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Puljko A, Barišić I, Dekić Rozman S, Križanović S, Babić I, Jelić M, Maravić A, Udiković-Kolić N. Molecular epidemiology and mechanisms of carbapenem and colistin resistance in Klebsiella and other Enterobacterales from treated wastewater in Croatia. ENVIRONMENT INTERNATIONAL 2024; 185:108554. [PMID: 38479059 DOI: 10.1016/j.envint.2024.108554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/30/2024] [Accepted: 03/02/2024] [Indexed: 03/26/2024]
Abstract
Among the most problematic bacteria with clinical relevance are the carbapenem-resistant Enterobacterales (CRE), as there are very limited options for their treatment. Treated wastewater can be a route for the release of these bacteria into the environment and the population. The aim of this study was to isolate CRE from treated wastewater from the Zagreb wastewater treatment plant and to determine their phenotypic and genomic characteristics. A total of 200 suspected CRE were isolated, 148 of which were confirmed as Enterobacterales by MALDI-TOF MS. The predominant species was Klebsiella spp. (n = 47), followed by Citrobacter spp. (n = 40) and Enterobacter cloacae complex (cplx.) (n = 35). All 148 isolates were carbapenemase producers with a multidrug-resistant phenotype. Using multi-locus sequence typing and whole-genome sequencing (WGS), 18 different sequence types were identified among these isolates, 14 of which were associated with human-associated clones. The virulence gene analysis of the sequenced Klebsiella isolates (n = 7) revealed their potential pathogenicity. PCR and WGS showed that the most frequent carbapenemase genes in K. pneumoniae were blaOXA-48 and blaNDM-1, which frequently occurred together, while blaKPC-2 together with blaNDM-1 was mainly detected in K. oxytoca, E. cloacae cplx. and Citrobacter spp. Colistin resistance was observed in 40% of Klebsiella and 57% of Enterobacter isolates. Underlying mechanisms identified by WGS include known and potentially novel intrinsic mechanisms (point mutations in the pmrA/B, phoP/Q, mgrB and crrB genes) and acquired mechanisms (mcr-4.3 gene). The mcr-4.3 gene was identified for the first time in K. pneumoniae and is probably located on the conjugative IncHI1B plasmid. In addition, WGS analysis of 13 isolates revealed various virulence genes and resistance genes to other clinically relevant antibiotics as well as different plasmids possibly associated with carbapenemase genes. Our study demonstrates the important role that treated municipal wastewater plays in harboring and spreading enterobacterial pathogens that are resistant to last-resort antibiotics.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210 Vienna, Austria
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000 Split, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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Bai S, Fang L, Xiao H, Zhang Y, Guo W, Zhang J, Liu J, Zhang Y, Wang M, Sun R, Han L, Yu Y, Sun J, Liu Y, Liao X. Genomics analysis of KPC-2 and NDM-5-producing Enterobacteriaceae in migratory birds from Qinghai Lake, China. Appl Microbiol Biotechnol 2023; 107:7531-7542. [PMID: 37861819 DOI: 10.1007/s00253-023-12746-3] [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: 03/22/2023] [Revised: 07/02/2023] [Accepted: 08/24/2023] [Indexed: 10/21/2023]
Abstract
The study examined the epidemiological characteristics of carbapenem-resistant Enterobacteriaceae (CRE) isolated from migratory birds and surroundings in Qinghai Lake, China. We identified 69 (15.7%) CRE isolates from a total of 439 samples including 29 (6.6%) blaNDM-5 Escherichia coli and 40 (9.1%) blaKPC-2 Klebsiella pneumoniae. WGS analysis indicated that ST746, ST48, ST1011, and ST167 were the primary sequence types (ST) for blaNDM-5 E. coli, while all blaKPC-2 K. pneumoniae were ST11 and harbored numerous antibiotic resistance gene types including blaCTX-M, qnrS, and rmtB. A phylogenetic tree based on core genomes revealed that blaNDM-5 E. coli was highly heterogeneous while the blaKPC-2 K. pneumoniae was highly genetically similar within the group and to human Chinese isolates. IncX3, IncHI2, and IncFIB-HI2 plasmid replicon types were associated with blaNDM-5 spread, while IncFII-R and IncFII plasmids mediated blaKPC-2 spread. We also identified IncFII-R hybrid plasmids most likely formed by IS26-mediated integration of IncFII into IncR plasmid backbones. This also facilitated the persistence of IncFII-R plasmids and antibiotic resistance genes including blaKPC-2. In addition, all of the blaKPC-2 K. pneumoniae isolates harbored a pLVKP-like virulence plasmid carrying a combination of two or more hypervirulence markers that included peg-344, iroB, iucA, rmpA, and rmpA2. This is the first description of ST11 K. pneumoniae that co-carried blaKPC-2- and pLVKP-like virulence plasmids from migratory birds. The blaKPC-2 K. pneumoniae carried by migratory birds displayed high genetic relatedness to human isolates highlighting a high risk of transmission of these K. pneumoniae. KEY POINTS: • Multidrug resistance plasmids (blaKPC-2, bla436NDM-5, bla CTX-M, qnrS, and rmtB). • Co-occurrence of plasmid-mediated resistance and virulence genes. • High similarity between migratory bird genomes and humans.
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Affiliation(s)
- Shuancheng Bai
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Liangxing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Hongliang Xiao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yin Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Wenying Guo
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jixing Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Juan Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yan Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Minge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ruanyang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lu Han
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Yu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yahong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaoping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.
- Veterinary Pharmacology Department, College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues, South China Agricultural University, Guangzhou, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.
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Ramírez-Castillo FY, Guerrero-Barrera AL, Avelar-González FJ. An overview of carbapenem-resistant organisms from food-producing animals, seafood, aquaculture, companion animals, and wildlife. Front Vet Sci 2023; 10:1158588. [PMID: 37397005 PMCID: PMC10311504 DOI: 10.3389/fvets.2023.1158588] [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: 02/04/2023] [Accepted: 05/23/2023] [Indexed: 07/04/2023] Open
Abstract
Carbapenem resistance (CR) is a major global health concern. CR is a growing challenge in clinical settings due to its rapid dissemination and low treatment options. The characterization of its molecular mechanisms and epidemiology are highly studied. Nevertheless, little is known about the spread of CR in food-producing animals, seafood, aquaculture, wildlife, their environment, or the health risks associated with CR in humans. In this review, we discuss the detection of carbapenem-resistant organisms and their mechanisms of action in pigs, cattle, poultry, seafood products, companion animals, and wildlife. We also pointed out the One Health approach as a strategy to attempt the emergency and dispersion of carbapenem-resistance in this sector and to determine the role of carbapenem-producing bacteria in animals among human public health risk. A higher occurrence of carbapenem enzymes in poultry and swine has been previously reported. Studies related to poultry have highlighted P. mirabilis, E. coli, and K. pneumoniae as NDM-5- and NDM-1-producing bacteria, which lead to carbapenem resistance. OXA-181, IMP-27, and VIM-1 have also been detected in pigs. Carbapenem resistance is rare in cattle. However, OXA- and NDM-producing bacteria, mainly E. coli and A. baumannii, are cattle's leading causes of carbapenem resistance. A high prevalence of carbapenem enzymes has been reported in wildlife and companion animals, suggesting their role in the cross-species transmission of carbapenem-resistant genes. Antibiotic-resistant organisms in aquatic environments should be considered because they may act as reservoirs for carbapenem-resistant genes. It is urgent to implement the One Health approach worldwide to make an effort to contain the dissemination of carbapenem resistance.
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Affiliation(s)
- Flor Y. Ramírez-Castillo
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags, Mexico
| | - Alma L. Guerrero-Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags, Mexico
| | - Francisco J. Avelar-González
- Laboratorio de Estudios Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags, Mexico
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Usman M, Rasool MH, Khurshid M, Aslam B, Baloch Z. Co-Occurrence of mcr-1 and Carbapenem Resistance in Avian Pathogenic E. coli Serogroup O78 ST95 from Colibacillosis-Infected Broiler Chickens. Antibiotics (Basel) 2023; 12:antibiotics12050812. [PMID: 37237715 DOI: 10.3390/antibiotics12050812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023] Open
Abstract
Avian pathogenic Escherichia coli (APEC) is responsible for significant economic losses in the poultry industry. This study aimed to molecularly detect carbapenem-resistant co-harboring mcr-1 avian pathogenic E. coli in broiler chickens infected with colibacillosis. A total of 750 samples were collected from colibacillosis-infected broilers, and conventional microbiological techniques were used to isolate and identify APEC. MALDI-TOF and virulence-associated genes (VAGs) were used for further identification. Phenotypic carbapenem resistance profiling was followed by molecular detection of carbapenem resistance genes (CRGs) and other resistance genes through PCR using specific primers. Isolates were also subjected to PCR for O typing, followed by allele-specific PCR to detect sequence type (ST) 95. Results showed that 154 (37%) isolates were confirmed as APEC, with 13 (8.4%) isolates found to be carbapenem-resistant (CR)-APEC. Among CR-APEC isolates, 5 (38%) were observed to co-harbor mcr-1. All CR-APEC showed the presence of five markers (ompT, hylF, iutA, iroN, and iss) APEC VAGs, and 89% of CR-APEC isolates displayed O78 type. Furthermore, 7 (54%) CR-APEC isolates were observed with ST95, all displaying O78 type. These results suggest that the improper use of antibiotics in poultry production systems is contributing to the emergence of pathogens such as CR-APEC co-harboring the mcr-1 gene.
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Affiliation(s)
- Muhammad Usman
- Institute of Microbiology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Hidayat Rasool
- Institute of Microbiology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Mohsin Khurshid
- Institute of Microbiology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Bilal Aslam
- Institute of Microbiology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
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Zhang W, Lu X, Chen S, Liu Y, Peng D, Wang Z, Li R. Molecular epidemiology and population genomics of tet(X4), bla NDM or mcr-1 positive Escherichia coli from migratory birds in southeast coast of China. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 244:114032. [PMID: 36084501 DOI: 10.1016/j.ecoenv.2022.114032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/20/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
The emergence of multidrug-resistant (MDR) bacteria harboring tet(X4), blaNDM or mcr-1 posed a serious threat to public health. Wild birds, especially migratory birds, were considered as one of important transmission vectors for antibiotic resistance genes (ARGs) globally, however, few studies were performed on the genomic epidemiology of critical resistance genes among them. Isolates harboring tet(X4), mcr-1 or blaNDM from migratory birds were identified and characterized by PCR, antimicrobial susceptibility testing, conjugation assays, whole genome sequencing and bioinformatics analysis. A total of 14 tet(X4)-bearing E. coli, 4 blaNDM-bearing E. coli and 23 mcr-1-bearing E. coli isolates were recovered from 1060 fecal samples of migratory birds. All isolates were MDR bacteria and most plasmids carrying tet(X4), blaNDM or mcr-1 were conjugative. We first identified an E. coli of migratory bird origin carrying blaNDM-4, which was located on a conjugative IncHI2 plasmid and embedded on a novel MDR region flanked by IS26 that could generate the circular intermediate. The emergency of E. coli isolates co-harboring mcr-1 and blaNDM-5 in migratory birds indicated the coexistence of ARGs in migratory birds was a novel threat. This study revealed the prevalence and molecular characteristics of three important ARGs in migratory birds, provided evidence that migratory birds were potential vectors of novel resistance genes and highlighted the monitoring of ARGs in migratory birds should be strengthened to prevent the spread of ARGs in a One Health strategy.
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Affiliation(s)
- Wenhui Zhang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Xiaoyu Lu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Sujuan Chen
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Yuan Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, PR China
| | - Daxin Peng
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, PR China.
| | - Ruichao Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, PR China.
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Yitayew B, Woldeamanuel Y, Asrat D, Rahman A, Mihret A, Aseffa A, Olsson PE, Jass J. Antimicrobial resistance genes in microbiota associated with sediments and water from the Akaki river in Ethiopia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:70040-70055. [PMID: 35583762 PMCID: PMC9512891 DOI: 10.1007/s11356-022-20684-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
The spread of antimicrobial-resistant pathogens is a global health concern. Most studies report high levels of antimicrobial resistance genes (ARGs) in the aquatic environment; however, levels associated with sediments are limited. This study aimed to investigate the distribution of ARGs in the sediments and water of the Akaki river in Addis Ababa, Ethiopia. The diversity and abundance of 84 ARGs and 116 clinically important bacteria were evaluated from the sediments and water collected from five sites in the Akaki river. Most of the ARGs were found in the city close to anthropogenic activities. Water samples collected in the middle catchment of the river contained 71-75% of targeted ARGs, with genes encoding aminoglycoside acetyltransferase (aac(6)-Ib-cr), aminoglycoside adenylyl transferase (aadA1), β-lactamase (blaOXA-10), quinolone resistance S (qnrS), macrolide efflux protein A (mefA), and tetracycline resistance (tetA), were detected at all sampling sites. Much fewer ARGs were detected in all sediments, and those near the hospitals had the highest diversity and level. Despite the lower levels and diversity, there were no unique ARGs detected in the sediments that were also not detected in the waters. A wide range of clinically relevant pathogens were also detected in the Akaki river. The findings suggest that the water phase, rather than the sediments in the Akaki river, is a potential conduit for the spread of ARGs and antibiotic-resistant bacteria.
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Affiliation(s)
- Berhanu Yitayew
- College of Health Sciences, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- School of Science and Technology, The Life Science Center - Biology, Örebro University, 701 82, Örebro, Sweden
| | | | - Daniel Asrat
- College of Health Sciences, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aminur Rahman
- School of Science and Technology, The Life Science Center - Biology, Örebro University, 701 82, Örebro, Sweden
| | - Adane Mihret
- College of Health Sciences, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Per-Erik Olsson
- School of Science and Technology, The Life Science Center - Biology, Örebro University, 701 82, Örebro, Sweden
| | - Jana Jass
- School of Science and Technology, The Life Science Center - Biology, Örebro University, 701 82, Örebro, Sweden.
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Vezina B, Judd LM, McDougall FK, Boardman WSJ, Power ML, Hawkey J, Brisse S, Monk JM, Holt KE, Wyres KL. Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies. Environ Microbiol 2022; 24:4425-4436. [PMID: 35590448 PMCID: PMC9790207 DOI: 10.1111/1462-2920.16047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/11/2022] [Indexed: 12/30/2022]
Abstract
The grey-headed flying fox (Pteropus poliocephalus) is an endemic Australian fruit bat, known to carry zoonotic pathogens. We recently showed they harbour bacterial pathogen Klebsiella pneumoniae and closely related species in the K. pneumoniae species complex (KpSC); however, the dynamics of KpSC transmission and gene flow within flying fox colonies are poorly understood. High-resolution genome comparisons of 39 KpSC isolates from grey-headed flying foxes identified five putative strain transmission clusters (four intra- and one inter-colony). The instance of inter-colony strain transmission of K. africana was found between two flying fox populations within flying distance, indicating either direct or indirect transmission through a common food/water source. All 11 plasmids identified within the KpSC isolates showed 73% coverage (mean) and ≥95% identity to human-associated KpSC plasmids, indicating gene flow between human clinical and grey-headed flying fox isolates. Along with strain transmission, inter-species horizontal plasmid transmission between K. pneumoniae and Klebsiella africana was also identified within a flying fox colony. Finally, genome-scale metabolic models were generated to predict and compare substrate usage to previously published KpSC models, from human and environmental sources. These models indicated no distinction on the basis of metabolic capabilities. Instead, metabolic capabilities were consistent with population structure and ST/lineage.
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Affiliation(s)
- Ben Vezina
- Department of Infectious Diseases, Central Clinical SchoolMonash UniversityMelbourneVic.Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Central Clinical SchoolMonash UniversityMelbourneVic.Australia
| | | | | | - Michelle L. Power
- Department of Biological SciencesMacquarie UniversityNSW2109Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical SchoolMonash UniversityMelbourneVic.Australia
| | - Sylvain Brisse
- Institut PasteurUniversité de Paris, Biodiversity and Epidemiology of Bacterial PathogensParisFrance
| | | | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical SchoolMonash UniversityMelbourneVic.Australia,Department of Infection BiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Kelly L. Wyres
- Department of Infectious Diseases, Central Clinical SchoolMonash UniversityMelbourneVic.Australia
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Sellera FP, Cardoso B, Fuentes-Castillo D, Esposito F, Sano E, Fontana H, Fuga B, Goldberg DW, Seabra LAV, Antonelli M, Sandri S, Kolesnikovas CKM, Lincopan N. Genomic Analysis of a Highly Virulent NDM-1-Producing Escherichia coli ST162 Infecting a Pygmy Sperm Whale ( Kogia breviceps) in South America. Front Microbiol 2022; 13:915375. [PMID: 35755998 PMCID: PMC9231830 DOI: 10.3389/fmicb.2022.915375] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/18/2022] [Indexed: 11/29/2022] Open
Abstract
Carbapenemase-producing Enterobacterales are rapidly spreading and adapting to different environments beyond hospital settings. During COVID-19 lockdown, a carbapenem-resistant NDM-1-positive Escherichia coli isolate (BA01 strain) was recovered from a pygmy sperm whale (Kogia breviceps), which was found stranded on the southern coast of Brazil. BA01 strain belonged to the global sequence type (ST) 162 and carried the blaNDM–1, besides other medically important antimicrobial resistance genes. Additionally, genes associated with resistance to heavy metals, biocides, and glyphosate were also detected. Halophilic behavior (tolerance to > 10% NaCl) of BA01 strain was confirmed by tolerance tests of NaCl minimal inhibitory concentration, whereas halotolerance associated genes katE and nhaA, which encodes for catalase and Na+/H+ antiporter cytoplasmic membrane, respectively, were in silico confirmed. Phylogenomics clustered BA01 with poultry- and human-associated ST162 lineages circulating in European and Asian countries. Important virulence genes, including the astA (a gene encoding an enterotoxin associated with human and animal infections) were detected, whereas in vivo experiments using the Galleria mellonella infection model confirmed the virulent behavior of the BA01 strain. WHO critical priority carbapenemase-producing pathogens in coastal water are an emerging threat that deserves the urgent need to assess the role of the aquatic environment in its global epidemiology.
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Affiliation(s)
- Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil.,One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Elder Sano
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | | | - Lourdes A V Seabra
- School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | | | | | | | - Nilton Lincopan
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
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9
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Loucif L, Chelaghma W, Cherak Z, Bendjama E, Beroual F, Rolain JM. Detection of NDM-5 and MCR-1 antibiotic resistance encoding genes in Enterobacterales in long-distance migratory bird species Ciconia ciconia, Algeria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152861. [PMID: 34998768 DOI: 10.1016/j.scitotenv.2021.152861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
β-lactams and colistin resistance in Enterobacterales is a global public health issue. In this study we aimed to investigate the occurrence and genetic determinants of Extended-Spectrum β-lactamases, carbapenemases and mcr-encoding-genes in Enterobacterales isolates recovered from the migratory bird species Ciconia ciconia in an Algerian city. A total of 62 faecal samples from white storks were collected. Samples were then subjected to selective isolation of β-lactams and colistin-resistant-Enterobacterales. The representative colonies were identified using Matrix-Assisted Laser Desorption-Ionisation Time-of-Flight Mass Spectrometry. Susceptibility testing was performed using the disk-diffusion method. ESBL, carbapenemases, and colistin resistance determinants were searched for by PCR and sequencing. The clonality relationships of the obtained isolates were investigated by multilocus sequence typing assays. Mating experiments were carried out to evaluate the transferability of the carbapenemase and mcr-genes. Forty-two isolates were identified as follows: Escherichia coli (n = 33), Klebsiella pneumoniae (n = 4), Proteus mirabilis (n = 4) and Citrobacter freundii (n = 1). Molecular analysis showed that twelve isolates carried the blaESBL genes alone, fifteen E. coli isolates were positive for the blaOXA-48 gene, six isolates were NDM-5-carriers (two P. mirabilis, two K. pneumoniae and two E. coli) and eight E. coli strains were positive for the mcr-1 gene. MLST results showed a high clonal diversity, where NDM-5-producing strains were assigned to two sequence types (ST167 for E. coli and ST198 for K. pneumoniae), whereas the mcr-1 positive E. coli isolates belonged to ST58, ST224, ST453, ST1286, ST2973, ST5542, ST9815 and the international high-risk resistant lineage ST101. To the best of our knowledge, this is the first report of blaNDM-5 gene in white storks and also the first describing the mcr-1 gene in white storks in Algeria. This study underlines the important role of migratory white storks as carriers of high-level drug-resistant bacteria, allowing their possible implication as indicators and sentinels for antimicrobial resistance surveillance.
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Affiliation(s)
- Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université Batna 2, Batna 05000, Algeria.
| | - Widad Chelaghma
- Département de Biologie, Université Abou Bekr Belkaid-, Tlemcen 13000, Algeria
| | - Zineb Cherak
- Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra 07000, Algeria
| | - Esma Bendjama
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université Batna 2, Batna 05000, Algeria
| | - Ferhat Beroual
- Département de Microbiologie et de Biochimie, Faculté des Sciences de la Nature et de la Vie, Université Batna 2, Batna 05000, Algeria
| | - Jean-Marc Rolain
- Aix Marseille Université, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, France; Assistance Publique des Hôpitaux de Marseille, Marseille 13000, France
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10
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Gu C, Li X, Zou H, Zhao L, Meng C, Yang C, Berglund B. Clonal and plasmid-mediated dissemination of environmental carbapenem-resistant Enterobacteriaceae in large animal breeding areas in northern China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 297:118800. [PMID: 35007671 DOI: 10.1016/j.envpol.2022.118800] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/06/2021] [Accepted: 01/04/2022] [Indexed: 05/05/2023]
Abstract
The emergence and dissemination of carbapenem-resistant Enterobacteriaceae (CRE) constitute a major global health problem. The environment plays an important role in the dissemination of CRE, but large-scale studies on CRE in groundwater environments in animal breeding areas are scarce. The aim of this study was to investigate CRE occurrence and environmental transmission of carbapenem resistance genes in large animal breeding areas in northern China. In total, 280 well water and 102 animal feces samples in large animal breeding areas in six counties from the two provinces Inner Mongolia and Shandong in China, were screened for CRE. A total of 39 CRE were isolated and characterized with next-generation sequencing. 5.3% of well water samples were contaminated with CRE. The well water in chicken farms had the highest number of detections of CRE (15.9%). More than half of the isolates carried closely related, conjugative IncX3 plasmids with blaNDM-genes from multiple geographic areas, indicating that this kind of plasmid plays an important role in dissemination of carbapenem resistance determinants. The clonal expansion of various CRE isolates in well water and animal feces were demonstrated; clonally related CRE were isolated from different wells within the same county, from different counties in the same province, and even from different provinces. In addition to harboring various ARGs, two closely related K. pneumoniae belonging to ST11 isolated from well water carried genetic hypervirulence determinants on a virulence plasmid, highlighting the potential health risk posed by further dissemination of this strain. These findings suggest that groundwater may be an underappreciated reservoir and source of dissemination of CRE, from which resistance genes may disseminate among different bacterial strains and over large geographic distances. Further research and multi-sectorial monitoring, with a "One health" perspective, is urgently needed to investigate the need for interventions aimed at preventing CRE dissemination.
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Affiliation(s)
- Congcong Gu
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
| | - Huiyun Zou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ling Zhao
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chen Meng
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Chengxia Yang
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Björn Berglund
- Department of Biomedical and Clinical Sciences, Linköping University, 58185, Linköping, Sweden
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11
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Detection of a NDM-5-producing Klebsiella pneumoniae sequence type 340 (CG258) high-risk clone in swine. Vet Microbiol 2021; 262:109218. [PMID: 34481222 DOI: 10.1016/j.vetmic.2021.109218] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/27/2021] [Indexed: 11/21/2022]
Abstract
The emergence and rapid increase of carbapenem-resistant Enterobacteriaceae among food-producing animals poses a serious threat to public health. The aim of this study was to investigate the presence and dissemination of blaNDM-5 in porcine Klebsiella pneumoniae isolates. Of 19 meropenem-resistant K. pneumoniae isolates, 18 were blaNDM-5-positive and one carried blaNDM-1. Susceptibility testing indicated that all blaNDM-carrying K. pneumoniae showed a multiple drug resistance (MDR) profile. The blaNDM-5 gene was located on a conjugative IncX3 plasmid of ∼46-kb in all 18 blaNDM-5-carrying isolates. MLST analysis revealed that ST340 (n = 8), a member of the worldwide existing high-risk epidemic clonal group 258 (CG258), was predominant. Furthermore, whole genome sequence (WGS) analysis for one representative ST340 K. pneumoniae Kp19110124 showed a MDR profile for a wide range of antimicrobial agents, including meropenem, various cephalosporins, azteonam, gentamicin, ciprofloxacin, and florfenicol. Phylogenetic analysis exhibited that K. pneumoniae ST340 strains were clustered into one branch, which had spread across host species and across continents. Among them, K. pneumoniae Kp19110124 displayed a very close relationship with a clinical isolate collected from a patient in Canada. In conclusion, these results reveal the presence of a blaNDM-5-carrying conjugative IncX3 type plasmid into K. pneumoniae ST340 clone, which then may accelerate the dissemination of the blaNDM-5 gene in porcine K. pneumoniae isolates. The detection of high-risk blaNDM-5-carrying K. pneumoniae ST340 in food-producing animal poses a serious threat to public health.
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12
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Wang MG, Yu Y, Wang D, Yang RS, Jia L, Cai DT, Zheng SL, Fang LX, Sun J, Liu YH, Liao XP. The Emergence and Molecular Characteristics of New Delhi Metallo β-Lactamase-Producing Escherichia coli From Ducks in Guangdong, China. Front Microbiol 2021; 12:677633. [PMID: 34290681 PMCID: PMC8287858 DOI: 10.3389/fmicb.2021.677633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/31/2021] [Indexed: 12/24/2022] Open
Abstract
This study aimed to determine the prevalence and transmission characteristics of New Delhi metallo β-lactamase (NDM)-producing Escherichia coli from ducks in Guangdong, China. In this study, a total of 28 NDM-producing E. coli isolates were recovered from 88 unduplicated diseased duck samples (31.8%) from veterinary clinics in Guangzhou, Foshan, Qingyuan, and Huizhou. Two variants, bla NDM-1 and bla NDM-5, were detected and the latter was present in 89.6% of the isolates (25/28). Multilocus sequence typing (MLST) analysis indicated that these E. coli isolates possessed six distinct STs, and ST156 was the most prevalent followed by ST648, ST746, ST354, ST10, and ST162. In addition, phylogenomic analysis found that two of the isolates that were recovered from a single sample possessed different genomes, and the bla NDM-carrying IncX3 plasmids may be horizontal transfer between E. coli isolates in the intestinal tracts of ducks. Whole-genome sequencing (WGS) analysis further revealed that bla NDM co-existed with other 25 types of antimicrobial resistance genes (ARGs), of which 16 ARGs were highly prevalent with detection rates >50%, and a high incidence of coproducing bla NDM and mcr-1 E. coli isolates (22/88, 25.0%) was detected in ducks. This study underscores the importance of surveillance for bla NDM-harboring microbes in ducks.
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Affiliation(s)
- Min-Ge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yang Yu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Dong Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Run-Shi Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou, China
| | - Ling Jia
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Da-Tong Cai
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Si-Lin Zheng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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13
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Carramaschi IN, Dos S B Ferreira V, Chagas TPG, Corrêa LL, Picão RC, de C Queiroz MM, Rangel K, Jardim R, da Mota FF, Zahner V. Multidrug-resistant Klebsiella quasipneumoniae subsp. similipneumoniae carrying bla NDM-bla CTX-M15 isolated from flies in Rio de Janeiro, Brazil. J Glob Antimicrob Resist 2020; 24:1-5. [PMID: 33302000 DOI: 10.1016/j.jgar.2020.11.021] [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: 08/30/2020] [Revised: 10/25/2020] [Accepted: 11/21/2020] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Flies have been implicated in the dispersal of medically important bacteria including members of the genus Klebsiella between different environmental compartments. The aim of this study was to retrieve and characterize antibiotic-resistant bacteria from flies collected near to hospitals. METHODS Flies were collected in the vicinity of medical facilities and examined for bacteria demonstrating phenotypic resistance to ceftriaxone, followed by determination of phenotypic and genotypic resistance profiles. In addition, whole genome sequencing followed by phylogenetic analysis and resistance genotyping were performed with the multidrug-resistant (MDR) strain Lemef23, identified as Klebsiella quasipneumoniae subsp. similipneumoniae. RESULTS The strain Lemef23, classified by multiple locus sequence typing as novel ST 3397, harboured numerous resistance genes. The blaNDM was located on a Tn3000 element, a common genetic platform for the carriage of this gene in Brazil. Inference of phylogenetic orthology of strain Lemef23 and other clinical isolates suggested an anthropogenic origin. CONCLUSIONS The findings of this study support the role of flies as vectors of MDR bacteria of clinical importance and provide the first record of blaNDM-1 and blaCTXM-15 in a Brazilian isolate of K. quasipneumoniae subsp. similipneumoniae, demonstrating the value of surveying insects as reservoirs of antibiotic resistance.
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Affiliation(s)
- Isabel N Carramaschi
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Cep 21040-360, Rio de Janeiro, RJ, Brazil
| | - Vítor Dos S B Ferreira
- Universidade Federal do Rio de Janeiro, Instituto de Biologia, Centro de Ciências da Saúde, Avenida Carlos Chagas Filho, 373, Cidade Universitária, Cep 21941-599, Rio de Janeiro, RJ, Brazil
| | - Thiago P G Chagas
- Departamento de Patologia, Faculdade de Medicina, Universidade Federal Fluminense, Rua Marquês de Paraná, 303, Centro, Cep 24220-000, Niterói, RJ, Brazil
| | - Lais L Corrêa
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Avenida Carlos Chagas Filho, 373, Cidade Universitária, Cep 21941-902, Rio de Janeiro, RJ, Brazil
| | - Renata C Picão
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Centro de Ciências da Saúde, Avenida Carlos Chagas Filho, 373, Cidade Universitária, Cep 21941-902, Rio de Janeiro, RJ, Brazil
| | - Margareth M de C Queiroz
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Cep 21040-360, Rio de Janeiro, RJ, Brazil
| | - Karyne Rangel
- Centro de Desenvolvimento Tecnológico em Saúde (CDTS) Laboratório de Bioquímica de Proteínas e Peptídeos, Fiocruz, Avenida Brasil, 4365, Manguinhos, Cep 21040-360, Rio de Janeiro, RJ, Brazil
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Cep 21040-360, Rio de Janeiro, RJ, Brazil
| | - Fabio F da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Cep 21040-360, Rio de Janeiro, RJ, Brazil
| | - Viviane Zahner
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Cep 21040-360, Rio de Janeiro, RJ, Brazil.
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14
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Haenni M, Métayer V, Jarry R, Drapeau A, Puech MP, Madec JY, Keck N. Wide Spread of bla CTX-M-9/ mcr-9 IncHI2/ST1 Plasmids and CTX-M-9-Producing Escherichia coli and Enterobacter cloacae in Rescued Wild Animals. Front Microbiol 2020; 11:601317. [PMID: 33329492 PMCID: PMC7717979 DOI: 10.3389/fmicb.2020.601317] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022] Open
Abstract
Wildlife has recently been pinpointed as one of the drivers of dissemination of genes conferring resistances to clinically important antimicrobials. The presence of both extended-spectrum beta-lactamase- (ESBL) and carbapenemase-encoding genes has notably been reported in wild birds, that can act as sentinels of antimicrobial resistance (AMR) contamination but also as long-distance spreaders in case of migratory birds. Here, 424 wild birds brought to a rescue center in France were sampled over a 6-month period. These birds encompassed 62 different sedentary or migratory species. A further 16 wild mammals present in the center were also investigated. No carbapenemase-producer was found, but we identified a surprisingly high proportion (24.1%) of ESBL-positive isolates. A total of 144 non-duplicate isolates were collected, including Escherichia coli (n = 88), Enterobacter cloacae (n = 51), and Citrobacter freundii (n = 5), of which 123 carried the blaCTX–M–9 gene. PFGE, phylogroup, and MLST revealed the presence of a limited number of ESBL-positive clones circulating in these animals, all presenting multiple associated resistances. Next-generation sequencing on a subset of isolates, followed by Southern blot hybridization, showed the wide dissemination of an IncHI2/ST1 plasmid carrying the blaCTX–M–9, blaSHV–12 and mcr-9 genes. In all, our results undoubtedly reflect cross transmissions of ESC-resistance (ESC-R) Enterobacteriaceae within the rescue center – similarly to nosocomial spreads observed at hospital, rather than the true bacterial flora of birds. We also showed that the spread of ESC-R in this rescue center did not only rely on clonal but also on a highly successful plasmidic transmission. Since most animals are intended to get back to nature after a few days or weeks, this is obviously an issue with regard to ESBL dissemination in natural environments.
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Affiliation(s)
- Marisa Haenni
- ANSES, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes - Université de Lyon, Lyon, France
| | - Véronique Métayer
- ANSES, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes - Université de Lyon, Lyon, France
| | - Romane Jarry
- Laboratoire Départemental Vétérinaire de l'Hérault, Montpellier, France
| | - Antoine Drapeau
- ANSES, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes - Université de Lyon, Lyon, France
| | | | - Jean-Yves Madec
- ANSES, Laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes - Université de Lyon, Lyon, France
| | - Nicolas Keck
- Laboratoire Départemental Vétérinaire de l'Hérault, Montpellier, France
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15
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Microorganisms Resistant to Antimicrobials in Wild Canarian Egyptian Vultures ( Neophron percnopterus majorensis). Animals (Basel) 2020; 10:ani10060970. [PMID: 32503222 PMCID: PMC7341323 DOI: 10.3390/ani10060970] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Antibiotics are used to prevent and treat bacterial infections in both animals and humans. If bacteria become resistant to them, in particular as the result of the misuse and overuse of antibiotics, the infections that they cause are harder to treat. Therefore, the detection of microorganisms resistant to antimicrobial drugs is an important issue, considering the interaction among domestic animals, human, the ecosystem and wild animals. Wild birds, and particularly birds-of-prey, are sentinels, reservoirs, spreaders and a source of infection for human beings and other animals. Wildlife can also act as an asymptomatic reservoir for zoonotic bacteria (e.g., Salmonella). The presence of antimicrobial-resistant microorganisms was investigated for a period of three years and the differences between chicks in the nest (n = 81) and adult and immature birds (n = 61) were analyzed. Gram negative bacteria were isolated in all the samples. Escherichia coli was obtained in 80.28% of the samples, where the prevalence of Salmonella in our study was 6.3%. The results of our study support the idea that raptors could act as reservoirs of Salmonella and antimicrobial-resistant bacteria, posing a risk not only to wildlife but also to livestock and the human population. Abstract Due to their predatory habits, raptors may serve as indicators of the presence of antimicrobial-resistant bacteria in the environment, but they also represent a public health risk for livestock and humans because they can act as reservoirs, sources and spreaders of these bacteria. Our objective was to determine the presence of antimicrobial-resistant bacteria in cloacal samples of Canarian Egyptian vultures (Neophron percnopterus majorensis), an endemic bird of prey. One hundred and forty-two cloacal swabs were obtained; Escherichia coli was isolated from 80.28% and Salmonella from 6.3% of these samples. Low levels of susceptibility to ampicillin, tetracycline and trimethoprim/sulfamethoxazole were found. About 20% of the isolates were resistant or presented intermediate susceptibility to fluoroquinolones. Surprisingly, we found isolates resistant to imipenem (6.96%). Isolates from chicks were more susceptible to antimicrobial drugs than adult and immature birds. About 50% of E. coli isolates were resistant to ampicillin, tetracycline and trimethoprim/sulfamethoxazole, and about 20% to piperacillin, enrofloxacin and marbofloxacin. High percentages of isolates of Salmonella were found to be resistant to cephalexin (88%) and aminoglycosides (greater than 77%). Our results support the idea that raptors could act as reservoirs of Salmonella and antimicrobial-resistant bacteria, posing a risk not only to wildlife but also to livestock and the human population, thus reinforcing the need to minimize the exposure of wildlife to antimicrobial agent through human and livestock waste.
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16
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Wang H, Li X, Liu BT. Occurrence and characterization of KPC-2-producing ST11 Klebsiella pneumoniae isolate and NDM-5-producing Escherichia coli isolate from the same horse of equestrian clubs in China. Transbound Emerg Dis 2020; 68:224-232. [PMID: 32386080 DOI: 10.1111/tbed.13614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/18/2020] [Accepted: 04/30/2020] [Indexed: 11/27/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have been rapidly increasing among animals in many countries and have been a great threat to public health. Horse riding is becoming increasingly popular worldwide; however, reports of CRE producing NDM or KPC-2, two prevalent types of carbapenemases, from horses of equestrian club are extremely scarce and KPC-2-producing Klebsiella pneumoniae in animals is still rarely characterized. In this study, we identified four NDM-5-producing Escherichia coli isolates from horses in equestrian club in Qingdao, China, and one horse possessing NDM-5-producing E. coli also carried ST11 KPC-2-producing K. pneumoniae. Transferability of the plasmids producing carbapenemases was determined by conjugation, and the sequences of all CRE isolates and their transconjugants were then analysed by using whole-genome sequencing. blaNDM-5 was located on a highly similar ~ 46 kb self-transmissible IncX3 plasmid in all isolates, and these plasmids were nearly identical to IncX3 plasmids from different bacterial species of clinical patients in several countries, even including plasmid from clinical E. coli in Qingdao, China. The chromosome of the ST11 K. pneumoniae in this study was highly similar to ST11 clinical K. pneumoniae reported worldwide including the ST11 KPC-2-producing WCHKP020098 from Chengdu, China, and the blaKPC-2 -bearing plasmid in our study was a novel F33:A-:B- non-conjugative multidrug resistance plasmid. The presence of CRE from horses in equestrian club is alarming due to the potential for transmitting these isolates to humans during horse riding, and the prevalence of CRE among equestrian clubs in the whole country requires further monitoring.
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Affiliation(s)
- Han Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xuyong Li
- College of Agricultural, Liaocheng University, Liaocheng, China
| | - Bao-Tao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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Emergence and Comparative Genomics Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Carrying mcr-1 in Fennec Fox Imported from Sudan to China. mSphere 2019; 4:4/6/e00732-19. [PMID: 31748247 PMCID: PMC6887861 DOI: 10.1128/msphere.00732-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The aim of this study was to investigate the occurrence and genomic characteristics of extended-spectrum-β-lactamase-producing Escherichia coli (ESBL-EC) in fennec fox imported from Sudan to China. We screened 88 fecal samples from fennec fox for ESBL-EC, using cefotaxime- and meropenem-supplemented selective medium. Antimicrobial susceptibility testing was performed by the agar dilution method except for colistin and tigecycline; for colistin and tigecycline, testing was conducted by the broth microdilution method. ESBL-EC bacteria were sequenced, and their genomes were characterized. Plasmid conjugation, S1 nuclease pulsed-field gel electrophoresis (PFGE), and Southern blotting were performed for a MCR-1-producing isolate. The genetic environment of mcr-1 and ESBL genes was also investigated. A total of 29 ESBL-EC bacteria were isolated from 88 fennec fox (32.9%), while no carbapenemase producers were found. The most prevalent genotypes were the bla CTX-M-55 and bla CTX-M-14 genes, followed by bla CTX-M-15 and bla CTX-M-64 We detected nine sequence types among 29 ESBL-EC. Furthermore, the mcr-1 gene was detected in isolate EcFF273. Conjugation analysis confirmed that the mcr-1 gene was transferable. S1 PFGE, Southern blotting, and whole-genome sequencing revealed that mcr-1 and bla CTX-M-64 were both located on a 65-kb IncI2 plasmid. This study reports for the first time the occurrence of ESBL-EC in fennec fox. The high prevalence of ESBL producers and the occurrence of MCR-1 producer in fennec fox imported into China from Sudan are unexpected. In addition, it clearly demonstrated that commensal E. coli strains can be reservoirs of bla CTX-M and mcr-1, potentially contributing to the dissemination and transfer of such genes to pathogenic bacteria among fennec fox. Our results support the implication of fennec fox as a biological vector for ESBL-producing members of the Enterobacteriaceae family.IMPORTANCE The extended-spectrum-β-lactamase (ESBL)-producing members of the Enterobacteriaceae family are a global concern for both animal and human health. There is some information indicating a high prevalence of ESBL producers in food animals. Moreover, there have been an increasing number of reports on ESBL-producing strains resistant to the last-resort antibiotic colistin with the global dissemination of the plasmid-mediated mcr-1 gene, which is believed to have originated in animal breeding. However, little is known regarding the burden of ESBL-producing Enterobacteriaceae on wild animals. No data were available on the prevalence of antimicrobial resistance (AMR) among wild animals imported into China. This is the first study to investigate the microbiological and genomics surveillance investigation of ESBL colonization among fennec fox (Vulpes zerda) imported from Sudan to China, and we uncovered a high prevalence of ESBL-EC. Furthermore, the underlying mechanism of colistin resistance in an isolate that harbored mcr-1 was also investigated. Results of characterization and analysis of 29 ESBL-producing E. coli may have important implications on our understanding of the transmission dynamics of these bacteria. We emphasize the importance of improved multisectoral surveillance for colistin-resistant E. coli in this region.
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