1
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Li W, He Z, Di W, Xu W, Li Y, Sun B. Transposition mechanism of IS Apl1-the determinant of colistin resistance dissemination. Antimicrob Agents Chemother 2024; 68:e0123123. [PMID: 38289082 PMCID: PMC10916398 DOI: 10.1128/aac.01231-23] [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: 09/25/2023] [Accepted: 12/18/2023] [Indexed: 03/07/2024] Open
Abstract
Multidrug-resistant Enterobacteriaceae, a prominent family of gram-negative pathogenic bacteria, causes a wide range of severe diseases. Strains carrying the mobile colistin resistance (mcr-1) gene show resistance to polymyxin, the last line of defense against multidrug-resistant gram-negative bacteria. However, the transmission of mcr-1 is not well understood. In this study, genomes of mcr-1-positive strains were obtained from the NCBI database, revealing their widespread distribution in China. We also showed that ISApl1, a crucial factor in mcr-1 transmission, is capable of self-transposition. Moreover, the self-cyclization of ISApl1 is mediated by its own encoded transposase. The electrophoretic mobility shift assay experiment validated that the transposase can bind to the inverted repeats (IRs) on both ends, facilitating the cyclization of ISApl1. Through knockout or shortening of IRs at both ends of ISApl1, we demonstrated that the cyclization of ISApl1 is dependent on the sequences of the IRs at both ends. Simultaneously, altering the ATCG content of the bases at both ends of ISApl1 can impact the excision rate by modifying the binding ability between IRs and ISAPL1. Finally, we showed that heat-unstable nucleoid protein (HU) can inhibit ISApl1 transposition by binding to the IRs and preventing ISAPL1 binding and expression. In conclusion, the regulation of ISApl1-self-circling is predominantly controlled by the inverted repeat (IR) sequence and the HU protein. This molecular mechanism deepens our comprehension of mcr-1 dissemination.
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Affiliation(s)
- Wei Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhien He
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei Di
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Weifeng Xu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yujie Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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Amaro A, Leão C, Guerra V, Albuquerque T, Clemente L. Plasmid-Mediated Colistin Resistance Genes mcr-1 and mcr-4 in Multidrug-Resistant Escherichia coli Strains Isolated from a Healthy Pig in Portugal. Microb Drug Resist 2023; 29:78-84. [PMID: 36930202 DOI: 10.1089/mdr.2022.0228] [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] [Indexed: 03/18/2023] Open
Abstract
Antimicrobial resistance encoded by mobile colistin resistance (mcr) genes is a global and emergent threat. In this study, we report the occurrence of two different populations of colistin-resistant Escherichia coli harboring mcr-1 and mcr-4 variants in the intestinal microbiome of a healthy pig. Following antimicrobial susceptibility determination, the presence of mcr genes in two E. coli strains, isolated according to different selective microbiological procedures, was screened by PCR. Whole-genome sequencing confirmed that both strains were multidrug-resistant; INIAV_002EC was an AmpC producer carrying blaCMY-2, blaTEM-1B, qnrS1, mcr-1.1 genes, and INIAV_001EC carrying blaTEM-1A, tetB, and mcr-4.1 genes, along with mutations in quinolone resistance-determining regions. In addition, both strains harbored sul3, dfrA, and aadA1 determinants. Further genome analysis revealed different plasmid replicons associated with the mcr genes, IncX4 associated with mcr-1.1, and ColE10 with mcr-4.1. In addition, other replicons, including IncFIA, IncI1-Iγ, IncX1, IncY, in INIAV_002EC, and IncX1, IncI1, and p0111, in INIAV_001EC, were identified. Furthermore, both strains belonged to ST215 serotype O68:H12 and ST156 serotype O25:H28, respectively. This finding highlights the pig gut flora as a potential reservoir of mobile colistin resistance genes and reports the presence of the mcr-4.1 gene found for the first time in Portugal.
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Affiliation(s)
- Ana Amaro
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
| | - Célia Leão
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
- University of Évora, MED-Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Vanessa Guerra
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
- Faculty of Science, University of Lisbon, Lisbon, Portugal
| | - Teresa Albuquerque
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
- Faculty of Veterinary Science, CIISA-Centre for Interdisciplinary Research in Animal Health, Lisbon, Portugal
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3
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Dantas Palmeira J, V. Cunha M, Ferreira H, Fonseca C, Tinoco Torres R. Worldwide Disseminated IncX4 Plasmid Carrying mcr-1 Arrives to Wild Mammal in Portugal. Microbiol Spectr 2022; 10:e0124522. [PMID: 36394330 PMCID: PMC9769835 DOI: 10.1128/spectrum.01245-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022] Open
Abstract
The mcr-1 gene spread is worldwide recognized as a public health threat at multidrug-resistant infections therapy level. Here, we report for the first time, to the best of our knowledge, the detection of the globally distributed IncX4 plasmid carrying mcr-1 (mcr-1/IncX4) in Escherichia coli isolated from a wild mammal in Portugal and Europe. This plasmid was found in a ST533 E. coli isolate with a multidrug-resistant profile, virulence potential, and possibly phylogenetically related to human isolates. Our work contributes to highlight the importance of antimicrobial resistance (AMR) surveillance in wildlife, an important compartment of the whole ecosystem often overlooked in the fight against AMR. IMPORTANCE Colistin resistance mediated by plasmids is recognized worldwide as an emergency problem connected with the whole ecosystem, since is well described in the interface of the human-animal-environment. The plasmid IncX4 is reported as one of the most prevalent plasmids harboring the gene mcr-1. On an European scale the plasmid IncX4 carrying mcr-1 has been described in humans, the environment, and animals, including wildlife, but only in wild birds. This study shows the first report of the plasmid IncX4 harboring mcr-1 in a wild mammal in Portugal and Europe, identified in a ST533 E. coli commensal that is, curiously, more related to isolates from humans than from livestock. Our findings show that the plasmid IncX4 harboring mcr-1 is well established in a colistin resistance drive embracing the whole ecosystem.
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Affiliation(s)
- Josman Dantas Palmeira
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Helena Ferreira
- UCIBIO Applied Molecular Biosciences Unit, REQUIMTE, University of Porto, Porto, Portugal
- Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carlos Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal
- ForestWISE Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, Vila Real, Portugal
| | - Rita Tinoco Torres
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal
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Ferreira M, Leão C, Clemente L, Albuquerque T, Amaro A. Antibiotic Susceptibility Profiles and Resistance Mechanisms to β-Lactams and Polymyxins of Escherichia coli from Broilers Raised under Intensive and Extensive Production Systems. Microorganisms 2022; 10:microorganisms10102044. [PMID: 36296320 PMCID: PMC9608943 DOI: 10.3390/microorganisms10102044] [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: 09/11/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023] Open
Abstract
The intensive and extensive broiler production systems imply different veterinary interventions, including the use of antimicrobials. This study aimed to compare the antimicrobial susceptibility profiles of Escherichia coli isolated from both systems, characterize resistance mechanisms to β-lactams and polymyxins, and identify genetic elements such as integrons. E. coli isolates recovered from broiler cecal samples were assayed for antimicrobial susceptibility through the broth microdilution technique. The molecular characterization of acquired resistance mechanisms to β-lactams and colistin and the detection of integrons was performed by a multiplex PCR. For most antibiotics tested, the prevalence of reduced susceptibility is higher in commensal and extended-spectrum β-lactamases (ESBL)/AmpC producers from broilers raised in the intensive system, compared with those raised under extensive conditions. SHV-12 was the most common ESBL enzyme found in both production systems. Other ESBL variants such as CTX-M-1, CTX-M-55, CTX-M-14, CTX-M-32, CTX-M-9, TEM-52, and plasmid-encoded AmpC enzyme CMY-2 were also present. MCR-1 was identified in a colistin-resistant isolate from broilers raised under the intensive system. This study highlights the differences in E. coli antibiotic susceptibility from both production types and emphasizes that a great deal of work remains to decrease consumption and antimicrobial resistance levels.
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Affiliation(s)
- Mariana Ferreira
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- University of Évora, 7004-516 Évora, Portugal
| | - Célia Leão
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, Portugal
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, University of Lisbon, 1300-477 Lisbon, Portugal
| | - Teresa Albuquerque
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- Correspondence:
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5
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Occurrence and Biological Cost of mcr-1-Carrying Plasmids Co-harbouring Beta-Lactamase Resistance Genes in Zoonotic Pathogens from Intensive Animal Production. Antibiotics (Basel) 2022; 11:antibiotics11101356. [PMID: 36290014 PMCID: PMC9598650 DOI: 10.3390/antibiotics11101356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
Colistin is classified as a high-priority critical antimicrobial by the World Health Organization (WHO). A better understanding of the biological cost imposed by mcr-plasmids is paramount to comprehending their spread and may facilitate the decision about the ban of colistin in livestock. This study aimed to assess the prevalence of mcr and ESBL genes from 98 Escherichia coli and 142 Salmonella enterica isolates from food-producing animals and the impact of the mcr-1 acquisition on bacterial fitness. Only mcr-1 was identified by multiplex PCR (mcr-1 to mcr-10) in 15.3% of E. coli. Colistin MICs ranged between 8−32 mg/L. In four isolates, blaTEM-1, blaCTX-M-1, and blaCTX-M-15 co-existed with mcr-1. The IncH12, IncHI1, IncP, IncN, and IncI plasmids were transferred by conjugation to E. coli J53 at frequencies of 10−7 to 10−2 cells/recipient. Growth kinetics assays showed that transconjugants had a significantly lower growth rate than the recipient (p < 0.05), and transconjugants’ average growth rate was higher in the absence than in the presence of colistin (1.66 versus 1.32 (p = 0.0003)). Serial transfer assay during 10 days demonstrated that plasmid retention ranged from complete loss to full retention. Overall, mcr-1-bearing plasmids impose a fitness cost, but the loss of plasmids is highly variable, suggesting that other factors beyond colistin pressure regulate the plasmid maintenance in a bacterial population, and colistin withdrawal will not completely lead to a decrease of mcr-1 levels.
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6
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Teixeira P, Pinto N, Henriques I, Tacão M. KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19105848. [PMID: 35627386 PMCID: PMC9141432 DOI: 10.3390/ijerph19105848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 01/27/2023]
Abstract
Carbapenems are antibiotics of pivotal importance in human medicine, the efficacy of which is threatened by the increasing prevalence of carbapenem-resistant Enterobacterales (CRE). Urban ponds may be reservoirs of CRE, although this hypothesis has been poorly explored. We assessed the proportion of CRE in urban ponds over a one-year period and retrieved 23 isolates. These were submitted to BOX-PCR, PFGE, 16S rDNA sequencing, antibiotic susceptibility tests, detection of carbapenemase-encoding genes, and conjugation assays. Isolates were affiliated with Klebsiella (n = 1), Raoultella (n = 11), Citrobacter (n = 8), and Enterobacter (n = 3). Carbapenemase-encoding genes were detected in 21 isolates: blaKPC (n = 20), blaGES-5 (n = 6), and blaVIM (n = 1), with 7 isolates carrying two carbapenemase genes. Clonal isolates were collected from different ponds and in different campaigns. Citrobacter F6, Raoultella N9, and Enterobacter N10 were predicted as pathogens from whole-genome sequence analysis, which also revealed the presence of several resistance genes and mobile genetic elements. We found that blaKPC-3 was located on Tn4401b (Citrobacter F6 and Enterobacter N10) or Tn4401d (Raoultella N9). The former was part of an IncFIA-FII pBK30683-like plasmid. In addition, blaGES-5 was in a class 3 integron, either chromosomal (Raoultella N9) or plasmidic (Enterobacter N10). Our findings confirmed the role of urban ponds as reservoirs and dispersal sites for CRE.
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Affiliation(s)
- Pedro Teixeira
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, 3810-193 Aveiro, Portugal; (P.T.); (M.T.)
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Nuno Pinto
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Isabel Henriques
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3004-531 Coimbra, Portugal
- Correspondence:
| | - Marta Tacão
- CESAM (Centre for Marine and Environmental Studies), University of Aveiro, 3810-193 Aveiro, Portugal; (P.T.); (M.T.)
- Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal;
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7
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Li Q, Qian C, Zhang X, Zhu T, Shi W, Gao M, Feng C, Xu M, Lin H, Lin L, Lu J, Lin X, Li K, Xu T, Bao Q, Li C, Zhang H. Colistin Resistance and Molecular Characterization of the Genomes of mcr-1-Positive Escherichia coli Clinical Isolates. Front Cell Infect Microbiol 2022; 12:854534. [PMID: 35601104 PMCID: PMC9120429 DOI: 10.3389/fcimb.2022.854534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Research on resistance against polymyxins induced by the mcr-1 gene is gaining interest. In this study, using agar dilution method, polymerase chain reaction, and comparative genomic analysis, we investigated the colistin resistance mechanism of clinical E. coli isolates. The minimum inhibitory concentration (MIC) analysis results revealed that of the 515 isolates tested, bacteria with significantly increased MIC levels against colistin were isolated in 2019. Approximately one-fifth (17.14% to 19.65%) of the isolates showed MIC values ≥1 mg/L against colistin in 2015, 2016, and 2017. However, in 2019, up to three-quarters (74.11%, 146/197) of the isolates showed MIC values ≥1 mg/L against colistin indicating an increase in colistin resistance. Six isolates (EC7518, EC4968, EC3769, EC16, EC117, EC195, 1.13%, 6/515) were found to carry the mcr-1 gene and a novel mcr-1 variant with Met2Ile mutation was identified in EC3769. All six strains showed higher MIC levels (MIC=4 mg/L) than any mcr-1-negative strains (MIC ≤ 2 mg/L). Whole-genome sequencing of the six mcr-1-positive isolates revealed that EC195 carried the highest number of resistance genes (n = 28), nearly a half more than those of the following EC117 (n = 19). Thus, EC195 showed a wider resistance spectrum and higher MIC levels against the antimicrobials tested than the other five isolates. Multi-locus sequence typing demonstrated that these mcr-1-positive strains belonged to six different sequence types. The six mcr-1 genes were located in three different incompatibility group plasmids (IncI2, IncHI2 and IncX4). The genetic context of mcr-1 was related to a sequence derived from Tn6330 (ISApl1-mcr-1-pap2-ISApl1). Investigations into the colistin resistance mechanism and characterization of the molecular background of the mcr genes may help trace the development and spread of colistin resistance in clinical settings.
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Affiliation(s)
- Qiaoling Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Changrui Qian
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tingting Zhu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ming Xu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hailong Lin
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Li Lin
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Qiyu Bao
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Hailin Zhang, ; Changchong Li, ; Qiyu Bao,
| | - Changchong Li
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Hailin Zhang, ; Changchong Li, ; Qiyu Bao,
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Hailin Zhang, ; Changchong Li, ; Qiyu Bao,
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8
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Teixeira P, Tacão M, Henriques I. Occurrence and distribution of Carbapenem-resistant Enterobacterales and carbapenemase genes along a highly polluted hydrographic basin. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 300:118958. [PMID: 35131334 DOI: 10.1016/j.envpol.2022.118958] [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: 12/10/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
We determined the distribution and temporal variation of Carbapenem Resistant Enterobacterales (CRE), carbapenemase-encoding genes and other antibiotic resistance genes (ARGs) in a highly polluted river (Lis River; Portugal), also assessing the potential influence of water quality to this distribution. Water samples were collected in two sampling campaigns performed one year apart (2018/2019) from fifteen sites and water quality was analyzed. CRE were isolated and characterized. The abundance of four ARGs (blaNDM, blaKPC, tetA, blaCTX-M), two Microbial Source Tracking (MST) indicators (HF183 and Pig-2-Bac) and the class 1 integrase gene (IntI1) was measured by qPCR. RESULTS: confirmed the poor quality of the Lis River water, particularly in sites near pig farms. A collection of 23 CRE was obtained: Klebsiella (n = 19), Enterobacter (n = 2) and Raoultella (n = 2). PFGE analysis revealed a clonal relationship between isolates obtained in different sampling years and sites. All CRE isolates exhibited multidrug resistance profiles. Klebsiella and Raoultella isolates carried blaKPC while Enterobacter harbored blaNDM. Conjugation experiments were successful for only four Klebsiella isolates. All ARGs were detected by qPCR on both sampling campaigns. An increase in ARGs and IntI1 abundances was detected in sites located downstream of wastewater treatment plants. Strong correlations were observed between blaCTX-M, IntI1 and the human-pollution marker HF183, and also between tetA and the pig-pollution marker Pig-2-bac, suggesting that both human- and animal-derived pollution in the Lis River are a potential source of ARGs. Plus, water quality parameters related to eutrophication and land use were significantly correlated with ARGs abundances. Our findings demonstrated that the Lis River encloses high levels of antibiotic resistant bacteria and ARGs, including CRE and carbapenemase-encoding genes. Overall, this study provides a better understanding on the impacts of water pollution resulting from human and animal activities on the resistome of natural aquatic systems.
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Affiliation(s)
- Pedro Teixeira
- Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal
| | - Marta Tacão
- Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal.
| | - Isabel Henriques
- University of Coimbra, Centre for Functional Ecology and Department of Life Sciences, Faculty of Science and Technology, Coimbra, Portugal
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9
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Spreading Advantages of Coresident Plasmids blaCTX-M-Bearing IncFII and mcr-1-Bearing IncI2 in Escherichia coli. Microbiol Spectr 2022; 10:e0170621. [PMID: 35171014 PMCID: PMC8849077 DOI: 10.1128/spectrum.01706-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two diverse conjugative plasmids can interact within bacterial cells. However, to the best of our knowledge, the interaction between blaCTX-M-bearing IncFII plasmid and mcr-1-carrying IncI2 plasmid colocated on the same bacterial host has not been reported. This study was initiated to explore the interaction and to analyze the reasons that these two plasmids are often coresident in multidrug-resistant Escherichia coli. To assess the interactions on plasmid stabilities, fitness costs, and transfer rates, we constructed two groups of isogenic derivatives, C600FII, C600I2, and C600FII+I2 of E. coli C600 and J53FII, J53I2, and J53FII+I2 of E. coli J53, respectively. We found that carriage of FII and I2 plasmids, independently and together, had not impaired the growth of the bacterial host. It was difficult for the single plasmid FII or I2 in E. coli C600 to reach stable persistence for a long time in an antibiotic-free environment, while the stability would be striking improved when they coresided. Meanwhile, plasmids FII and I2, whether together or apart, could notably enhance the fitness advantage of the host; moreover, E. coli coharboring plasmids FII and I2 presented more obvious fitness advantage than that carrying single plasmid FII. Coresident plasmids FII and I2 could accelerate horizontal cotransfer by conjugation. The transfer rates from a strain carrying coresident FII and I2 plasmids increased significantly when it mated with a recipient cell carrying one of them. Our findings highlight the advantages of coinhabitant FII and I2 plasmids in E. coli to drive the persistence and spread of plasmid-carried blaCTX-M and mcr-1 genes, although the molecular mechanisms of their coresidence warrant further study. IMPORTANCE More and more Enterobacteriaceae carry both blaCTX-M and mcr-1, which are usually located on IncFII-type and IncI2-type plasmids in the same bacterial host, respectively. However, the study on advantages of coresident plasmids in bacterial host is still sparse. Here, we investigated the stability, fitness cost, and cotransfer traits associated with coresident IncFII-type and IncI2-type plasmids in E. coli. Our results show that coinhabitant plasmids in E. coli are more stable, confer more fitness advantages, and are easier to transfer and cotransfer than a single plasmid IncFII or IncI2. Our findings confirm the advantages of coresident plasmids of blaCTX-M-bearing IncFII and mcr-1-bearing IncI2 in clinical E. coli, which will pose a serious threat to clinical therapy and public health.
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Occurrence and Characteristics of Mcrs among Gram-Negative Bacteria Causing Bloodstream Infections of Infant Inpatients between 2006 and 2019 in China. Microbiol Spectr 2022; 10:e0193821. [PMID: 35138190 PMCID: PMC8826862 DOI: 10.1128/spectrum.01938-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to determine the occurrence of mobilized colistin resistance (mcr) genes in Gram-negative bacteria causing bloodstream infections of child inpatients in China. Bacteria were collected between 2006 and 2019 in a maternal and child health hospital, and mcr genes were screened by PCR. Five of 252 isolates were mcr-positive, including one mcr-1-positive colistin-resistant Escherichia coli isolate, two mcr-9-positive colistin-susceptible Salmonella enterica isolates, and two mcr-9-positive colistin-susceptible Enterobacter hormaechei isolates. These were obtained from two neonate and three infant patients admitted between 2009 and 2018. The E. coli isolate was obtained from a neonate aged 20 min, suggestive of a possible mother-to-neonate transmission. The five mcr-positive isolates were multidrug resistant, and two S. enterica and one E. hormaechei isolate showed a hypervirulent phenotype compared to a hypervirulent Klebsiella pneumoniae type strain in a Galleria mellonella infection model. The mcr-1 gene was carried by an IncX4-type pA1-like epidemic plasmid, and the mcr-9 gene was detected on IncHI2/2A-type novel plasmids co-carrying multiple resistance genes. The four IncHI2/2A-type plasmids shared a backbone and a high similarity (≥77% coverage and ≥ 90% nucleotide identity), suggesting that they were derived from a common ancestor with cross-species transmission and have circulated locally over a long period. The conjugation assay showed that the mcr-1-encoding plasmid and one mcr-9-encoding plasmid were self-transmissible to E. coli with high conjugation frequencies. Our findings demonstrate that mcr genes have disseminated in the community and/or hospitals, mediated by epidemic/endemic plasmids over a long period. The study shows that continuous monitoring of mcr genes is imperative for understanding and tackling their dissemination. IMPORTANCE Antimicrobial resistance, especially the spread of carbapenemase-producing Enterobacteriaceae (CPE), represents one of the largest challenges to One Health coverage of environmental, animal, and human sectors. Colistin is one of the last-line antibiotics for clinical treatment of CPE. However, the emergence of the mobilized colistin resistance (mcr) gene largely threatens the usage of colistin in the clinical setting. In this study, we investigated the existence of mcr genes in 252 Gram-negative bacteria collected between 2006 and 2019 which caused bloodstream infections of child inpatients in China. We found a high prevalence of mcr carriage among children inpatients in the absence of professional exposure, and mcr might have widely disseminated in the community via different routes. This study emphasizes the importance of rational use of colistin in the One Health frame, and highlights both the urgent need for understanding the prevalence and dissemination of mcr genes in different populations and the importance of effective measures to control their spread.
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Fortini D, Owczarek S, Dionisi AM, Lucarelli C, Arena S, Carattoli A, Villa L, García-Fernández A. Colistin Resistance Mechanisms in Human Salmonella enterica Strains Isolated by the National Surveillance Enter-Net Italia (2016–2018). Antibiotics (Basel) 2022; 11:antibiotics11010102. [PMID: 35052978 PMCID: PMC8772777 DOI: 10.3390/antibiotics11010102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Background: A collection of human-epidemiologically unrelated S. enterica strains collected over a 3-year period (2016 to 2018) in Italy by the national surveillance Enter-Net Italia was analysed. Methods: Antimicrobial susceptibility tests, including the determination of minimal inhibitory concentrations (MICs) for colistin, were performed. Colistin resistant strains were analysed by PCR to detect mobile colistin resistance (mcr) genes. In mcr-negative S. enterica serovar Enteritidis strains, chromosomal mutations potentially involved in colistin resistance were identified by a genomic approach. Results: The prevalence of colistin-resistant S. enterica strains was 7.7%, the majority (87.5%) were S. Enteritidis. mcr genes were identified only in one strain, a S. Typhimurium monophasic variant, positive for both mcr-1.1 and mcr-5.1 genes in an IncHI2 ST4 plasmid. Several chromosomal mutations were identified in the colistin-resistant mcr-negative S. Enteritidis strains in proteins involved in lipopolysaccharide and outer membrane synthesis and modification (RfbN, LolB, ZraR) and in a component of a multidrug efflux pump (MdsC). These mutated proteins were defined as possible candidates for colistin resistance in mcr-negative S. Enteritidis of our collection. Conclusions: The colistin national surveillance in Salmonella spp. in humans, implemented with genomic-based surveillance, permitted to monitor colistin resistance, determining the prevalence of mcr determinants and the study of new candidate mechanisms for colistin resistance.
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Affiliation(s)
- Daniela Fortini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Slawomir Owczarek
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Anna Maria Dionisi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Claudia Lucarelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Sergio Arena
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Alessandra Carattoli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy;
| | | | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Aurora García-Fernández
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
- Correspondence:
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Uddin MB, Alam MN, Hasan M, Hossain SMB, Debnath M, Begum R, Samad MA, Hoque SF, Chowdhury MSR, Rahman MM, Hossain MM, Hassan MM, Lundkvist Å, Järhult JD, El Zowalaty ME, Ahmed SSU. Molecular Detection of Colistin Resistance mcr-1 Gene in Multidrug-Resistant Escherichia coli Isolated from Chicken. Antibiotics (Basel) 2022; 11:antibiotics11010097. [PMID: 35052973 PMCID: PMC8772701 DOI: 10.3390/antibiotics11010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 11/29/2022] Open
Abstract
Zoonotic and antimicrobial-resistant Escherichia coli (hereafter, E. coli) is a global public health threat which can lead to detrimental effects on human health. Here, we aim to investigate the antimicrobial resistance and the presence of mcr-1 gene in E. coli isolated from chicken feces. Ninety-four E. coli isolates were obtained from samples collected from different locations in Bangladesh, and the isolates were identified using conventional microbiological tests. Phenotypic disk diffusion tests using 20 antimicrobial agents were performed according to CLSI-EUCAST guidelines, and minimum inhibitory concentrations (MICs) were determined for a subset of samples. E. coli isolates showed high resistance to colistin (88.30%), ciprofloxacin (77.66%), trimethoprim/sulfamethoxazole (76.60%), tigecycline (75.53%), and enrofloxacin (71.28%). Additionally, the pathotype eaeA gene was confirmed in ten randomly selected E. coli isolates using primer-specific polymerase chain reaction (PCR). The presence of mcr-1 gene was confirmed using PCR and sequencing analysis in six out of ten E. coli isolates. Furthermore, sequencing and phylogenetic analyses revealed a similarity between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, indicating that the six tested isolates were colistin resistant. Finally, the findings of the present study showed that E. coli isolated from chicken harbored mcr-1 gene, and multidrug and colistin resistance. These findings accentuate the need to implement strict measures to limit the imprudent use of antibiotics, particularly colistin, in agriculture and poultry farms.
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
| | - Mohammad Nurul Alam
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.H.); (S.F.H.)
| | - S. M. Bayejed Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mita Debnath
- Kazi Farms Poultry Laboratory, Gazipur 1700, Bangladesh;
| | - Ruhena Begum
- Bangladesh Livestock Research Institute (BLRI), Savar 1341, Bangladesh; (R.B.); (M.A.S.)
| | - Mohammed A. Samad
- Bangladesh Livestock Research Institute (BLRI), Savar 1341, Bangladesh; (R.B.); (M.A.S.)
| | - Syeda Farjana Hoque
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.H.); (S.F.H.)
| | - Md. Shahidur Rahman Chowdhury
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mahfujur Rahman
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mukter Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mohammad Mahmudul Hassan
- Department of Physiology, Biochemistry and Pharmacology, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
| | - Josef D. Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
| | - Mohamed E. El Zowalaty
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet 3100, Bangladesh
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
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Dierikx CM, Meijs AP, Hengeveld PD, van der Klis FRM, van Vliet J, Gijsbers EF, Rozwandowicz M, van Hoek AHAM, Hendrickx APA, Hordijk J, Van Duijkeren E. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac041. [PMID: 35445193 PMCID: PMC9015910 DOI: 10.1093/jacamr/dlac041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives Plasmid-mediated colistin resistance can be transferred from animals to humans. We investigated the prevalence of carriage of mcr-mediated colistin-resistant Escherichia coli and Klebsiella pneumoniae (ColR-E/K) in veterinary healthcare workers and in the general population in the Netherlands. Methods Two cross-sectional population studies were performed: one among veterinary healthcare workers and one in the general population. Participants sent in a faecal sample and filled in a questionnaire. Samples were analysed using selective enrichment and culture. Mobile colistin resistance genes (mcr) were detected by PCR and ColR-E/K were sequenced using Illumina and Nanopore technologies. Results The prevalence of mcr-mediated ColR-E/K was 0.2% (1/482, 95% CI 0.04%–1.17%) among veterinary personnel and 0.8% (5/660, 95% CI 0.3%–1.8%) in the population sample. mcr-1 was found in E. coli from four persons, mcr-8 in K. pneumoniae from one person and another person carried both mcr-1 and mcr-8 in a K. pneumoniae isolate. mcr-1 was found on different plasmid types (IncX4, IncI1 and IncI2), while mcr-8 was found on IncF plasmids only. Conclusions mcr-mediated ColR-E/K resistance was uncommon in both populations. Professional contact with animals does not increase the chance of carriage of these bacteria in the Netherlands at present. mcr-8 was found for the first time in the Netherlands. Surveillance of colistin resistance and its underlying mechanisms in humans, livestock and food is important in order to identify emerging trends in time.
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Affiliation(s)
- C. M. Dierikx
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
- Corresponding author. E-mail:
| | - A. P. Meijs
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - P. D. Hengeveld
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - F. R. M. van der Klis
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - J. van Vliet
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - E. F. Gijsbers
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - M. Rozwandowicz
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - A. H. A. M. van Hoek
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - A. P. A. Hendrickx
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - J. Hordijk
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - E. Van Duijkeren
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
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Majewski P, Gutowska A, Smith DGE, Hauschild T, Majewska P, Hryszko T, Gizycka D, Kedra B, Kochanowicz J, Glowiński J, Drewnowska J, Swiecicka I, Sacha PT, Wieczorek P, Iwaniuk D, Sulewska A, Charkiewicz R, Makarewicz K, Zebrowska A, Czaban S, Radziwon P, Niklinski J, Tryniszewska EA. Plasmid Mediated mcr-1.1 Colistin-Resistance in Clinical Extraintestinal Escherichia coli Strains Isolated in Poland. Front Microbiol 2021; 12:547020. [PMID: 34956105 PMCID: PMC8703133 DOI: 10.3389/fmicb.2021.547020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2021] [Indexed: 01/27/2023] Open
Abstract
Objectives: The growing incidence of multidrug-resistant (MDR) bacteria is an inexorable and fatal challenge in modern medicine. Colistin is a cationic polypeptide considered a “last-resort” antimicrobial for treating infections caused by MDR Gram-negative bacterial pathogens. Plasmid-borne mcr colistin resistance emerged recently, and could potentially lead to essentially untreatable infections, particularly in hospital and veterinary (livestock farming) settings. In this study, we sought to establish the molecular basis of colistin-resistance in six extraintestinal Escherichia coli strains. Methods: Molecular investigation of colistin-resistance was performed in six extraintestinal E. coli strains isolated from patients hospitalized in Medical University Hospital, Bialystok, Poland. Complete structures of bacterial chromosomes and plasmids were recovered with use of both short- and long-read sequencing technologies and Unicycler hybrid assembly. Moreover, an electrotransformation assay was performed in order to confirm IncX4 plasmid influence on colistin-resistance phenotype in clinical E. coli strains. Results: Here we report on the emergence of six mcr-1.1-producing extraintestinal E. coli isolates with a number of virulence factors. Mobile pEtN transferase-encoding gene, mcr-1.1, has been proved to be encoded within a type IV secretion system (T4SS)-containing 33.3 kbp IncX4 plasmid pMUB-MCR, next to the PAP2-like membrane-associated lipid phosphatase gene. Conclusion: IncX4 mcr-containing plasmids are reported as increasingly disseminated among E. coli isolates, making it an “epidemic” plasmid, responsible for (i) dissemination of colistin-resistance determinants between different E. coli clones, and (ii) circulation between environmental, industrial, and clinical settings. Great effort needs to be taken to avoid further dissemination of plasmid-mediated colistin resistance among clinically relevant Gram-negative bacterial pathogens.
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Affiliation(s)
- Piotr Majewski
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anna Gutowska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Tomasz Hauschild
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | | | - Tomasz Hryszko
- Second Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Białystok, Białystok, Poland
| | - Dominika Gizycka
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Boguslaw Kedra
- Second Department of General and Gastroenterological Surgery, Medical University of Białystok, Białystok, Poland
| | - Jan Kochanowicz
- Department of Neurology, Medical University of Białystok, Białystok, Poland
| | - Jerzy Glowiński
- Department of Vascular Surgery and Transplantation, Medical University of Białystok, Białystok, Poland
| | - Justyna Drewnowska
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Pawel T Sacha
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Piotr Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Dominika Iwaniuk
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | | | | | - Slawomir Czaban
- Department of Anesthesiology and Intensive Care, Medical University of Białystok, Białystok, Poland
| | - Piotr Radziwon
- Regional Centre for Transfusion Medicine, Białystok, Poland.,Department of Hematology, Medical University of Białystok, Białystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Elzbieta A Tryniszewska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
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Mobile Colistin Resistance Genetic Determinants of Non-Typhoid Salmonella enterica Isolates from Russia. Microorganisms 2021; 9:microorganisms9122515. [PMID: 34946117 PMCID: PMC8705591 DOI: 10.3390/microorganisms9122515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Polymyxin resistance, determined by mcr genes located on plasmid DNA, currently poses a high epidemiological threat. Non-typhoid Salmonella (NTS) are one of the key pathogens causing diarrheal diseases. Here, we report the isolation and whole genome sequencing of multidrug colistin-resistant/susceptible isolates of non-typhoid Salmonella enterica serovars carrying mcr genes. Non-typhoid strains of Salmonella enterica subsp. enterica were isolated during microbiological monitoring of the environment, food, and diarrheal disease patients between 2018 and 2020 in Russia (n = 586). mcr-1 genes were detected using a previously developed qPCR assay, and whole genome sequencing of mcr positive isolates was performed by both short-read (Illumina) and long-read (Oxford Nanopore) approaches. Three colistin-resistant isolates, including two isolates of S. Enteritidis and one isolate of S. Bovismorbificans, carried the mcr-1.1 gene located on IncX4 and IncI2 conjugative plasmids, respectively. The phenotypically colistin-susceptible isolate of S. Typhimurium carried a mcr-9 gene on plasmid IncHI2. In conclusion, we present the first three cases of mcr gene-carrying NTS isolates detected in Russia with both outbreak and sporadic epidemiological backgrounds.
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Occurrence of mcr-mediated colistin resistance in Salmonella clinical isolates in Thailand. Sci Rep 2021; 11:14170. [PMID: 34238964 PMCID: PMC8266838 DOI: 10.1038/s41598-021-93529-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/25/2021] [Indexed: 01/01/2023] Open
Abstract
Nontyphoidal Salmonella, an important zoonotic pathogen and a major cause of foodborne illnesses, could be a potential reservoir of plasmids harbouring mobile colistin resistance gene (mcr). This study reported, for the first time, a high rate of mcr-carrying Salmonella clinical isolates (3.3%, 24/724) in Thailand, associated with mcr-3 gene (3.0%, 22/724) in S. 4,[5],12:i:-(15.4%, 4/26), S. Typhimurium (8.8%, 5/57), and S. Choleraesuis (5.6%, 13/231). Remarkably, the increasing trends of colistin and extended-spectrum cephalosporin resistances have displayed a high agreement over the years, with a dramatic rise in the mcr-carrying Salmonella from 1.1% (6/563) during 2005–2007 to 11.2% (18/161) during 2014–2018 when CTX-M-55 became abundant. Clonal and plasmid analysis revealed that the self-transferable IncA/C and a novel hybrid IncA/C-FIIs MDR plasmids were the major vehicles to disseminate both mcr-3 and blaCTX-M55 genes among diverse Salmonella strains, from as early as 2007. To our knowledge the occurrence of mcr-3 and the co-existence of it with blaCTX-M-55 in S. Choleraesuis are reported here for the first time, leading to clinical concern over the treatment of the invasive salmonellosis. This study provides evidence of the potential reservoirs and vectors in the dissemination of the mcr and highlights the co-selection by colistin and/or cephalosporins.
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Li W, Li Y, Jia Y, Sun H, Zhang C, Hu G, Yuan L. Genomic characteristics of mcr-1 and bla CTX-M-type in a single multidrug-resistant Escherichia coli ST93 from chicken in China. Poult Sci 2021; 100:101074. [PMID: 33774373 PMCID: PMC8025056 DOI: 10.1016/j.psj.2021.101074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
This study was undertaken to discern the transmission characteristics of mcr-1 and blaCTX-M-type in one multidrug-resistant Escherichia coli LWY24 from chicken in China. The genetic profiles of LWY24 isolate were determined by conjugation, S1-pulsed-field gel electrophoresis, southern blot hybridization, and whole genome sequencing analysis. Meanwhile, co-transfer of plasmids in LWY24 isolate was screened by dual conjugation assays. The LWY24 isolate was identified as ST93, and harbored 3 conjugative plasmids, pLWY24J-3 (blaCTX-M-55-bearing IncFⅡ), pLWY24J-mcr-1 (mcr-1-carrying IncI2), and pLWY24J-4 (non-resistance-conferring IncI1), and one nonconjugative plasmid pLWY24 (blaCTX-M-14-containing IncHI2/IncHI2A). Numerous resistance genes, insertion sequences (especially IS26), and transposons were found in the 4 plasmids, suggesting that horizontal transmission have occurred by plasmid mating, homologous recombination, and transpositions. Under the selection pressure of cefotaxime and colistin or cefotaxime alone, the mcr-1-bearing plasmid and the blaCTX-M-55-harboring plasmid could be co-transferred at a similar frequency, with 8.00 × 10−4 or 9.00 × 10−4 transconjugants per donor cell, respectively. The specific shufflon region in mcr-1-encoding plasmid could generate up to 6 diverse PilV structures, which may further accelerate the horizontal transfer of plasmid. In conclusion, the transmission characteristics of mcr-1 and blaCTX-M-type in LWY24 isolate could due to clonal spread of ST93, selective pressure of cefotaxime, IS26-mediate homologous recombination and transposition, and the specific shufflon region.
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Affiliation(s)
- Wenya Li
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yinshu Li
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yating Jia
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Huarun Sun
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Chunhui Zhang
- College of Animal Medicine, Henan University of Animal Husbandry & Economy, Zhengzhou 450046, China
| | - Gongzheng Hu
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Li Yuan
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China.
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18
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Chaalal N, Touati A, Yahiaoui-Martinez A, Aissa MA, Sotto A, Lavigne JP, Pantel A. Colistin-Resistant Enterobacterales Isolated from Chicken Meat in Western Algeria. Microb Drug Resist 2021; 27:991-1002. [PMID: 33428521 DOI: 10.1089/mdr.2020.0109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aim: In Algeria, colistin is used as a metaphylactic treatment in the poultry industry for the treatment of Gram-negative gastrointestinal infections and also as a feed additive to promote animal growth. The aim of this study was to investigate the importance and genetic characteristics of colistin-resistant Enterobacterales from chicken meat in Western Algeria. Results: A total of 181 samples of chicken meat were collected from three poultry farms across three provinces in Western Algeria. The presence of colistin-resistant Enterobacterales isolates was screened on selective media. Resistance and virulence profiles were characterised by PCR and sequencing. The clonal relatedness of the different mcr positive isolates was studied using repetitive sequence-based PCR (Rep-PCR) and multilocus sequence typing. Transferability and characteristics of plasmids harboring mcr-1 positive gene were performed using conjugation, PCR-based replicon typing, and whole-genome sequencing. A total of 22 isolates with acquired colistin resistance were identified giving an overall prevalence of 12.2% (22/181): 17 Escherichia coli (predominantly ST224 [n = 4, 23.5%]) and 5 Klebsiella pneumoniae (ST17 [n = 2, 40%], ST646 [n = 2, 40%], and ST944 [n = 1, 20%]). mcr-1 gene was exclusively found in 11 E. coli (prevalence of 6.1% [11/181]) and was associated with IncFV (n = 7) and IncFIIK (n = 4) plasmids. All the isolates had a commensal origin (n = 11). One isolate harbored virulence profile, a high colistin resistance (minimum inhibitory concentration = 96 mg/L), with some new mutations in the chromosomic colistin-resistant genes and different pathogenicity islands typically identified in uropathogenic E. coli. Conclusions: This study reports the diffusion of mcr-1 producing Enterobacterales from chicken meat in Western Algeria. This represents a worrisome situation needing continuous monitoring.
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Affiliation(s)
- Nadia Chaalal
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria.,VBMI, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University of Montpellier, Nîmes, France
| | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria
| | - Alex Yahiaoui-Martinez
- VBMI, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University of Montpellier, Nîmes, France
| | - Mohamed Amine Aissa
- Laboratory of Microbiology, National Institute of Veterinarian Sciences, Tiaret, Algeria
| | - Albert Sotto
- VBMI, INSERM U1047, Department of Infectious Diseases, CHU Nîmes, University of Montpellier, Nîmes, France
| | - Jean-Philippe Lavigne
- VBMI, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University of Montpellier, Nîmes, France
| | - Alix Pantel
- VBMI, INSERM U1047, Department of Microbiology and Hospital Hygiene, CHU Nîmes, University of Montpellier, Nîmes, France
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19
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El-Sayed Ahmed MAEG, Zhong LL, Shen C, Yang Y, Doi Y, Tian GB. Colistin and its role in the Era of antibiotic resistance: an extended review (2000-2019). Emerg Microbes Infect 2020; 9:868-885. [PMID: 32284036 PMCID: PMC7241451 DOI: 10.1080/22221751.2020.1754133] [Citation(s) in RCA: 324] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 03/28/2020] [Accepted: 04/04/2020] [Indexed: 12/17/2022]
Abstract
Increasing antibiotic resistance in multidrug-resistant (MDR) Gram-negative bacteria (MDR-GNB) presents significant health problems worldwide, since the vital available and effective antibiotics, including; broad-spectrum penicillins, fluoroquinolones, aminoglycosides, and β-lactams, such as; carbapenems, monobactam, and cephalosporins; often fail to fight MDR Gram-negative pathogens as well as the absence of new antibiotics that can defeat these "superbugs". All of these has prompted the reconsideration of old drugs such as polymyxins that were reckoned too toxic for clinical use. Only two polymyxins, polymyxin E (colistin) and polymyxin B, are currently commercially available. Colistin has re-emerged as a last-hope treatment in the mid-1990s against MDR Gram-negative pathogens due to the development of extensively drug-resistant GNB. Unfortunately, rapid global resistance towards colistin has emerged following its resurgence. Different mechanisms of colistin resistance have been characterized, including intrinsic, mutational, and transferable mechanisms.In this review, we intend to discuss the progress over the last two decades in understanding the alternative colistin mechanisms of action and different strategies used by bacteria to develop resistance against colistin, besides providing an update about what is previously recognized and what is novel concerning colistin resistance.
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Affiliation(s)
- Mohamed Abd El-Gawad El-Sayed Ahmed
- Department of Microbiology, Zhongshan School of
Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of
China
- Key Laboratory of Tropical Diseases Control, Sun
Yat-sen University, Ministry of Education, Guangzhou, People’s
Republic of China
- Department of Microbiology and Immunology,
Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science
and Technology (MUST), Cairo, Egypt
| | - Lan-Lan Zhong
- Department of Microbiology, Zhongshan School of
Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of
China
- Key Laboratory of Tropical Diseases Control, Sun
Yat-sen University, Ministry of Education, Guangzhou, People’s
Republic of China
| | - Cong Shen
- Department of Microbiology, Zhongshan School of
Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of
China
- Key Laboratory of Tropical Diseases Control, Sun
Yat-sen University, Ministry of Education, Guangzhou, People’s
Republic of China
| | - Yongqiang Yang
- Department of Microbiology, Zhongshan School of
Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of
China
- Key Laboratory of Tropical Diseases Control, Sun
Yat-sen University, Ministry of Education, Guangzhou, People’s
Republic of China
| | - Yohei Doi
- University of Pittsburgh School of
Medicine, Pittsburgh, PA, USA
- Department of Microbiology and Infectious
Diseases, Fujita Health University, School of Medicine, Aichi,
Japan
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of
Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of
China
- Key Laboratory of Tropical Diseases Control, Sun
Yat-sen University, Ministry of Education, Guangzhou, People’s
Republic of China
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20
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Ngbede EO, Poudel A, Kalalah A, Yang Y, Adekanmbi F, Adikwu AA, Adamu AM, Mamfe LM, Daniel ST, Useh NM, Kwaga JK, Adah MI, Kelly P, Butaye P, Wang C. Identification of mobile colistin resistance genes (mcr-1.1, mcr-5 and mcr-8.1) in Enterobacteriaceae and Alcaligenes faecalis of human and animal origin, Nigeria. Int J Antimicrob Agents 2020; 56:106108. [DOI: 10.1016/j.ijantimicag.2020.106108] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/14/2020] [Accepted: 07/19/2020] [Indexed: 01/29/2023]
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21
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Adiguzel MC, Baran A, Wu Z, Cengiz S, Dai L, Oz C, Ozmenli E, Goulart DB, Sahin O. Prevalence of Colistin Resistance in Escherichia coli in Eastern Turkey and Genomic Characterization of an mcr-1 Positive Strain from Retail Chicken Meat. Microb Drug Resist 2020; 27:424-432. [PMID: 32721263 DOI: 10.1089/mdr.2020.0209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Colistin is one of the most effective antibiotics against multidrug resistant Gram-negative bacteria. However, the recent emergence of plasmid-borne mobilized colistin resistance (mcr) genes is considered a serious antimicrobial resistance challenge worldwide. In this study, we report detection of an mcr-1 carrying Escherichia coli isolate (named ATAVET mcr-1 Turkey) from retail raw chicken meat in Turkey. Of the 11 (from 500 total tested) phenotypically colistin-resistant isolates, 1 was shown to carry the mcr-1 gene by PCR. Whole-genome sequencing indicated that mcr-1 was located on a ∼13 kb-long contig that was almost identical to the corresponding part in pZJ1635, an IncI2 plasmid encoding mcr-1 in the same genetic context in another E. coli strain. In addition, ATAVET mcr-1 Turkey harbored blaCTX-M-8, qnrB19, mdf(A), tet(A), sul2, aph(3″)-Ib, aph(6)-Id, and floR resistance genes. Phylogenetic analysis based on whole genome and multilocus sequence typing indicated that ATAVET mcr-1 Turkey was more closely related to mcr-1 carrying E. coli isolates from food and human clinical samples previously reported from different parts of the world than to those from Turkey. These findings further emphasize the worldwide emergence and spread of mcr meditated colistin resistance in bacteria with zoonotic potential within animals and the food chain.
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Affiliation(s)
- Mehmet Cemal Adiguzel
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey.,Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Alper Baran
- Department of Food Quality Control and Analysis, Erzurum Vocational School, Ataturk University, Erzurum, Turkey
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Seyda Cengiz
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Cihan Oz
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey
| | - Esma Ozmenli
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey
| | - Debora Brito Goulart
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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22
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Luo Q, Wang Y, Xiao Y. Prevalence and transmission of mobilized colistin resistance (mcr) gene in bacteria common to animals and humans. BIOSAFETY AND HEALTH 2020. [DOI: 10.1016/j.bsheal.2020.05.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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23
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García-Meniño I, Díaz-Jiménez D, García V, de Toro M, Flament-Simon SC, Blanco J, Mora A. Genomic Characterization of Prevalent mcr-1, mcr-4, and mcr-5 Escherichia coli Within Swine Enteric Colibacillosis in Spain. Front Microbiol 2019; 10:2469. [PMID: 31736909 PMCID: PMC6838222 DOI: 10.3389/fmicb.2019.02469] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 10/15/2019] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial agents are crucial for the treatment of many bacterial diseases in pigs, however, the massive use of critically important antibiotics such as colistin, fluoroquinolones and 3rd-4th-generation cephalosporins often selects for co-resistance. Based on a comprehensive characterization of 35 colistin-resistant Escherichia coli from swine enteric colibacillosis, belonging to prevalent Spanish lineages, the aims of the present study were to investigate the characteristics of E. coli clones successfully spread in swine and to assess the correlation of the in vitro results with in silico predictions from WGS data. The resistome analysis showed six different mcr variants: mcr-1.1; mcr-1.10; mcr-4.1; mcr-4.2; mcr-4.5; and mcr-5.1. Additionally, bla CTX-M- 14, bla CTX-M- 32 and bla SHV- 12 genes were present in seven genomes. PlasmidFinder revealed that mcr-1.1 genes located mainly on IncHI2 and IncX4 types, and mcr-4 on ColE10-like plasmids. Twenty-eight genomes showed a gyrA S83L substitution, and 12 of those 28 harbored double-serine mutations gyrA S83L and parC S80I, correlating with in vitro quinolone-resistances. Notably, 16 of the 35 mcr-bearing genomes showed mutations in the PmrA (S39I) and PmrB (V161G) proteins. The summative presence of mechanisms, associated with high-level of resistance to quinolones/fluoroquinolones and colistin, could be conferring adaptive advantages to prevalent pig E. coli lineages, such as the ST10-A (CH11-24), as presumed for ST131. SerotypeFinder allowed the H-antigen identification of in vitro non-mobile (HNM) isolates, revealing that 15 of the 21 HNM E. coli analyzed were H39. Since the H39 is associated with the most prevalent O antigens worldwide within swine colibacillosis, such as O108 and O157, it would be probably playing a role in porcine colibacillosis to be considered as a valuable subunit antigen in the formulation of a broadly protective Enterotoxigenic E. coli (ETEC) vaccine. Our data show common features with other European countries in relation to a prevalent clonal group (CC10), serotypes (O108:H39, O138:H10, O139:H1, O141:H4), high plasmid content within the isolates and mcr location, which would support global alternatives to the use of antibiotics in pigs. Here, we report for first time a rare finding so far, which is the co-occurrence of double colistin-resistance mechanisms in a significant number of E. coli isolates.
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Affiliation(s)
- Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Saskia C Flament-Simon
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Jorge Blanco
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli, Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
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24
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Acquisition of mcr-1 and Cocarriage of Virulence Genes in Avian Pathogenic Escherichia coli Isolates from Municipal Wastewater Influents in Japan. Appl Environ Microbiol 2019; 85:AEM.01661-19. [PMID: 31492666 DOI: 10.1128/aem.01661-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
This study focused on the detection of the plasmid-mediated mcr colistin resistance gene in Escherichia coli isolates from wastewater treatment plants (WWTPs). Seven influent samples were collected from three WWTPs in Nagano Prefecture, Japan, during August and December 2018. Colistin-resistant E. coli isolates were selected on colistin-supplemented CHROMagar ECC plates. mcr-1-positive isolates were subjected to whole-genome sequencing (WGS) analysis. From six influent samples, seven mcr-1-positive but extended-spectrum β-lactamase (ESBL)-negative isolates belonging to different genetic lineages, namely, B2-O25:H4-ST131-fimH22, B2-O2:H1-ST135-fimH2, B1-O8:H9-ST764-fimH32, B1-O23:H16-ST453-fimH31, A-O81:H27-ST10-fimH54, A-O16:H5-ST871-fimH25, and F-O11:H6-ST457-fimH145, were detected. The MICs of colistin for these isolates ranged from 4 to 16 mg/liter. The mcr-1 genes were located on plasmids belonging to IncX4 and IncI2 in five and two isolates, respectively. Four IncX4 plasmids with the same size (33,309 bp) showed high sequence similarity (4 single-nucleotide variations). The remaining one IncX4 plasmid, with a size of 33,858 bp, carried the mcr-1 gene with the single synonymous nucleic substitution T27C. Two IncI2 plasmids with sizes of 60,710 bp and 60,733 bp had high sequence similarity (99.9% identity; 100% query coverage). Two of five isolates carrying IncX4 plasmids and both of the isolates carrying IncI2 plasmids harbored ColV plasmids carrying virulence-associated genes of avian pathogenic E. coli (APEC). In addition, another isolate of the B2-O25:H4-ST131-fimH22 lineage had those APEC-associated virulence genes on its chromosome. In conclusion, mcr-1-positive E. coli environmental isolates were mostly characterized as positive for APEC-associated virulence genes. The copresence of those genes may suggest the existence of a common source in animals and/or their associated environments.IMPORTANCE Colistin is considered a last-line therapeutic option in severe infections due to multidrug-resistant Gram-negative bacteria, in particular carbapenemase-producing Enterobacteriaceae and multidrug-resistant Acinetobacter baumannii An increasing prevalence of mcr genes in diverse Enterobacteriaceae species, mainly Escherichia coli and Klebsiella pneumoniae from humans and food animals, has become a significant concern to public health all over the world. In Japan, mcr genes have so far been detected in food animals, raw meat, wastewater, and human clinical samples. This study reports the copresence of mcr-1 and avian pathogenic E. coli (APEC)-associated virulence genes in five of seven E. coli isolates recovered from aquatic environments in Japan. Our study highlights the importance and urgency of action to reduce environmental contamination by mcr genes that may likely occur due to exposure to untreated wastewater through combined sewer overflow by recent unusual weather.
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Characteristics of Carbapenem-Resistant and Colistin-Resistant Escherichia coli Co-Producing NDM-1 and MCR-1 from Pig Farms in China. Microorganisms 2019; 7:microorganisms7110482. [PMID: 31652858 PMCID: PMC6920953 DOI: 10.3390/microorganisms7110482] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/14/2019] [Accepted: 10/22/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of carbapenem-resistant and colistin-resistant Enterobacteriaceae represents a great risk for public health. In this study, the phenotypical and genetic characteristics of eight carbapenem-resistant and colistin-resistant isolates from pig farms in China were determined by the broth microdilution method and whole genome sequencing. Antimicrobial susceptibility testing showed that the eight carbapenem-resistant and colistin-resistant strains were resistant to three aminoglycosides, twelve β-lactams, one of the phenicols, one of the tetracyclines, and one of the fluoroquinolones tested, simultaneously. The prediction of acquired resistant genes using the whole genome sequences revealed the co-existence of blaNDM-1 and mcr-1 as well as the other genes that were responsible for the multidrug-resistant phenotypes. Bioinformatics analysis also showed that the carbapenem-resistant gene blaNDM-1 was located on a putative IncFII-type plasmid, which also carried the other acquired resistant genes identified, including fosA3, blaTEM-1B and rmtB, while the colistin-resistant gene mcr-1 was carried by a putative IncX4-type plasmid. Finally, we found that these resistant genes/plasmids were conjugative, and they could be co-conjugated, conferring resistance to multiple types of antibiotics, including the carbapenems and colistin, to the recipient Escherichia coli strains.
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