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Liu S, Yang X, Li R, Wang S, Han Z, Yang M, Zhang Y. IS6 family insertion sequences promote optrA dissemination between plasmids varying in transfer abilities. Appl Microbiol Biotechnol 2024; 108:132. [PMID: 38229329 DOI: 10.1007/s00253-023-12858-w] [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: 05/26/2023] [Revised: 09/25/2023] [Accepted: 11/13/2023] [Indexed: 01/18/2024]
Abstract
Plasmids are the primary vectors for intercellular transfer of the oxazolidinone and phenicol cross-resistance gene optrA, while insertion sequences (ISs) are mobile genetic elements that can mobilize plasmid-borne optrA intracellularly. However, little is known about how the IS-mediated intracellular mobility facilitates the dissemination of the optrA gene between plasmid categories that vary in transfer abilities, including non-mobilizable, mobilizable, and conjugative plasmids. Here, we performed a holistic genomic study of 52 optrA-carrying plasmids obtained from searches guided by the Comprehensive Antibiotic Resistance Database. Among the 132 ISs identified within 10 kbp from the optrA gene in the plasmids, IS6 family genes were the most prevalent (86/132). Homologous gene arrays containing IS6 family genes were shared between different plasmids, especially between mobilizable and conjugative plasmids. All these indicated the central role of IS6 family genes in disseminating plasmid-borne optrA. Thirty-three of the 52 plasmids were harbored by Enterococcus faecalis found mainly in humans and animals. By Nanopore sequencing and inverse PCR, the potential of the enterococcal optrA to be transmitted from a mobilizable plasmid to a conjugative plasmid mediated by IS6 family genes was further confirmed in Enterococcus faecalis strains recovered from the effluents of anaerobic digestion systems for treating chicken manure. Our findings highlight the increased intercellular transfer abilities and dissemination risk of plasmid-borne optrA gene caused by IS-mediated intracellular mobility, and underscore the importance of routinely monitoring the dynamic genetic contexts of clinically important antibiotic resistance genes to effectively control this critical public health threat. KEY POINTS: • IS6 was prevalent in optrA-plasmids varying in intercellular transfer abilities. • Enterococcal optrA-plasmids were widespread among human, animal, and the environment. • IS6 elevated the dissemination risk of enterococcal optrA-plasmids.
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Affiliation(s)
- Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Shaolin Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- National Engineering Research Center of Industrial Wastewater Detoxication and Resource Recovery, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Yang P, Li J, Lv M, He P, Song G, Shan B, Yang X. Molecular Epidemiology and Horizontal Transfer Mechanism of optrA-Carrying Linezolid-Resistant Enterococcus faecalis. Pol J Microbiol 2024; 73:349-362. [PMID: 39268957 PMCID: PMC11395433 DOI: 10.33073/pjm-2024-031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 07/06/2024] [Indexed: 09/15/2024] Open
Abstract
The aim of this work was to provide a theoretical and scientific basis for the treatment, prevention, and control of clinical drug-resistant bacterial infections by studying the molecular epidemiology and horizontal transfer mechanism of optrA-carrying linezolid-resistant Enterococcus faecalis strains (LREfs) that were clinically isolated in a tertiary hospital in Kunming, China. Non-repetitive LREfs retained in a tertiary A hospital in Kunming, China. The strains were identified by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The transferability and horizontal transfer mechanism of optrA gene were analyzed using polymerase chain reaction (PCR), whole-genome sequencing (WGS), and conjugation experiments. A total of 39 LREfs strains were collected, and all of them were multi-drug resistant. There were 30 LREfs strains (76.9%) carrying the optrA gene, The cfr, poxtA genes and mutations in the 23S rRNA gene were not detected. The conjugation experiments showed that only three of 10 randomly selected optrA-carrying LREfs were successfully conjugated with JH2-2. Further analysis of one successfully conjugated strain revealed that the optrA gene, located in the donor bacterium, formed the IS1216E-erm(A)-optrA-fexA-IS1216E transferable fragment under the mediation of the mobile genetic element (MGE) IS1216E, which was then transferred to the recipient bacterium via horizontal plasmid transfer. Carrying the optrA gene is the primary resistance mechanism of LREfs strains. The optrA gene could carry the erm(A) and fexA genes to co-transfer among E. faecalis. MGEs such as insertion sequence IS1216E play an important role in the horizontal transfer of the optrA gene.
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Affiliation(s)
- Peini Yang
- 1Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jiang Li
- 2Department of Blood Transfusion, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Mei Lv
- 1Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Pingan He
- 1Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Guibo Song
- 3Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Bin Shan
- 3Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xu Yang
- 1Department of Clinical Laboratory, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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Cinthi M, Coccitto SN, Massacci FR, Albini E, Binucci G, Gobbi M, Tentellini M, D'Avino N, Ranucci A, Papa P, Magistrali CF, Brenciani A, Giovanetti E. Genomic analysis of enterococci carrying optrA, poxtA, and vanA resistance genes from wild boars, Italy. J Appl Microbiol 2024; 135:lxae193. [PMID: 39076010 DOI: 10.1093/jambio/lxae193] [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: 07/03/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
AIMS To investigate enterococci carrying linezolid and vancomycin resistance genes from fecal samples recovered from wild boars. METHODS AND RESULTS Florfenicol- and vancomycin-resistant enterococci, isolated on selective agar plates, were screened by PCR for the presence of linezolid and vancomycin resistance genes. Five isolates carried optrA or poxtA linezolid resistance genes; one strain was resistant to vancomycin for the presence of vanA gene. All isolates were tested for their antibiotic susceptibility and subjected to Whole Genome Sequencing (WGS) analysis. In Enterococcus faecalis (E. faecalis) V1344 and V1676, the optrA was located on the new pV1344-optrA and pV1676-optrA plasmids, respectively, whereas in Enterococcus faecium (E. faecium) V1339 this gene was on a 22 354-bp chromosomal genetic context identical to the one detected in a human E. faecium isolate. In both E. faecium V1682 and E. durans V1343, poxtA was on the p1818-c plasmid previously found in a human E. faecium isolate. In E. faecium V1328, the vanA gene was on the Tn1546 transposon in turn located on a new pV1328-vanA plasmid. Only E. faecium V1682 successfully transferred the poxtA gene to an enterococcal recipient in filter mating assays. CONCLUSIONS The occurrence of genetic elements carrying linezolid and vancomycin resistance genes in enterococci from wild boars is a matter of concern, moreover, the sharing of plasmids and transposons between isolates from wild animals, human, and environment indicates an exchange of genetic material between these settings.
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Affiliation(s)
- Marzia Cinthi
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Sonia Nina Coccitto
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Via Tronto 10/A, 60126 Ancona, Italy
| | - Francesca Romana Massacci
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Elisa Albini
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Giorgia Binucci
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Marco Gobbi
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Michele Tentellini
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Nicoletta D'Avino
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Alice Ranucci
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Paola Papa
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) "Togo Rosati", 06126 Perugia, Italy
| | - Chiara Francesca Magistrali
- Department of Sede Territoriale Lodi-Milano, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", 25124 Brescia, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Via Tronto 10/A, 60126 Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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Brenciani A, Cinthi M, Coccitto SN, Massacci FR, Albini E, Cucco L, Paniccià M, Freitas AR, Schwarz S, Giovanetti E, Magistrali CF. Global spread of the linezolid-resistant Enterococcus faecalis ST476 clonal lineage carrying optrA. J Antimicrob Chemother 2024; 79:846-850. [PMID: 38366373 DOI: 10.1093/jac/dkae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
OBJECTIVES To investigate the global distribution of an optrA-harbouring linezolid-resistant Enterococcus faecalis ST476 clonal lineage. METHODS Comprehensive searches of the NCBI database were performed to identify published peer-reviewed articles and genomes of E. faecalis ST476. Each genome was analysed for resistome, virulome, OptrA variant and optrA genetic contexts. A phylogenetic comparison of ST476 genomes with publicly available genomes of other STs was also performed. RESULTS Sixty-six E. faecalis ST476 isolates from 15 countries (China, Japan, South Korea, Austria, Denmark, Spain, Czech Republic, Colombia, Tunisia, Italy, Malaysia, Belgium, Germany, United Arab Emirates and Switzerland) mainly of human and animal origin were identified. Thirty available ST476 genomes compared with genomes of 591 STs indicated a progressive radiation of E. faecalis STs starting from ST21. The closest ancestral node for ST476 was ST1238. Thirty E. faecalis ST476 genomes exhibited 3-916 SNP differences. Several antimicrobial resistance and virulence genes were conserved among the ST476 genomes. The optrA genetic context exhibited a high degree of or complete identity to the chromosomal transposon Tn6674. Only three isolates displayed an optrA-carrying plasmid with complete or partial Tn6674. The WT OptrA protein was most widespread in the ST476 lineage. CONCLUSIONS Linezolid-resistant optrA-carrying E. faecalis of the clonal lineage ST476 is globally distributed in human, animal and environmental settings. The presence of such an emerging clone can be of great concern for public health. Thus, a One Health approach is needed to counteract the spread and the evolution of this enterococcal clonal lineage.
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Affiliation(s)
- Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Unit of Microbiology, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marzia Cinthi
- Department of Life and Environmental Sciences, Unit of Microbiology, Polytechnic University of Marche, Ancona, Italy
| | - Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Unit of Microbiology, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Francesca Romana Massacci
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy
| | - Elisa Albini
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy
| | - Lucilla Cucco
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy
| | - Marta Paniccià
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy
| | - Ana R Freitas
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, Institute for Health and Bioeconomy, University of Porto, Porto, Portugal
- 1H-TOXRUN-One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra 4585-116, Portugal
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, MARA, College of Veterinary Medicine, China Agricultural University, Beijing, People's Republic of China
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Unit of Microbiology, Polytechnic University of Marche, Ancona, Italy
| | - Chiara Francesca Magistrali
- Department of Research and Development, Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy
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Cinthi M, Coccitto SN, Simoni S, Vignaroli C, Brenciani A, Giovanetti E. An Enterococcus faecium Isolated from Bovine Feces in Italy Shares optrA- and poxtA-Carrying Plasmids with Enterococci from Switzerland. Microb Drug Resist 2023; 29:438-442. [PMID: 37523292 DOI: 10.1089/mdr.2023.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023] Open
Abstract
To investigate the occurrence of oxazolidinone resistance genes, 18 florfenicol-resistant enterococci were isolated from 66 fecal samples collected from several cattle farms in central Italy. The PCR screening indicated that only a bovine florfenicol-resistant isolate, Enterococcus faecium 249031-C, was positive for the presence of optrA and poxtA genes. The strain was tested for its susceptibility to florfenicol, chloramphenicol, linezolid, tedizolid, tetracycline, erythromycin, and vancomycin. Whole Genome Sequencing analysis showed that E. faecium 249031-C, belonging to the ST22 lineage, harbored two plasmids: the optrA-carrying p249031-S (179 kb) and the poxtA-carrying p1818-c (23 kb). p249031-S, containing a new optrA-carrying Tn7695 transposon, was closely related to the plasmid pF88_1 of E. faecium F88, whereas p1818-c had already been detected in a human E. faecium, both enterococci were from Switzerland. The linezolid resistance genes were cotransferred to the E. faecium 64/3 recipient. Circular forms from both optrA- and poxtA-carrying genetic contexts were obtained. The occurrence of oxazolidinone resistance genes in a bovine E. faecium isolate and their localization on conjugative and mobilizable plasmids pose a risk for public health.
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Affiliation(s)
- Marzia Cinthi
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
| | - Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Serena Simoni
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
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Li XS, Qi Y, Li PH, Xue JZ, Li XY, Muhammad I, Li YZ, Zhu DM, Ma Y, Kong LC, Ma HX. Genetic characterization of MDR genomic elements carrying two aac(6')- aph(2″) genes in feline-derived clinical Enterococcus faecalis isolate. Front Microbiol 2023; 14:1191837. [PMID: 37577435 PMCID: PMC10413266 DOI: 10.3389/fmicb.2023.1191837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Multidrug-resistant Enterococcus faecalis (E. faecalis) often cause intestinal infections in cats. The aim of this study was to investigate a multidrug-resistant E. faecalis isolate for plasmidic and chromosomal antimicrobial resistance and their genetic environment. E. faecalis strain ESC1 was obtained from the feces of a cat. Antimicrobial susceptibility testing was carried out using the broth microdilution method. Conjugation experiments were performed using Escherichia coli and Staphylococcus aureus as receptors. Complete sequences of chromosomal DNA and plasmids were generated by whole genome sequencing (WGS) and bioinformatics analysis for the presence of drug resistance genes and mobile elements. Multidrug-resistant E. faecalis ESC1 contained a chromosome and three plasmids. The amino acid at position 80 of the parC gene on the chromosome was mutated from serine to isoleucine, and hence the amino acid mutation at this site led to the resistance of ESC1 strain to fluoroquinolones. Eleven antibiotic resistance genes were located on two plasmids. We identified a novel composite transposon carrying two aminoglycoside resistance genes aac(6')-aph(2″). This study reported the coexistence of a novel 5.4 kb composite transposon and a resistance plasmid with multiple homologous recombination in an isolate of E. faecalis ESC1. This data provides a basis for understanding the genomic signature and antimicrobial resistance mechanisms of this pathogen.
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Affiliation(s)
- Xue-Song Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Yu Qi
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Peng-hui Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Jun-ze Xue
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Xuan-yu Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Inam Muhammad
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
- Department of Zoology, Shaheed Benazir Bhutto University, Sheringal, Pakistan
| | - Ya-zhuo Li
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Dao-mi Zhu
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Ying Ma
- Liaoyuan Animal Disease Prevention and Control Center, Liaoyuan, China
| | - Ling-Cong Kong
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
| | - Hong-Xia Ma
- Department of Veterinary Medicine, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Changchun, China
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Changchun, China
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Tang B, Zou C, Schwarz S, Xu C, Hao W, Yan XM, Huang Y, Ni J, Yang H, Du XD, Shan X. Linezolid-Resistant Enterococcus faecalis of Chicken Origin Harbored Chromosome-Borne optrA and Plasmid-Borne cfr, cfr(D), and poxtA2 Genes. Microbiol Spectr 2023; 11:e0274122. [PMID: 36995237 PMCID: PMC10269796 DOI: 10.1128/spectrum.02741-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/26/2023] [Indexed: 03/31/2023] Open
Abstract
The aim of this study was to investigate the transferability of acquired linezolid resistance genes and associated mobile genetic elements in an Enterococcus faecalis isolate QZ076, cocarrying optrA, cfr, cfr(D), and poxtA2 genes. MICs were determined by broth microdilution. Whole-genome sequencing (WGS) was performed using the Illumina and Nanopore platforms. The transfer of linezolid resistance genes was investigated by conjugation, using E. faecalis JH2-2 and clinical methicillin-resistant Staphylococcus aureus (MRSA) 109 as recipients. E. faecalis QZ076 harbors four plasmids, designated pQZ076-1 to pQZ076-4, with optrA located in the chromosomal DNA. The gene cfr was located on a novel pseudocompound transposon, designated Tn7515, integrated into the 65,961-bp pCF10-like pheromone-responsive conjugative plasmid pQZ076-1. Tn7515 generated 8-bp direct target duplications (5'-GATACGTA-3'). The genes cfr(D) and poxtA2 were colocated on the 16,397-bp mobilizable broad-host-range Inc18 plasmid pQZ076-4. The cfr-carrying plasmid pQZ076-1 could transfer from E. faecalis QZ076 to E. faecalis JH2-2, along with the cfr(D)- and poxtA2-cocarrying plasmid pQZ076-4, conferring the corresponding resistant phenotype to the recipient. Moreover, pQZ076-4 could also transfer to MRSA 109. To the best of our knowledge, this study presented the first report of four acquired linezolid resistance genes [optrA, cfr, cfr(D), and poxtA2] being simultaneously present in the same E. faecalis isolate. The location of the cfr gene on a pseudocompound transposon in a pheromone-responsive conjugative plasmid will accelerate its rapid dissemination. In addition, the cfr-carrying pheromone-responsive conjugative plasmid in E. faecalis was also able to mobilize the interspecies transfer of the cfr(D)- and poxtA2-cocarrying plasmid between enterococci and staphylococci. IMPORTANCE In this study, the simultaneous occurrence of four acquired oxazolidinone resistance genes [optrA, cfr, cfr(D), and poxtA2] was identified in an E. faecalis isolate of chicken origin. The association of the cfr gene with a novel pseudocompound transposon Tn7515 integrated into a pCF10-like pheromone-responsive conjugative plasmid will accelerate its dissemination. Moreover, the location of the resistance genes cfr(D) and poxtA2 on a mobilizable broad-host-range Inc18 family plasmid represents the basis for their intra- and interspecies dissemination with the aid of a conjugative plasmid and further accelerates the spreading of acquired oxazolidinone resistance genes, such as cfr, cfr(D), and poxtA2, among Gram-positive pathogens.
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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, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chenhui Zou
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Chunyan Xu
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Wenbo Hao
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xiao-Mei Yan
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuting Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Agro-product Safety and Nutrition, Zhejiang 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, Zhejiang Academy of Agricultural Sciences, 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, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiang-Dang Du
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Xinxin Shan
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
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Dai X, Sun J, Zhu B, Lv M, Chen L, Chen L, Wang X, Huang J, Wang L. Various Mobile Genetic Elements Involved in the Dissemination of the Phenicol-Oxazolidinone Resistance Gene optrA in the Zoonotic Pathogen Streptococcus suis: a Nonignorable Risk to Public Health. Microbiol Spectr 2023; 11:e0487522. [PMID: 37070987 PMCID: PMC10269897 DOI: 10.1128/spectrum.04875-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/17/2023] [Indexed: 04/19/2023] Open
Abstract
The rapid increase of phenicol-oxazolidinone (PhO) resistance in Streptococcus suis due to transferable resistance gene optrA is a matter of concern. However, genetic mechanisms for the dissemination of the optrA gene remain to be discovered. Here, we selected 33 optrA-positive S. suis isolates for whole-genome sequencing and analysis. The IS1216E element was present in 85% of the optrA-carrying contigs despite genetic variation observed in the flanking region. IS1216E-optrA-carrying segments could be inserted into larger mobile genetic elements (MGEs), including integrative and conjugative elements, plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated circularization occurred to form the IS1216E-optrA-carrying translocatable units, suggesting a crucial role of IS1216E in optrA spreading. Three optrA-carrying MGEs (ICESsuAKJ47_SSU1797, plasmid pSH0918, and prophage ΦSsuFJSM5_rum) were successfully transferred via conjugation at different transfer frequencies. Interestingly, two types of transconjugants were observed due to the multilocus integration of ICESsuAKJ47 into an alternative SSU1943 attachment site along with the primary SSU1797 attachment site (type 1) or into the single SSU1797 attachment site (type 2). In addition, conjugative transfer of an optrA-carrying plasmid and prophage in streptococci was validated for the first time. Considering the abundance of MGEs in S. suis and the mobility of IS1216E-optrA-carrying translocatable units, attention should be paid to the potential risks to public health from the emergence and spread of PhO-resistant S. suis. IMPORTANCE Antimicrobial resistance to phenicols and oxazolidinones by the dissemination of the optrA gene leads to treatment failure in both veterinary and human medicine. However, information about the profile of these MGEs (mobilome) that carry optrA and their transferability in streptococci was limited, especially for the zoonotic pathogen S. suis. This study showed that the optrA-carrying mobilome in S. suis includes integrative and conjugative elements (ICEs), plasmids, prophages, and antibiotic resistance-associated genomic islands. IS1216E-mediated formation of optrA-carrying translocatable units played important roles in optrA spreading between types of MGEs, and conjugative transfer of various optrA-carrying MGEs (ICEs, plasmids, and prophages) further facilitated the transfer of optrA across strains, highlighting a nonignorable risk to public health of optrA dissemination to other streptococci and even to bacteria of other genera.
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Affiliation(s)
- Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Boqin Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mingsiyi Lv
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liye Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Li Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing, China
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9
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Idola D, Mori H, Nagata Y, Nonaka L, Yano H. Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria. Mob DNA 2023; 14:7. [PMID: 37237359 DOI: 10.1186/s13100-023-00295-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague. RESULTS To corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA, tfp, intB) and srap located at the left end of SEs were identified as essential for attL × attR recombination. The synteny blocks of tfp and srap homologs were detected in 3.6% of the replicons of Gammaproteobacteria but not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the orders Vibrionales (19% of replicons), Pseudomonadales (18%), Alteromonadales (17%), and Aeromonadales (12%). Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, like tmexCD-toprJ, mcr-9, and blaGMA-1. Further experiments validated that three new SE members possess the strand-biased attL × attR recombination activity. CONCLUSIONS This study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-living Gammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.
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Affiliation(s)
- Desmila Idola
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Hiroshi Mori
- Department of Informatics, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Japan
| | - Yuji Nagata
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan
| | - Lisa Nonaka
- Faculty of Human Life Sciences, Shokei University, 2-6-78 Kuhonji, Kumamoto, 862-8678, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aobaku, Sendai, 980-8577, Japan.
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aobacho, Higashimurayama, Tokyo, 189-0002, Japan.
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10
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Hou Z, Liu L, Wei J, Xu B. Progress in the Prevalence, Classification and Drug Resistance Mechanisms of Methicillin-Resistant Staphylococcus aureus. Infect Drug Resist 2023; 16:3271-3292. [PMID: 37255882 PMCID: PMC10226514 DOI: 10.2147/idr.s412308] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/12/2023] [Indexed: 06/01/2023] Open
Abstract
Staphylococcus aureus is a common human pathogen with a variety of virulence factors, which can cause multiple infectious diseases. In recent decades, due to the constant evolution and the abuse of antibiotics, Staphylococcus aureus was becoming more resistant, the infection rate of MRSA remained high, and clinical treatment of MRSA became more difficult. The genetic diversity of MRSA was mainly represented by the continuous emergence of epidemic strains, resulting in the constant changes of epidemic clones. Different classes of MRSA resulted in different epidemics and resistance characteristics, which could affect the clinical symptoms and treatments. MRSA had also spread from traditional hospitals to community and livestock environments, and the new clones established a relationship between animals and humans, promoting further evolution of MRSA. Since the resistance mechanism of MRSA is very complex, it is important to clarify these resistance mechanisms at the molecular level for the treatment of infectious diseases. We firstly described the diversity of SCCmec elements, and discussed the types of SCCmec, its drug resistance mechanisms and expression regulations. Then, we described how the vanA operon makes Staphylococcus aureus resistant to vancomycin and its expression regulation. Finally, a brief introduction was given to the drug resistance mechanisms of biofilms and efflux pump systems. Analyzing the resistance mechanism of MRSA can help study new anti-infective drugs and alleviate the evolution of MRSA. At the end of the review, we summarized the treatment strategies for MRSA infection, including antibiotics, anti-biofilm agents and efflux pump inhibitors. To sum up, here we reviewed the epidemic characteristics of Staphylococcus aureus, summarized its classifications, drug resistance mechanisms of MRSA (SCCmec element, vanA operon, biofilm and active efflux pump system) and novel therapy strategies, so as to provide a theoretical basis for the treatment of MRSA infection.
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Affiliation(s)
- Zhuru Hou
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, People’s Republic of China
| | - Ling Liu
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, People’s Republic of China
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, People’s Republic of China
| | - Jianhong Wei
- Department of Basic Medicine, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
| | - Benjin Xu
- Key Laboratory of Lvliang for Clinical Molecular Diagnostics, Fenyang, People’s Republic of China
- Department of Medical Laboratory Science, Fenyang College of Shanxi Medical University, Fenyang, People’s Republic of China
- Department of Clinical Laboratory, Fenyang Hospital of Shanxi Province, Fenyang, People’s Republic of China
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11
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Han N, Li J, Wan P, Pan Y, Xu T, Xiong W, Zeng Z. Co-Existence of Oxazolidinone Resistance Genes cfr(D) and optrA on Two Streptococcus parasuis Isolates from Swine. Antibiotics (Basel) 2023; 12:antibiotics12050825. [PMID: 37237728 DOI: 10.3390/antibiotics12050825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
This study was performed to investigate the presence and characteristics of the oxazolidinone resistance genes optrA and cfr(D) in Streptococcus parasuis. In total, 36 Streptococcus isolates (30 Streptococcus suis isolates, 6 Streptococcus parasuis isolates) were collected from pig farms in China in 2020-2021, using PCR to determine the presence of optrA and cfr. Then, 2 of the 36 Streptococcus isolates were further processed as follows. Whole-genome sequencing and de novo assembly were employed to analyze the genetic environment of the optrA and cfr(D) genes. Conjugation and inverse PCR were employed to verify the transferability of optrA and cfr(D). The optrA and cfr(D) genes were identified in two S. parasuis strains named SS17 and SS20, respectively. The optrA of the two isolates was located on chromosomes invariably associated with the araC gene and Tn554, which carry the resistance genes erm(A) and ant(9). The two plasmids that carry cfr(D), pSS17 (7550 bp) and pSS20-1 (7550 bp) have 100% nucleotide sequence identity. The cfr(D) was flanked by GMP synthase and IS1202. The findings of this study extend the current knowledge of the genetic background of optrA and cfr(D) and indicate that Tn554 and IS1202 may play an important role in the transmission of optrA and cfr(D), respectively.
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Affiliation(s)
- Ning Han
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Peng Wan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Tiantian Xu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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12
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Mowlaboccus S, Daley DA, Coombs GW. Genomic characterisation of linezolid-resistant Enterococcus faecalis from Western Australia 2016-2021. Pathology 2023; 55:397-399. [PMID: 36085088 DOI: 10.1016/j.pathol.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 10/15/2022]
Affiliation(s)
- Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases Laboratory, Murdoch University, Perth, WA, Australia; PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, WA, Australia; School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
| | - Denise A Daley
- PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, WA, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases Laboratory, Murdoch University, Perth, WA, Australia; PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Perth, WA, Australia.
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13
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Deng L, Zhen W, Wang J, Lin D. Bile Carriage of optrA-Positive Enterococcus faecium in a Patient with Choledocholith. Microbiol Spectr 2023; 11:e0285222. [PMID: 36976027 PMCID: PMC10101025 DOI: 10.1128/spectrum.02852-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
We isolated one Enterococcus faecium isolate SZ21B15 from a bile sample of a patient with choledocholith in Shenzhen, China in 2021. It was positive for oxazolidinone resistance gene optrA and was intermediate to linezolid. The whole genome of E. faecium SZ21B15 was sequenced by Illumina Hiseq. It belonged to ST533 within the clonal complex 17. The optrA gene and additional two resistance genes fexA and erm(A) were located within a 25,777-bp multiresistance region, which was inserted into the chromosomal radC gene, being chromosomal intrinsic resistance genes. The chromosomal optrA gene cluster found in E. faecium SZ21B15 was closely related to the corresponding regions of multiple optrA-carrying plasmids or chromosomes from Enterococcus, Listeria, Staphylococcus, and Lactococcus strains. It further highlights the ability of the optrA cluster that transfers between plasmids and chromosomes and evolves by a series of molecular recombination events. IMPORTANCE Oxazolidinone are effective antimicrobial agents for the treatment of infections caused by multidrug-resistant Gram-positive bacteria, including vancomycin-resistant enterococci. The emergence and global spread of transferable oxazolidinone resistance genes such as optrA is worrisome. Enterococcus spp. can become causes of hospital-associated infections and are also widely distributed in the gastrointestinal tracts of animals and the natural environment. In this study, one E. faecium isolate from bile sample carried chromosomal optrA, being intrinsic resistance gene. optrA-positive E. faecium in bile not only makes the treatment of gallstones difficult, but also may become a reservoir of resistance genes in the body.
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Affiliation(s)
- Li Deng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Wendong Zhen
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Jing Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Dachuan Lin
- Guangdong Key Laboratory of Regional Immunity and Diseases, Shenzhen University School of Medicine, Shenzhen University, Shenzhen, China
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14
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Xuan H, Xia L, Schwarz S, Jia H, Yao X, Wang S, Li R, Wei J, Li Z, Shao D, Liu K, Qiu Y, Ma Z, Li B. Various mobile genetic elements carrying optrA in Enterococcus faecium and Enterococcus faecalis isolates from swine within the same farm. J Antimicrob Chemother 2023; 78:504-511. [PMID: 36508313 DOI: 10.1093/jac/dkac421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/20/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES In this study, the distribution of the oxazolidinone/phenicol resistance gene optrA and the mobile genetic elements involved in its dissemination were analysed among enterococcal isolates from a farrow-to-finish swine farm. METHODS Enterococcus faecium and Enterococcus faecalis isolates were obtained from all pig production stages in the farm. The optrA-carrying E. faecium and E. faecalis isolates were subjected to PFGE and antimicrobial susceptibility testing. Complete sequences of the genetically unrelated optrA-carrying E. faecium and E. faecalis isolates were determined using Illumina HiSeq and MinION platforms. RESULTS The optrA gene was present in 12.2% (23/188) of the E. faecium and E. faecalis isolates, most of which originated from nursery and finishing stages. The 23 optrA-positive Enterococcus isolates represented 15 PFGE types. WGS of representative isolates of the 15 PFGE types showed that optrA was carried by diverse genetic elements either located in the chromosomal DNA or on plasmids. A novel optrA-bearing genetic element was identified on two distinct multi-resistance plasmids from E. faecium. Two new hybrid plasmids carrying several resistance genes were found in two E. faecalis isolates. pC25-1-like plasmids and chromosomally integrated Tn6674 and Tn6823-like transposons were prevalent in the remaining Enterococcus isolates. CONCLUSIONS The gene optrA was found in genetically unrelated E. faecium and E. faecalis isolates from the same farm. Analysis of the genetic contexts of optrA suggested that horizontal transfer including different plasmids and transposons played a key role in the dissemination of optrA in this farm.
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Affiliation(s)
- Huiyong Xuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Stefan Schwarz
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany.,Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Haiyan Jia
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xiaohui Yao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Shufeng Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 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, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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15
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Li G, Walker MJ, De Oliveira DMP. Vancomycin Resistance in Enterococcus and Staphylococcus aureus. Microorganisms 2022; 11:microorganisms11010024. [PMID: 36677316 PMCID: PMC9866002 DOI: 10.3390/microorganisms11010024] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.
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16
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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.
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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
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17
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Tn 560, a Novel Tn 554 Family Transposon from Porcine Methicillin-Resistant Staphylococcus aureus ST398, Carries a Multiresistance Gene Cluster Comprising a Novel spc Gene Variant and the Genes lsa(E) and lnu(B). Antimicrob Agents Chemother 2022; 66:e0194721. [PMID: 35315688 DOI: 10.1128/aac.01947-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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18
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McHugh MP, Parcell BJ, Pettigrew KA, Toner G, Khatamzas E, El Sakka N, Karcher AM, Walker J, Weir R, Meunier D, Hopkins KL, Woodford N, Templeton KE, Gillespie SH, Holden MTG. Presence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35130141 PMCID: PMC8941993 DOI: 10.1099/mic.0.001137] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Transferable linezolid resistance due to optrA, poxtA, cfr and cfr-like genes is increasingly detected in enterococci associated with animals and humans globally. We aimed to characterize the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland. Six linezolid-resistant E. faecalis isolated from urogenital samples were confirmed to carry the optrA gene by PCR. Short read (Illumina) sequencing showed the isolates were genetically distinct (>13900 core SNPs) and belonged to different MLST sequence types. Plasmid contents were examined using hybrid assembly of short and long read (Oxford Nanopore MinION) sequencing technologies. The optrA gene was located on distinct plasmids in each isolate, suggesting that transfer of a single plasmid did not contribute to optrA dissemination in this collection. pTM6294-2, BX5936-1 and pWE0438-1 were similar to optrA-positive plasmids from China and Japan, while the remaining three plasmids had limited similarity to other published examples. We identified the novel Tn6993 transposon in pWE0254-1 carrying linezolid (optrA), macrolide (ermB) and spectinomycin [ANT(9)-Ia] resistance genes. OptrA amino acid sequences differed by 0–20 residues. We report multiple variants of optrA on distinct plasmids in diverse strains of E. faecalis. It is important to identify the selection pressures driving the emergence and maintenance of resistance against linezolid to retain the clinical utility of this antibiotic.
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Affiliation(s)
- Martin P McHugh
- School of Medicine, University of St Andrews, St Andrews, UK.,NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Benjamin J Parcell
- School of Medicine, University of St Andrews, St Andrews, UK.,Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK.,Present address: Medical Microbiology, Ninewells Hospital, Dundee, UK
| | - Kerry A Pettigrew
- School of Medicine, University of St Andrews, St Andrews, UK.,Present address: School of Social and Behavioural Sciences, Erasmus University, Rotterdam, Netherlands
| | - Geoff Toner
- NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Elham Khatamzas
- NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK.,Present address: Department of Medicine III, University Hospital, LMU Munich, Germany
| | - Noha El Sakka
- Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Anne Marie Karcher
- Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK.,Present address: Medical Microbiology, Ninewells Hospital, Dundee, UK
| | - Joanna Walker
- Medical Microbiology, Aberdeen Royal Infirmary, Aberdeen, UK
| | - Robert Weir
- Medical Microbiology, Forth Valley Royal Hospital, Larbert, UK
| | - Danièle Meunier
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - Kate E Templeton
- NHS Lothian Infection Service, Royal Infirmary of Edinburgh, Edinburgh, UK
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Gargis AS, Spicer LM, Kent AG, Zhu W, Campbell D, McAllister G, Ewing TO, Albrecht V, Stevens VA, Sheth M, Padilla J, Batra D, Johnson JK, Halpin AL, Rasheed JK, Elkins CA, Karlsson M, Lutgring JD. Sentinel Surveillance Reveals Emerging Daptomycin-Resistant ST736 Enterococcus faecium and Multiple Mechanisms of Linezolid Resistance in Enterococci in the United States. Front Microbiol 2022; 12:807398. [PMID: 35178041 PMCID: PMC8846945 DOI: 10.3389/fmicb.2021.807398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/09/2021] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecalis and faecium with resistance to daptomycin and/or linezolid are emerging globally. We present the genomic characterization of daptomycin- and linezolid-resistant E. faecalis and E. faecium surveillance isolates from the United States, 2013-2016. Daptomycin resistance was low among E. faecalis (2/364, 0.5%) and E. faecium (17/344, 5%). The majority (71%, 12/17) of daptomycin-resistant E. faecium isolates belonged to the emerging ST736 clone and contained mutations in liaFSR and cls previously associated with resistance. However, 1/2 E. faecalis and 3/17 E. faecium did not contain these mutations previously associated with daptomycin resistance. Linezolid resistance was rare among E. faecalis (1/364, 0.3%) and E. faecium (2/344, 0.6%). These two E. faecium isolates, one of which was also resistant to daptomycin and vancomycin, contained the 23S rRNA nucleotide mutation (G2576T) associated with linezolid resistance. Long-read sequencing revealed the linezolid-resistant E. faecalis isolate contained chromosomal- and plasmid-encoded copies of optrA. The chromosomal optrA was located on the recently described Tn6674 multiresistance transposon. The second copy of optrA was encoded on an ∼65 kb mosaic plasmid, with component regions sharing high sequence identity to optrA-encoding multiresistance plasmids of animal origin. The optrA-encoding plasmid contained open reading frames predicted to encode proteins associated with a pheromone-responsive plasmid transfer system, and filter mating experiments confirmed the plasmid was conjugative. Continued surveillance of enterococci is necessary to assess the prevalence and trends of daptomycin and linezolid resistance in the United States, characterize resistance mechanisms and how they transfer, and monitor for emerging sequence types associated with resistance.
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Affiliation(s)
- Amy S. Gargis
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lori M. Spicer
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
- Goldbelt C6, LLC, Chesapeake, VA, United States
| | - Alyssa G. Kent
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
- Goldbelt C6, LLC, Chesapeake, VA, United States
| | - Wenming Zhu
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Davina Campbell
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Thomas O. Ewing
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
- Goldbelt C6, LLC, Chesapeake, VA, United States
| | - Valerie Albrecht
- Office of the Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Valerie A. Stevens
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jasmine Padilla
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States
- ASRT Incorporated, Atlanta, GA, United States
| | - Dhwani Batra
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - J. Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - J. Kamile Rasheed
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Christopher A. Elkins
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Maria Karlsson
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joseph D. Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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20
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Yi M, Zou J, Zhao J, Tang Y, Yuan Y, Yang B, Huang J, Xia P, Xia Y. Emergence of optrA-Mediated Linezolid Resistance in Enterococcus faecium: A Molecular Investigation in a Tertiary Hospital of Southwest China from 2014-2018. Infect Drug Resist 2022; 15:13-20. [PMID: 35018102 PMCID: PMC8742577 DOI: 10.2147/idr.s339761] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/14/2021] [Indexed: 01/06/2023] Open
Abstract
Purpose To investigate the potential mechanism and molecular characteristics of linezolid-non-sensitive Enterococcus faecium from a tertiary hospital in southwest China and characterize the relevant plasmids. Patients and Methods Linezolid-non-sensitive Enterococcus faecium (LNSEFM) isolates collected from January 2014 to December 2018 were screened for resistant genes 23s rRNA, rplC, rplD, rplV, optrA, cfr, poxtA, by PCR. Molecular epidemiological analysis was performed by multilocus sequence typing (MLST). The optrA-and-poxtA co-harboring strain EFM_7150 was subjected to the whole genome sequencing (WGS) by Illumina HiSeq and Oxford Nanopore MinION. Results A total of 15 LNSEFM with linezolid MICs ranging from 4 to 16 mg/L were identified. About 66.7% (10/15) of isolates were linezolid-resistant. About 46.7% (7/15) of strains were positive for optrA. Two types of optrA variants (P and EYDNDM) were identified. About 13.3% (2/15) of isolates had poxtA. 1 harbored a L22 protein alteration (Ser77Thr). One isolate coharbored optrA (EYDNDM variant) and poxtA. There was no mutation in the gene that encoded the ribosomal protein L3/L4 or the domain V of 23S rRNA. No cfr gene was detected. Based on WGS data, optrA was associated with Tn558 inserted to radC gene and poxtA was flanked by IS1216E. Conclusion OptrA is primary mechanism in linezolid-resistant Enterococcus faecium. This is the first report ofoptrA variants P and EYDNDM identified in Enterococcus faecium and optrA-and-poxtA co-harboring Enterococcus faecium clinically in southwest China. Besides, Tn558 and IS1216Es may play an important role in the dissemination of optrA and poxtA, respectively. The findings revealed the potential threat to nosocomial infection by optrA and coexistence of optrA and poxtA in Enterococcus faecium. Thus, clinical surveillance of linezolid-resistant Enterococcus is urgently needed.
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Affiliation(s)
- Miao Yi
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Jiaqi Zou
- Department of Clinical Laboratory, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Jinxin Zhao
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yu Tang
- Department of Laboratory Medicine, Chongqing University Three Gorges Hospital, Chongqing, People's Republic of China
| | - Yaling Yuan
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Bingxue Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Jinzhu Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Peiwen Xia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yun Xia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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21
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Ross K, Varani AM, Snesrud E, Huang H, Alvarenga DO, Zhang J, Wu C, McGann P, Chandler M. TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis. mBio 2021; 12:e0206021. [PMID: 34517763 PMCID: PMC8546635 DOI: 10.1128/mbio.02060-21] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/11/2021] [Indexed: 01/03/2023] Open
Abstract
We describe here the structure and organization of TnCentral (https://tncentral.proteininformationresource.org/ [or the mirror link at https://tncentral.ncc.unesp.br/]), a web resource for prokaryotic transposable elements (TE). TnCentral currently contains ∼400 carefully annotated TE, including transposons from the Tn3, Tn7, Tn402, and Tn554 families; compound transposons; integrons; and associated insertion sequences (IS). These TE carry passenger genes, including genes conferring resistance to over 25 classes of antibiotics and nine types of heavy metal, as well as genes responsible for pathogenesis in plants, toxin/antitoxin gene pairs, transcription factors, and genes involved in metabolism. Each TE has its own entry page, providing details about its transposition genes, passenger genes, and other sequence features required for transposition, as well as a graphical map of all features. TnCentral content can be browsed and queried through text- and sequence-based searches with a graphic output. We describe three use cases, which illustrate how the search interface, results tables, and entry pages can be used to explore and compare TE. TnCentral also includes downloadable software to facilitate user-driven identification, with manual annotation, of certain types of TE in genomic sequences. Through the TnCentral homepage, users can also access TnPedia, which provides comprehensive reviews of the major TE families, including an extensive general section and specialized sections with descriptions of insertion sequence and transposon families. TnCentral and TnPedia are intuitive resources that can be used by clinicians and scientists to assess TE diversity in clinical, veterinary, and environmental samples. IMPORTANCE The ability of bacteria to undergo rapid evolution and adapt to changing environmental circumstances drives the public health crisis of multiple antibiotic resistance, as well as outbreaks of disease in economically important agricultural crops and animal husbandry. Prokaryotic transposable elements (TE) play a critical role in this. Many carry "passenger genes" (not required for the transposition process) conferring resistance to antibiotics or heavy metals or causing disease in plants and animals. Passenger genes are spread by normal TE transposition activities and by insertion into plasmids, which then spread via conjugation within and across bacterial populations. Thus, an understanding of TE composition and transposition mechanisms is key to developing strategies to combat bacterial pathogenesis. Toward this end, we have developed TnCentral, a bioinformatics resource dedicated to describing and exploring the structural and functional features of prokaryotic TE whose use is intuitive and accessible to users with or without bioinformatics expertise.
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Affiliation(s)
- Karen Ross
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Alessandro M. Varani
- School of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil
| | - Erik Snesrud
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Hongzhan Huang
- Protein Information Resource, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Danillo Oliveira Alvarenga
- School of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Jaboticabal, Sao Paulo, Brazil
| | - Jian Zhang
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Cathy Wu
- Protein Information Resource, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Patrick McGann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mick Chandler
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
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22
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Zhu Y, Zhang W, Wang C, Liu W, Yang Q, Luan T, Wang L, Schwarz S, Liu S. Identification of a novel optrA-harbouring transposon, Tn6823, in Staphylococcus aureus. J Antimicrob Chemother 2021; 75:3395-3397. [PMID: 32728701 DOI: 10.1093/jac/dkaa323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yao Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wanjiang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Changzhen Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Wenyu Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Qin Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Tian Luan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Lingli Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
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23
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Krüger H, Ji X, Wang Y, Feßler AT, Wang Y, Wu C, Schwarz S. Identification of Tn553, a novel Tn554-related transposon that carries a complete blaZ-blaR1-blaI β-lactamase operon in Staphylococcus aureus. J Antimicrob Chemother 2021; 76:2733-2735. [PMID: 34164661 DOI: 10.1093/jac/dkab210] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/31/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Henrike Krüger
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Xing Ji
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yaxin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Congming Wu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - 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, China
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24
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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.
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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
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25
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Bakthavatchalam YD, Vasudevan K, Babu P, Neeravi AR, Narasiman V, Veeraraghavan B. Genomic insights of optrA-carrying linezolid-resistant Enterococcus faecium using hybrid assembly: first report from India. J Glob Antimicrob Resist 2021; 25:331-336. [PMID: 33957286 DOI: 10.1016/j.jgar.2021.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Linezolid resistance in Enterococcus faecium is emerging worldwide. In this study, we aimed to characterise two linezolid-resistant E. faecium isolates using whole-genome sequencing. METHODS Antimicrobial susceptibility testing was performed by the broth microdilution method. A hybrid assembly approach of IonTorrent and MinION sequencing reads was used to generate the complete genome of linezolid-resistant E. faecium isolates VB3025 and VB3240. RESULTS VB3025 and VB3240 had minimum inhibitory concentration (MICs) for linezolid of 1024 μg/mL and 512 μg/mL, respectively. In addition, VB3025 was found to be resistant to both vancomycin and teicoplanin, while VB3240 was susceptible to these antibiotics. A hybrid assembly approach was used to generate the complete genome of VB3025 and VB3240 isolates harbouring the optrA gene. Notably, VB3025 carried two copies of optrA (chromosomal and plasmid), while in VB3240 optrA was identified on the chromosome. Interestingly, the plasmid pVB3025_2 co-carried the resistance gene clusters aph(3)-IIIa-sat4-ant(6)-Ia-ermB, the vanHAX operon and a copy of the optrA gene. Moreover, the optrA gene inserted into a Tn554 transposon carrying the ermA gene was identified in both VB3025 and VB3240 isolates. Furthermore, mutation analysis revealed the presence of a G2592T mutation in the 23S rRNA of both isolates. CONCLUSION This is the first study reporting optrA-positive linezolid-resistant E. faecium from India. A novel plasmid co-carrying vancomycin and linezolid resistance determinants highlights the threat for potential dissemination.
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Affiliation(s)
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632 004, Tamil Nadu, India
| | - Priyanka Babu
- Department of Clinical Microbiology, Christian Medical College, Vellore 632 004, Tamil Nadu, India
| | - Ayyan Raj Neeravi
- Department of Clinical Microbiology, Christian Medical College, Vellore 632 004, Tamil Nadu, India
| | - Vignesh Narasiman
- Department of Clinical Microbiology, Christian Medical College, Vellore 632 004, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632 004, Tamil Nadu, India.
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26
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Elghaieb H, Tedim AP, Abbassi MS, Novais C, Duarte B, Hassen A, Peixe L, Freitas AR. From farm to fork: identical clones and Tn6674-like elements in linezolid-resistant Enterococcus faecalis from food-producing animals and retail meat. J Antimicrob Chemother 2021; 75:30-35. [PMID: 31605129 DOI: 10.1093/jac/dkz419] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Increasing numbers of linezolid-resistant Enterococcus carrying optrA are being reported across different niches worldwide. We aimed to characterize the first optrA-carrying Enterococcus faecalis obtained from food-producing animals and retail meat samples in Tunisia. METHODS Seven optrA-carrying E. faecalis obtained from chicken faeces (n=3, August 2017) and retail chicken meat (n=4, August 2017) in Tunisia were analysed. Antimicrobial susceptibility was determined by disc diffusion, broth microdilution and Etest against 13 antibiotics, linezolid and tedizolid, respectively (EUCAST/CLSI). optrA stability (∼600 bacterial generations), transfer (filter mating) and location (S1-PFGE/hybridization) were characterized. WGS (Illumina-HiSeq) was done for four representatives that were analysed through in silico and genomic mapping tools. RESULTS Four MDR clones carrying different virulence genes were identified in chicken faeces (ST476) and retail meat (the same ST476 clone plus ST21 and ST859) samples. MICs of linezolid and tedizolid were stably maintained at 8 and 1-2 mg/L, respectively. optrA was located in the same transferable chromosomal Tn6674-like element in ST476 and ST21 clones, similar to isolates from pigs in Malaysia and humans in China. ST859 carried a non-conjugative plasmid of ∼40 kb with an impB-fexA-optrA segment, similar to plasmids from pigs and humans in China. CONCLUSIONS The same chromosomal and transferable Tn6674-like element was identified in different E. faecalis clones from humans and animals. The finding of retail meat contaminated with the same linezolid-resistant E. faecalis strain obtained from a food-producing animal highlights the potential role of the food chain in the worrisome dissemination of optrA that can be stably maintained without selective pressure over generations.
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Affiliation(s)
- Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Ana P Tedim
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Mohamed S Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Soliman, Tunisia
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Nüesch-Inderbinen M, Raschle S, Stevens MJA, Schmitt K, Stephan R. Linezolid-resistant Enterococcus faecalis ST16 harbouring optrA on a Tn6674-like element isolated from surface water. J Glob Antimicrob Resist 2021; 25:89-92. [PMID: 33705941 DOI: 10.1016/j.jgar.2021.02.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/21/2021] [Accepted: 02/25/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES The objective of this work was to characterise an optrA-carrying Enterococcus faecalis ST16 isolate recovered from a river water sample in Switzerland. METHODS Linezolid-resistant E. faecalis F102 was recovered from surface water in Switzerland and was subjected to comprehensive genotypic characterisation and analysis of the genetic environment of the oxazolidinone/phenicol resistance gene optrA. Whole-genome sequencing (WGS) was performed to detect linezolid resistance mechanisms, including mutations in 23S rRNA and ribosomal protein genes as well as acquired resistance genes. The isolate was further characterised by multilocus sequence typing (MLST) and identification of virulence genes. RESULTS WGS detected the presence of optrA identical to the original optrA gene from E. faecalis E349. Analysis of the genetic environment revealed the association of optrA with fexA and a Tn6674-like transposon in co-existence with spc and erm(A) resistance genes. Sequence alignment indicated that the genetic environment of optrA was identical to a Tn6674-like variant from E. faecalis previously isolated from diseased and healthy humans and food-producing animals in the Asia-Pacific region. Enterococcus faecalis F102 did not contain any mutations in 23S rRNA or in genes encoding ribosomal proteins L3, L4 and L22. A total of 14 other resistance genes and 16 virulence genes were detected. Enterococcus faecalis F102 was assigned in silico to ST16. CONCLUSION The spread of optrA-carrying E. faecalis ST16 with a high pathogenic potential in surface water is a worrisome aspect from a public-health perspective.
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Affiliation(s)
- Magdalena Nüesch-Inderbinen
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 272, CH-8057 Zürich, Switzerland.
| | - Susanne Raschle
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 272, CH-8057 Zürich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 272, CH-8057 Zürich, Switzerland
| | - Kira Schmitt
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 272, CH-8057 Zürich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 272, CH-8057 Zürich, Switzerland
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Fioriti S, Morroni G, Coccitto SN, Brenciani A, Antonelli A, Di Pilato V, Baccani I, Pollini S, Cucco L, Morelli A, Paniccià M, Magistrali CF, Rossolini GM, Giovanetti E. Detection of Oxazolidinone Resistance Genes and Characterization of Genetic Environments in Enterococci of Swine Origin, Italy. Microorganisms 2020; 8:E2021. [PMID: 33348682 PMCID: PMC7766396 DOI: 10.3390/microorganisms8122021] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 11/16/2022] Open
Abstract
One hundred forty-five florfenicol-resistant enterococci, isolated from swine fecal samples collected from 76 pig farms, were investigated for the presence of optrA, cfr, and poxtA genes by PCR. Thirty florfenicol-resistant Enterococcus isolates had at least one linezolid resistance gene. optrA was found to be the most widespread linezolid resistance gene (23/30), while cfr and poxtA were detected in 6/30 and 7/30 enterococcal isolates, respectively. WGS analysis also showed the presence of the cfr(D) gene in Enterococcus faecalis (n = 2 isolates) and in Enterococcus avium (n = 1 isolate). The linezolid resistance genes hybridized both on chromosome and plasmids ranging from ~25 to ~240 kb. Twelve isolates were able to transfer linezolid resistance genes to enterococci recipient. WGS analysis displayed a great variability of optrA genetic contexts identical or related to transposons (Tn6628 and Tn6674), plasmids (pE035 and pWo27-9), and chromosomal regions. cfr environments showed identities with Tn6644-like transposon and a region from p12-2300 plasmid; cfr(D) genetic contexts were related to the corresponding region of the plasmid 4 of Enterococcus faecium E8014; poxtA was always found on Tn6657. Circular forms were obtained only for optrA- and poxtA-carrying genetic contexts. Clonality analysis revealed the presence of E. faecalis (ST16, ST27, ST476, and ST585) and E. faecium (ST21) clones previously isolated from humans. These results demonstrate a dissemination of linezolid resistance genes in enterococci of swine origin in Central Italy and confirm the spread of linezolid resistance in animal settings.
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Affiliation(s)
- Simona Fioriti
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Gianluca Morroni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy; (S.F.); (G.M.); (S.N.C.)
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50139 Florence, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, 16126 Genoa, Italy;
| | - Ilaria Baccani
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50139 Florence, Italy
| | - Lucilla Cucco
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Alessandra Morelli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Marta Paniccià
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Chiara Francesca Magistrali
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, 06126 Perugia, Italy; (L.C.); (A.M.); (M.P.); (C.F.M.)
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, 50121 Florence, Italy; (A.A.); (I.B.); (S.P.); (G.M.R.)
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, 50139 Florence, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60121 Ancona, Italy;
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Yoon S, Son SH, Kim YB, Seo KW, Lee YJ. Molecular characteristics of optrA-carrying Enterococcus faecalis from chicken meat in South Korea. Poult Sci 2020; 99:6990-6996. [PMID: 33248615 PMCID: PMC7704738 DOI: 10.1016/j.psj.2020.08.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
The purpose of this study was to identify the genetic environment of optrA gene in linezolid (LZD)-resistant Enterococcus faecalis from chicken meat and to describe the probable mechanism of dissemination of the optrA gene through plasmid or chromosomal integration. Whole genome sequencing and analysis revealed that all 3 E. faecalis isolates confirmed as LZD- and chloramphenicol-resistant carried fexA adjacent to the optrA gene as well as a variety of resistance genes for macrolides, tetracyclines, and aminoglycosides, simultaneously. But, the other genes conferring LZD resistance, cfr and poxtA, were not detected in those strains. Two isolates harboring the optrA gene in their chromosomal DNA showed >99% similarity in arrangement to the transposon Tn6674 and the transposase genes, tnpA, tnpB, and tnpC and were located in the first open reading frame for transposase. One isolate harboring an optrA-carrying plasmid also showed >99% similarity with the previously reported pE439 plasmid but had 2 amino acid changes (Thr96Lys and Tyr160Asp) and a higher minimum inhibitory concentration against LZD of 16 mg/L than that of pE439 (8 mg/L). Mobile genetic elements such as transposons or plasmids flanking the optrA gene conduct a crucial role in the dissemination of antimicrobial resistance genes. Further investigations are required to identify the way by which optrA is integrated into chromosomal DNA and plasmids.
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Affiliation(s)
- Sunghyun Yoon
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Se Hyun Son
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Yeong Bin Kim
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kwang Won Seo
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Young Ju Lee
- College of Veterinary Medicine & Zoonoses Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea.
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Kerschner H, Rosel AC, Hartl R, Hyden P, Stoeger A, Ruppitsch W, Allerberger F, Apfalter P. Oxazolidinone Resistance Mediated by optrA in Clinical Enterococcus faecalis Isolates in Upper Austria: First Report and Characterization by Whole Genome Sequencing. Microb Drug Resist 2020; 27:685-690. [PMID: 33090061 DOI: 10.1089/mdr.2020.0098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genetic mechanisms associated with acquisition of linezolid (LZD) resistance are diverse, including point mutations in the V domain of the 23S rRNA and the 50S ribosomal proteins as well as cfr, optrA, and/or poxtA genes, which may be plasmid- or chromosomally encoded. The aim of this study was to investigate through Whole Genome Sequencing (WGS)-based typing the presence and location of genes and point mutations associated with LZD resistance in two Enterococcus faecalis isolates from Upper Austrian patients. The isolates were retrieved during screening by LZD disk diffusion test of a total of 911 clinical E. faecalis isolates in 2017. The two E. faecalis isolates had LZD minimum inhibitory concentrations of 8 and 32 mg/L and were optrA-positive (ST476 and ST585). Bioinformatic analysis revealed the presence of optrA located in the chromosome of both isolates. One isolate carried the optrA gene in the transposon 6674, previously reported as chromosomally encoded, and the second isolate in fragments originating from the integrative plasmid pEF10748. Additional mechanisms of LZD resistance on the 23S rRNA and the 50S ribosomal proteins were detected. None of the patients reported travels to geographical areas with high LZD resistance or previous LZD treatments. This is the first report of optrA carrying E. faecalis, including characterization by WGS from Austria. LZD resistance in a low-prevalence setting is of concern and should be further monitored.
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Affiliation(s)
- Heidrun Kerschner
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Adriana Cabal Rosel
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Rainer Hartl
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
| | - Patrick Hyden
- CUBE, Division of Computational Systems Biology, University of Vienna, Vienna, Austria
| | - Anna Stoeger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Werner Ruppitsch
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Franz Allerberger
- AGES-Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Vienna, Austria
| | - Petra Apfalter
- National Reference Center for Antimicrobial Resistance and Nosocomial Infections (NRZ), Institute for Hygiene, Microbiology and Tropical Medicine, Ordensklinikum Linz Elisabethinen, Linz, Austria
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Saavedra SY, Bernal JF, Montilla-Escudero E, Torres G, Rodríguez MK, Hidalgo AM, Ovalle MV, Rivera S, Perez-Gutierrez E, Duarte C. [National surveillance of clinical isolates of Enterococcus faecalis resistant to linezolid carrying the optrA gene in Colombia, 2014-2019]. Rev Panam Salud Publica 2020; 44:e104. [PMID: 32968369 PMCID: PMC7505479 DOI: 10.26633/rpsp.2020.104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 07/16/2020] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE To describe the epidemiological, phenotypical and genetic characteristics of clinical isolates carrying the optrA gene identified in antimicrobial resistance surveillance by the laboratory of the National Institute of Health of Colombia. METHODS Between October 2014 and February 2019, 25 isolates of Enterococcus spp. resistant to linezolid were received. Antimicrobial identification and sensitivity were determined using Vitek 2 and the minimum inhibitory concentration (MIC) to linezolid was established with E-test. The optrA gene was detected by PCR, and the genetic diversity of optrA-positive isolates was tested with Diversilab®. Six isolates were selected to perform whole genome sequencing. RESULTS The optrA gene was confirmed in 23/25 isolates of E. faecalis from seven departments in Colombia. The isolates presented a MIC to linezolid between 8 and >256µg/mL. Typing by Diversilab® showed a wide genetic variability. All the isolates analyzed by whole genome sequencing showed the resistance genes fexA, ermB, lsaA, tet(M), tet(L) and dfrG in addition to optrA and were negative for other mechanisms of resistance to linezolid. Three type sequences and three optrA variants were identified: ST16 (optrA-2), ST476 (optrA-5) and ST618 (optrA-6). The genetic environment of the optrA-2 (ST16) isolates presented the impB, fex, optrA segment, associated with plasmid, while in two isolates (optrA-6 and optrA-5) the transferable chromosomal element Tn6674-like was found. CONCLUSION OptrA-positive clinical isolates present a high genetic diversity, with different optrA clones and variants related to two types of structures and different mobile genetic elements.
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Affiliation(s)
- Sandra Yamile Saavedra
- Grupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS)BogotáColombiaGrupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Johan Fabian Bernal
- Grupo de resistencia antimicrobiana, Centro de investigación Tibaitata Corporación colombiana de investigación agropecuaria (AGROSAVIA)BogotáColombiaGrupo de resistencia antimicrobiana, Centro de investigación Tibaitata Corporación colombiana de investigación agropecuaria (AGROSAVIA), Bogotá, Colombia
| | - Efrain Montilla-Escudero
- Grupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS)BogotáColombiaGrupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - German Torres
- Equipo de infecciones asociadas a la atención en salud. Dirección Vigilancia y análisis del Riesgo en Salud Pública. Instituto Nacional de Salud (INS)BogotáColombiaEquipo de infecciones asociadas a la atención en salud. Dirección Vigilancia y análisis del Riesgo en Salud Pública. Instituto Nacional de Salud (INS), Bogotá, Colombia.
| | - Mabel Karina Rodríguez
- Grupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS)BogotáColombiaGrupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Andrea Melissa Hidalgo
- Grupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS)BogotáColombiaGrupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - María Victoria Ovalle
- Grupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS)BogotáColombiaGrupo de Microbiología, Dirección Redes en Salud Pública. Instituto Nacional de Salud (INS), Bogotá, Colombia
| | - Sandra Rivera
- Equipo de infecciones asociadas a la atención en salud. Dirección Vigilancia y análisis del Riesgo en Salud Pública. Instituto Nacional de Salud (INS)BogotáColombiaEquipo de infecciones asociadas a la atención en salud. Dirección Vigilancia y análisis del Riesgo en Salud Pública. Instituto Nacional de Salud (INS), Bogotá, Colombia.
| | - Enrique Perez-Gutierrez
- Organización Panamericana de la SaludWashington DCEstados Unidos de AméricaOrganización Panamericana de la Salud, Washington DC, Estados Unidos de América
| | - Carolina Duarte
- Grupo de resistencia antimicrobiana, Centro de investigación Tibaitata Corporación colombiana de investigación agropecuaria (AGROSAVIA)BogotáColombiaGrupo de resistencia antimicrobiana, Centro de investigación Tibaitata Corporación colombiana de investigación agropecuaria (AGROSAVIA), Bogotá, Colombia
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Drug Resistance Determinants in Clinical Isolates of Enterococcus faecalis in Bangladesh: Identification of Oxazolidinone Resistance Gene optrA in ST59 and ST902 Lineages. Microorganisms 2020; 8:microorganisms8081240. [PMID: 32824090 PMCID: PMC7463919 DOI: 10.3390/microorganisms8081240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/06/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
Enterococcus faecalis is one of the major causes of urinary tract infection, showing acquired resistance to various classes of antimicrobials. The objective of this study was to determine the prevalence of drug resistance and its genetic determinants for E. faecalis clinical isolates in north-central Bangladesh. Among a total of 210 E. faecalis isolates, isolated from urine, the resistance rates to erythromycin, levofloxacin, and gentamicin (high level) were 85.2, 45.7, and 11.4%, respectively, while no isolates were resistant to ampicillin, vancomycin and teicoplanin. The most prevalent resistance gene was erm(B) (97%), and any of the four genes encoding aminoglycoside modifying enzyme (AME) were detected in 99 isolates (47%). The AME gene aac(6′)-Ie-aph(2”)-Ia was detected in 46 isolates (21.9%) and was diverse in terms of IS256-flanking patterns, which were associated with resistance level to gentamicin. Tetracycline resistance was ascribable to tet(M) (61%) and tet(L) (38%), and mutations in the quinolone resistance-determining region of both GyrA and ParC were identified in 44% of isolates. Five isolates (2.4%) exhibited non-susceptibility to linezolide (MIC, 4 μg/mL), and harbored the oxazolidinone resistance gene optrA, which was located in a novel genetic cluster containing the phenicol exporter gene fexA. The optrA-positive isolates belonged to ST59, ST902, and ST917 (CC59), while common lineages of other multiple drug-resistant isolates were ST6, ST28, CC16, and CC116. The present study first revealed the prevalence of drug resistance determinants of E. faecalis and their genetic profiles in Bangladesh.
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Yao TG, Li BY, Luan RD, Wang HN, Lei CW. Whole genome sequence of Enterococcus gallinarum EG81, a porcine strain harbouring the oxazolidinone-phenicol resistance gene optrA with chromosomal and plasmid location. J Glob Antimicrob Resist 2020; 22:598-600. [PMID: 32603905 DOI: 10.1016/j.jgar.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVE The aim of this study was to characterise the whole genome sequence of linezolid-intermediate Enterococcus gallinarum strain EG81 of swine origin in China. METHODS Whole genome of EG81 was sequenced using Illumina MiSeq platform combined with the Nanopore PromethION platform, and assembled de novo using Canu v1.5. NCBI Prokaryotic Genome Annotation Pipeline (PGAP) was used to annotate the genome of EG81. Antimicrobial resistance genes were identified using CGE ResFinder 3.2. RESULTS The genome of EG81 consists of one 3,433,237-bp chromosome and two plasmids, pEG81-1 (51,632 bp) and pEG81-2 (3425 bp). A total of 3285 coding sequences and 80 RNA genes were predicted by PGAP. The oxazolidinone-phenicol resistance gene optrA is located on both the chromosome and plasmid pEG81-1 associated with Tn554 and Tn558, respectively. In addition, EG81 harbours vanC1XY (vancomycin resistance), fexA (phenicol), dfrG (trimethoprim), aadD, ant(6)-Ia and ant(9)-Ia (aminoglycoside), erm(A) and erm(B) (macrolide), and tet(L) and tet(M) (tetracycline). CONCLUSION Here, we first report the oxazolidinone-phenicol gene optrA in E. gallinarum that is intrinsically resistant to vancomycin, which poses a great threat to public health. The genome sequence of E. gallinarum EG81 provides valuable information for the dissemination of optrA among vancomycin-resistant enterococci.
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Affiliation(s)
- Tian-Ge Yao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Bo-Yang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Ren-Dong Luan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hong-Ning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Chang-Wei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China.
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Transferable Resistance Gene optrA in Enterococcus faecalis from Swine in Brazil. Antimicrob Agents Chemother 2020; 64:AAC.00142-20. [PMID: 32253215 DOI: 10.1128/aac.00142-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
OptrA is an ATP-binding cassette (ABC)-F protein that confers resistance to oxazolidinones and phenicols and can be either plasmid-encoded or chromosomally encoded. Here, we isolated 13 Enterococcus faecalis strains possessing a linezolid MIC of ≥4 mg/liter from nursery pigs in swine herds located across Brazil. Genome sequence comparison showed that these strains possess optrA in different genetic contexts occurring in 5 different E. faecalis sequence type backgrounds. The optrA gene invariably occurred in association with an araC regulator and a gene encoding a hypothetical protein. In some contexts, this genetic island was able to excise and form a covalently closed circle within the cell; this circle appeared to occur in high abundance and to be transmissible by coresident plasmids.
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Freitas AR, Tedim AP, Novais C, Lanza VF, Peixe L. Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes. Microb Genom 2020; 6. [PMID: 32149599 PMCID: PMC7371108 DOI: 10.1099/mgen.0.000350] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
| | - Ana P Tedim
- Grupo de Investigación Biomédica en Sepsis - BioSepsis. Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
| | - Val F Lanza
- Departamento de Bioinformática. Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
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Ruiz-Ripa L, Feßler AT, Hanke D, Sanz S, Olarte C, Eichhorn I, Schwarz S, Torres C. Detection of poxtA- and optrA-carrying E. faecium isolates in air samples of a Spanish swine farm. J Glob Antimicrob Resist 2019; 22:28-31. [PMID: 31884049 DOI: 10.1016/j.jgar.2019.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 12/16/2019] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVE Two linezolid-resistant Enterococcus faecium isolates, C10004 and C10009, were recovered from air samples of a Spanish swine farm and comprehensively characterized. METHODS Detection of linezolid resistance mechanisms (mutations and acquisition of resistance genes) was performed by PCR/sequencing. Isolates were characterized by multilocus sequence typing (MLST), antimicrobial susceptibility testing, detection of antimicrobial resistance and virulence genes, and analysis of the genetic environment of the linezolid resistance genes. The characterization of isolate C10009 was performed by Whole-Genome-Sequencing and of isolate C10004 by PCR and amplicon sequencing, where applicable. Conjugation experiments to assess the transferability of the optrA and poxtA genes implicated in linezolid resistance were performed. RESULTS The linezolid-resistant E. faecium isolates C10004 and C10009, assigned to ST128 and ST437, respectively, harbored the optrA and poxtA genes. Neither mutations in the 23S rRNA nor in the genes for the ribosomal proteins L3, L4 and L22 were detected. C10004 and C10009 carried fourteen and thirteen antimicrobial resistance genes, respectively. The sequence alignment indicated that the genetic environment of the poxtA gene was identical in both isolates, with a downstream-located fexB gene. The poxtA gene was transferred by conjugation together with the fexB gene, and also with tet(M) and tet(L) in the case of isolate C10004. The optrA gene could not be transferred. CONCLUSIONS This is the first report of the poxtA gene in Spain. The presence of poxtA- and optrA-carrying E. faecium isolates in air samples represents a public health concern, indicating an involvement of swine farms in the spread of linezolid-resistant bacteria.
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Affiliation(s)
- Laura Ruiz-Ripa
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Susana Sanz
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Carmen Olarte
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Carmen Torres
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain.
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