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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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Harmer CJ, Hall RM. IS 26 and the IS 26 family: versatile resistance gene movers and genome reorganizers. Microbiol Mol Biol Rev 2024; 88:e0011922. [PMID: 38436262 DOI: 10.1128/mmbr.00119-22] [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] [Indexed: 03/05/2024] Open
Abstract
SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Michaelis C, Berger TMI, Kuhlmann K, Ghulam R, Petrowitsch L, Besora Vecino M, Gesslbauer B, Pavkov-Keller T, Keller W, Grohmann E. Effect of TraN key residues involved in DNA binding on pIP501 transfer rates in Enterococcus faecalis. Front Mol Biosci 2024; 11:1268647. [PMID: 38380428 PMCID: PMC10877727 DOI: 10.3389/fmolb.2024.1268647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024] Open
Abstract
Conjugation is a major mechanism that facilitates the exchange of antibiotic resistance genes among bacteria. The broad-host-range Inc18 plasmid pIP501 harbors 15 genes that encode for a type IV secretion system (T4SS). It is a membrane-spanning multiprotein complex formed between conjugating donor and recipient cells. The penultimate gene of the pIP501 operon encodes for the cytosolic monomeric protein TraN. This acts as a transcriptional regulator by binding upstream of the operon promotor, partially overlapping with the origin of transfer. Additionally, TraN regulates traN and traO expression by binding upstream of the PtraNO promoter. This study investigates the impact of nine TraN amino acids involved in binding to pIP501 DNA through site-directed mutagenesis by exchanging one to three residues by alanine. For three traN variants, complementation of the pIP501∆traN knockout resulted in an increase of the transfer rate by more than 1.5 orders of magnitude compared to complementation of the mutant with native traN. Microscale thermophoresis (MST) was used to assess the binding affinities of three TraN double-substituted variants and one triple-substituted variant to its cognate pIP501 double-stranded DNA. The MST data strongly correlated with the transfer rates obtained by biparental mating assays in Enterococcus faecalis. The TraN variants TraN_R23A-N24A-Q28A, TraN_H82A-R86A, and TraN_G100A-K101A not only exhibited significantly lower DNA binding affinities but also, upon complementation of the pIP501∆traN knockout, resulted in the highest pIP501 transfer rates. This confirms the important role of the TraN residues R23, N24, Q28, H82, R86, G100, and K101 in downregulating pIP501 transfer. Although TraN is not part of the mating pair formation complex, TraE, TraF, TraH, TraJ, TraK, and TraM were coeluted with TraN in a pull-down. Moreover, TraN homologs are present not only in Inc18 plasmids but also in RepA_N and Rep_3 family plasmids, which are frequently found in enterococci, streptococci, and staphylococci. This points to a widespread role of this repressor in conjugative plasmid transfer among Firmicutes.
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Affiliation(s)
- Claudia Michaelis
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | | | - Kirill Kuhlmann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Rangina Ghulam
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | - Lukas Petrowitsch
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Bernd Gesslbauer
- Institute of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Elisabeth Grohmann
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
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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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Coccitto SN, Cinthi M, Simoni S, Vignaroli C, Massacci FR, Albini E, Garofalo C, Aquilanti L, Magistrali CF, Brenciani A, Giovanetti E. Identification of plasmids co-carrying cfr(D)/optrA and cfr(D2)/poxtA linezolid resistance genes in two Enterococcus avium isolates from swine brain. Vet Microbiol 2023; 282:109749. [PMID: 37116421 DOI: 10.1016/j.vetmic.2023.109749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 04/30/2023]
Abstract
Oxazolidinones are critically important antibiotics to treat human infections caused by multidrug-resistant bacteria, therefore the occurrence of linezolid-resistant enterococci from food-producing animals poses a serious risk to human health. In this study, Enterococcus avium 38157 and 44917 strains, isolated from the brain of two unrelated piglets, were found to carry the linezolid resistance genes cfr(D)-optrA, and cfr(D2)-poxtA, respectively. Whole genome sequencing analysis of E. avium 38157 revealed that the genes were co-located on the 36.5-kb pEa_cfr(D)-optrA plasmid showing high identity with the pAT02-c of Enterococcus faecium AT02 from pet food. The optrA region, was 99% identical to the one of the pAv-optrA plasmid from a bovine Aerococcus viridans strain, whereas the cfr(D) genetic context was identical to that of the plasmid 2 of E. faecium 15-307.1. pEa_cfr(D)-optrA was not transferable to enterococcal recipients. In E. avium 44917 a cfr(D)-like gene, named cfr(D2), and the poxtA gene were co-located on the transferable 42.6-kb pEa-cfr(D2)-poxtA plasmid 97% identical to the Tn6349 transposon of the human MRSA AOUC-0915. The cfr(D2) genetic context, fully replaced the Tn6644 that in S. aureus AOUC-0915 harbor the cfr gene. In conclusion, this is, the best of our knowledge, the first report of the new cfr(D2) gene variant. The occurrence of plasmids co-carrying two linezolid resistance genes in enterococci from food-producing animals needs close surveillance to prevent their spread to human pathogens.
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Affiliation(s)
- Sonia Nina Coccitto
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marzia Cinthi
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Serena Simoni
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesca Romana Massacci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) 'Togo Rosati', Perugia, Italy
| | - Elisa Albini
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) 'Togo Rosati', Perugia, Italy
| | - Cristiana Garofalo
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Lucia Aquilanti
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy.
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Cinthi M, Coccitto SN, Simoni S, Garofalo C, Cesaro C, Vignaroli C, Brenciani A, Giovanetti E. Letter to the Editor: A Porcine Enterococcus hirae Shares a poxtA-Carrying Plasmid with a Human Enterococcus faecium Isolate. Microb Drug Resist 2023. [PMID: 36695758 DOI: 10.1089/mdr.2022.0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Marzia Cinthi
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Sonia Nina Coccitto
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Serena Simoni
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cristiana Garofalo
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cristiana Cesaro
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Cinthi M, Coccitto SN, Morroni G, D’Achille G, Brenciani A, Giovanetti E. Detection of an Enterococcus faecium Carrying a Double Copy of the PoxtA Gene from Freshwater River, Italy. Antibiotics (Basel) 2022; 11:1618. [PMID: 36421262 PMCID: PMC9686737 DOI: 10.3390/antibiotics11111618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 08/02/2023] Open
Abstract
Oxazolidinones are valuable antimicrobials that are used to treat severe infections due to multidrug-resistant (MDR) Gram-positive bacteria. However, in recent years, a significant spread of clinically relevant linezolid-resistant human bacteria that is also present in animal and environmental settings has been detected and is a cause for concern. This study aimed to investigate the presence, genetic environments, and transferability of oxazolidinone resistance genes in enterococci from freshwater samples. A total of 10 samples were collected from a river in Central Italy. Florfenicol-resistant enterococci were screened for the presence of oxazolidinone resistance genes by PCR. Enterococcus faecium M1 was positive for the poxtA gene. The poxtA transfer (filter mating and aquaria microcosm assays), localization (S1-PFGE/hybridization), genetic context, and clonality of the isolate (WGS) were analyzed. Two poxtA copies were located on the 30,877-bp pEfM1, showing high-level identity and synteny to the pEfm-Ef3 from an E. faecium collected from an Italian coastal area. The isolate was able to transfer the poxtA to enterococcal recipients both in filter mating and aquaria microcosm assays. This is-to the best of our knowledge-the first detection of an enterococcus carrying a linezolid resistance gene from freshwater in Italy.
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Affiliation(s)
- Marzia Cinthi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60121 Ancona, Italy
| | - Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy
| | - Gianluca Morroni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy
| | - Gloria D’Achille
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60121 Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, 60121 Ancona, Italy
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Carvalhaes CG, Sader HS, Rhomberg PR, Castanheira M, DeVries S, Mendes RE. Activity of Tedizolid and Comparator Agents Against Gram-positive Isolates Causing Skin and Skin Structure Infections in Pediatric Patients in United States Hospitals (2015-2019). Pediatr Infect Dis J 2022; 41:731-735. [PMID: 35703275 DOI: 10.1097/inf.0000000000003597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Tedizolid was approved by the United States Food and Drug Administration to treat acute bacterial skin and skin structure infections in adults in 2014, and in 2020, United States Food and Drug Administration expanded the approval of tedizolid to treat pediatric patients 12 years of age and older. This study assessed the activity of tedizolid and comparator agents against clinical surveillance isolates collected from pediatric patients with skin and skin structure infection in the United States. METHODS A total of 2747 gram-positive organisms (1 per patient) were collected in 2015 to 2019 from pediatric (≤17 years old) patients with skin and skin structure infections. The isolates were collected from 33 US medical centers and susceptibility tested against tedizolid and comparators by reference broth microdilution methods. Susceptibility results for main pathogens were stratified by patient age: ≤1 years old (851 isolates), 2 to 5 years old (623), 6 to 12 years old (754) and 13 to 17 years old (519). RESULTS Staphylococcus aureus (n = 2163) was the main pathogen recovered from all age groups, followed by β-hemolytic streptococci (n = 460). Tedizolid inhibited all S. aureus , including methicillin-resistant S. aureus (MRSA) isolates (41.0%), regardless of the age group. MRSA rates varied by age group; MRSA was highest among ≤1 years old (45.0%) and lowest in the 13 to 17 years old (32.7%) groups. Linezolid, daptomycin and vancomycin also displayed susceptibility rates of 100% against S. aureus isolates. Clindamycin (81.3%-98.5%), tetracycline (91.6%-97.1%) and trimethoprim-sulfamethoxazole (97.0%-100%) susceptibility rates varied among age groups and methicillin resistance profiles. Overall, tedizolid, linezolid, daptomycin and vancomycin inhibited all gram-positive pathogens in this collection. CONCLUSIONS Tedizolid was very active against a large collection of gram-positive pathogens causing skin and skin structure infection in pediatric patients, including MRSA isolates.
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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: 37] [Impact Index Per Article: 18.5] [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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Li P, Gao M, Feng C, Yan T, Sheng Z, Shi W, Liu S, Zhang L, Li A, Lu J, Lin X, Li K, Xu T, Bao Q, Sun C. Molecular characterization of florfenicol and oxazolidinone resistance in Enterococcus isolates from animals in China. Front Microbiol 2022; 13:811692. [PMID: 35958123 PMCID: PMC9360786 DOI: 10.3389/fmicb.2022.811692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/07/2022] [Indexed: 11/24/2022] Open
Abstract
Florfenicol is widely used for the treatment of bacterial infections in domestic animals. The aim of this study was to analyze the molecular mechanisms of florfenicol and oxazolidinone resistance in Enterococcus isolates from anal feces of domestic animals. The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method. Polymerase chain reaction (PCR) was performed to analyze the distribution of the resistance genes. Whole-genome sequencing and comparative plasmid analysis was conducted to analyze the resistance gene environment. A total of 351 non-duplicated enteric strains were obtained. Among these isolates, 22 Enterococcus isolates, including 19 Enterococcus. faecium and 3 Enterococcus. faecalis, were further studied. 31 florfenicol resistance genes (13 fexA, 3 fexB, 12 optrA, and 3 poxtA genes) were identified in 15 of the 19 E. faecium isolates, and no florfenicol or oxazolidinone resistance genes were identified in 3 E. faecalis isolates. Whole-genome sequencing of E. faecium P47, which had all four florfenicol and oxazolidinone resistance genes and high MIC levels for both florfenicol (256 mg/L) and linezolid (8 mg/L), revealed that it contained a chromosome and 3 plasmids (pP47-27, pP47-61, and pP47-180). The four florfenicol and oxazolidinone resistance genes were all related to the insertion sequences IS1216 and located on two smaller plasmids. The genes fexB and poxtA encoded in pP47-27, while fexA and optrA encoded in the conjugative plasmid pP47-61. Comparative analysis of homologous plasmids revealed that the sequences with high identities were plasmid sequences from various Enterococcus species except for the Tn6349 sequence from a Staphylococcus aureus chromosome (MH746818.1). The current study revealed that florfenicol and oxazolidinone resistance genes (fexA, fexB, poxtA, and optrA) were widely distributed in Enterococcus isolates from animal in China. The mobile genetic elements, including the insertion sequences and conjugative plasmid, played an important role in the horizontal transfer of florfenicol and oxazolidinone resistance.
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Affiliation(s)
- Pingping Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Nursing Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Department of Clinical Laboratory, Zhoukou Maternal and Child Health Hospital, Zhoukou, China
| | - Mengdi Gao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chunlin Feng
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tielun Yan
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhiqiong Sheng
- School of Nursing, Wenzhou Medical University, Wenzhou, China
| | - Weina Shi
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shuang Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lei Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Anqi Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
- Teng Xu,
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- Qiyu Bao,
| | - Caixia Sun
- Nursing Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- Institute of Biomedical Informatics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
- *Correspondence: Caixia Sun,
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Coccitto SN, Cinthi M, Fioriti S, Morroni G, Simoni S, Vignaroli C, Garofalo C, Mingoia M, Brenciani A, Giovanetti E. Linezolid-resistant Enterococcus gallinarum isolate of swine origin carrying cfr, optrA and poxtA genes. J Antimicrob Chemother 2022; 77:331-337. [PMID: 35076077 DOI: 10.1093/jac/dkab408] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/12/2021] [Indexed: 10/21/2023] Open
Abstract
OBJECTIVES To characterize a linezolid-resistant Enterococcus gallinarum isolate of porcine origin co-carrying cfr, optrA and poxtA genes. METHODS The genome was sequenced using the Illumina and Nanopore platforms. The presence of circular intermediates was examined by inverse PCR. Transferability of oxazolidinone resistance genes was investigated by transformation and conjugation. RESULTS Two plasmids, the cfr- and optrA-carrying pEgFS4-1 (35 kb) and the poxtA-harbouring pEgFS4-2 (38 kb), were identified. pEgFS4-1 disclosed a distinctive mosaic structure with two cargo regions bounded by identical IS1216 elements interpolated into a backbone related to that of Enterococcus faecium vanA-containing pVEF2. The first cargo region included the cfr and optrA contexts, whereas the second one carried a Tn554 remnant and the lnu(A) gene. Both regions were able to excise in circular form as a unique translocable unit. pEgFS4-2 plasmid was 99% identical to a not fully described E. faecium pSBC1 plasmid. The poxtA environment, flanked by IS1216, was proved to be unstable. pEgFS4-2 also exhibited another cargo region containing the tet(M)-tet(L) genes arranged in tandem and its circular form was detected. Transformation and conjugation experiments failed to demonstrate the transferability of both plasmids to enterococcal recipients. Both plasmids persisted in the absence of selective pressure. CONCLUSIONS To the best of our knowledge, this is the first description of a linezolid-resistant E. gallinarum isolate of swine origin carrying cfr, optrA and poxtA genes. The co-presence of three linezolid resistance determinants in an intrinsically vancomycin-resistant enterococcal species is cause of concern.
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Affiliation(s)
- Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marzia Cinthi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Simona Fioriti
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Serena Simoni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Cristiana Garofalo
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Marina Mingoia
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Plasmid Fusion and Recombination Events That Occurred during Conjugation of poxtA-Carrying Plasmids in Enterococci. Microbiol Spectr 2022; 10:e0150521. [PMID: 35044200 PMCID: PMC8768628 DOI: 10.1128/spectrum.01505-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Linezolid plays a crucial role in the treatment of infections caused by multiresistant Gram-positive bacteria. The poxtA gene not only confers oxazolidinone and phenicol resistance but also decreases susceptibility to tetracycline. In this study, we investigated structural changes in mobilizable poxtA-carrying plasmids in enterococci which occurred during conjugation experiments using S1-PFGE (pulsed-field gel electrophoresis), Southern blot hybridization, and whole-genome sequencing (WGS) analysis. Two poxtA-carrying strains were identified in Enterococcus faecalis E006 and Enterococcus lactis E843, respectively. E. faecalis E006 contains the 121,520-bp conjugative plasmid pE006-121 and the 19,832-bp mobilizable poxtA-carrying plasmid pE006-19, while E. lactis E843 contains the 171,930-bp conjugative plasmid pE843-171 and the 27,847-bp mobilizable poxtA-carrying plasmid pE843-27. Moreover, both poxtA-carrying plasmids were mobilized by their respective conjugative plasmid in enterococci by plasmid fusion; one was generated by homologous recombination in E. faecalis through an identical 864-bp homologous region in the plasmids of the parental strain, while another was generated by an IS1216E-mediated plasmid integration in E. lactis, involving a replicative transposition. IMPORTANCE Until now, all the poxtA genes described in enterococci, including E. faecalis, E. faecium, and E. hirae, are plasmid-borne, suggesting that plasmids play an important role in the dissemination of the poxtA gene among enterococci. This study showed that the mobilizable poxtA-carrying plasmid could transfer with the help of conjugative plasmid in enterococci via plasmid fusion, with one generated by homologous recombination in E. faecalis, and another by replicative transposition in E. lactis. During both the fusion events, the poxtA-carrying plasmids changed from nonconjugative to conjugative, leading to the generation and enhanced dissemination of the larger phenicol-oxazolidinone-tetracycline resistance-encoding plasmids in enterococci.
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13
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Cinthi M, Coccitto SN, Fioriti S, Morroni G, Simoni S, Vignaroli C, Magistrali CF, Albini E, Brenciani A, Giovanetti E. Occurrence of a plasmid co-carrying cfr(D) and poxtA2 linezolid resistance genes in Enterococcus faecalis and Enterococcus casseliflavus from porcine manure, Italy. J Antimicrob Chemother 2021; 77:598-603. [PMID: 34910146 DOI: 10.1093/jac/dkab456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To investigate the genetic elements and the transferability of linezolid resistance genes in three enterococci co-carrying cfr(D) and poxtA2 isolates from manure of a swine farm in central Italy. METHODS Two Enterococcus faecalis isolates and one Enterococcus casseliflavus isolate carrying both cfr(D) and poxtA genes were tested for their susceptibility to florfenicol, chloramphenicol, linezolid, tedizolid, tetracycline and vancomycin. Linezolid resistance genes transfer (filter mating), localization (S1-PFGE/hybridization), genetic elements and relatedness between isolates (WGS) were analysed. RESULTS Two E. faecalis isolates and one E. casseliflavus isolate carried the cfr(D) gene and the recently described poxtA2 variant. In the three enterococci, cfr(D) and poxtA2 were co-located on a 33 480 bp plasmid, pV386, 95%-100% identical (coverage 84%) to the Tn6349 transposon of Staphylococcus aureus AOUC-0915. In all isolates, both genes also showed a chromosomal location. Same sequence identities were found from the comparison with currently known poxtA2 genetic elements. In the plasmid pV386, poxtA2 gene was not bounded by two IS1216, as described in pIB-BOL, but closely associated to the cfr(D) and fexA genes. pV386 was always transferred by filter mating to Enterococcus faecium 64/3 recipient. CONCLUSIONS The occurrence of the pV386 plasmid in E. faecalis and E. casseliflavus from swine manure is of great concern and highlights the need for control measures to contain its spread to other enterococcal species.
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Affiliation(s)
- Marzia Cinthi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Simona Fioriti
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Serena Simoni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Elisa Albini
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche 'Togo Rosati', Perugia, Italy
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Characterization of the specific DNA-binding properties of Tnp26, the transposase of insertion sequence IS26. J Biol Chem 2021; 297:101165. [PMID: 34487761 PMCID: PMC8477213 DOI: 10.1016/j.jbc.2021.101165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022] Open
Abstract
The bacterial insertion sequence (IS) IS26 mobilizes and disseminates antibiotic resistance genes. It differs from bacterial IS that have been studied to date as it exclusively forms cointegrates via either a copy-in (replicative) or a recently discovered targeted conservative mode. To investigate how the Tnp26 transposase recognizes the 14-bp terminal inverted repeats (TIRs) that bound the IS, amino acids in two domains in the N-terminal (amino acids M1-P56) region were replaced. These changes substantially reduced cointegration in both modes. Tnp26 was purified as a maltose-binding fusion protein and shown to bind specifically to dsDNA fragments that included an IS26 TIR. However, Tnp26 with an R49A or a W50A substitution in helix 3 of a predicted trihelical helix-turn-helix domain (amino acids I13-R53) or an F4A or F9A substitution replacing the conserved amino acids in a unique disordered N-terminal domain (amino acids M1-D12) did not bind. The N-terminal M1-P56 fragment also bound to the TIR but only at substantially higher concentrations, indicating that other parts of Tnp26 enhance the binding affinity. The binding site was confined to the internal part of the TIR, and a G to T nucleotide substitution in the TGT at positions 6 to 8 of the TIR that is conserved in most IS26 family members abolished binding of both Tnp26 (M1-M234) and Tnp26 M1-P56 fragment. These findings indicate that the helix-turn-helix and disordered domains of Tnp26 play a role in Tnp26-TIR complex formation. Both domains are conserved in all members of the IS26 family.
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Di Lallo G, Falconi M, Iacovelli F, Frezza D, D'Addabbo P. Analysis of Four New Enterococcus faecalis Phages and Modeling of a Hyaluronidase Catalytic Domain from Saphexavirus. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:131-141. [PMID: 36161247 PMCID: PMC9041502 DOI: 10.1089/phage.2021.0003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Background: Phage therapy (PT), as a method to treat bacterial infections, needs identification of bacteriophages targeting specific pathogenic host. Enterococcus faecalis, a Gram-positive coccus resident in the human gastrointestinal tract, may become pathogenic in hospitalized patients showing acquired resistance to vancomycin and thus representing a possible target for PT. Materials and Methods: We isolated four phages that infect E. faecalis and characterized them by host range screening, transmission electron microscopy, and genome sequencing. We also identified and three-dimensional modeled a new hyaluronidase enzyme. Results: The four phages belong to Siphoviridae family: three Efquatrovirus (namely vB_EfaS_TV51, vB_EfaS_TV54, and vB_EfaS_TV217) and one Saphexavirus (vB_EfaS_TV16). All of them are compatible with lytic cycle. vB_EfaS_TV16 moreover presents a gene encoding for a hyaluronidase enzyme. Conclusions: The identified phages show features suggesting their useful application in PT, particularly the Saphexavirus that may be of enhanced relevance in PT because of its potential biofilm-digestion capability.
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Affiliation(s)
- Gustavo Di Lallo
- Laboratory of Microbiology, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Mattia Falconi
- Structural Bioinformatics Group, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Federico Iacovelli
- Structural Bioinformatics Group, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Domenico Frezza
- Laboratory of Microbiology, Department of Biology, University of Roma Tor Vergata, Roma, Italy
| | - Pietro D'Addabbo
- Computational Biology Unit, Department of Biology, University of Bari, Bari, Italy
- Address correspondence to: Pietro D'Addabbo, PhD, Computational Biology Unit, Department of Biology, University of Bari, Via E. Orabona 4, Bari 70125, Italy
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16
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Dejoies L, Sassi M, Schutz S, Moreaux J, Zouari A, Potrel S, Collet A, Lecourt M, Auger G, Cattoir V. Genetic features of the poxtA linezolid resistance gene in human enterococci from France. J Antimicrob Chemother 2021; 76:1978-1985. [PMID: 33895846 DOI: 10.1093/jac/dkab116] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/14/2021] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES To describe the prevalence of poxtA among clinical linezolid-resistant enterococci (LRE) collected in France from 2016 to 2020 and to extensively characterize its genetic supports and environments. METHODS All LRE clinical isolates received at the National Reference Centre for Enterococci from French hospitals between 2016 and 2020 were included. LRE isolates were screened for linezolid resistance genes (cfr-like, optrA and poxtA) by real-time PCR and phenotypically characterized. A collection of 11 representative poxtA-positive isolates (10 Enterococcus faecium and 1 Enterococcus faecalis) underwent WGS by hybrid assembly combining short-read (Illumina MiSeq) and long-read (MinION) approaches. Transferability of poxtA was attempted by filter-mating experiments. RESULTS Out of 466 LRE received at the National Reference Centre for Enterococci over the period, 47 (10.1%) were poxtA-positive, including 42 E. faecium. The 11 isolates characterized by WGS were confirmed to be epidemiologically unrelated by core genome analysis and eight different STs were assigned to E. faecium isolates. The poxtA gene was found to be plasmid carried and flanked by IS1216E transposase genes in all isolates and frequently linked with fexB, tet(M) and tet(L). A total of seven distinct poxtA-harbouring plasmids were obtained after hybrid assembly and plasmid transfer of poxtA was successful in three cases. For the two poxtA/optrA-positive isolates, those genes were carried by different plasmids. CONCLUSIONS The poxtA gene has been circulating among clinical enterococci in France since at least 2016, mostly in E. faecium and independently from optrA. The poxtA-carrying plasmids often co-carried resistance genes to phenicols and tetracyclines, and could have been co-selected through their veterinary use.
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Affiliation(s)
- Loren Dejoies
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,Université de Rennes 1, Inserm U1230, Rennes, France
| | - Mohamed Sassi
- Université de Rennes 1, Inserm U1230, Rennes, France
| | - Sacha Schutz
- Université de Brest, INSERM, EFS, UMR 1078, GGB, Brest, France.,CHU Brest, Laboratoire de Génétique Moléculaire, Brest, France
| | - Julie Moreaux
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France
| | - Asma Zouari
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Sophie Potrel
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Anaïs Collet
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Maxime Lecourt
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Gabriel Auger
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
| | - Vincent Cattoir
- CHU de Rennes, Service de Bactériologie-Hygiène hospitalière, Rennes, France.,Université de Rennes 1, Inserm U1230, Rennes, France.,CNR de la Résistance aux Antibiotiques (laboratoire associé 'Entérocoques'), Rennes, France
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17
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Shan X, Li XS, Wang N, Schwarz S, Zhang SM, Li D, Du XD. Studies on the role of IS1216E in the formation and dissemination of poxtA-carrying plasmids in an Enterococcus faecium clade A1 isolate. J Antimicrob Chemother 2021; 75:3126-3130. [PMID: 32772071 DOI: 10.1093/jac/dkaa325] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To analyse the role of IS1216E in the dissemination of the phenicol-oxazolidinone-tetracycline resistance gene poxtA in an Enterococcus faecium clade A1 isolate. METHODS MICs were determined by broth microdilution. The poxtA-positive isolate was typed by MLST. The two plasmids were characterized by PCR, conjugation, S1-PFGE, Southern blot hybridization and WGS analysis. The presence of translocatable units (TUs) was examined by PCR and sequencing. RESULTS Isolate E1077 contains the 217661 bp conjugative plasmid pE1077-217 and the 23710 bp mobilizable plasmid pE1077-23. pE1077-217 harbours erm(B), aac(A)-aph(D), aadE, spw, lsa(E), lnu(B), aphA3 and dfrG, whereas pE1077-23 carries a Tn6657-like transposon containing poxtA and fexB. pE1077-23 was apparently formed by an IS1216E-mediated composite transposon-plasmid fusion event, involving a replicative transposition process. Conjugation experiments showed that pE1077-23 is mobilizable by pE1077-217. Moreover, a novel 31742 bp plasmid, pT-E1077-31, was found in a transconjugant. WGS analysis indicated that pT-E1077-31 was formed by the integration of a Tn6657-derived, IS1216E-based translocatable unit, which carried fexB and poxtA, into a copy of pE1077-23. CONCLUSIONS This study showed the presence of two cointegrate formation events in the formation and spread of a poxtA/fexB-carrying plasmid in E. faecium. One was the integration of a transposon into a plasmid while the other was the integration of a TU into a different site of the same type of plasmid-borne transposon from which it originated. In both events, IS1216E played a major role, suggesting that IS1216E-mediated transposition and translocation processes aid the dissemination and persistence of important antimicrobial resistance genes, such as poxtA, among enterococci.
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Affiliation(s)
- Xinxin Shan
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Xin-Sheng Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Nannan Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Su-Mei Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Dexi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Xiang-Dang Du
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
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Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria. Clin Microbiol Rev 2021; 34:e0018820. [PMID: 34076490 DOI: 10.1128/cmr.00188-20] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [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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Linezolid Resistance Genes in Enterococci Isolated from Sediment and Zooplankton in Two Italian Coastal Areas. Appl Environ Microbiol 2021; 87:AEM.02958-20. [PMID: 33608287 DOI: 10.1128/aem.02958-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/08/2021] [Indexed: 12/19/2022] Open
Abstract
Linezolid is a last-resort antibiotic for the treatment of severe infections caused by multidrug-resistant Gram-positive organisms; although linezolid resistance remains uncommon, the number of linezolid-resistant enterococci has increased in recent years due to worldwide spread of acquired resistance genes (cfr, optrA, and poxtA) in clinical, animal, and environmental settings. In this study, we investigated the occurrence of linezolid-resistant enterococci in marine samples from two coastal areas in Italy. Isolates grown on florfenicol-supplemented Slanetz-Bartley agar plates were investigated for their carriage of optrA, poxtA, and cfr genes; optrA was found in one Enterococcus faecalis isolate, poxtA was found in three Enterococcus faecium isolates and two Enterococcus hirae isolates, and cfr was not found. Two of the three poxtA-carrying E. faecium isolates and the two E. hirae isolates showed related pulsed-field gel electrophoresis (PFGE) profiles. Two E. faecium isolates belonged to the new sequence type 1710, which clustered in clonal complex 94, encompassing nosocomial strains. S1 PFGE/hybridization assays showed a double (chromosome and plasmid) location of poxtA and a plasmid location of optrA Whole-genome sequencing revealed that poxtA was contained in a Tn6657-like element carried by two plasmids (pEfm-EF3 and pEh-GE2) of similar size, found in different species, and that poxtA was flanked by two copies of IS1216 in both plasmids. In mating experiments, all but one strain (E. faecalis EN3) were able to transfer the poxtA gene to E. faecium 64/3. The occurrence of linezolid resistance genes in enterococci from marine samples is of great concern and highlights the need to improve practices aimed at limiting the transmission of linezolid-resistant strains to humans from environmental reservoirs.IMPORTANCE Linezolid is one of the few antimicrobials available to treat severe infections due to drug-resistant Gram-positive bacteria; therefore, the emergence of linezolid-resistant enterococci carrying transferable resistance determinants is of great concern for public health. Linezolid resistance genes (cfr, optrA, and poxtA), often plasmid located, can be transmitted via horizontal gene transfer and have the potential to spread globally. This study highlights the detection of enterococci carrying linezolid resistance genes from sediment and zooplankton samples from two coastal urban areas in Italy. The presence of clinically relevant resistant bacteria, such as linezolid-resistant enterococci, in marine environments could reflect their spillover from human and/or animal reservoirs and could indicate that coastal seawaters also might represent a source of these resistance genes.
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Turner AM, Lee JYH, Gorrie CL, Howden BP, Carter GP. Genomic Insights Into Last-Line Antimicrobial Resistance in Multidrug-Resistant Staphylococcus and Vancomycin-Resistant Enterococcus. Front Microbiol 2021; 12:637656. [PMID: 33796088 PMCID: PMC8007764 DOI: 10.3389/fmicb.2021.637656] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/25/2021] [Indexed: 12/17/2022] Open
Abstract
Multidrug-resistant Staphylococcus and vancomycin-resistant Enterococcus (VRE) are important human pathogens that are resistant to most clinical antibiotics. Treatment options are limited and often require the use of 'last-line' antimicrobials such as linezolid, daptomycin, and in the case of Staphylococcus, also vancomycin. The emergence of resistance to these last-line antimicrobial agents is therefore of considerable clinical concern. This mini-review provides an overview of resistance to last-line antimicrobial agents in Staphylococcus and VRE, with a particular focus on how genomics has provided critical insights into the emergence of resistant clones, the molecular mechanisms of resistance, and the importance of mobile genetic elements in the global spread of resistance to linezolid.
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Affiliation(s)
- Adrianna M Turner
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Claire L Gorrie
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Department of Infectious Diseases, Austin Health, Melbourne, VIC, Australia
| | - Glen P Carter
- Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia.,Antimicrobial Reference and Research Unit, Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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21
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Jung YH, Cha MH, Woo GJ, Chi YM. Characterization of oxazolidinone and phenicol resistance genes in non-clinical enterococcal isolates from Korea. J Glob Antimicrob Resist 2021; 24:363-369. [PMID: 33515778 DOI: 10.1016/j.jgar.2021.01.009] [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: 02/29/2020] [Revised: 11/29/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES To investigate the distribution and genetic characteristics of linezolid-resistant enterococci. METHODS Enterococcus faecalis and Enterococcus faecium strains were isolated from pigs, equipment, grounds, and employees of 19 Korean swine farms in 2017. Antimicrobial susceptibility testing was then performed and linezolid resistance genes were detected via PCR. For genetic epidemiological characterization, multilocus sequence typing and whole-genome sequencing data were analysed. RESULTS Twenty-eightE. faecalis and five E. faecium strains were isolated from 1026 samples obtained from the 19 farms. Ten sequence types were identified among the E. faecalis strains, of which ST256 (42.9%) and ST86 (25%) were the most abundant. The oxazolidinone and phenicol resistance genes poxtA, optrA, and fexA were detected in isolates of E. faecalis (100%, 85.7%, and 67.9%, respectively) and E. faecium (100%, 60%, and 80%, respectively). The minimum inhibitory concentrations of linezolid in these isolates ranged from 2 mg/L to 12 mg/L. The whole-genome sequencing data indicated that fexA was located upstream of poxtA. CONCLUSIONS This is the first study to report the detection of poxtA in isolates that were both susceptible and resistant to linezolid in Korea. These results demonstrate the importance of antimicrobial resistance monitoring programmes, including regular antimicrobial susceptibility testing and resistance gene expression analysis, to facilitate the control of the spread of antibiotic resistance in non-clinical settings in Korea.
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Affiliation(s)
- Young-Hee Jung
- Division of Biotechnology, College of Life Sciences, Korea University, Seoul, 02841, Republic of Korea
| | - Min-Hyeok Cha
- Laboratory of Food Safety and Evaluation, Department of Biotechnology, Korea University Graduate School, Seoul, 02841, Republic of Korea
| | - Gun-Jo Woo
- Laboratory of Food Safety and Evaluation, Department of Biotechnology, Korea University Graduate School, Seoul, 02841, Republic of Korea.
| | - Young-Min Chi
- Division of Biotechnology, College of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
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Wu C, Zhang X, Liang J, Li Q, Lin H, Lin C, Liu H, Zhou D, Lu W, Sun Z, Lin X, Zhang H, Li K, Xu T, Bao Q, Lu J. Characterization of florfenicol resistance genes in the coagulase-negative Staphylococcus (CoNS) isolates and genomic features of a multidrug-resistant Staphylococcus lentus strain H29. Antimicrob Resist Infect Control 2021; 10:9. [PMID: 33413633 PMCID: PMC7791814 DOI: 10.1186/s13756-020-00869-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
Background With the wide use of florfenicol to prevent and treat the bacterial infection of domestic animals, the emergence of the florfenicol resistance bacteria is increasingly serious. It is very important to elucidate the molecular mechanism of the bacteria’s resistance to florfenicol. Methods The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method, and polymerase chain reaction was conducted to analyze the distribution of florfenicol resistance genes in 39 CoNS strains isolated from poultry and livestock animals and seafood. The whole genome sequence of one multidrug resistant strain, Staphylococcus lentus H29, was characterized, and comparative genomics analysis of the resistance gene-related sequences was also performed. Results As a result, the isolates from the animals showed a higher resistance rate (23/28, 82.1%) and much higher MIC levels to florfenicol than those from seafood. Twenty-seven animal isolates carried 37 florfenicol resistance genes (including 26 fexA, 6 cfr and 5 fexB genes) with one carrying a cfr gene, 16 each harboring a fexA gene, 5 with both a fexA gene and a fexB gene and the other 5 with both a fexA gene and a cfr gene. On the other hand, all 11 isolates from seafood were sensitive to florfenicol, and only 3 carried a fexA gene each. The whole genome sequence of S. lentus H29 was composed of a chromosome and two plasmids (pH29-46, pH29-26) and harbored 11 resistance genes, including 6 genes [cfr, fexA, ant(6)-Ia, aacA-aphD, mecA and mph(C)] encoded on the chromosome, 4 genes [cfr, fexA, aacA-aphD and tcaA] on pH29-46 and 1 gene (fosD) on pH29-26. We found that the S. lentus H29 genome carried two identical copies of the gene arrays of radC-tnpABC-hp-fexA (5671 bp) and IS256-cfr (2690 bp), of which one copy of the two gene arrays was encoded on plasmid pH29-46, while the other was encoded on the chromosome. Conclusions The current study revealed the wide distribution of florfenicol resistance genes (cfr, fexA and fexB) in animal bacteria, and to the best of our knowledge, this is the first report that one S. lentus strain carried two identical copies of florfenicol resistance-related gene arrays.
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Affiliation(s)
- Chongyang Wu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.,Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xueya Zhang
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jialei Liang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Qiaoling Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hailong Lin
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Chaoqin Lin
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hongmao Liu
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Danying Zhou
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Wei Lu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Zhewei Sun
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Xi Lin
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Kewei Li
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, 014040, China.
| | - Qiyu Bao
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.
| | - Junwan Lu
- School of Laboratory Medicine and Life Science/Institute of Biomedical Informatics, Wenzhou Medical University, Chashan University Town, Wenzhou, 325035, Zhejiang, China.
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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: 21] [Impact Index Per Article: 5.3] [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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Ruiz-Ripa L, Feßler AT, Hanke D, Eichhorn I, Azcona-Gutiérrez JM, Alonso CA, Pérez-Moreno MO, Aspiroz C, Bellés A, Schwarz S, Torres C. Mechanisms of Linezolid Resistance Among Clinical Staphylococcus spp. in Spain: Spread of Methicillin- and Linezolid-Resistant S. epidermidis ST2. Microb Drug Resist 2020; 27:145-153. [PMID: 32456543 DOI: 10.1089/mdr.2020.0122] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This study aimed at determining the mechanisms of linezolid resistance and the molecular characteristics of clinical Staphylococcus aureus (n = 2) and coagulase-negative staphylococci (n = 15) isolates obtained from four Spanish hospitals. The detection of linezolid resistance mechanisms (mutations and acquisition of resistance genes) was performed by PCR/sequencing. The antimicrobial resistance and virulence profile was determined, and the isolates were typed by different molecular techniques. Moreover, the genetic environment of the cfr gene was determined by whole-genome sequencing. The cfr gene was detected in one methicillin-resistant S. aureus (MRSA) that also displayed the amino acid change Val118Ala in the ribosomal protein L4. The second S. aureus isolate was methicillin susceptible and showed different alterations in the ribosomal protein L4. All remaining linezolid-resistant Staphylococcus epidermidis (n = 14) and Staphylococcus hominis isolates (n = 1) showed the mutation G2576T (n = 14) or C2534T (n = 1) in the 23S rRNA. Moreover, different amino acid changes were detected in the ribosomal proteins L3 and L4 in S. epidermidis isolates. All S. epidermidis isolates belonged to the multilocus sequence type ST2. Linezolid-resistant staphylococci (LRS) showed a multiresistance phenotype, including methicillin resistance that was detected in all isolates but one, and was mediated by the mecA gene. The cfr gene in the MRSA isolate was located together with the fexA gene on a conjugative 38,864 bp plasmid. Linezolid- and methicillin-resistant S. epidermidis ST2 showing mutations in the 23S rRNA and in the ribosomal proteins L3 and L4 are spread among Spanish hospitals, whereas LRS carrying acquired linezolid resistance genes are rarely detected.
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Affiliation(s)
- Laura Ruiz-Ripa
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | | | | | - Carmen Aspiroz
- Servicio Microbiología, Hospital Royo-Villanova, Zaragoza, Spain
| | - Alba Bellés
- Sección Microbiología, Hospital Universitari Arnau Vilanova, Lleida, Spain
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
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IS 26 Family Members IS 257 and IS 1216 Also Form Cointegrates by Copy-In and Targeted Conservative Routes. mSphere 2020; 5:5/1/e00811-19. [PMID: 31915227 PMCID: PMC6952201 DOI: 10.1128/msphere.00811-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
IS26 differs from other studied ISs in the reactions that it can undertake. The differences make IS26 uniquely suited to its key role in the recruitment and spread of antibiotic resistance genes in Gram-negative bacteria. However, whether other ISs in the IS6/IS26 family can perform the same reactions is not known. IS257/IS431 and IS1216 isoforms found associated with antibiotic resistance genes in the Gram-positive bacteria staphylococci, enterococci, streptococci, and clostridia are related to IS26. However, the way that they move had not been investigated, limiting interpretation of their role in resistance gene dissemination and in the formation of cointegrates and complex resistance regions in staphylococci and enterococci. Here, they are shown to share the broad catalytic capabilities of IS26, demonstrating that it is likely that all members of the redefined IS6/IS26 family of bacterial ISs likewise are able to use both the copy-in and conservative routes. IS26 has been shown to form cointegrates both by a copy-in mechanism involving one insertion sequence (IS) and a target and by a targeted conservative mechanism involving two ISs. IS26 is the flagship of a group of 65 bacterial ISs in the recently redefined IS6/IS26 family. Here, whether other family members can also use two mechanisms was examined using members of the IS257/IS431 and IS1216 isoform groups, which are associated with antibiotic resistance genes in staphylococci and enterococci, respectively. Transposases Tnp257 and Tnp1216 have 39% and 47% amino acid identities, respectively, with Tnp26 and are 62% identical to one another. Using a novel transposition assay, pUC-based plasmids carrying these ISs integrated into the chromosome of a temperature-sensitive polAEscherichia coli strain grown at the restrictive temperature. In the cointegrates, the plasmid carrying IS257 was flanked by various 8-bp target site duplications, consistent with random target selection. However, in a mating-out assay, only the targeted conservative reaction was detectable at a low frequency in a recA-negative E. coli strain, indicating that IS257 is at least 100-fold less active than IS26. For IS1216, in mating-out assays, both copy-in and targeted conservative cointegrate formation were detectable at frequencies similar to those observed for IS26. Duplication of various 8-bp target sites was detected for the copy-in route. For both IS257 and IS1216, when both of the plasmids carried an IS, the targeted conservative route occurred at a significantly higher frequency than the copy-in route, and only cointegrates formed by the conservative route were detected. IMPORTANCE IS26 differs from other studied ISs in the reactions that it can undertake. The differences make IS26 uniquely suited to its key role in the recruitment and spread of antibiotic resistance genes in Gram-negative bacteria. However, whether other ISs in the IS6/IS26 family can perform the same reactions is not known. IS257/IS431 and IS1216 isoforms found associated with antibiotic resistance genes in the Gram-positive bacteria staphylococci, enterococci, streptococci, and clostridia are related to IS26. However, the way that they move had not been investigated, limiting interpretation of their role in resistance gene dissemination and in the formation of cointegrates and complex resistance regions in staphylococci and enterococci. Here, they are shown to share the broad catalytic capabilities of IS26, demonstrating that it is likely that all members of the redefined IS6/IS26 family of bacterial ISs likewise are able to use both the copy-in and conservative routes.
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