1
|
Latif H, Pazra DF, Basri C, Wibawan IWT, Rahayu P. Whole genome sequencing analysis on antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia. J Vet Sci 2024; 25:e44. [PMID: 38834513 PMCID: PMC11156600 DOI: 10.4142/jvs.24031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 06/06/2024] Open
Abstract
IMPORTANCE The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics. OBJECTIVE This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia. METHODS Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNA-barcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder. RESULTS Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fifty-one ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%. CONCLUSIONS AND RELEVANCE The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.
Collapse
Affiliation(s)
- Hadri Latif
- Veterinery Public Health and Epidemology Division, School of Veterinary Medicine and Biomedical Sciences (SVMBS), IPB University, Bogor 16680, Indonesia
| | - Debby Fadhilah Pazra
- Animal Health Division, Bogor Agricultural Development Polytechnic, Bogor 16730, Indonesia.
| | - Chaerul Basri
- Veterinery Public Health and Epidemology Division, School of Veterinary Medicine and Biomedical Sciences (SVMBS), IPB University, Bogor 16680, Indonesia
| | - I Wayan Teguh Wibawan
- Medical Microbiology Division, School of Veterinary Medicine and Biomedical Sciences (SVMBS), IPB University, Bogor 16680, Indonesia
| | - Puji Rahayu
- Quality Control Laboratory and Certification of Animal Products, Bogor 16161, Indonesia
| |
Collapse
|
2
|
Gauba A, Rahman KM. Evaluation of Antibiotic Resistance Mechanisms in Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:1590. [PMID: 37998792 PMCID: PMC10668847 DOI: 10.3390/antibiotics12111590] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Multidrug-resistant Gram-negative bacterial infections are exponentially increasing, posing one of the most urgent global healthcare and economic threats. Due to the lack of new therapies, the World Health Organization classified these bacterial species as priority pathogens in 2017, known as ESKAPE pathogens. This classification emphasizes the need for urgent research and development of novel targeted therapies. The majority of these priority pathogens are Gram-negative species, which possess a structurally dynamic cell envelope enabling them to resist multiple antibiotics, thereby leading to increased mortality rates. Despite 6 years having passed since the WHO classification, the progress in generating new treatment ideas has not been sufficient, and antimicrobial resistance continues to escalate, acting as a global ticking time bomb. Numerous efforts and strategies have been employed to combat the rising levels of antibiotic resistance by targeting specific resistance mechanisms. These mechanisms include antibiotic inactivating/modifying enzymes, outer membrane porin remodelling, enhanced efflux pump action, and alteration of antibiotic target sites. Some strategies have demonstrated clinical promise, such as the utilization of beta-lactamase inhibitors as antibiotic adjuvants, as well as recent advancements in machine-based learning employing artificial intelligence to facilitate the production of novel narrow-spectrum antibiotics. However, further research into an enhanced understanding of the precise mechanisms by which antibiotic resistance occurs, specifically tailored to each bacterial species, could pave the way for exploring narrow-spectrum targeted therapies. This review aims to introduce the key features of Gram-negative bacteria and their current treatment approaches, summarizing the major antibiotic resistance mechanisms with a focus on Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Additionally, potential directions for alternative therapies will be discussed, along with their relative modes of action, providing a future perspective and insight into the discipline of antimicrobial resistance.
Collapse
Affiliation(s)
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, London SE1 9NH, UK;
| |
Collapse
|
3
|
Zhang F, Ye X, Yin Z, Hu M, Wang B, Liu W, Li B, Ren H, Jin Y, Yue J. Comparative genomics reveals new insights into the evolution of the IncA and IncC family of plasmids. Front Microbiol 2022; 13:1045314. [PMID: 36466664 PMCID: PMC9709138 DOI: 10.3389/fmicb.2022.1045314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 06/13/2024] Open
Abstract
Incompatibility groups IncA and IncC plasmids are of great concern due to their ability to disseminate antibiotic resistance in bacteria via conjugative transfer. A deep understanding of their genomic structures and evolutionary characteristics is of great significance for improving our knowledge about its multidrug-resistance evolution and dissemination. However, current knowledge of their backbone structure, features of core functional modules and the characteristics of variable regions is based on a few plasmids, which highlights the need for a comprehensive systematic study. The present study thoroughly compared and analysed 678 IncA and IncC plasmid genomes. We found that their core functional genes were occasionally deficient and sometimes existed as multiple functional copies/multiple families, which resulted in much diversity. The phylogeny of 13 core functional genes corresponded well to the plasmid subtypes. The conjugative transfer system gained diverse complexity and exhibited many previously unnoticed types with multiple combinations. The insertion of mobile genetic elements (MGEs) in plasmids varied between types and was present in 4 insertion spots in different types of plasmids with certain types of transposons, integrons and insertion sequences. The impact of gene duplication, deletion, the insertion of MGEs, genome rearrangement and recombination resulted in the complex dynamic variable backbone of IncA and IncC plasmids. And IncA and IncC plasmids were more complex than their closest relative SXT/R391 integrative conjugative elements (ICEs), which included nearly all of the diversity of SXT/R391 in key systems. Our work demonstrated a global and systematic view of the IncA and IncC plasmids and provides many new insights into their genome evolution.
Collapse
Affiliation(s)
- Fengwei Zhang
- Medical College of Guizhou University, Guiyang, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Xianwei Ye
- Medical College of Guizhou University, Guiyang, China
- Guizhou Provincial People’s Hospital, Guiyang, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Tai’an, China
| | - Mingda Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Boqian Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Wenting Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Beiping Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hongguang Ren
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yuan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Junjie Yue
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| |
Collapse
|
4
|
Tang B, Ni J, Lin J, Sun Y, Lin H, Wu Y, Yang H, Yue M. Genomic characterization of multidrug-resistance gene cfr in Escherichia coli recovered from food animals in Eastern China. Front Microbiol 2022; 13:999778. [PMID: 36160268 PMCID: PMC9493366 DOI: 10.3389/fmicb.2022.999778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022] Open
Abstract
The plasmid-borne cfr gene, mediating multiple drug resistance (MDR), has been observed in many Gram-positive bacteria. The prevalence of cfr and its co-occurrence with additional antimicrobial resistance (AMR) determinants in Escherichia coli is an ongoing issue. Additionally, the prevalence and transfer mechanism of the cfr gene remain partially investigated. Here, eight cfr-positive E. coli strains were screened using PCR from an extensive collection of E. coli (n = 2,165) strains isolated from pigs and chickens in 2021 in China, with a prevalence rate of 0.37%. All of them were MDR and resistant to florfenicol and tetracycline. These strains can transfer the cfr gene to E. coli J53 by conjugation (1.05 × 10−1 – 1.01 × 10−6). Moreover, the IncX4 plasmid p727A3-62 K-cfr (62,717 bp) harboring cfr in strain EC727A3 was confirmed using Oxford Nanopore Technology. The unknown type plasmid p737A1-27K-cfr (27,742 bp) harboring cfr in strain EC737A1 was also identified. Notably, it was verified by PCR that three of the eight E. coli strains were able to form the cfr-IS26 circular intermediate. It was 2,365 bp in length in strains EC727A3 and ECJHZ21-173, and 2,022 bp in length in EC737A1. Collectively, this study demonstrated that IS26 plays a vital role in transmitting the MDR gene cfr in E. coli via conjugation and provided updated knowledge regarding cfr in E. coli in Eastern China.
Collapse
Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Academy of Agricultural Sciences, Hangzhou, China
| | - Juan Ni
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Academy of Agricultural Sciences, Hangzhou, China
- School of Food and Pharmacy, Ningbo University, Ningbo, China
| | - Jiahui Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yangying Sun
- School of Food and Pharmacy, Ningbo University, Ningbo, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Academy of Agricultural Sciences, Hangzhou, China
| | - Yuehong Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Hua Yang,
| | - Min Yue
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Min Yue,
| |
Collapse
|
5
|
Brenciani A, Morroni G, Schwarz S, Giovanetti E. Oxazolidinones: mechanisms of resistance and mobile genetic elements involved. J Antimicrob Chemother 2022; 77:2596-2621. [PMID: 35989417 DOI: 10.1093/jac/dkac263] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The oxazolidinones (linezolid and tedizolid) are last-resort antimicrobial agents used for the treatment of severe infections in humans caused by MDR Gram-positive bacteria. They bind to the peptidyl transferase centre of the bacterial ribosome inhibiting protein synthesis. Even if the majority of Gram-positive bacteria remain susceptible to oxazolidinones, resistant isolates have been reported worldwide. Apart from mutations, affecting mostly the 23S rDNA genes and selected ribosomal proteins, acquisition of resistance genes (cfr and cfr-like, optrA and poxtA), often associated with mobile genetic elements [such as non-conjugative and conjugative plasmids, transposons, integrative and conjugative elements (ICEs), prophages and translocatable units], plays a critical role in oxazolidinone resistance. In this review, we briefly summarize the current knowledge on oxazolidinone resistance mechanisms and provide an overview on the diversity of the mobile genetic elements carrying oxazolidinone resistance genes in Gram-positive and Gram-negative bacteria.
Collapse
Affiliation(s)
- Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| |
Collapse
|
6
|
Feßler AT, Scholtzek AD, Schug AR, Kohn B, Weingart C, Hanke D, Schink AK, Bethe A, Lübke-Becker A, Schwarz S. Antimicrobial and Biocide Resistance among Canine and Feline Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii Isolates from Diagnostic Submissions. Antibiotics (Basel) 2022; 11:antibiotics11020152. [PMID: 35203754 PMCID: PMC8868471 DOI: 10.3390/antibiotics11020152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/12/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
A total of 215 isolates from infections of dogs and cats, including 49 Enterococcus faecalis, 37 Enterococcus faecium, 59 Escherichia coli, 56 Pseudomonas aeruginosa, and 14 Acinetobacter baumannii, were investigated for their susceptibility to 27 (Gram-positive bacteria) or 20 (Gram-negative bacteria) antimicrobial agents/combinations of antimicrobial agents by broth microdilution according to the recommendations of the Clinical and Laboratory Standards Institute. Moreover, all isolates were analysed for their susceptibility to the biocides benzalkonium chloride, chlorhexidine, polyhexanide, and octenidine by a recently published broth microdilution biocide susceptibility testing method. While the E. faecalis isolates did not show expanded resistances, considerable numbers of the E. faecium isolates were resistant to penicillins, macrolides, tetracyclines, and fluoroquinolones. Even a single vancomycin-resistant isolate that carried the vanA gene cluster was detected. Expanded multiresistance phenotypes were also detected among the E. coli isolates, including a single carbapenem-resistant, blaOXA-48-positive isolate. In addition, multiresistant A. baumannii isolates were detected. The minimal inhibitory concentrations of the biocides showed unimodal distributions but differed with respect to the biocide and the bacterial species investigated. Although there were no indications of a development of biocide resistance, some P. aeruginosa isolates exhibited benzalkonium MICs higher than the highest test concentration.
Collapse
Affiliation(s)
- Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Anissa D Scholtzek
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
- Unit Bacterial Toxins, Food Service, Department Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Angela R Schug
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Barbara Kohn
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
- Small Animal Clinic, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Christiane Weingart
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
- Small Animal Clinic, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Anne-Kathrin Schink
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| |
Collapse
|
7
|
Jiang BW, Ji X, Lyu ZQ, Liang B, Li JH, Zhu LW, Guo XJ, Liu J, Sun Y, Liu YJ. Detection of Two Copies of a blaNDM-1-Encoding Plasmid in Escherichia coli Isolates from a Pediatric Patient with Diarrhea. Infect Drug Resist 2022; 15:223-232. [PMID: 35115791 PMCID: PMC8801394 DOI: 10.2147/idr.s346111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/11/2022] [Indexed: 11/30/2022] Open
Abstract
Purpose To elucidate the contribution of a transferable plasmid harboring the blaNDM-1 gene in an Escherichia coli clinical isolate to the spread of resistance determinants. Methods Nine extended-spectrum β-lactamase-producing E. coli were collected from diarrhea samples from a pediatric patient and genetic linkage was investigated through enterobacteriaceae repetitive intragenic consensus polymerase chain reaction (PCR). Bacterial species were identified by 16s rRNA sequencing, susceptibility testing with the use of a BD PhoenixTM-100 Automated Microbiology System, and assessment of virulence genes by PCR. The transferability of blaNDM-1 in E. coli strain TCM3e1 was confirmed by conjugation experiments. Complete sequencing of E. coli strain TCM3e1 was determined with the PacBio and Illumina NovaSeq platforms and the characteristics were analyzed with bioinformatics software. Results The results showed that all nine E. coli strains were the same clone. E. coli strain TCM3e1 was resistant to 12 antimicrobial agents and carried the virulence gene EAST-1. Conjugation transfer analysis showed that blaNDM-1 was carried on a self-transmissible plasmid. Two copies of the blaNDM-1 gene were present on an IncC plasmid and some resistance genes with two or three copies were located downstream of the blaNDM-1 gene and formed a tandem repeat fragment (blaDNM-1-bleo-sul1- aadA17- dfrA12). Conclusion A transmissible plasmid harboring two copies of the blaNDM-1 gene, including clonal dispersions of the blaNDM-1 gene, was identified in clinical isolates. These findings emphasized the necessity of surveillance of the plasmid-borne blaNDM-1 to prevent dissemination.
Collapse
Affiliation(s)
- Bo-Wen Jiang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People’s Republic of China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, People’s Republic of China
| | - Xue Ji
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People’s Republic of China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, People’s Republic of China
| | - Zhong-Qing Lyu
- Third Affiliated Clinical Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, People’s Republic of China
| | - Bing Liang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People’s Republic of China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, People’s Republic of China
| | - Jian-Hang Li
- Third Affiliated Clinical Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, People’s Republic of China
| | - Ling-Wei Zhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People’s Republic of China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, People’s Republic of China
| | - Xue-Jun Guo
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People’s Republic of China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, People’s Republic of China
| | - Jun Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People’s Republic of China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, People’s Republic of China
| | - Yang Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, People’s Republic of China
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, Jilin, People’s Republic of China
- Correspondence: Yang Sun; Yan-Jing Liu, Tel +86 431-86986933, Email ;
| | - Yan-Jing Liu
- Third Affiliated Clinical Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, People’s Republic of China
| |
Collapse
|
8
|
Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Ru G, Simmons M, Skandamis P, Suffredini E, Andersson DI, Bampidis V, Bengtsson‐Palme J, Bouchard D, Ferran A, Kouba M, López Puente S, López‐Alonso M, Nielsen SS, Pechová A, Petkova M, Girault S, Broglia A, Guerra B, Innocenti ML, Liébana E, López‐Gálvez G, Manini P, Stella P, Peixe L. Maximum levels of cross-contamination for 24 antimicrobial active substances in non-target feed. Part 8: Pleuromutilins: tiamulin and valnemulin. EFSA J 2021; 19:e06860. [PMID: 34729088 PMCID: PMC8546795 DOI: 10.2903/j.efsa.2021.6860] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The specific concentrations of tiamulin and valnemulin in non-target feed for food-producing animals, below which there would not be an effect on the emergence of, and/or selection for, resistance in bacteria relevant for human and animal health, as well as the specific antimicrobial concentrations in feed which have an effect in terms of growth promotion/increased yield were assessed by EFSA in collaboration with EMA. Details of the methodology used for this assessment, associated data gaps and uncertainties, are presented in a separate document. To address antimicrobial resistance, the Feed Antimicrobial Resistance Selection Concentration (FARSC) model developed specifically for the assessment was applied. However, due to the lack of data on the parameters required to calculate the FARSC, it was not possible to conclude the assessment until further experimental data become available. To address growth promotion, data from scientific publications obtained from an extensive literature review were used. Levels in feed that showed to have an effect on growth promotion/increased yield were reported for tiamulin, while for valnemulin no suitable data for the assessment were available. It was recommended to carry out studies to generate the data that are required to fill the gaps which prevented the calculation of the FARSC for these two antimicrobials.
Collapse
|
9
|
Schwarz S, Zhang W, Du XD, Krüger H, Feßler AT, Ma S, Zhu Y, Wu C, Shen J, Wang Y. Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 PMCID: PMC8262807 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Seven mobile oxazolidinone resistance genes, including cfr, cfr(B), cfr(C), cfr(D), cfr(E), optrA, and poxtA, have been identified to date. The cfr genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The optrA and poxtA genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones. The optrA gene confers resistance to oxazolidinones and phenicols, while the poxtA gene confers elevated MICs or resistance to oxazolidinones, phenicols, and tetracycline. These oxazolidinone resistance genes are most frequently found on plasmids, but they are also located on transposons, integrative and conjugative elements (ICEs), genomic islands, and prophages. In these mobile genetic elements (MGEs), insertion sequences (IS) most often flanked the cfr, optrA, and poxtA genes and were able to generate translocatable units (TUs) that comprise the oxazolidinone resistance genes and occasionally also other genes. MGEs and TUs play an important role in the dissemination of oxazolidinone resistance genes across strain, species, and genus boundaries. Most frequently, these MGEs also harbor genes that mediate resistance not only to antimicrobial agents of other classes, but also to metals and biocides. Direct selection pressure by the use of antimicrobial agents to which the oxazolidinone resistance genes confer resistance, but also indirect selection pressure by the use of antimicrobial agents, metals, or biocides (the respective resistance genes against which are colocated on cfr-, optrA-, or poxtA-carrying MGEs) may play a role in the coselection and persistence of oxazolidinone resistance genes.
Collapse
Affiliation(s)
- Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Henrike Krüger
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Shizhen Ma
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| |
Collapse
|
10
|
Cadel-Six S, Cherchame E, Douarre PE, Tang Y, Felten A, Barbet P, Litrup E, Banerji S, Simon S, Pasquali F, Gourmelon M, Mensah N, Borowiak M, Mistou MY, Petrovska L. The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe. Front Microbiol 2021; 12:651124. [PMID: 34093465 PMCID: PMC8175864 DOI: 10.3389/fmicb.2021.651124] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/16/2021] [Indexed: 01/23/2023] Open
Abstract
The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3' end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.
Collapse
Affiliation(s)
- Sabrina Cadel-Six
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Emeline Cherchame
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | | | - Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Arnaud Felten
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Pauline Barbet
- Anses, Laboratory for Food Safety, Salmonella and Listeria Unit, Maisons-Alfort, France
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sangeeta Banerji
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Sandra Simon
- Robert Koch-Institute, Division of Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Wernigerode, Germany
| | - Federique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna, Bologna, Italy
| | - Michèle Gourmelon
- Ifremer, RBE, SGMM, Health, Environment and Microbiology Laboratory, Plouzané, France
| | - Nana Mensah
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Maria Borowiak
- Department for Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Michel-Yves Mistou
- Université Paris-Saclay, INRAE, Centre International de Ressource Microbienne (CIRM) MaIAGE, Jouy-en-Josas, France
| | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| |
Collapse
|
11
|
Abdelfattah EM, Ekong PS, Okello E, Chamchoy T, Karle BM, Black RA, Sheedy D, ElAshmawy WR, Williams DR, Califano D, Tovar LFD, Ongom J, Lehenbauer TW, Byrne BA, Aly SS. Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows. PeerJ 2021; 9:e11108. [PMID: 33976962 PMCID: PMC8063881 DOI: 10.7717/peerj.11108] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/23/2021] [Indexed: 12/17/2022] Open
Abstract
Background This study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400–14408 (formerly known as Senate Bill, SB 27) in California (CA). Methods The study was conducted on ten dairies distributed across CA’s three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials. Results The E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%). Conclusions Our findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season.
Collapse
Affiliation(s)
- Essam M Abdelfattah
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA.,Department of Animal Hygiene, and Veterinary Management, Faculty of Veterinary Medicine, Benha University, Moshtohor, Qalyubia, Egypt
| | - Pius S Ekong
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA.,Department of Epidemiology, National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Emmanuel Okello
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA.,Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Tapakorn Chamchoy
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA
| | - Betsy M Karle
- Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Davis, Orland, CA, USA
| | - Randi A Black
- Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Davis, Santa Rosa, CA, USA
| | - David Sheedy
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA
| | - Wagdy R ElAshmawy
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA.,Department of Internal Medicine and Infectious Diseases, Cairo University, Giza, Giza, Egypt
| | - Deniece R Williams
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA
| | - Daniela Califano
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA
| | - Luis Fernando Durán Tovar
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA
| | - Jonathan Ongom
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA
| | - Terry W Lehenbauer
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA.,Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Barbara A Byrne
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Sharif S Aly
- Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Davis, Tulare, CA, USA.,Department of Population Health & Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| |
Collapse
|
12
|
Liu Y, Tong Z, Shi J, Li R, Upton M, Wang Z. Drug repurposing for next-generation combination therapies against multidrug-resistant bacteria. Theranostics 2021; 11:4910-4928. [PMID: 33754035 PMCID: PMC7978324 DOI: 10.7150/thno.56205] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance has been a global health challenge that threatens our ability to control and treat life-threatening bacterial infections. Despite ongoing efforts to identify new drugs or alternatives to antibiotics, no new classes of antibiotic or their alternatives have been clinically approved in the last three decades. A combination of antibiotics and non-antibiotic compounds that could inhibit bacterial resistance determinants or enhance antibiotic activity offers a sustainable and effective strategy to confront multidrug-resistant bacteria. In this review, we provide a brief overview of the co-evolution of antibiotic discovery and the development of bacterial resistance. We summarize drug-drug interactions and uncover the art of repurposing non-antibiotic drugs as potential antibiotic adjuvants, including discussing classification and mechanisms of action, as well as reporting novel screening platforms. A pathogen-by-pathogen approach is then proposed to highlight the critical value of drug repurposing and its therapeutic potential. Finally, general advantages, challenges and development trends of drug combination strategy are discussed.
Collapse
Affiliation(s)
- Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ziwen Tong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jingru Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Mathew Upton
- School of Biomedical Sciences, University of Plymouth, Drake Circus, Plymouth, UK
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
| |
Collapse
|
13
|
Rapid Increase in the IS 26-Mediated cfr Gene in E. coli Isolates with IncP and IncX4 Plasmids and Co-Existing cfr and mcr-1 Genes in a Swine Farm. Pathogens 2021; 10:pathogens10010033. [PMID: 33401636 PMCID: PMC7823714 DOI: 10.3390/pathogens10010033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 01/13/2023] Open
Abstract
This paper aimed to investigate the molecular epidemiological features of the cfr gene in E. coli isolates in a typical swine farm during 2014–2017. A total of 617 E. coli isolates were screened for the cfr gene using PCR amplification. A susceptibility test, pulsed-field gel electrophoresis (PFGE), S1-PFGE, southern blotting hybridization, and the genetic context of the cfr gene were all used for analyzing all cfr-positive E. coli isolates. A conjugation experiment was conducted with the broth mating method using E. coli C600 as the recipient strain and 45 mcr-1-cfr-bearing E. coli isolates as the donor strain. Plasmids pHNEP124 and pHNEP129 were revealed by Illumina Miseq 2500. Eighty-five (13.7%) E. coli isolates were positive for the cfr gene and the prevalence of the cfr gene had significantly increased from 1.6% in 2014 to 29.1% in 2017. The Pulsed-Field Gel Electrophoresis (PFGE) analysis indicated that the spread of the cfr gene among E. coli isolates was mainly due to horizontal transfer. In addition, the cfr gene was primarily located on the plasmids between 28.8-kb to 60-kb in size, and the cfr gene was flanked by two copies of IS26 with the same orientation. Sequence analysis suggested that the plasmids pHNEP124 and pHNEP129 co-harboring the cfr and mcr-1 genes belonged to the plasmids IncP plasmid and IncX4 plasmid, respectively. In conclusion, this is the first study to report the high prevalence of the cfr gene among E. coli isolates and the first report of the complete genome sequence of IncP and IncX4 plasmids carrying the mcr-1 and cfr genes. The occurrence and dissemination of the cfr/mcr-1-carrying plasmids among E. coli isolates need further surveillance.
Collapse
|
14
|
Chen H, Deng H, Cheng L, Liu R, Fu G, Shi S, Wan C, Fu Q, Huang Y, Huang X. First report of the multiresistance gene cfr in Pasteurella multocida strains of avian origin from China. J Glob Antimicrob Resist 2020; 23:251-255. [PMID: 33045440 DOI: 10.1016/j.jgar.2020.09.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/21/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES The aim of this study was to investigate the presence and genetic environment of the multiresistance gene cfr gene in Pasteurella multocida of avian origin from China. METHODS A total of 113 P. multocida isolates were collected from sick poultries (ducks, chickens and geese) from 2003 to 2016 in Southern China and were screened for the presence of the cfr gene by PCR. The cfr-carrying P. multocida strains were subjected to antimicrobial susceptibility testing, S1 nuclease PFGE and Southern blot hybridisation, conjugative transfer and analysis of genetic environment of the cfr gene. RESULTS Among 113 P. multocida isolates, strains FJ6671 and FJ6683 from Muscovy duck harboured the cfr gene and presented a multiresistant phenotype. The cfr gene in the two strains was located on an ∼40-kb conjugative plasmid in different genetic environments, including ISApl12-cfr-IS26 and IS26-cfr-IS256. CONCLUSIONS These results demonstrate plasmid-carried cfr in P. multocida and suggest that transposition and homologous recombination mediated by IS26, ISApl1 and IS256 might have played an important role in transfer of the cfr gene in P. multocida. To the best of our knowledge, this is the first report of the cfr gene in P. multocida. Active and ongoing surveillance of cfr in P. multocida is urgently warranted.
Collapse
Affiliation(s)
- Hongmei Chen
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China; Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Hui Deng
- Fujian Provincial Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences (College of Bee Sciences), Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Longfei Cheng
- Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Rongchang Liu
- Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Guanghua Fu
- Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Shaohua Shi
- Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Chunhe Wan
- Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Qiuling Fu
- Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China
| | - Yu Huang
- Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, PR China.
| | - Xiaohong Huang
- Fujian Provincial Key Laboratory of Traditional Chinese Veterinary Medicine and Animal Health, College of Animal Sciences (College of Bee Sciences), Fujian Agriculture and Forestry University, Fuzhou 350002, PR China.
| |
Collapse
|
15
|
Moo CL, Yang SK, Yusoff K, Ajat M, Thomas W, Abushelaibi A, Lim SHE, Lai KS. Mechanisms of Antimicrobial Resistance (AMR) and Alternative Approaches to Overcome AMR. Curr Drug Discov Technol 2020; 17:430-447. [PMID: 30836923 DOI: 10.2174/1570163816666190304122219] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 01/21/2023]
Abstract
Antimicrobials are useful compounds intended to eradicate or stop the growth of harmful microorganisms. The sustained increase in the rates of antimicrobial resistance (AMR) worldwide is worrying and poses a major public health threat. The development of new antimicrobial agents is one of the critical approaches to overcome AMR. However, in the race towards developing alternative approaches to combat AMR, it appears that the scientific community is falling behind when pitched against the evolutionary capacity of multi-drug resistant (MDR) bacteria. Although the "pioneering strategy" of discovering completely new drugs is a rational approach, the time and effort taken are considerable, the process of drug development could instead be expedited if efforts were concentrated on enhancing the efficacy of existing antimicrobials through: combination therapies; bacteriophage therapy; antimicrobial adjuvants therapy or the application of nanotechnology. This review will briefly detail the causes and mechanisms of AMR as background, and then provide insights into a novel, future emerging or evolving strategies that are currently being evaluated and which may be developed in the future to tackle the progression of AMR.
Collapse
Affiliation(s)
- Chew-Li Moo
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Shun-Kai Yang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Khatijah Yusoff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mokrish Ajat
- Department of Veterinary Pre Clinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Warren Thomas
- Perdana University-Royal College of Surgeons in Ireland School of Medicine, Perdana University, MAEPS Building, Serdang, Selangor, Malaysia
| | - Aisha Abushelaibi
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012 Abu Dhabi, United Arab Emirates
| | - Swee-Hua-Erin Lim
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012 Abu Dhabi, United Arab Emirates
| | - Kok-Song Lai
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| |
Collapse
|
16
|
Zhu Y, Zhang W, Schwarz S, Wang C, Liu W, Chen F, Luan T, Liu S. Characterization of a blaIMP-4-carrying plasmid from Enterobacter cloacae of swine origin. J Antimicrob Chemother 2020; 74:1799-1806. [PMID: 30879063 DOI: 10.1093/jac/dkz107] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/28/2019] [Accepted: 02/25/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To characterize an MDR blaIMP-4-harbouring plasmid from Enterobacter cloacae EC62 of swine origin in China. METHODS Plasmid pIMP-4-EC62 from E. cloacae EC62 was transferred by conjugation via filter mating into Escherichia coli J53. Plasmid DNA was extracted from an E. coli J53 transconjugant and sequenced using single-molecule real-time (SMRT) technology. MIC values for both the isolate EC62 and the transconjugant were determined using the broth microdilution and agar dilution methods. Plasmid stability in both the isolate EC62 and the transconjugant was assessed through a series of passages on antibiotic-free media. RESULTS Plasmid pIMP-4-EC62 is 314351 bp in length, encodes 369 predicted proteins and harbours a novel class 1 integron carrying blaIMP-4 and a group II intron. The blaIMP-4-bearing plasmid belongs to the IncHI2/ST1 incompatibility group. Sequence analysis showed that pIMP-4-EC62 carries four MDR regions and several gene clusters encoding heavy metal resistance. Plasmid pIMP-4-EC62 was stably maintained in both the E. cloacae EC62 isolate and the transconjugant E. coli J53-pIMP-4-EC62 in the absence of selective pressure. Analysis of the evolutionary relatedness of selected IncHI2 plasmids indicates that ST1-type plasmids are key carriers of carbapenemase genes among IncHI2 plasmids. CONCLUSIONS pIMP-4-EC62 represents the first fully sequenced IncHI2-type blaIMP-4-harbouring plasmid from E. cloacae in China. Co-location of blaIMP-4 with other resistance genes on an MDR plasmid is likely to further accelerate the dissemination of blaIMP-4 by co-selection among bacteria from humans, animals and the environment under the selective pressure of other antimicrobial agents, heavy metals and disinfectants.
Collapse
Affiliation(s)
- Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Stefan Schwarz
- Department of Veterinary Medicine, Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Changzhen Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wenyu Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Fuguang Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tian Luan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| |
Collapse
|
17
|
Li P, Zhu T, Zhou D, Lu W, Liu H, Sun Z, Ying J, Lu J, Lin X, Li K, Ying J, Bao Q, Xu T. Analysis of Resistance to Florfenicol and the Related Mechanism of Dissemination in Different Animal-Derived Bacteria. Front Cell Infect Microbiol 2020; 10:369. [PMID: 32903722 PMCID: PMC7438884 DOI: 10.3389/fcimb.2020.00369] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/16/2020] [Indexed: 12/26/2022] Open
Abstract
Bacterial resistance to antibiotics has become an important concern for public health. This study was aimed to investigate the characteristics and the distribution of the florfenicol-related resistance genes in bacteria isolated from four farms. A total of 106 florfenicol-resistant Gram-negative bacilli were examined for florfenicol-related resistance genes, and the positive isolates were further characterized. The antimicrobial sensitivity results showed that most of them (100, 94.33%) belonged to multidrug resistance Enterobacteriaceae. About 91.51% of the strains carried floR gene, while 4.72% carried cfr gene. According to the pulsed-field gel electrophoresis results, 34 Escherichia coli were subdivided into 22 profiles, the genetic similarity coefficient of which ranged from 80.3 to 98.0%. The multilocus sequence typing (MLST) results revealed 17 sequence types (STs), with ST10 being the most prevalent. The genome sequencing result showed that the Proteus vulgaris G32 genome consists of a 4.06-Mb chromosome, a 177,911-bp plasmid (pG32-177), and a 51,686-bp plasmid (pG32-51). A floR located in a drug-resistant region on the chromosome of P. vulgaris G32 was with IS91 family transposase, and the other floR gene on the plasmid pG32-177 was with an ISCR2 insertion sequence. The cfr gene was located on the pG32-51 flanked by IS26 element and TnpA26. This study suggested that the mobile genetic elements played an important role in the replication of resistance genes and the horizontal resistance gene transfer.
Collapse
Affiliation(s)
- Peizhen Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Tingyuan Zhu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jun Ying
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,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, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Jianchao Ying
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| |
Collapse
|
18
|
Chen F, Zhang W, Schwarz S, Zhu Y, Li R, Hua X, Liu S. Genetic characterization of an MDR/virulence genomic element carrying two T6SS gene clusters in a clinical Klebsiella pneumoniae isolate of swine origin. J Antimicrob Chemother 2020; 74:1539-1544. [PMID: 30903161 DOI: 10.1093/jac/dkz093] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/16/2019] [Accepted: 02/11/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Multiresistant Klebsiella pneumoniae isolates rarely cause infections in pigs. The aim of this study was to investigate a multiresistant porcine K. pneumoniae isolate for plasmidic and chromosomal antimicrobial resistance and virulence genes and their genetic environment. METHODS K. pneumoniae strain ZYST1 originated from a pig with pneumonia. Antimicrobial susceptibility testing was performed using broth microdilution. Conjugation experiments were conducted using Escherichia coli J53 as the recipient. The complete sequences of the chromosomal DNA and the plasmids were generated by WGS and analysed for the presence of resistance and virulence genes. RESULTS The MDR K. pneumoniae ST1 strain ZYST1 contained three plasmids belonging to incompatibility groups IncFIIk5-FIB, IncI1 and IncX4, respectively. The IncFIIk5-FIB plasmid carried the resistance genes aadA2, mph(A), sul1 and aph(3')-Ia, and the IncI1 plasmid carried aadA22 and erm(B). No resistance genes were present on the IncX4 plasmid. Plasmids related to the aforementioned three plasmids were also present in other Enterobacteriaceae species from humans, animals and the environment. Bioinformatic analyses identified a chromosomal 904 kb MDR element flanked by two copies of ISKpn26. This element included virulence factors, such as a type VI secretion system (T6SS) and genes for type 1 fimbriae, the toxin-antitoxin system HipA/HipB, antimicrobial resistance genes, such as blaSHV-187, mdtk, catA and the multiple antibiotic resistance operon marRABC, and heavy metal resistance determinants, such as chrB/chrA and tehA/tehB. CONCLUSIONS This study reports a novel 904 kb MDR/virulence genomic element and three important plasmids coexisting in a clinical K. pneumoniae isolate of animal origin.
Collapse
Affiliation(s)
- Fuguang Chen
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| | - Wanjiang Zhang
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Yao Zhu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. 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, Jiangsu, P.R. China
| | - Xin Hua
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| | - Siguo Liu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, P.R. China
| |
Collapse
|
19
|
Zhu T, Liu S, Ying Y, Xu L, Liu Y, Jin J, Ying J, Lu J, Lin X, Li K, Xu T, Bao Q, Li P. Genomic and functional characterization of fecal sample strains of Proteus cibarius carrying two floR antibiotic resistance genes and a multiresistance plasmid-encoded cfr gene. Comp Immunol Microbiol Infect Dis 2020; 69:101427. [PMID: 32058867 DOI: 10.1016/j.cimid.2020.101427] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/24/2020] [Accepted: 01/24/2020] [Indexed: 11/26/2022]
Abstract
The objective of this study was to investigate the molecular characteristics and horizontal transfer of florfenicol resistance gene-related sequences in Proteus strains isolated from animals. A total of six Proteus strains isolated from three farms between 2015 and 2016 were screened by polymerase chain reaction (PCR) for known florfenicol resistance genes. Proteus cibarius G11, isolated from the fecal material of a goose, was found to harbor both cfr and floR genes. Whole genome sequencing revealed that the strain harbored two copies of the floR gene: one was located on the chromosome and the other was located on a plasmid named pG11-152. Two floR-containing fragments 4028 bp in length were identical and showed transposon-like structures. The cfr gene was found on a plasmid named pG11-51 and flanked by a pair of IS26s. Thus, mobile genetic elements played an important role in floR replication and horizontal resistance gene transfer. Therefore, increasing attention should be paid to monitoring the spread of resistance genes and resistance in real time.
Collapse
Affiliation(s)
- Tingyuan Zhu
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Suzhen Liu
- Wenzhou Vocational College of Science and Technology, Wenzhou, 325000, China
| | - Yuanyuan Ying
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Lei Xu
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yabo Liu
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Junjie Jin
- Wenzhou Vocational College of Science and Technology, Wenzhou, 325000, China
| | - Jun Ying
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Junwan Lu
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xi Lin
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kewei Li
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, 014040, China.
| | - Qiyu Bao
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Peizhen Li
- Institute of Biomedical Informatics, Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| |
Collapse
|
20
|
Lu J, Zhang Y, Wu J, Wang J, Cai Y. Fate of antibiotic resistance genes in reclaimed water reuse system with integrated membrane process. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:121025. [PMID: 31446351 DOI: 10.1016/j.jhazmat.2019.121025] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
The fate of antibiotic resistance genes (ARGs) in reclaimed water reuse system with integrated membrane process (IMR) was firstly investigated. Results indicated that ARGs, class 1 integrons (intI1) and 16S rRNA gene could be reduced efficiently in the IMR system. The absolute abundance of all detected ARGs in the reuse water after reverse osmosis (RO) filtration of the IMR system was 4.03 × 104 copies/mL, which was about 2-3 orders of magnitude lower than that in the raw influent of the wastewater treatment plants (WWTPs). Maximum removal efficiency of the detected genes was up to 3.8 log removal values. Daily flux of the summation of all selected ARGs in the IMR system decreased sharply to (1.02 ± 1.37) ×1014 copies/day, which was 1-3 orders of magnitude lower than that in the activated sludge system (CAS) system. The strong clustering based on ordination analysis separated the reuse water from other water samples in the WWTPs. Network analysis revealed the existence of potential multi-antibiotic resistant bacteria. The potential multi-antibiotic resistant bacteria, including Clostridium and Defluviicoccus, could be removed effectively by microfiltration and RO filtration. These findings suggested that the IMR system was efficient to remove ARGs and potential multi-antibiotic resistant bacteria in the wastewater reclamation system.
Collapse
Affiliation(s)
- Jian Lu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, PR China.
| | - Yuxuan Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Wu
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong 264025, PR China
| | - Jianhua Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China
| | - Ying Cai
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, PR China
| |
Collapse
|
21
|
Zhang Y, Lei CW, Wang HN. Identification of a novel conjugative plasmid carrying the multiresistance gene cfr in Proteus vulgaris isolated from swine origin in China. Plasmid 2019; 105:102440. [DOI: 10.1016/j.plasmid.2019.102440] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 10/26/2022]
|
22
|
Fang H, Huang K, Yu J, Ding C, Wang Z, Zhao C, Yuan H, Wang Z, Wang S, Hu J, Cui Y. Metagenomic analysis of bacterial communities and antibiotic resistance genes in the Eriocheir sinensis freshwater aquaculture environment. CHEMOSPHERE 2019; 224:202-211. [PMID: 30822726 DOI: 10.1016/j.chemosphere.2019.02.068] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/02/2019] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
Aquaculture has attracted significant attention as an environmental gateway to the development of antibiotic resistance. The industry of Chinese mitten crab Eriocheir sinensis contributes significantly to the freshwater aquaculture industry in China. However, the situation of antibiotic resistance in the E. sinensis aquaculture environment is not known. In this study, high-throughput sequencing based metagenomic approaches were used to comprehensively investigate the structure of bacterial communities, the abundance and diversity of antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs) in three E. sinensis aquaculture ponds in Jiangsu Province, China. The dominant phyla were Proteobacteria, Actinobacteria, and Bacteroidetes in water samples and Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes in sediment samples. Bacitracin and multidrug were predominant ARG types in water and sediment samples, respectively. There was a significant correlation between MGEs and ARGs. In particular, plasmids were the most abundant MGEs and strongly correlated with ARGs. This is the first study of antibiotic resistome that uses metagenomic approaches in the E. sinensis aquaculture environment. The results indicate that the opportunistic pathogens may acquire ARGs via horizontal gene transfer, intensifying the potential risk to human health.
Collapse
Affiliation(s)
- Hao Fang
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Junnan Yu
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Chengcheng Ding
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing, 210042, China
| | - Zhifeng Wang
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Cheng Zhao
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Hezhong Yuan
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Zhuang Wang
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Se Wang
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Jianlin Hu
- Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing, 210044, China
| | - Yibin Cui
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing, 210042, China.
| |
Collapse
|
23
|
Abstract
Multidrug resistance in Escherichia coli has become a worrying issue that is increasingly observed in human but also in veterinary medicine worldwide. E. coli is intrinsically susceptible to almost all clinically relevant antimicrobial agents, but this bacterial species has a great capacity to accumulate resistance genes, mostly through horizontal gene transfer. The most problematic mechanisms in E. coli correspond to the acquisition of genes coding for extended-spectrum β-lactamases (conferring resistance to broad-spectrum cephalosporins), carbapenemases (conferring resistance to carbapenems), 16S rRNA methylases (conferring pan-resistance to aminoglycosides), plasmid-mediated quinolone resistance (PMQR) genes (conferring resistance to [fluoro]quinolones), and mcr genes (conferring resistance to polymyxins). Although the spread of carbapenemase genes has been mainly recognized in the human sector but poorly recognized in animals, colistin resistance in E. coli seems rather to be related to the use of colistin in veterinary medicine on a global scale. For the other resistance traits, their cross-transfer between the human and animal sectors still remains controversial even though genomic investigations indicate that extended-spectrum β-lactamase producers encountered in animals are distinct from those affecting humans. In addition, E. coli of animal origin often also show resistances to other-mostly older-antimicrobial agents, including tetracyclines, phenicols, sulfonamides, trimethoprim, and fosfomycin. Plasmids, especially multiresistance plasmids, but also other mobile genetic elements, such as transposons and gene cassettes in class 1 and class 2 integrons, seem to play a major role in the dissemination of resistance genes. Of note, coselection and persistence of resistances to critically important antimicrobial agents in human medicine also occurs through the massive use of antimicrobial agents in veterinary medicine, such as tetracyclines or sulfonamides, as long as all those determinants are located on the same genetic elements.
Collapse
|
24
|
Madec JY, Haenni M. Antimicrobial resistance plasmid reservoir in food and food-producing animals. Plasmid 2018; 99:72-81. [PMID: 30194944 DOI: 10.1016/j.plasmid.2018.09.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/24/2018] [Accepted: 09/03/2018] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance (AMR) plasmids have been recognized as important vectors for efficient spread of AMR phenotypes. The food reservoir includes both food-producing animals and food products, and a huge diversity of AMR plasmids have been reported in this sector. Based on molecular typing methods and/or whole genome sequencing approaches, certain AMR genes/plasmids combinations were found more frequently in food compared to other settings. However, the food source of a definite AMR plasmid is highly complex to confirm due to cross-sectorial transfers and international spread of AMR plasmids. For risk assessment purposes related to human health, AMR plasmids found in food and bearing genes conferring resistances to critically important antibiotics in human medicine - such as to extended-spectrum cephalosporins, carbapenems or colistin - have been under specific scrutiny these last years. Those plasmids are often multidrug resistant and their dissemination can be driven by the selective pressure exerted by any of the antibiotics concerned. Also, AMR plasmids carry numerous other genes conferring vital properties to the bacterial cell and are recurrently subjected to evolutionary steps such as hybrid plasmids, making the epidemiology of AMR plasmids in food a moving picture.
Collapse
Affiliation(s)
- Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon - Université de Lyon, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon - Université de Lyon, Lyon, France.
| |
Collapse
|
25
|
Ambrose SJ, Harmer CJ, Hall RM. Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria. Plasmid 2018; 99:40-55. [PMID: 30081066 DOI: 10.1016/j.plasmid.2018.08.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/12/2018] [Accepted: 08/02/2018] [Indexed: 01/14/2023]
Abstract
The large, broad host range IncC plasmids are important contributors to the spread of key antibiotic resistance genes and over 200 complete sequences of IncC plasmids have been reported. To track the spread of these plasmids accurate typing to identify the closest relatives is needed. However, typing can be complicated by the high variability in resistance gene content and various typing methods that rely on features of the conserved backbone have been developed. Plasmids can be broadly typed into two groups, type 1 and type 2, using four features that differentiate the otherwise closely related backbones. These types are found in many different countries in bacteria from humans and animals. However, hybrids of type 1 and type 2 are also occasionally seen, and two further types, each represented by a single plasmid, were distinguished. Generally, the antibiotic resistance genes are located within a small number of resistance islands, only one of which, ARI-B, is found in both type 1 and type 2. The introduction of each resistance island generates a new lineage and, though they are continuously evolving via the loss of resistance genes or introduction of new ones, the island positions serve as valuable lineage-specific markers. A current type 2 lineage of plasmids is derived from an early type 2 plasmid but the sequences of early type 1 plasmids include features not seen in more recent type 1 plasmids, indicating a shared ancestor rather than a direct lineal relationship. Some features, including ones essential for maintenance or for conjugation, have been examined experimentally.
Collapse
Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|
26
|
Wang X, Zhu Y, Hua X, Chen F, Wang C, Zhang Y, Liu S, Zhang W. F14:A-:B- and IncX4 Inc group cfr -positive plasmids circulating in Escherichia coli of animal origin in Northeast China. Vet Microbiol 2018; 217:53-57. [DOI: 10.1016/j.vetmic.2018.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 12/25/2022]
|
27
|
Impact of co-carriage of IncA/C plasmids with additional plasmids on the transfer of antimicrobial resistance in Salmonella enterica isolates. Int J Food Microbiol 2018; 271:77-84. [DOI: 10.1016/j.ijfoodmicro.2018.01.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/22/2017] [Accepted: 01/19/2018] [Indexed: 11/22/2022]
|
28
|
Plasmids of Diverse Inc Groups Disseminate the Fosfomycin Resistance Gene fosA3 among Escherichia coli Isolates from Pigs, Chickens, and Dairy Cows in Northeast China. Antimicrob Agents Chemother 2017; 61:AAC.00859-17. [PMID: 28674050 DOI: 10.1128/aac.00859-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/27/2017] [Indexed: 11/20/2022] Open
Abstract
Thirty-nine fosfomycin-resistant Escherichia coli isolates carrying fosA3 were obtained from pigs, chickens, dairy cows, and staff in four northeastern provinces of China between June 2015 and April 2016. The fosA3 gene was colocated with blaCTX-M genes on conjugative plasmids of the incompatibility groups IncN (n = 12), IncN-F33:A-:B-(n = 2), IncF33:A-:B-(n = 14), IncF14:A-:B-(n = 2), and IncI1/sequence type 136 (ST136) (n = 9). Four different genetic contexts of fosA3 were detected among the 39 E. coli isolates. Three potential epidemic plasmids circulated among E. coli strains from this region.
Collapse
|
29
|
Characterization of pHeBE7, an IncFII-type virulence-resistance plasmid carrying bla CTX-M-98b , bla TEM-1, and rmtB genes, detected in Escherichia coli from a chicken isolate in China. Plasmid 2017; 92:37-42. [DOI: 10.1016/j.plasmid.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/02/2017] [Accepted: 07/05/2017] [Indexed: 11/20/2022]
|
30
|
Argudín MA, Deplano A, Meghraoui A, Dodémont M, Heinrichs A, Denis O, Nonhoff C, Roisin S. Bacteria from Animals as a Pool of Antimicrobial Resistance Genes. Antibiotics (Basel) 2017; 6:antibiotics6020012. [PMID: 28587316 PMCID: PMC5485445 DOI: 10.3390/antibiotics6020012] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/12/2017] [Accepted: 06/01/2017] [Indexed: 01/14/2023] Open
Abstract
Antimicrobial agents are used in both veterinary and human medicine. The intensive use of antimicrobials in animals may promote the fixation of antimicrobial resistance genes in bacteria, which may be zoonotic or capable to transfer these genes to human-adapted pathogens or to human gut microbiota via direct contact, food or the environment. This review summarizes the current knowledge of the use of antimicrobial agents in animal health and explores the role of bacteria from animals as a pool of antimicrobial resistance genes for human bacteria. This review focused in relevant examples within the ESC(K)APE (Enterococcus faecium, Staphylococcus aureus, Clostridium difficile (Klebsiella pneumoniae), Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae) group of bacterial pathogens that are the leading cause of nosocomial infections throughout the world.
Collapse
Affiliation(s)
- Maria Angeles Argudín
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Alaeddine Meghraoui
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Magali Dodémont
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Amelie Heinrichs
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Olivier Denis
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
- Ecole de Santé Publique, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050 Bruxelles, Belgium.
| | - Claire Nonhoff
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Sandrine Roisin
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| |
Collapse
|
31
|
Liu XQ, Wang J, Li W, Zhao LQ, Lu Y, Liu JH, Zeng ZL. Distribution of cfr in Staphylococcus spp. and Escherichia coli Strains from Pig Farms in China and Characterization of a Novel cfr-Carrying F43:A-:B- Plasmid. Front Microbiol 2017; 8:329. [PMID: 28293235 PMCID: PMC5329041 DOI: 10.3389/fmicb.2017.00329] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/17/2017] [Indexed: 11/18/2022] Open
Abstract
The multi-resistance gene cfr is widely distributed among various gram-positive and gram-negative species in livestock in China. To better understand the epidemiology of cfr among Staphylococcus spp. and E. coli isolates, 254 Staphylococcus spp. and 398 E. coli strains collected from six swine farms in China were subjected to prevalence and genetic analysis. Forty (15.7%) Staphylococcus spp. isolates, including 38 Staphylococcus sciuri strains, one Staphylococcus chromogenes strain, and one Staphylococcus lentus strain, and two (0.5%) E. coli isolates were found to contain the cfr gene. Most of the 38 S. sciuri strains were clonally unrelated; however, clonal dissemination of cfr-positive S. sciuri was detected at the same farm. In eight randomly selected cfr-positive staphylococci, a cfr-harboring module (IS21-558-cfr-ΔtnpB) was detected in six S. sciuri isolates; cfr was bracketed by two copies of ISEnfa4 or IS256 in the remaining two S. sciuri isolates. In the two E. coli isolates, EP25 and EP28, cfr was flanked by two IS26 elements in the same or opposite orientation, respectively. Complete sequence analysis of the novel F43:A-:B- plasmid pHNEP28 revealed that it contains two multi-resistance regions: cfr together with floR, qnrS1 interspersed with IS26, ΔISCR2 and ISKpn19, and blaTEM-1 together with tet(M) interspersed with IS26, ISApl1, ΔTn2, and ΔIS1B. The coexistence of cfr with other resistance genes on a conjugative plasmid may contribute to the dissemination of these genes by co-selection. Thus, rational drug use and continued surveillance of cfr in swine farms are warranted.
Collapse
Affiliation(s)
- Xiao-Qin Liu
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Jing Wang
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Wei Li
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Li-Qing Zhao
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Yan Lu
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Jian-Hua Liu
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Zhen-Ling Zeng
- National Reference Laboratory of Veterinary Drug Residues, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| |
Collapse
|
32
|
Richard D, Ravigné V, Rieux A, Facon B, Boyer C, Boyer K, Grygiel P, Javegny S, Terville M, Canteros BI, Robène I, Vernière C, Chabirand A, Pruvost O, Lefeuvre P. Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements. Mol Ecol 2017; 26:2131-2149. [PMID: 28101896 DOI: 10.1111/mec.14007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 11/28/2016] [Accepted: 12/08/2016] [Indexed: 12/17/2022]
Abstract
Copper-based antimicrobial compounds are widely used to control plant bacterial pathogens. Pathogens have adapted in response to this selective pressure. Xanthomonas citri pv. citri, a major citrus pathogen causing Asiatic citrus canker, was first reported to carry plasmid-encoded copper resistance in Argentina. This phenotype was conferred by the copLAB gene system. The emergence of resistant strains has since been reported in Réunion and Martinique. Using microsatellite-based genotyping and copLAB PCR, we demonstrated that the genetic structure of the copper-resistant strains from these three regions was made up of two distant clusters and varied for the detection of copLAB amplicons. In order to investigate this pattern more closely, we sequenced six copper-resistant X. citri pv. citri strains from Argentina, Martinique and Réunion, together with reference copper-resistant Xanthomonas and Stenotrophomonas strains using long-read sequencing technology. Genes involved in copper resistance were found to be strain dependent with the novel identification in X. citri pv. citri of copABCD and a cus heavy metal efflux resistance-nodulation-division system. The genes providing the adaptive trait were part of a mobile genetic element similar to Tn3-like transposons and included in a conjugative plasmid. This indicates the system's great versatility. The mining of all available bacterial genomes suggested that, within the bacterial community, the spread of copper resistance associated with mobile elements and their plasmid environments was primarily restricted to the Xanthomonadaceae family.
Collapse
Affiliation(s)
- D Richard
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France.,Plant Health Laboratory, ANSES, F-97410, St Pierre, Réunion, France.,Université de la Réunion, UMR PVBMT, F-97490, St Denis, Réunion, France
| | - V Ravigné
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - A Rieux
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - B Facon
- INRA, UMR PVBMT, F-97410, St Pierre, Réunion, France.,INRA, UMR CBGP, F-34090, Montpellier, France
| | - C Boyer
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - K Boyer
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - P Grygiel
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - S Javegny
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - M Terville
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - B I Canteros
- INTA, Estación Experimental Agropecuaria Bella Vista, Bella Vista, Argentina
| | - I Robène
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - C Vernière
- CIRAD, UMR BGPI, F-34398, Montpellier, France
| | - A Chabirand
- Plant Health Laboratory, ANSES, F-97410, St Pierre, Réunion, France
| | - O Pruvost
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| | - P Lefeuvre
- UMR PVBMT, CIRAD, F-97410, St Pierre, Réunion, France
| |
Collapse
|
33
|
Schwarz S, Shen J, Kadlec K, Wang Y, Brenner Michael G, Feßler AT, Vester B. Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance. Cold Spring Harb Perspect Med 2016; 6:a027037. [PMID: 27549310 PMCID: PMC5088508 DOI: 10.1101/cshperspect.a027037] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lincosamides, streptogramins, phenicols, and pleuromutilins (LSPPs) represent four structurally different classes of antimicrobial agents that inhibit bacterial protein synthesis by binding to particular sites on the 50S ribosomal subunit of the ribosomes. Members of all four classes are used for different purposes in human and veterinary medicine in various countries worldwide. Bacteria have developed ways and means to escape the inhibitory effects of LSPP antimicrobial agents by enzymatic inactivation, active export, or modification of the target sites of the agents. This review provides a comprehensive overview of the mode of action of LSPP antimicrobial agents as well as of the mutations and resistance genes known to confer resistance to these agents in various bacteria of human and animal origin.
Collapse
Affiliation(s)
- Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Birte Vester
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| |
Collapse
|
34
|
Gomes C, Martínez-Puchol S, Palma N, Horna G, Ruiz-Roldán L, Pons MJ, Ruiz J. Macrolide resistance mechanisms in Enterobacteriaceae: Focus on azithromycin. Crit Rev Microbiol 2016; 43:1-30. [DOI: 10.3109/1040841x.2015.1136261] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Cláudia Gomes
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Sandra Martínez-Puchol
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Noemí Palma
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| | - Gertrudis Horna
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Maria J Pons
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Joaquim Ruiz
- ISGlobal, Barcelona Ctr. Int. Health Res. (CRESIB), Hospital Clínic ? Universitat de Barcelona, Spain
| |
Collapse
|
35
|
Schwarz S, Enne VI, van Duijkeren E. 40 years of veterinary papers inJAC– what have we learnt? J Antimicrob Chemother 2016; 71:2681-90. [DOI: 10.1093/jac/dkw363] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
|
36
|
Stability of the cargo regions of the cfr-carrying, multiresistance plasmid pSP01 from Staphylococcus epidermidis. Int J Med Microbiol 2016; 306:717-721. [PMID: 27554790 DOI: 10.1016/j.ijmm.2016.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/20/2016] [Accepted: 08/14/2016] [Indexed: 11/20/2022] Open
Abstract
This study investigated the stability or instability - i.e. the ability or inability to undergo excision in circular form - of the four cargo regions (cr1 to cr4) of the novel cfr-carrying, multiresistance plasmid pSP01, arboured by a clinical Staphylococcus epidermidis isolate. Only cr4 proved unstable. The stability of cr1 and cr2 was substantially expected. Insertion sequences (ISs) played an important role in the stability of cr3 (the cfr gene context) and in the instability of cr4. Whereas the stability of cfr genetic contexts is associated with the presence of a single IS copy (istAS-istBS in cr3), their instability is associated with two identical, flanking ISs with the same orientation. cr4 is bracketed between two identical IS257 elements, and appears to behave as a composite transposon. Its instability is of interest because of the existence of a closely related cfr plasmid from S. epidermidis (pSP01.1) that differs from pSP01 only by the lack of cr4. An integration/recombination mechanism is suggested to explain how cr4 may have moved to pSP01.1 to form pSP01.
Collapse
|
37
|
Wyrsch ER, Roy Chowdhury P, Chapman TA, Charles IG, Hammond JM, Djordjevic SP. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis. Front Microbiol 2016; 7:843. [PMID: 27379026 PMCID: PMC4908116 DOI: 10.3389/fmicb.2016.00843] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/22/2016] [Indexed: 11/18/2022] Open
Abstract
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.
Collapse
Affiliation(s)
- Ethan R Wyrsch
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, SydneyNSW, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Ian G Charles
- Institute of Food Research, Norwich Research Park Norwich, UK
| | - Jeffrey M Hammond
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
| |
Collapse
|
38
|
Abstract
In staphylococci and other Firmicutes, resistance to numerous classes of antimicrobial agents, which are commonly used in human and veterinary medicine, is mediated by genes that are associated with mobile genetic elements. The gene products of some of these antimicrobial resistance genes confer resistance to only specific members of a certain class of antimicrobial agents, whereas others confer resistance to the entire class or even to members of different classes of antimicrobial agents. The resistance mechanisms specified by the resistance genes fall into any of three major categories: active efflux, enzymatic inactivation, and modification/replacement/protection of the target sites of the antimicrobial agents. Among the mobile genetic elements that carry such resistance genes, plasmids play an important role as carriers of primarily plasmid-borne resistance genes, but also as vectors for nonconjugative and conjugative transposons that harbor resistance genes. Plasmids can be exchanged by horizontal gene transfer between members of the same species but also between bacteria belonging to different species and genera. Plasmids are highly flexible elements, and various mechanisms exist by which plasmids can recombine, form cointegrates, or become integrated in part or in toto into the chromosomal DNA or into other plasmids. As such, plasmids play a key role in the dissemination of antimicrobial resistance genes within the gene pool to which staphylococci and other Firmicutes have access. This chapter is intended to provide an overview of the current knowledge of plasmid-mediated antimicrobial resistance in staphylococci and other Firmicutes.
Collapse
|
39
|
Michael GB, Freitag C, Wendlandt S, Eidam C, Feßler AT, Lopes GV, Kadlec K, Schwarz S. Emerging issues in antimicrobial resistance of bacteria from food-producing animals. Future Microbiol 2016; 10:427-43. [PMID: 25812464 DOI: 10.2217/fmb.14.93] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
During the last decade, antimicrobial resistance in bacteria from food-producing animals has become a major research topic. In this review, different emerging resistance properties related to bacteria of food-producing animals are highlighted. These include: extended-spectrum β-lactamase-producing Enterobacteriaceae; carbapenemase-producing bacteria; bovine respiratory tract pathogens, such as Pasteurella multocida and Mannheimia haemolytica, which harbor the multiresistance mediating integrative and conjugative element ICEPmu1; Gram-positive and Gram-negative bacteria that carry the multiresistance gene cfr; and the occurrence of numerous novel antimicrobial resistance genes in livestock-associated methicillin-resistant Staphylococcus aureus. The emergence of the aforementioned resistance properties is mainly based on the exchange of mobile genetic elements that carry the respective resistance genes.
Collapse
|
40
|
Characterization of a cfr-Carrying Plasmid from Porcine Escherichia coli That Closely Resembles Plasmid pEA3 from the Plant Pathogen Erwinia amylovora. Antimicrob Agents Chemother 2015; 60:658-61. [PMID: 26525796 DOI: 10.1128/aac.02114-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/26/2015] [Indexed: 12/24/2022] Open
Abstract
The multiresistance gene cfr was found in two porcine Escherichia coli isolates, one harboring it on the conjugative 33,885-bp plasmid pFSEC-01, the other harboring it in the chromosomal DNA. Sequence analysis of pFSEC-01 revealed that a 6,769-bp fragment containing the cfr gene bracketed by two IS26 elements was inserted into a plasmid closely related to pEA3 from the plant pathogen Erwinia amylovora, suggesting that pFSEC-01 may be transferred between different bacterial genera of both animal and plant origin.
Collapse
|
41
|
Zhou G, Shi QS, Huang XM, Xie XB. The Three Bacterial Lines of Defense against Antimicrobial Agents. Int J Mol Sci 2015; 16:21711-33. [PMID: 26370986 PMCID: PMC4613276 DOI: 10.3390/ijms160921711] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/21/2015] [Accepted: 08/31/2015] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial agents target a range of extra- and/or intracellular loci from cytoplasmic wall to membrane, intracellular enzymes and genetic materials. Meanwhile, many resistance mechanisms employed by bacteria to counter antimicrobial agents have been found and reported in the past decades. Based on their spatially distinct sites of action and distribution of location, antimicrobial resistance mechanisms of bacteria were categorized into three groups, coined the three lines of bacterial defense in this review. The first line of defense is biofilms, which can be formed by most bacteria to overcome the action of antimicrobial agents. In addition, some other bacteria employ the second line of defense, the cell wall, cell membrane, and encased efflux pumps. When antimicrobial agents permeate the first two lines of defense and finally reach the cytoplasm, many bacteria will make use of the third line of defense, including alterations of intracellular materials and gene regulation to protect themselves from harm by bactericides. The presented three lines of defense theory will help us to understand the bacterial resistance mechanisms against antimicrobial agents and design efficient strategies to overcome these resistances.
Collapse
Affiliation(s)
- Gang Zhou
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Qing-Shan Shi
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Xiao-Mo Huang
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| | - Xiao-Bao Xie
- Guangdong Institute of Microbiology, Guangzhou 510070, Guangdong, China.
- State Key Laboratory of Applied Microbiology Southern China, Guangzhou 510070, Guangdong, China.
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangzhou 510070, Guangdong, China.
| |
Collapse
|
42
|
Zhang SH, Lv X, Han B, Gu X, Wang PF, Wang C, He Z. Prevalence of antibiotic resistance genes in antibiotic-resistant Escherichia coli isolates in surface water of Taihu Lake Basin, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:11412-21. [PMID: 25813640 DOI: 10.1007/s11356-015-4371-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/12/2015] [Indexed: 05/12/2023]
Abstract
The rapid development of antibiotic-resistant bacteria (ARB) has been of concern worldwide. In this study, antibiotic resistance genes (ARGs) were investigated in antibiotic-resistant Escherichia coli isolated from surface water samples (rivers, n = 17; Taihu Lake, n = 16) and from human, chicken, swine, and Egretta garzetta sources in the Taihu Basin. E. coli showing resistance to at least five drugs occurred in 31, 67, 58, 27, and 18% of the isolates from surface water (n = 665), chicken (n = 27), swine (n = 29), human (n = 45), and E. garzetta (n = 15) sources, respectively. The mean multi-antibiotic resistance (MAR) index of surface water samples (0.44) was lower than that of chicken (0.64) and swine (0.57) sources but higher than that of human (0.30) and E. garzetta sources (0.15). Ten tetracycline, four sulfonamide, four quinolone, five β-lactamase, and two streptomycin resistance genes were detected in the corresponding antibiotic-resistant isolates. Most antibiotic-resistant E. coli harbored at least two similar functional ARGs. Int-I was detected in at least 57% of MAR E. coli isolates. The results of multiple correspondence analysis and Spearman correlation analysis suggest that antibiotic-resistant E. coli in water samples were mainly originated from swine, chicken, and/or human sources. Most of the ARGs detected in E. garzetta sources were prevalent in other sources. These data indicated that human activities may have contributed to the spread of ARB in the aquatic environment.
Collapse
Affiliation(s)
- Song He Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Xikang Road No. 1, Gulou District, Nanjing, 210098, China,
| | | | | | | | | | | | | |
Collapse
|
43
|
Wendlandt S, Shen J, Kadlec K, Wang Y, Li B, Zhang WJ, Feßler AT, Wu C, Schwarz S. Multidrug resistance genes in staphylococci from animals that confer resistance to critically and highly important antimicrobial agents in human medicine. Trends Microbiol 2015; 23:44-54. [DOI: 10.1016/j.tim.2014.10.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 10/04/2014] [Accepted: 10/07/2014] [Indexed: 10/24/2022]
|
44
|
Abstract
Antibiotic-resistant bacteria that are difficult or impossible to treat are becoming increasingly common and are causing a global health crisis. Antibiotic resistance is encoded by several genes, many of which can transfer between bacteria. New resistance mechanisms are constantly being described, and new genes and vectors of transmission are identified on a regular basis. This article reviews recent advances in our understanding of the mechanisms by which bacteria are either intrinsically resistant or acquire resistance to antibiotics, including the prevention of access to drug targets, changes in the structure and protection of antibiotic targets and the direct modification or inactivation of antibiotics.
Collapse
|
45
|
Novel conjugative plasmid from Escherichia coli of swine origin that coharbors the multiresistance gene cfr and the extended-spectrum-β-lactamase gene blaCTX-M-14b. Antimicrob Agents Chemother 2014; 59:1337-40. [PMID: 25421479 DOI: 10.1128/aac.04631-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Two porcine Escherichia coli isolates harbored the cfr gene on conjugative plasmids of 38,405 bp (pGXEC6) and 41,646 bp (pGXEC3). In these two plasmids, the cfr gene was located within a 4,612-bp region containing a tnpA-IS26-cfr-IS26-Δhyp element. Plasmid pGXEC3 was almost identical to pGXEC6 except for a 3,235-bp ISEcp1-blaCTX-M-14b insertion. The colocation of the multiresistance cfr gene with an extended-spectrum-β-lactamase gene on a conjugative plasmid may support the dissemination of these genes by coselection.
Collapse
|
46
|
Complete nucleotide sequence of cfr-carrying IncX4 plasmid pSD11 from Escherichia coli. Antimicrob Agents Chemother 2014; 59:738-41. [PMID: 25403661 DOI: 10.1128/aac.04388-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We report the complete nucleotide sequence of a plasmid carrying the multiresistance gene cfr. This plasmid was isolated from an Escherichia coli strain of swine origin in 2011. This 37,672-bp plasmid, pSD11, had an IncX4 backbone similar to those of the IncX4 plasmids obtained from the United States and Australia, in which the cfr gene was flanked by two copies of IS26 and a truncated Tn1331 was inserted.
Collapse
|
47
|
Harmer CJ, Hall RM. pRMH760, a Precursor of A/C2 Plasmids Carrying blaCMY and blaNDM Genes. Microb Drug Resist 2014; 20:416-23. [DOI: 10.1089/mdr.2014.0012] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Ruth M. Hall
- School of Molecular Bioscience, The University of Sydney, Sydney, Australia
| |
Collapse
|
48
|
Identification of the multi-resistance gene cfr in Escherichia coli isolates of animal origin. PLoS One 2014; 9:e102378. [PMID: 25036029 PMCID: PMC4103833 DOI: 10.1371/journal.pone.0102378] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/17/2014] [Indexed: 11/23/2022] Open
Abstract
Previous study indicated that the multi-resistance gene cfr was mainly found in gram-positive bacteria, such as Staphylococcus and Enterococcus, and was sporadically detected in Escherichia coli. Little is known about the prevalence and transmission mechanism of cfr in E. coli. In this study, the presence of cfr in E. coli isolates collected during 2010–2012 from food-producing animals in Guangdong Province of China was investigated, and the cfr-positive E. coli isolates were characterized by PFGE, plasmid profiling, and genetic environment analysis. Of the 839 E. coli isolates, 10 isolates from pig were cfr positive. All the cfr-positive isolates presented a multi-resistance phenotype and were genetically divergent as determined by PFGE. In 8 out of the 10 strains, the cfr gene was located on plasmids of ∼30 kb. Restriction digestion of the plasmids with EcoRI and sequence hybridization with a cfr-specific probe revealed that the cfr-harboring fragments ranged from 6 to 23 kb and a ∼18 kb cfr-carrying fragment was common for the plasmids that were ∼30 kb. Four different genetic environments of cfr were detected, in which cfr is flanked by two identical copies of IS26, which may loop out the intervening sequence through homologous recombination. Among the 8 plasmids of ∼30 kb, 7 plasmids shared the same genetic environment. These results demonstrate plasmid-carried cfr in E. coli and suggest that transposition and homologous recombination mediated by IS26 might have played a rule in the transfer of the cfr gene in E. coli.
Collapse
|
49
|
Mendes RE, Deshpande LM, Jones RN. Linezolid update: stable in vitro activity following more than a decade of clinical use and summary of associated resistance mechanisms. Drug Resist Updat 2014; 17:1-12. [PMID: 24880801 DOI: 10.1016/j.drup.2014.04.002] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Linezolid, approved for clinical use since 2000, has become an important addition to the anti-Gram-positive infection armamentarium. This oxazolidinone drug has in vitro and in vivo activity against essentially all Gram-positive organisms, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). The in vitro activity of linezolid was well documented prior to its clinical application, and several ongoing surveillance studies demonstrated consistent and potent results during the subsequent years of clinical use. Emergence of resistance has been limited and associated with invasive procedures, deep organ involvement, presence of foreign material and mainly prolonged therapy. Non-susceptible organisms usually demonstrate alterations in the 23S rRNA target, which remain the main resistance mechanism observed in enterococci; although a few reports have described the detection of cfr-mediated resistance in Enterococcus faecalis. S. aureus isolates non-susceptible to linezolid remain rare in large surveillance studies. Most isolates harbour 23S rRNA mutations; however, cfr-carrying MRSA isolates have been observed in the United States and elsewhere. It is still uncertain whether the occurrences of such isolates are becoming more prevalent. Coagulase-negative isolates (CoNS) resistant to linezolid were uncommon following clinical approval. Surveillance data have indicated that CoNS isolates, mainly Staphylococcus epidermidis, currently account for the majority of Gram-positive organisms displaying elevated MIC results to linezolid. In addition, these isolates frequently demonstrate complex and numerous resistance mechanisms, such as alterations in the ribosomal proteins L3 and/or L4 and/or presence of cfr and/or modifications in 23S rRNA. The knowledge acquired during the past decades on this initially used oxazolidinone has been utilized for developing new candidate agents, such as tedizolid and radezolid, and as linezolid patents soon begin to expire, generic brands will certainly become available. These events will likely establish a new chapter for this successful class of antimicrobial agents.
Collapse
Affiliation(s)
| | | | - Ronald N Jones
- JMI Laboratories, North Liberty, IA 52317, USA; Tufts University School of Medicine, Boston, MA 02111, USA
| |
Collapse
|
50
|
Pyörälä S, Baptiste KE, Catry B, van Duijkeren E, Greko C, Moreno MA, Pomba MCMF, Rantala M, Ružauskas M, Sanders P, Threlfall EJ, Torren-Edo J, Törneke K. Macrolides and lincosamides in cattle and pigs: use and development of antimicrobial resistance. Vet J 2014; 200:230-9. [PMID: 24685099 DOI: 10.1016/j.tvjl.2014.02.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 02/10/2014] [Accepted: 02/14/2014] [Indexed: 10/25/2022]
Abstract
Macrolides and lincosamides are important antibacterials for the treatment of many common infections in cattle and pigs. Products for in-feed medication with these compounds in combination with other antimicrobials are commonly used in Europe. Most recently approved injectable macrolides have very long elimination half-lives in both pigs and cattle, which allows once-only dosing regimens. Both in-feed medication and use of long-acting injections result in low concentrations of the active substance for prolonged periods, which causes concerns related to development of antimicrobial resistance. Acquired resistance to macrolides and lincosamides among food animal pathogens, including some zoonotic bacteria, has now emerged. A comparison of studies on the prevalence of resistance is difficult, since for many micro-organisms no agreed standards for susceptibility testing are available. With animal pathogens, the most dramatic increase in resistance has been seen in the genus Brachyspira. Resistance towards macrolides and lincosamides has also been detected in staphylococci isolated from pigs and streptococci from cattle. This article reviews the use of macrolides and lincosamides in cattle and pigs, as well as the development of resistance in target and some zoonotic pathogens. The focus of the review is on European conditions.
Collapse
Affiliation(s)
- Satu Pyörälä
- Department of Production Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, 04920 Saarentaus, Finland.
| | | | - Boudewijn Catry
- Scientific Institute of Public Health, Healthcare Associated Infections and Antimicrobial Resistance, 1050 Brussels, Belgium
| | - Engeline van Duijkeren
- National Institute for Public Health and the Environment, PO Box 13720, BA, Bilthoven, The Netherlands
| | | | - Miguel A Moreno
- Veterinary Faculty, Complutense University of Madrid, 28040 Madrid, Spain
| | | | - Merja Rantala
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, 00014, Finland
| | | | - Pascal Sanders
- Agence Nationale de Sécurité Sanitaire (ANSES), 35302 Fougères Cedex, France
| | - E John Threlfall
- Health Protection Agency, Centre for Infections, Laboratory of Enteric Pathogens, London NW9 5EQ, UK
| | - Jordi Torren-Edo
- European Medicines Agency, Animal and Public Health, London E14 8HB, UK
| | | |
Collapse
|