Nwakaeze
- Department of Applied Microbiology, Ebonyi State University, Abakaliki, Nigeria
| | - Peter Eze
- Department of Environmental Health Science, Nnamdi Azikiwe University, Awka, Nigeria
| | - Eniola Oni
- Department of Microbiology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Chidiebere Obi
- Department of Microbiology, Federal University, Birnin Kebbi, Nigeria
| | - Ifeanyichukwu Iroha
- Department of Applied Microbiology, Ebonyi State University, Abakaliki, Nigeria
| | - Charles Esimone
- Department of Pharmaceutical Microbiology and Biotechnology, Nnamdi Azikiwe University, Awka, Nigeria
| | - Michael U Adikwu
- Department of Pharmaceutics, University of Nigeria, Nsukka, Nigeria
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20
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Shang D, Zhao H, Xu X, Arunachalam K, Chang J, Bai L, Shi C. Conjugative IncHI2 plasmid harboring novel class 1 integron mediated dissemination of multidrug resistance genes in Salmonella Typhimurium. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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21
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Mthembu TP, Zishiri OT, El Zowalaty ME. Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species. Animals (Basel) 2021; 11:ani11030872. [PMID: 33803844 PMCID: PMC8003163 DOI: 10.3390/ani11030872] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In the era of the COVID-19 global pandemic, antimicrobial resistance is looming as an imminent threat and challenge to human public health. Antimicrobial resistance is a major global threat of increasing concern to human and animal health. It also has implications for both food safety and food security and the economic well-being of millions of humans. Among other zoonotic infectious diseases, antimicrobial resistance in food chain and livestock-associated pathogens such as Salmonella is of great concern. In the present study, the genomic characterization of antimicrobial resistance in food chain and livestock-associated Salmonella was summarized. Several antimicrobial resistance determinants were reported in Salmonella isolated from food chain animals and livestock. Monitoring of antimicrobial resistance in Salmonella in livestock and food chain animals through genomic characterization is significant to control and protect humans from the threat of antimicrobial resistance. Salmonella, a foodborne zoonotic enterobacterium species can transmit antimicrobial resistance from the microbiome of animals to humans. This study summarizes the genomic characterization of antimicrobial resistance in Salmonella species with special focus on resistance against carbapenems and colistin which are the last resort antibiotics used against infections caused by multidrug resistant bacteria. The present review aims to draw attention to prudent use of antibiotics, a good example of the One Health concept. Abstract The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.
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Affiliation(s)
- Thobeka P. Mthembu
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa; (T.P.M.); (O.T.Z.)
| | - Oliver T. Zishiri
- Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa; (T.P.M.); (O.T.Z.)
| | - Mohamed E. El Zowalaty
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala SE 751 23, Sweden
- Correspondence:
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22
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Pauly N, Hammerl JA, Grobbel M, Tenhagen BA, Käsbohrer A, Bisenius S, Fuchs J, Horlacher S, Lingstädt H, Mauermann U, Mitro S, Müller M, Rohrmann S, Schiffmann AP, Stührenberg B, Zimmermann P, Schwarz S, Meemken D, Irrgang A. ChromID ® CARBA Agar Fails to Detect Carbapenem-Resistant Enterobacteriaceae With Slightly Reduced Susceptibility to Carbapenems. Front Microbiol 2020; 11:1678. [PMID: 32849351 PMCID: PMC7432429 DOI: 10.3389/fmicb.2020.01678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/26/2020] [Indexed: 02/02/2023] Open
Abstract
After first detections of carbapenemase-producing Enterobacteriaceae (CPE) in animals, the European Union Reference Laboratory for Antimicrobial Resistance has provided a protocol for the isolation of carbapenemase-producing Escherichia (E.) coli from cecum content and meat. Up to now, only few isolates were recovered using this procedure. In our experience, the choice of the selective agar is important for the efficacy of the method. Currently, the use of the prevailing method fails to detect CPE that exhibit a low resistance against carbapenems. Thus, this study aims to evaluate the suitability of selective media with antibiotic supplements and commercial ChromID® CARBA agar for a reliable CPE detection. For comparative investigations, detection of freeze-dried carbapenemase-resistant bacteria was studied on different batches of the ChromID® CARBA agar as well as on MacConkey agar supplemented with 1 mg/L cefotaxime and 0.125 mg/L meropenem (McC+CTX+MEM). The suitability of the different media was assessed within a time of 25 weeks, starting at least six weeks before expiration of the media. Carbapenem-resistant isolates exhibiting a serine-based hydrolytic resistance mechanism (e.g., bla KPC genes) were consistently detected over 25 weeks on the different media. In contrast, carbapenemase producers with only slightly reduced susceptibility and exhibiting a zinc-catalyzed activity (e.g., bla VIM, bla NDM, and bla IMP) could only be cultivated on long-time expired ChromID® CARBA, but within the whole test period on McC+CTX+MEM. Thus, ChromID® CARBA agar appears to be not suitable for the detection of CPE with slightly increased minimum inhibitory concentrations (MIC) against carbapenems, which have been detected in German livestock and thus, are of main interest in the national monitoring programs. Our data are in concordance with the results of eleven state laboratories that had participated in this study with their ChromID® CARBA batches routinely used for the German CPE monitoring. Based on the determined CPE detection rate, we recommend the use of McC+CTX+MEM for monitoring purposes. This study indicates that the use of ChromID® CARBA agar might lead to an underestimation of the current CPE occurrence in food and livestock samples.
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Affiliation(s)
- Natalie Pauly
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens A Hammerl
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mirjam Grobbel
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Annemarie Käsbohrer
- German Federal Institute for Risk Assessment, Berlin, Germany.,Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, Vienna, Austria
| | - Sandra Bisenius
- Institute for Fish and Fishery Products (LAVES), Cuxhaven, Germany
| | - Jannika Fuchs
- Chemical and Veterinary Investigation Office, Karlsruhe, Germany
| | | | - Holger Lingstädt
- State Office for Consumer Protection Saxony-Anhalt, Stendal, Germany
| | | | - Silke Mitro
- State Investigation Institute for Health and Veterinary Services, Chemnitz, Germany
| | - Margit Müller
- Chemical and Veterinary Investigation Office Rhein-Ruhr-Wupper, Krefeld, Germany
| | - Stefan Rohrmann
- Chemical and Veterinary Investigation Office, Arnsberg, Germany
| | | | | | - Pia Zimmermann
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Diana Meemken
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, Berlin, Germany
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23
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Zingali T, Chapman TA, Webster J, Roy Chowdhury P, Djordjevic SP. Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia. Microorganisms 2020; 8:microorganisms8060896. [PMID: 32545892 PMCID: PMC7355605 DOI: 10.3390/microorganisms8060896] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 01/16/2023] Open
Abstract
Antibiotic resistance genes (ARGs) including those from the blaCTX-M family and mcr-1 that encode resistance to extended spectrum β–lactams and colistin, respectively, have been linked with IncHI2 plasmids isolated from swine production facilities globally but not in IncHI2 plasmids from Australia. Here we describe the first complete sequence of a multiple drug resistance Australian IncHI2-ST4 plasmid, pTZ41_1P, from a commensal E. coli from a healthy piglet. pTZ41_1P carries genes conferring resistance to heavy-metals (copper, silver, tellurium and arsenic), β-lactams, aminoglycosides and sulphonamides. The ARGs reside within a complex resistance locus (CRL) that shows considerable sequence identity to a CRL in pSDE_SvHI2, an IncHI2:ST3 plasmid from an enterotoxigenic E. coli with serotype O157:H19 of porcine origin that caused substantial losses to swine production operations in Australia in 2007. pTZ41_1P is closely related to IncHI2 plasmids found in E. coli and Salmonella enterica from porcine, avian and human sources in Europe and China but it does not carry genes encoding resistance to clinically-important antibiotics. We identified regions of IncHI2 plasmids that contribute to the genetic plasticity of this group of plasmids and highlight how they may readily acquire new resistance gene cargo. Genomic surveillance should be improved to monitor IncHI2 plasmids.
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Affiliation(s)
- Tiziana Zingali
- The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; (T.Z.); (P.R.C.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
| | - Toni A. Chapman
- NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia; (T.A.C.); (J.W.)
| | - John Webster
- NSW Department of Primary Industries, Elizabeth MacArthur Agricultural Institute, Menangle, NSW 2568, Australia; (T.A.C.); (J.W.)
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; (T.Z.); (P.R.C.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
| | - Steven P. Djordjevic
- The ithree Institute, University of Technology Sydney, City Campus, Ultimo, NSW 2007, Australia; (T.Z.); (P.R.C.)
- Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, P.O. Box 123, Broadway, NSW 2007, Australia
- Correspondence: ; Tel.: +61-2-9514-4127
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24
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Han YH, Yin DX, Jia MR, Wang SS, Chen Y, Rathinasabapathi B, Chen DL, Ma LQ. Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:1178-1189. [PMID: 31470481 DOI: 10.1016/j.scitotenv.2019.07.098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/06/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Microbial arsenic transformation is important in As biogeochemical cycles in the environment. In this study, a new As-resistant bacterial strain Leclercia adecarboxylata As3-1 was isolated and its associated mechanisms in As resistance and detoxification were evaluated based on genome sequencing and gene annotations. After subjecting strain As3-1 to medium containing arsenate (AsV), AsV reduction occurred and an AsV-enhanced bacterial growth was observed. Strain As3-1 lacked arsenite (AsIII) oxidation ability and displayed lower AsIII resistance than AsV, probably due to its higher AsIII accumulation. Polymerase chain reaction and phylogenetic analysis showed that strain As3-1 harbored a typical AsV reductase gene (arsC) on the plasmids. Genome sequencing and gene annotations identified four operons phoUpstBACS, arsHRBC, arsCRDABC and ttrRSBCA, with 8 additional genes outside the operons that might have involved in As resistance and detoxification in strain As3-1. These included 5 arsC genes explaining why strain As3-1 tolerated high AsV concentrations. Besides ArsC, TtrB, TtrC and TtrA proteins could also be involved in AsV reduction and consequent energy acquisition for bacterial growth. Our data provided a new example of diverse As-regulating systems and AsV-enhanced growth without ArrA in bacteria. The information helps to understand the role of As in selecting microbial systems that can transform and utilize As.
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Affiliation(s)
- Yong-He Han
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, China
| | - Dai-Xia Yin
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Meng-Ru Jia
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Shan-Shan Wang
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China
| | - Yanshan Chen
- School of the Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Bala Rathinasabapathi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Deng-Long Chen
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; Innovative Center for Eco-Friendly Polymeric Materials, Quanzhou, Fujian 362801, China.
| | - Lena Q Ma
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States.
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25
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Irrgang A, Tenhagen BA, Pauly N, Schmoger S, Kaesbohrer A, Hammerl JA. Characterization of VIM-1-Producing E. coli Isolated From a German Fattening Pig Farm by an Improved Isolation Procedure. Front Microbiol 2019; 10:2256. [PMID: 31632372 PMCID: PMC6779854 DOI: 10.3389/fmicb.2019.02256] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/17/2019] [Indexed: 01/08/2023] Open
Abstract
A few reports indicate that livestock might represent a new reservoir for carbapenemase-producing Enterobacteriaceae (CPE). In 2015, VIM-1-producing Escherichia coli were detected at slaughter in colon contents of animals from a German fattening pig farm within the national monitoring on ESBL-producing E. coli. In this study, pooled faces samples from pigs, as well as samples from the barn surrounding environment of this fattening farm were taken, to evaluate the dissemination of CPEs. Several modifications of the culture-dependent detection procedure were investigated for their potential to improve the sensitivity of the CPE isolation method. The current reference procedure was adapted by adding a real-time PCR pre-screening and additional enrichment steps. It was possible to isolate 32 VIM-1-producing E. coli from four fecal samples of three different barns using two serial enrichment steps in combination with real-time PCR and selective agar plates. By genetic typing, we confirmed the presence of two E. coli clonal lineages circulating on this particular farm: one was harboring the blaVIM–1 on an IncHI2 plasmid while the second lineage carried the gene on the chromosome. Despite its different locations, the blaVIM–1 gene was harbored on a class 1 integron in both clonal lineages. Whole-genome sequencing revealed that the VIM-1-carrying plasmids exhibited only slight variability in its compositions and sizes. We assume that the prevalence of CPEs in animal production in Germany and other European countries might be underestimated and there is a concern of further spread of VIM-1-producing bacteria in German livestock and food.
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Affiliation(s)
- A Irrgang
- Unit of Epidemiology, Zoonoses and Antimicrobial Resistance, Department of Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR), Berlin, Germany
| | - B-A Tenhagen
- Unit of Epidemiology, Zoonoses and Antimicrobial Resistance, Department of Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR), Berlin, Germany
| | - N Pauly
- Unit of Epidemiology, Zoonoses and Antimicrobial Resistance, Department of Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR), Berlin, Germany
| | - S Schmoger
- Unit of Epidemiology, Zoonoses and Antimicrobial Resistance, Department of Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR), Berlin, Germany
| | - Annemarie Kaesbohrer
- Unit of Epidemiology, Zoonoses and Antimicrobial Resistance, Department of Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR), Berlin, Germany.,Institute for Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - J A Hammerl
- Unit of Epidemiology, Zoonoses and Antimicrobial Resistance, Department of Biological Safety, German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR), Berlin, Germany
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26
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Roschanski N, Hadziabdic S, Borowiak M, Malorny B, Tenhagen BA, Projahn M, Kaesbohrer A, Guenther S, Szabo I, Roesler U, Fischer J. Detection of VIM-1-Producing Enterobacter cloacae and Salmonella enterica Serovars Infantis and Goldcoast at a Breeding Pig Farm in Germany in 2017 and Their Molecular Relationship to Former VIM-1-Producing S. Infantis Isolates in German Livestock Production. mSphere 2019; 4:e00089-19. [PMID: 31189558 PMCID: PMC6563352 DOI: 10.1128/msphere.00089-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/23/2019] [Indexed: 01/30/2023] Open
Abstract
In 2011, VIM-1-producing Salmonella enterica serovar Infantis and Escherichia coli were isolated for the first time in four German livestock farms. In 2015/2016, highly related isolates were identified in German pig production. This raised the issue of potential reservoirs for these isolates, the relation of their mobile genetic elements, and potential links between the different affected farms/facilities. In a piglet-producing farm suspicious for being linked to some blaVIM-1 findings in Germany, fecal and environmental samples were examined for the presence of carbapenemase-producing Enterobacteriaceae and Salmonella spp. Newly discovered isolates were subjected to Illumina whole-genome sequencing (WGS) and S1 pulsed-field gel electrophoresis (PFGE) hybridization experiments. WGS data of these isolates were compared with those for the previously isolated VIM-1-producing Salmonella Infantis isolates from pigs and poultry. Among 103 samples, one Salmonella Goldcoast isolate, one Salmonella Infantis isolate, and one Enterobacter cloacae isolate carrying the blaVIM-1 gene were detected. Comparative WGS analysis revealed that the blaVIM-1 gene was part of a particular Tn21-like transposable element in all isolates. It was located on IncHI2 (ST1) plasmids of ∼290 to 300 kb with a backbone highly similar (98 to 100%) to that of reference pSE15-SA01028. SNP analysis revealed a close relationship of all VIM-1-positive S Infantis isolates described since 2011. The findings of this study demonstrate that the occurrence of the blaVIM-1 gene in German livestock is restricted neither to a certain bacterial species nor to a certain Salmonella serovar but is linked to a particular Tn21-like transposable element located on transferable pSE15-SA01028-like IncHI2 (ST1) plasmids, being present in all of the investigated isolates from 2011 to 2017.IMPORTANCE Carbapenems are considered one of few remaining treatment options against multidrug-resistant Gram-negative pathogens in human clinical settings. The occurrence of carbapenemase-producing Enterobacteriaceae in livestock and food is a major public health concern. Particularly the occurrence of VIM-1-producing Salmonella Infantis in livestock farms is worrisome, as this zoonotic pathogen is one of the main causes for human salmonellosis in Europe. Investigations on the epidemiology of those carbapenemase-producing isolates and associated mobile genetic elements through an in-depth molecular characterization are indispensable to understand the transmission of carbapenemase-producing Enterobacteriaceae along the food chain and between different populations to develop strategies to prevent their further spread.
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Affiliation(s)
- Nicole Roschanski
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Sead Hadziabdic
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Bernd-Alois Tenhagen
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Michaela Projahn
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Annemarie Kaesbohrer
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
- Institute of Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Sebastian Guenther
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Istvan Szabo
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, BfR, Berlin, Germany
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27
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Bonardi S, Pitino R. Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: A challenge for human health. Ital J Food Saf 2019; 8:7956. [PMID: 31316921 PMCID: PMC6603432 DOI: 10.4081/ijfs.2019.7956] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/09/2019] [Indexed: 01/11/2023] Open
Abstract
Antimicrobial resistance is an increasing global health problem and one of the major concerns for economic impacts worldwide. Recently, resistance against carbapenems (doripenem, ertapenem, imipenem, meropenem), which are critically important antimicrobials for human cares, poses a great risk all over the world. Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and encoded by both chromosomal and plasmidic genes. They hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillins and aztreonam. Despite several studies in human patients and hospital settings have been performed in European countries, the role of livestock animals, wild animals and the terrestrial and aquatic environment in the maintenance and transmission of carbapenemase- producing bacteria has been poorly investigated. The present review focuses on the carbapenemase-producing bacteria detected in pigs, cattle, poultry, fish, mollusks, wild birds and wild mammals in Europe as well as in non-European countries, investigating the genetic mechanisms for their transmission among food-producing animals and wildlife. To shed light on the important role of the environment in the maintenance and genetic exchange of resistance determinants between environmental and pathogenic bacteria, studies on aquatic sources (rivers, lakes, as well as wastewater treatment plants) are described.
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Affiliation(s)
- Silvia Bonardi
- Department of Veterinary Science, University of Parma, Italy
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28
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Wyrsch ER, Reid CJ, DeMaere MZ, Liu MY, Chapman TA, Roy Chowdhury P, Djordjevic SP. Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017. EFSA J 2019; 17:e05598. [PMID: 32626224 PMCID: PMC7009238 DOI: 10.2903/j.efsa.2019.5598] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The data on antimicrobial resistance in zoonotic and indicator bacteria in 2017, submitted by 28 EU Member States (MSs), were jointly analysed by EFSA and ECDC. Resistance in zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as meticillin‐resistant Staphylococcus aureus in animals and food were addressed, and temporal trends assessed. ‘Microbiological’ resistance was assessed using epidemiological cut‐off (ECOFF) values; for some countries, qualitative data on human isolates were interpreted in a way which corresponds closely to the ECOFF‐defined ‘microbiological’ resistance. In Salmonella from humans, as well as in Salmonella and E. coli isolates from fattening pigs and calves of less than 1 year of age, high proportions of isolates were resistant to ampicillin, sulfonamides and tetracyclines, whereas resistance to third‐generation cephalosporins was uncommon. Varying occurrence/prevalence rates of presumptive extended‐spectrum beta‐lactamase (ESBL)/AmpC producers in Salmonella and E. coli monitored in meat (pork and beef), fattening pigs and calves, and Salmonella monitored in humans, were observed between countries. Carbapenemase‐producing E. coli were detected in one single
sample from fattening pigs in one MS. Resistance to colistin was observed at low levels in Salmonella and E. coli from fattening pigs and calves and meat thereof and in Salmonella from humans. In Campylobacter from humans, high to extremely high proportions of isolates were resistant to ciprofloxacin and tetracyclines, particularly in Campylobacter coli. In five countries, high to very high proportions of C. coli from humans were resistant also to erythromycin, leaving few options for treatment of severe Campylobacter infections. High resistance to ciprofloxacin and tetracyclines was observed in C. coli isolates from fattening pigs, whereas much lower levels were recorded for erythromycin. Combined resistance to critically important antimicrobials in both human and animal isolates was generally uncommon but very high to extremely high multidrug resistance levels were observed in S. Typhimurium and its monophasic variant in both humans and animals. S. Kentucky from humans exhibited high‐level resistance to ciprofloxacin, in addition to a high prevalence of ESBL.
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30
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Bonardi S, Cabassi CS, Longhi S, Pia F, Corradi M, Gilioli S, Scaltriti E. Detection of Extended- Spectrum Beta-Lactamase producing Escherichia coli from mesenteric lymph nodes of wild boars ( Sus scrofa). Ital J Food Saf 2019; 7:7707. [PMID: 30854342 PMCID: PMC6379689 DOI: 10.4081/ijfs.2018.7707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/15/2018] [Indexed: 12/20/2022] Open
Abstract
Wild boars (Sus scrofa) are increasing in several European countries, including Italy. In areas with intensive animal farming, like the Italian Emilia-Romagna region, they are likely to be exposed to antimicrobialresistant (AMR) bacteria of livestock origin. In 2017-2018, 108 mesenteric lymph nodes samples were collected from 108 wild boars hunted in Parma province, Emilia-Romagna region, to be tested for ESBL- and carbapenemase-producing Escherichia coli. One isolate (WB-21L) out of 108 (0.9%) was phenotypically confirmed as ESBLproducing E. coli. The strain WB-21L was tested by PCR for the genes blaSHV, blaCTX-M, blaTEM, blaAmpC, blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48, blaSPM, blaBIC, blaSIM, blaDIM, blaGIM, blaAIM, resulting positive for TEM β- lactamase. Resistance to ampicillin, amoxicillin/clavulanic acid, streptomycin, sulfasomidine, tetracycline and trimethoprim confirmed the multi-resistance nature of the strain WB-21L. Nine E.coli isolates showed resistance to meropenem by the Kirby Bauer test but none of them showed Meropenem MIC values indicative of resistance. In conclusion, the present study shows the presence of ESBL E. coli in wild boars and the possible risk of transfer to game meat handlers and consumers. Future studies are needed to better evaluate the sources of AMR bacteria in wildlife.
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Affiliation(s)
| | | | - Simona Longhi
- Department of Veterinary Sciences, University of Parma
| | - Federico Pia
- Department of Veterinary Sciences, University of Parma
| | - Margherita Corradi
- Management Body for Parks and Biodiversity "Emilia Occidentale", Sala Baganza (PR)
| | - Stefano Gilioli
- Management Body for Parks and Biodiversity "Emilia Occidentale", Sala Baganza (PR)
| | - Erika Scaltriti
- Experimental Institute for Zooprophylaxis of Lombardy and Emilia-Romagna Regions, Risk Analysis and Genomic Epidemiology Unit, Parma, Italy
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31
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Ben Fekih I, Zhang C, Li YP, Zhao Y, Alwathnani HA, Saquib Q, Rensing C, Cervantes C. Distribution of Arsenic Resistance Genes in Prokaryotes. Front Microbiol 2018; 9:2473. [PMID: 30405552 PMCID: PMC6205960 DOI: 10.3389/fmicb.2018.02473] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/27/2018] [Indexed: 12/13/2022] Open
Abstract
Arsenic is a metalloid that occurs naturally in aquatic and terrestrial environments. The high toxicity of arsenic derivatives converts this element in a serious problem of public health worldwide. There is a global arsenic geocycle in which microbes play a relevant role. Ancient exposure to arsenic derivatives, both inorganic and organic, has represented a selective pressure for microbes to evolve or acquire diverse arsenic resistance genetic systems. In addition, arsenic compounds appear to have been used as a toxin in chemical warfare for a long time selecting for an extended range of arsenic resistance determinants. Arsenic resistance strategies rely mainly on membrane transport pathways that extrude the toxic compounds from the cell cytoplasm. The ars operons, first discovered in bacterial R-factors almost 50 years ago, are the most common microbial arsenic resistance systems. Numerous ars operons, with a variety of genes and different combinations of them, populate the prokaryotic genomes, including their accessory plasmids, transposons, and genomic islands. Besides these canonical, widespread ars gene clusters, which confer resistance to the inorganic forms of arsenic, additional genes have been discovered recently, which broadens the spectrum of arsenic tolerance by detoxifying organic arsenic derivatives often used as toxins. This review summarizes the presence, distribution, organization, and redundance of arsenic resistance genes in prokaryotes.
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Affiliation(s)
- Ibtissem Ben Fekih
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chengkang Zhang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Ping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi Zhao
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hend A Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Quaiser Saquib
- Department of Zoology, College of Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.,Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Carlos Cervantes
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana, Morelia, Mexico
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Chalmers G, Rozas KM, Amachawadi RG, Scott HM, Norman KN, Nagaraja TG, Tokach MD, Boerlin P. Distribution of the pco Gene Cluster and Associated Genetic Determinants among Swine Escherichia coli from a Controlled Feeding Trial. Genes (Basel) 2018; 9:E504. [PMID: 30340352 PMCID: PMC6211086 DOI: 10.3390/genes9100504] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
Copper is used as an alternative to antibiotics for growth promotion and disease prevention. However, bacteria developed tolerance mechanisms for elevated copper concentrations, including those encoded by the pco operon in Gram-negative bacteria. Using cohorts of weaned piglets, this study showed that the supplementation of feed with copper concentrations as used in the field did not result in a significant short-term increase in the proportion of pco-positive fecal Escherichia coli. The pco and sil (silver resistance) operons were found concurrently in all screened isolates, and whole-genome sequencing showed that they were distributed among a diversity of unrelated E. coli strains. The presence of pco/sil in E. coli was not associated with elevated copper minimal inhibitory concentrations (MICs) under a variety of conditions. As found in previous studies, the pco/sil operons were part of a Tn7-like structure found both on the chromosome or on plasmids in the E. coli strains investigated. Transfer of a pco/sil IncHI2 plasmid from E. coli to Salmonella enterica resulted in elevated copper MICs in the latter. Escherichia coli may represent a reservoir of pco/sil genes transferable to other organisms such as S. enterica, for which it may represent an advantage in the presence of copper. This, in turn, has the potential for co-selection of resistance to antibiotics.
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Affiliation(s)
- Gabhan Chalmers
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E., Guelph, ON N1G 2W1, Canada.
| | - Kelly M Rozas
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Raghavendra G Amachawadi
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Harvey Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Keri N Norman
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA.
| | - Tiruvoor G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Mike D Tokach
- Department of Animal Sciences & Industry, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA.
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Rd. E., Guelph, ON N1G 2W1, Canada.
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Borowiak M, Szabo I, Baumann B, Junker E, Hammerl JA, Kaesbohrer A, Malorny B, Fischer J. VIM-1-producing Salmonella Infantis isolated from swine and minced pork meat in Germany. J Antimicrob Chemother 2018; 72:2131-2133. [PMID: 28369508 DOI: 10.1093/jac/dkx101] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Istvan Szabo
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Beatrice Baumann
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Ernst Junker
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Jens A Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Annemarie Kaesbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
| | - Jennie Fischer
- Department for Biological Safety, German Federal Institute for Risk Assessment, BfR, Max-Dohrn Strasse 8-10, D-10589 Berlin, Germany
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Madec JY, Haenni M. Antimicrobial resistance plasmid reservoir in food and food-producing animals. Plasmid 2018; 99:72-81. [PMID: 30194944 DOI: 10.1016/j.plasmid.2018.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 09/03/2018] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance (AMR) plasmids have been recognized as important vectors for efficient spread of AMR phenotypes. The food reservoir includes both food-producing animals and food products, and a huge diversity of AMR plasmids have been reported in this sector. Based on molecular typing methods and/or whole genome sequencing approaches, certain AMR genes/plasmids combinations were found more frequently in food compared to other settings. However, the food source of a definite AMR plasmid is highly complex to confirm due to cross-sectorial transfers and international spread of AMR plasmids. For risk assessment purposes related to human health, AMR plasmids found in food and bearing genes conferring resistances to critically important antibiotics in human medicine - such as to extended-spectrum cephalosporins, carbapenems or colistin - have been under specific scrutiny these last years. Those plasmids are often multidrug resistant and their dissemination can be driven by the selective pressure exerted by any of the antibiotics concerned. Also, AMR plasmids carry numerous other genes conferring vital properties to the bacterial cell and are recurrently subjected to evolutionary steps such as hybrid plasmids, making the epidemiology of AMR plasmids in food a moving picture.
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Affiliation(s)
- Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon - Université de Lyon, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon - Université de Lyon, Lyon, France.
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Fernández J, Guerra B, Rodicio MR. Resistance to Carbapenems in Non-Typhoidal Salmonella enterica Serovars from Humans, Animals and Food. Vet Sci 2018; 5:E40. [PMID: 29642473 PMCID: PMC6024723 DOI: 10.3390/vetsci5020040] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Non-typhoidal serovars of Salmonella enterica (NTS) are a leading cause of food-borne disease in animals and humans worldwide. Like other zoonotic bacteria, NTS have the potential to act as reservoirs and vehicles for the transmission of antimicrobial drug resistance in different settings. Of particular concern is the resistance to critical "last resort" antimicrobials, such as carbapenems. In contrast to other Enterobacteriaceae (e.g., Klebsiella pneumoniae, Escherichia coli, and Enterobacter, which are major nosocomial pathogens affecting debilitated and immunocompromised patients), carbapenem resistance is still very rare in NTS. Nevertheless, it has already been detected in isolates recovered from humans, companion animals, livestock, wild animals, and food. Five carbapenemases with major clinical importance-namely KPC (Klebsiella pneumoniae carbapenemase) (class A), IMP (imipenemase), NDM (New Delhi metallo-β-lactamase), VIM (Verona integron-encoded metallo-β-lactamase) (class B), and OXA-48 (oxacillinase, class D)-have been reported in NTS. Carbapenem resistance due to the production of extended spectrum- or AmpC β-lactamases combined with porin loss has also been detected in NTS. Horizontal gene transfer of carbapenemase-encoding genes (which are frequently located on self-transferable plasmids), together with co- and cross-selective adaptations, could have been involved in the development of carbapenem resistance by NTS. Once acquired by a zoonotic bacterium, resistance can be transmitted from humans to animals and from animals to humans through the food chain. Continuous surveillance of resistance to these "last resort" antibiotics is required to establish possible links between reservoirs and to limit the bidirectional transfer of the encoding genes between S. enterica and other commensal or pathogenic bacteria.
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Affiliation(s)
- Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo 33011, Spain.
- Instituto de Investigación del Principado de Asturias (ISPA), Oviedo 33011, Spain.
| | | | - M Rosario Rodicio
- Instituto de Investigación del Principado de Asturias (ISPA), Oviedo 33011, Spain.
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo 33006, Spain.
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Roschanski N, Fischer J, Falgenhauer L, Pietsch M, Guenther S, Kreienbrock L, Chakraborty T, Pfeifer Y, Guerra B, Roesler UH. Retrospective Analysis of Bacterial Cultures Sampled in German Chicken-Fattening Farms During the Years 2011-2012 Revealed Additional VIM-1 Carbapenemase-Producing Escherichia coli and a Serologically Rough Salmonella enterica Serovar Infantis. Front Microbiol 2018; 9:538. [PMID: 29636734 PMCID: PMC5880886 DOI: 10.3389/fmicb.2018.00538] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/08/2018] [Indexed: 11/30/2022] Open
Abstract
Carbapenems are last-resort antibiotics used in human medicine. The increased detection of carbapenem-resistant Enterobacteriaceae (CRE) is therefore worrying. In 2011 we reported the first livestock-associated VIM-1-producing Salmonella (S.) enterica serovar Infantis (R3) isolate from dust, sampled in a German chicken fattening farm. Due to this observation we retrospectively investigated more than 536 stored bacterial cultures, isolated from 45 chicken fattening farms during the years 2011 and 2012. After a non-selective overnight incubation, the bacteria were transferred to selective media. Escherichia (E.) coli and Salmonella growing on these media were further investigated, including antibiotic susceptibility testing, carbapenemase gene screening and whole genome sequencing (WGS). In total, four CRE were found in three out of 45 investigated farms: Besides R3, one additional Salmonella (G-336-1a) as well as two E. coli isolates (G-336-2, G-268-2). All but G-268-2 harbored the blaVIM-1 gene. Salmonella isolates R3 and G-336-1 were closely related although derived from two different farms. All three blaVIM-1-encoding isolates possessed identical plasmids and the blaVIM-1- containing transposon showed mobility at least in vitro. In isolate G-268-2, the AmpC beta-lactamase gene blaCMY-2 but no known carbapenemase gene was identified. However, a transfer of the phenotypic resistance was possible. Furthermore, G-268-2 contained the mcr-1 gene, combining phenotypical carbapenem- as well as colistin resistance in one isolate. Carbapenem-resistant Enterobacteriaceae have been found in three out of 45 investigated chicken flocks. This finding is alarming and emphasizes the importance of intervention strategies to contain the environmental spread of resistant bacteria in animals and humans.
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Affiliation(s)
- Nicole Roschanski
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Jennie Fischer
- Department for Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Linda Falgenhauer
- German Center for Infection Research, Institute of Medical Microbiology, Justus Liebig University Giessen, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Michael Pietsch
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Sebastian Guenther
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
| | - Lothar Kreienbrock
- Epidemiology and Information Processing and WHO Collaborating Center for Research and Training for Health at the Human-Animal-Environment Interface, Institute for Biometry, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Trinad Chakraborty
- German Center for Infection Research, Institute of Medical Microbiology, Justus Liebig University Giessen, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute, Wernigerode, Germany
| | - Beatriz Guerra
- Department for Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany
| | - Uwe H Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universitaet Berlin, Berlin, Germany
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High Genetic Plasticity in Multidrug-Resistant Sequence Type 3-IncHI2 Plasmids Revealed by Sequence Comparison and Phylogenetic Analysis. Antimicrob Agents Chemother 2018; 62:AAC.02068-17. [PMID: 29437633 DOI: 10.1128/aac.02068-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022] Open
Abstract
We report a novel fusion plasmid, pP2-3T, cointegrating sequence type 3 (ST3)-IncHI2 with an IncFII plasmid backbone mediating multidrug resistance (MDR) and virulence. Phylogenetic analysis and comparative genomics revealed that pP2-3T and other MDR ST3-IncHI2 plasmids clustered together, representing a unique IncHI2 lineage that exhibited high conservation in backbones of plasmids but possessed highly genetic plasticity in various regions by acquiring numerous antibiotic resistance genes and fusing with other plasmids. Surveillance studies should be performed to monitor multiresistance IncHI2 plasmids among Enterobacteriaceae.
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38
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Poole K. At the Nexus of Antibiotics and Metals: The Impact of Cu and Zn on Antibiotic Activity and Resistance. Trends Microbiol 2017; 25:820-832. [PMID: 28526548 DOI: 10.1016/j.tim.2017.04.010] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 12/14/2022]
Abstract
Environmental influences on antibiotic activity and resistance can wreak havoc with in vivo antibiotic efficacy and, ultimately, antimicrobial chemotherapy. In nature, bacteria encounter a variety of metal ions, particularly copper (Cu) and zinc (Zn), as contaminants in soil and water, as feed additives in agriculture, as clinically-used antimicrobials, and as components of human antibacterial responses. Importantly, there is a growing body of evidence for Cu/Zn driving antibiotic resistance development in metal-exposed bacteria, owing to metal selection of genetic elements harbouring both metal and antibiotic resistance genes, and metal recruitment of antibiotic resistance mechanisms. Many classes of antibiotics also form complexes with metal cations, including Cu and Zn, and this can hinder (or enhance) antibiotic activity. This review highlights the ways in which Cu/Zn influence antibiotic resistance development and antibiotic activity, and in so doing impact in vivo antibiotic efficacy.
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Affiliation(s)
- Keith Poole
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada, K7L 3N6.
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39
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Köck R, Kreienbrock L, van Duijkeren E, Schwarz S. Antimicrobial resistance at the interface of human and veterinary medicine. Vet Microbiol 2017; 200:1-5. [DOI: 10.1016/j.vetmic.2016.11.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Characterization of a Novel IncHI2 Plasmid Carrying Tandem Copies of blaCTX-M-2 in a fosA6-Harboring Escherichia coli Sequence Type 410 Strain. Antimicrob Agents Chemother 2016; 60:6742-6747. [PMID: 27572405 DOI: 10.1128/aac.01173-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/23/2016] [Indexed: 12/23/2022] Open
Abstract
The extended-spectrum β-lactamase gene blaCTX-M-2 is mainly associated with ISCR1 embedded in complex sul1-type integrons, but information on the genetic context of plasmids harboring the ISCR1-blaCTX-M-2 module remains limited. In this study, a blaCTX-M-2-harboring plasmid (pYD786-1) belonging to the sequence type 2 (ST2)-IncHI2 plasmid type and isolated from an Escherichia coli ST410 clinical strain was sequenced and analyzed. pYD786-1 belongs to the APEC-O1-R-type IncHI2 plasmids, which are widely distributed in human, poultry, and livestock strains. It contains a multidrug resistance mosaic region (MRR) consisting of a Tn21::In2 transposon backbone augmented by acquisition of duplicate ISCR1-blaCTX-M-2 modules. Tn2411, a Tn21::In2 precursor, likely played a role in the generation of the MRR in pN13-01290_23, the putative progenitor plasmid of pYD786-1, found in a foodborne Salmonella strain. Tn21/Tn2411::In::ISCR1-blaCTX-M-2 derivatives, including pYD786-1, have been identified in strains from Europe, South America, and the United States, suggesting potential global dissemination of the blaCTX-M-2 modules mediated by this vehicle.
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41
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Sun F, Zhou D, Sun Q, Luo W, Tong Y, Zhang D, Wang Q, Feng W, Chen W, Fan Y, Xia P. Genetic characterization of two fully sequenced multi-drug resistant plasmids pP10164-2 and pP10164-3 from Leclercia adecarboxylata. Sci Rep 2016; 6:33982. [PMID: 27658354 PMCID: PMC5034289 DOI: 10.1038/srep33982] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/06/2016] [Indexed: 02/04/2023] Open
Abstract
We previously reported the complete sequence of the resistance plasmid pP10164-NDM, harboring blaNDM (conferring carbapenem resistance) and bleMBL (conferring bleomycin resistance), which is recovered from a clinical Leclercia adecarboxylata isolate P10164 from China. This follow-up work disclosed that there were still two multidrug-resistant (MDR) plasmids pP10164-2 and pP10164-3 coexisting in this strain. pP10164-2 and pP10164-3 were completely sequenced and shown to carry a wealth of resistance genes, which encoded the resistance to at least 10 classes of antibiotics (β-lactams. macrolides, quinolones, aminoglycosides, tetracyclines, amphenicols, quaternary ammonium compounds, sulphonamides, trimethoprim, and rifampicin) and 7 kinds of heavy mental (mercury, silver, copper, nickel, chromate, arsenic, and tellurium). All of these antibiotic resistance genes are associated with mobile elements such as transposons, integrons, and insertion sequence-based transposable units, constituting a total of three novel MDR regions, two in pP10164-2 and the other one in pP10164-3. Coexistence of three resistance plasmids pP10164-NDM, pP10164-2 and pP10164-3 makes L. adecarboxylata P10164 tend to become extensively drug-resistant.
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Affiliation(s)
- Fengjun Sun
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Wenbo Luo
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Defu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.,College of Food Science and Project Engineering, Bohai University, Jinzhou 121013, China
| | - Qian Wang
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Wei Feng
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Weijun Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Yahan Fan
- Transfusion Department, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
| | - Peiyuan Xia
- Department of Pharmacy, Southwest Hospital, the Third Military Medical University, Chongqing 400038, China
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42
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Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Indiana C629, a Carbapenem-Resistant Bacterium Isolated from Chicken Carcass in China. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00662-16. [PMID: 27417837 PMCID: PMC4945797 DOI: 10.1128/genomea.00662-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The carbapenem-resistant Salmonella enterica subsp. enterica serovar Indiana strain C629 was isolated from a chicken carcass collected from a slaughterhouse in Qingdao, China. The complete genome sequence of C629 contains a circular 4,791,723-bp chromosome and a circular 210,106-bp plasmid. Genes involved in carbapenem resistance of this bacterium were identified by whole-genome analysis.
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