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Dehdashti S, Mohseni P, Ghanbarpour R, Aslani S, Moradiyan MS, Kalantar-Neyestanaki D. The emergence of carbapenem-resistance and New Delhi metallo-β-lactamase-1 ( blaNDM-1) among Salmonella spp. in Kerman, Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2024; 16:29-38. [PMID: 38682060 PMCID: PMC11055441 DOI: 10.18502/ijm.v16i1.14868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Background and Objectives Salmonella species (spp) are the most prevalent zoonotic pathogens that cause outbreaks of gastroenteritis worldwide. Therefore evaluation of the profile of antibiotic resistance, virulence factors, and plasmid replicon types in these bacteria is necessary to control and prevent the spread of potentially pathogenic and drug-resistant strains. Materials and Methods This study was performed on 39 Salmonella spp. The antibacterial susceptibility of isolates to various antibiotic agents was determined using disk diffusion test. β-lactamases (bla) including ESBLs, AmpC, MBLs, and virulence genes were detected by PCR methods. Plasmid incompatibility groups among the isolates were identified using PCR-based replicon typing (PBRT). Results The most prevalent virulent gene was phoP/Q (84.6%). slyA, sopB, and stn were identified in 79.4% (n=31), 69.2% (n=27), and 2.5% (n=1) of the isolates, respectively. The antibiotic susceptibility testing showed that 30.7% of the isolates were ESBL-producing. blaTEM (41%; n=16) was the most frequent β-lactamase gene among the isolates followed by blaNDM-1 (15.4%; n=6), blaDHA (7.7%; n=3), and blaCTX-M (1.5%; n=1). Six different plasmid replicon types, including IncP (n=9; 23%), IncFIC (n=3; 7.70%), IncY (n=3; 7.70%), IncI1-Iγ (n=2; 5.12%), IncFIIAs (n=1; 2.56%), and IncN (n=1; 2.56%) were observed among the isolates. Conclusion Our study showed the emergence of carbapenem-resistant and blaNDM-1 among Salmonella spp. for the first time in Kerman, Iran. Since Salmonella spp. plays an important role in the transmission of resistance genes in livestock and humans in the food chains, so more stringent control policies are recommended to prevent the circulation of drug-resistant and potentially pathogenic strains from animals to humans.
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Affiliation(s)
- Sanaz Dehdashti
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Parvin Mohseni
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Reza Ghanbarpour
- Molecular Microbiology Research Group, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Sajad Aslani
- Department of Pharmaceutics, Faculty of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Davood Kalantar-Neyestanaki
- Medical Mycology and Bacteriology Research Center, Kerman University of Medical Sciences, Kerman, Iran
- Department of Medical Microbiology (Bacteriology and Virology), Afzalipour Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
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Bartsch LJ, Borowiak M, Deneke C, Gruetzke J, Hammerl JA, Malorny B, Szabo I, Alter T, Nguyen KK, Fischer J. Genetic characterization of a multidrug-resistant Salmonella enterica serovar Agona isolated from a dietary supplement in Germany. Front Microbiol 2023; 14:1284929. [PMID: 38033583 PMCID: PMC10686068 DOI: 10.3389/fmicb.2023.1284929] [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: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Agona has a history of causing food-borne outbreaks and any emergence of multidrug-resistant (MDR) isolates in novel food products is of concern. Particularly, in food products frequently consumed without sufficient heating prior to consumption. Here, we report about the MDR isolate, 18-SA00377, which had been isolated from a dietary supplement in Germany in 2018 and submitted to the German National Reference Laboratory for Salmonella. WGS-based comparative genetic analyses were conducted to find a potential reservoir of the isolate itself or mobile genetic elements associated with MDR. As a phylogenetic analysis did not yield any closely related S. Agona isolates, either globally or from Germany, a detailed analysis of the largest plasmid (295,499 bp) was performed as it is the main carrier of resistances. A combined approach of long-read and short-read sequencing enabled the assembly of the isolate's chromosome and its four plasmids. Their characterization revealed the presence of 23 different antibiotic resistance genes (ARGs), conferring resistance to 12 different antibiotic drug classes, as well as genes conferring resistance to six different heavy metals. The largest plasmid, pSE18-SA00377-1, belongs to the IncHI2 plasmid family and carries 16 ARGs, that are organized as two distinct clusters, with each ARG associated with putative composite transposons. Through a two-pronged approach, highly similar plasmids to pSE18-SA00377-1 were identified in the NCBI database and a search for Salmonella isolates with a highly similar ARG resistance profile was conducted. Mapping and structural comparisons between pSE18-SA00377-1 and these plasmids and Salmonella isolates showed that both the plasmid backbone and identical or similar ARG clusters can be found not only in Salmonella isolates, originating mostly from a wide variety of livestock, but also in a diverse range of bacterial genera of varying geographical origins and isolation sources. Thus, it can be speculated that the host range of pSE18-SA00377-1 is not restricted to Salmonella and its spread already occurred in different bacterial populations. Overall, this hints at a complex history for pSE18-SA00377-1 and highlights the importance of surveilling multidrug-resistant S. enterica isolates, especially in novel food items that are not yet heavily regulated.
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Affiliation(s)
- Lee Julia Bartsch
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Maria Borowiak
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Josephine Gruetzke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens-Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Allain M, Mahérault AC, Gachet B, Martinez C, Condamine B, Magnan M, Kempf I, Denamur E, Landraud L. Dissemination of IncI plasmid encoding bla CTX-M-1 is not hampered by its fitness cost in the pig's gut. Antimicrob Agents Chemother 2023; 67:e0011123. [PMID: 37702541 PMCID: PMC10583664 DOI: 10.1128/aac.00111-23] [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: 02/02/2023] [Accepted: 07/01/2023] [Indexed: 09/14/2023] Open
Abstract
Multiresistance plasmids belonging to the IncI incompatibility group have become one of the most pervasive plasmid types in extended-spectrum beta-lactamase-producing Escherichia coli of animal origin. The extent of the burden imposed on the bacterial cell by these plasmids seems to modulate the emergence of "epidemic" plasmids. However, in vivo data in the natural environment of the strains are scarce. Here, we investigated the cost of a bla CTX-M-1-IncI1 epidemic plasmid in a commensal E. coli animal strain, UB12-RC, before and after oral inoculation of 15 6- to 8-week- old specific-pathogen-free pigs. Growth rate in rich medium was determined on (i) UB12-RC and derivatives, with or without plasmid, in vivo and/or in vitro evolved, and (ii) strains that acquired the plasmid in the gut during the experiment. Although bla CTX-M-1-IncI1 plasmid imposed no measurable burden on the recipient strain after conjugation and during the longitudinal carriage in the pig's gut, we observed a significant difference in the bacterial growth rate between IncI1 plasmid-carrying and plasmid-free isolates collected during in vivo carriage. Only a few mutations on the chromosome of the UB12-RC derivatives were detected by whole-genome sequencing. RNA-Seq analysis of a selected set of these strains showed that transcriptional responses to the bla CTX-M-1-IncI1 acquisition were limited, affecting metabolism, stress response, and motility functions. Our data suggest that the effect of IncI plasmid on host cells is limited, fitness cost being insufficient to act as a barrier to IncI plasmid spread among natural population of E. coli in the gut niche.
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Affiliation(s)
- Margaux Allain
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
| | - Anne Claire Mahérault
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
| | - Benoit Gachet
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Caroline Martinez
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Bénédicte Condamine
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Mélanie Magnan
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
| | - Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
| | - Erick Denamur
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Génétique Moléculaire, Hôpital Bichat, Paris, France
| | - Luce Landraud
- Université Paris Cité and Université Sorbonne Paris Nord, INSERM, IAME, Paris, France
- AP-HP, Laboratoire de Microbiologie Hygiène, Hôpital Louis Mourier, Colombes, France
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Huang E, Yang X, Leighton E, Li X. Carbapenem resistance in the food supply chain. J Food Prot 2023; 86:100108. [PMID: 37244353 DOI: 10.1016/j.jfp.2023.100108] [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: 02/03/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Carbapenems are critically important antibiotic agents because they are considered the "last-resort" antibiotics for treating serious infections. However, resistance to carbapenems is increasing throughout the world and has become an urgent problem. Some carbapenem-resistant bacteria are considered urgent threats by the United States Centers for Disease Control and Prevention. In this review, we searched and summarized studies published mostly in the recent five years related to carbapenem resistance in three main areas in the food supply chain: livestock, aquaculture, and fresh produce. We have found that many studies have shown a direct or indirect correlation between carbapenem resistance in the food supply chain and human infections. Our review also revealed the worrisome incidences of the cooccurrence of resistance to carbapenem and other "last-resort" antibiotics, such as colistin and/or tigecycline, in the food supply chain. Antibiotic resistance is a global public health challenge, and more effort related to carbapenem resistance in the food supply chain for different food commodities is still needed in some countries and regions, including the United States. In addition, antibiotic resistance in the food supply chain is a complicated issue. Based on the knowledge from current studies, only restricting the use of antibiotics in food animal production might not be enough. Additional research is needed to determine factors contributing to the introduction and persistence of carbapenem resistance in the food supply chain. Through this review, we hope to provide a better understanding of the current state of carbapenem resistance, and the niches of knowledge that are needed for developing strategies to mitigate antibiotic resistance, especially carbapenem resistance in the food supply chain.
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Affiliation(s)
- En Huang
- Department of Environmental Health Sciences, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, AR 72205, USA
| | - Xu Yang
- Department of Nutrition and Food Science, California State Polytechnic University Pomona, 3801 West Temple Ave, Pomona, CA 91768, USA
| | - Elizabeth Leighton
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, USA
| | - Xinhui Li
- Department of Microbiology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI 54601, USA.
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Surachat K, Kantachote D, Wonglapsuwan M, Chukamnerd A, Deachamag P, Mittraparp-arthorn P, Jeenkeawpiam K. Complete Genome Sequence of Weissella cibaria NH9449 and Comprehensive Comparative-Genomic Analysis: Genomic Diversity and Versatility Trait Revealed. Front Microbiol 2022; 13:826683. [PMID: 35663880 PMCID: PMC9161744 DOI: 10.3389/fmicb.2022.826683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Lactic acid bacteria (LAB) in the genus Weissella spp. contain traits in their genome that confer versatility. In particular, Weissella cibaria encodes several beneficial genes that are useful in biotechnological applications. The complete genome of W. cibaria NH9449 was sequenced and an in silico comparative analysis was performed to gain insight into the genomic diversity among members of the genus Weissella. A total of 219 Weissella genomes were used in a bioinformatics analysis of pan-genomes, phylogenetics, self-defense mechanisms, virulence factors, antimicrobial resistance, and carbohydrate-active enzymes. These investigations showed that the strain NH9449 encodes several restriction-modification-related genes and a CRISPR-Cas region in its genome. The identification of carbohydrate-active enzyme-encoding genes indicated that this strain could be beneficial in biotechnological applications. The comparative genomic analysis reveals the very high genomic diversity in this genus, and some marked differences in genetic variation and genes among Weissella species. The calculated average amino acid identity (AAI) and phylogenetic analysis of core and accessory genes shows the possible existence of three new species in this genus. These new genomic insights into Weissella species and their biological functions could be useful in the food industry and other applications.
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Affiliation(s)
- Komwit Surachat
- Division of Computational Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- *Correspondence: Komwit Surachat,
| | - Duangporn Kantachote
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Monwadee Wonglapsuwan
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Panchalika Deachamag
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Pimonsri Mittraparp-arthorn
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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6
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Wink PL, Lima-Morales D, Meurer R, Barth AL. Escherichia coli carrying bla NDM-1 obtained from a migratory penguin (Spheniscus magellanicus) in the Brazilian seacoast. Braz J Microbiol 2021; 53:499-502. [PMID: 34775575 DOI: 10.1007/s42770-021-00652-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/03/2021] [Indexed: 12/25/2022] Open
Abstract
The reservoirs for NDM-producing Enterobacterales are increasing, not only in hospitals, but also in the environment and in the community, challenging the therapeutic efficacy of carbapenems. We aimed to characterize an isolate of Escherichia coli harboring the blaNDM-1 gene recovered from the bloodstream of a penguin (Spheniscus magellanicus) in Southern Brazil. A total of 74 bacterial isolates recovered from arterial blood samples from dead birds were submitted to species identification and antibiotic susceptibility evaluation. One isolate presented resistance to carbapenems (E. coli 89PenNDM) and proved to harbor the blaNDM-1 gene by multiplex high-resolution melting real-time PCR (PCR-HRM). Conjugation experiments indicated that the blaNDM-1 was transmissible to E. coli J53. Whole genome sequencing (WGS) confirmed the presence of the blaNDM-1 gene in a conjugative plasmid (IncA/C2 plasmid) in both the E. coli 89PenNDM and its transconjugants. The isolate was classified as ST 156 and many other resistance genes (e.g., sul1, sul,2, strA, floR, tet(A)) were identified, all carried in the same IncA/C2 plasmid. This is the first report of blaNDM-1-producing E. coli isolated from a penguin in the Brazilian seacoast. The presence of a carbapenemase gene in wildlife animals is of concern as they may become reservoirs of multidrug-resistant bacteria and disseminate them to the environment.
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Affiliation(s)
- Priscila L Wink
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Porto Alegre, RS, 90.035-903, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Daiana Lima-Morales
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Porto Alegre, RS, 90.035-903, Brazil
| | - Rafael Meurer
- Curso de Especialização em Microbiologia Clínica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Associação R3 Animal, Florianópolis, Santa Catarina, Brazil
| | - Afonso L Barth
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, Porto Alegre, RS, 90.035-903, Brazil.
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
- Curso de Especialização em Microbiologia Clínica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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Zheng XR, Sun YH, Zhu JH, Wu SL, Ping C, Fang LX, Jiang HX. Two novel bla NDM-1-harbouring transposons on pPrY2001-like plasmids coexisting with a novel cfr-encoding plasmid in food animal source Enterobacteriaceae. J Glob Antimicrob Resist 2021; 26:222-226. [PMID: 34245899 DOI: 10.1016/j.jgar.2021.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 06/13/2021] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES This study reports identification of the carbapenemase-encoding gene from carbapenem-resistant Enterobacterales from food animals. METHODS A total of 40 bacterial isolates recovered from 475 faecal swabs obtained on one farm were tested for the presence of the blaNDM-1 gene by PCR. Species identification of three blaNDM-1-positive strains was conducted by MALDI-TOF/MS. Antimicrobial susceptibility testing was performed by broth microdilution. Transferability of the blaNDM-1 and cfr genes was determined by filter mating. The genetic environment of blaNDM-1 and cfr was analysed by whole-genome sequencing. RESULTS Two Proteus mirabilis (JPM24 and YPM35) and one Providencia rettgeri (YPR25) carried blaNDM-1. The blaNDM-1 genes were located on conjugable pPrY2001-like plasmids often reported to carry important antimicrobial resistance genes (ARGs). YPR25 and YPM35 shared two almost identical conjugable plasmids, one carrying blaNDM-1 and the other cfr. The blaNDM-1 gene in YPR25 (same as YPM35) and JPM24 was located in two novel transposons, designated Tn6922 and Tn6923, respectively. Tn6922 and Tn6923 carried 14 and 7 ARGs, respectively, and both contained multiple copies of IS26 in the same direction, with a high degree of similarity. Additionally, cfr was located on a plasmid with an unreported high frequency of conjugative transfer in YPR25 (same as YPM35). CONCLUSION We identified two novel blaNDM-1-containing transposons (Tn6922 and Tn6923) present on pPrY2001-like plasmids. The pPrY2001-like blaNDM-1 plasmids coexisted with a novel cfr plasmid, and both could transfer at high frequency, highlighting the importance of continuous surveillance of multiresistant Enterobacterales of animal origin that can serve as a reservoir for ARGs.
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Affiliation(s)
- Xing-Run Zheng
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Yin-Huan Sun
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Jia-Hang Zhu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Si-Li Wu
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Cai Ping
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Liang-Xing Fang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Hong-Xia Jiang
- Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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Aires-de-Sousa M, Ortiz de la Rosa JM, Goncalves ML, Costa A, Nordmann P, Poirel L. Occurrence of NDM-1-producing Morganella morganii and Proteus mirabilis in a single patient in Portugal: probable in vivo transfer by conjugation. J Antimicrob Chemother 2021; 75:903-906. [PMID: 31971235 DOI: 10.1093/jac/dkz542] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/28/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To decipher the genetics of acquisition of carbapenemase-encoding genes identified in two carbapenem-resistant Enterobacteriaceae recovered from a single patient in Portugal. METHODS Carbapenemase genes were searched by PCR assays and mating-out assays were performed to further characterize the plasmid support of the carbapenemase genes. Genetic characterization of the plasmid supports was performed by whole-plasmid sequencing using the Illumina technology. RESULTS We identified here two NDM-1-producing isolates, namely a Morganella morganii and a Proteus mirabilis, sharing the same blaNDM-1-positive plasmid. This 154 kb plasmid belonged to the IncA/C2 type, recently renamed IncC, and co-harboured two AmpC β-lactamase genes, namely blaCMY-4 and blaDHA-1, in addition to the 16S rRNA methylase gene armA encoding high-level resistance to aminoglycosides. In addition, the M. morganii isolate produced the CTX-M-33 extended-spectrum β-lactamase possessing weak carbapenemase activity, encoded by another plasmid. CONCLUSIONS We showed here that, in addition to KPC-type and OXA-181 carbapenemases, which have been identified as widespread in this country, another concern is the emergence of NDM-1-producing enterobacterial isolates in Portugal. We demonstrated here the in vivo plasmid transfer of a blaNDM-1-positive plasmid leading to dissemination of this carbapenemase gene within different enterobacterial species in a single patient.
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Affiliation(s)
- Marta Aires-de-Sousa
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,Escola Superior de Saúde da Cruz Vermelha Portuguesa (ESSCVP), Lisboa, Portugal.,Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - José Manuel Ortiz de la Rosa
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | | | | | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,Escola Superior de Saúde da Cruz Vermelha Portuguesa (ESSCVP), Lisboa, Portugal.,Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.,Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland.,INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland.,University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland.,Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland.,INSERM European Unit (IAME, France), University of Fribourg, Fribourg, Switzerland
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Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones. EcoSal Plus 2021; 9. [PMID: 33634776 DOI: 10.1128/ecosalplus.esp-0013-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.
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Anderson REV, Boerlin P. Carbapenemase-producing Enterobacteriaceae in animals and methodologies for their detection. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2020; 84:3-17. [PMID: 31920216 PMCID: PMC6921994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/08/2019] [Indexed: 06/10/2023]
Abstract
Carbapenemase-producing bacteria are difficult to treat and pose an important threat for public health. Detecting and identifying them can be a challenging and time-consuming task. Due to the recent rise in prevalence of infections with these organisms, there is an increased demand for rapid and accurate detection methods. This review describes and contrasts current methods used for the identification and detection of carbapenemase-producing bacteria to help control their spread in animal populations and along the food chain. The methods discussed include cultures used for screening clinical samples and primary isolation, susceptibility testing, culture-based and molecular confirmation tests. Advantages and disadvantages as well as limitations of the methods are discussed.
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Affiliation(s)
- Rebecca E V Anderson
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario NIG 2W1
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph, Ontario NIG 2W1
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The bla NDM-1-Carrying IncA/C 2 Plasmid Underlies Structural Alterations and Cointegrate Formation In Vivo. Antimicrob Agents Chemother 2019; 63:AAC.00380-19. [PMID: 31109975 PMCID: PMC6658791 DOI: 10.1128/aac.00380-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/09/2019] [Indexed: 01/04/2023] Open
Abstract
In 2012, a carbapenemase-producing Salmonella enterica serovar Corvallis isolate carrying a bla NDM-1 multiresistance IncA/C2 plasmid, apart from IncHI2 and ColE-like plasmids, was detected in a wild bird in Germany. In a recent broiler chicken infection study, we observed transfer of this bla NDM-1-carrying IncA/C2 plasmid to other Enterobacteriaceae Here, we focused on the stability of this plasmid and gained insight into the type and frequency of its structural alterations after an in vivo passage in a broiler chicken infection study.
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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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Characterization of mcr-5-Harboring Salmonella enterica subsp. enterica Serovar Typhimurium Isolates from Animal and Food Origin in Germany. Antimicrob Agents Chemother 2019; 63:AAC.00063-19. [PMID: 30910897 DOI: 10.1128/aac.00063-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/17/2019] [Indexed: 12/25/2022] Open
Abstract
We characterized eight mcr-5-positive Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) isolates obtained from pigs and meat in Germany. Five plasmid types were identified harboring mcr-5 on Tn6452 or putative mobile insertion cassettes. The mobility of mcr-5 was confirmed by integration of Tn6452 into the bacterial chromosomes of two strains and the detection of conjugative mcr-5 plasmids. The association with mobile genetic elements might further enhance mcr-5 distribution.
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Hadziabdic S, Borowiak M, Bloch A, Malorny B, Szabo I, Guerra B, Kaesbohrer A, Fischer J. Complete Genome Sequence of an Avian Native NDM-1-Producing Salmonella enterica subsp. enterica Serovar Corvallis Strain. GENOME ANNOUNCEMENTS 2018; 6:e00593-18. [PMID: 29954902 PMCID: PMC6025930 DOI: 10.1128/genomea.00593-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 11/20/2022]
Abstract
Carbapenems are an important class of β-lactams and one of the last options for treating severe human infections. We present here the complete genome sequence of avian native carbapenemase-producing Salmonella enterica subsp. enterica serovar Corvallis strain 12-01738, harboring a blaNDM-1-carrying IncA/C2 plasmid, isolated in 2012 from a wild bird (Milvus migrans) in Germany.
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Affiliation(s)
- Sead Hadziabdic
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Angelina Bloch
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Burkhard Malorny
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Istvan Szabo
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Annemarie Kaesbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Jennie Fischer
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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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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