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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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Wang Z, Fu Y, Zheng YL, Jiang N, Jiang H, Wu C, Lv Z, Krüger-Haker H, Feßler AT, Schwarz S, Wang Y. Fate of florfenicol and linezolid resistance genes and their bacterial hosts during two waste treatment models in swine feedlots. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 939:173645. [PMID: 38821272 DOI: 10.1016/j.scitotenv.2024.173645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/16/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
Florfenicol resistance genes (FRGs) are widely present in livestock farms. The aim of this study was to evaluate the removal efficiencies of FRGs as well as the relationships between FRGs, mobile genetic elements (MGEs) and bacterial communities during the natural drying (ND) and anaerobic digestion (AD) processes of manure treatment in swine farms by combining bacterial isolation, quantitative PCR and metagenomic approaches. Solid manure showed a higher abundance of FRGs than fresh manure and was the main contamination source of fexA and fexB in ND farms, whilst biogas slurry displayed a lower abundance of FRGs than the wastewater in AD farms. Moreover, fresh manure and wastewater showed a high abundance of optrA, and wastewater was the main contamination source of cfr in both ND and AD farms. Both optrA/fexA-positive enterococci and cfr/fexA-positive staphylococci were mainly isolated along the farms' treatment processes. The cfr-positive staphylococci were highly prevalent in wastewater (57.14 % - 100 %) and may be associated with nasal-derived cfr-positive porcine staphylococci. An increased abundance of Enterococcus, Jeotgalibaca and Vagococcus in the bacterial community structures may account for the high optrA abundance in wastewater and Jeotgalibaca may be another potential host of optrA. Furthermore, the abundance of FRG-related MGEs increased by 22.63 % after the ND process and decreased by 66.96 % in AD farms. A significant correlation was observed between cfr and ISEnfa4, whereas no significance was found between optrA and IS1216E, although IS1216E is the predominant insertion sequence involved in the transfer of optrA. In conclusion, manure and wastewater represented independent pollution sources of FRGs in swine farms. Associated MGEs might play a key role in the transfer and persistence of FRGs. The AD process was more efficient in the removal of FRGs than the ND method, nevertheless a longer storage of slurry may be required for a complete removal.
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Affiliation(s)
- Zheng Wang
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China.
| | - Yulin Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; Central Laboratory Department, Shenzhen Centre for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yong-Liang Zheng
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, China
| | - Nansong Jiang
- Research Center for Poultry Diseases of Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Haiyang Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ziquan Lv
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Henrike Krüger-Haker
- Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Stefan Schwarz
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China; Institute of Microbiology and Epizootics, Center for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre for Resistance Research, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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Zaidi SEZ, Zaheer R, Zovoilis A, McAllister TA. Enterococci as a One Health indicator of antimicrobial resistance. Can J Microbiol 2024; 70:303-335. [PMID: 38696839 DOI: 10.1139/cjm-2024-0024] [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: 05/04/2024]
Abstract
The rapid increase of antimicrobial-resistant bacteria in humans and livestock is concerning. Antimicrobials are essential for the treatment of disease in modern day medicine, and their misuse in humans and food animals has contributed to an increase in the prevalence of antimicrobial-resistant bacteria. Globally, antimicrobial resistance is recognized as a One Health problem affecting humans, animals, and environment. Enterococcal species are Gram-positive bacteria that are widely distributed in nature. Their occurrence, prevalence, and persistence across the One Health continuum make them an ideal candidate to study antimicrobial resistance from a One Health perspective. The objective of this review was to summarize the role of enterococci as an indicator of antimicrobial resistance across One Health sectors. We also briefly address the prevalence of enterococci in human, animal, and environmental settings. In addition, a 16S RNA gene-based phylogenetic tree was constructed to visualize the evolutionary relationship among enterococcal species and whether they segregate based on host environment. We also review the genomic basis of antimicrobial resistance in enterococcal species across the One Health continuum.
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Affiliation(s)
- Sani-E-Zehra Zaidi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Athanasios Zovoilis
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- University of Manitoba, Department of Biochemistry and Medical Genetics, 745 Bannatyne Ave, Winnipeg
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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Yang Q, Li L, Zhao G, Cui Q, Gong X, Ying L, Yang T, Fu M, Shen Z. Characterization of a multiresistance optrA- and lsa(E)-harbouring unconventional circularizable structure in Streptococcus suis. J Antimicrob Chemother 2024:dkae250. [PMID: 39086116 DOI: 10.1093/jac/dkae250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
OBJECTIVES To identify novel genetic elements facilitating the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA and the pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Streptococcus suis. METHODS The complete genomes of S. suis HB18 and two transconjugants were obtained using both the Illumina and Nanopore platforms. MICs were determined by broth microdilution. Inverse PCR was performed to identify circular forms of the novel unconventional circularizable structure (UCS), genomic island (GI) and integrative and conjugative element (ICE). Conjugation experiments assessed the transferability of optrA and lsa(E) genes in S. suis. RESULTS S. suis HB18 carried a multiresistance gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw. This gene cluster, flanked by intact and truncated erm(B) in the same orientation, resided on a novel ICESsuHB18. Inverse PCR revealed the existence of a novel UCS, named UCS-optrA + lsa(E), which could excise the gene cluster optrA-lsa(E)-lnu(B)-aphA-aadE-spw and one copy of erm(B) from ICESsuHB18. Two transconjugants with different characteristics were obtained. In transconjugant T-JH-GI, UCS-optrA + lsa(E) excised from ICESsuHB18 inserted into the erm(B)-positive GI, designated GISsuHB18, generating the novel GISsuHB18-1. Meanwhile, in T-JH-ICE, genetic rearrangement events occurred in ICESsuHB18 and GISsuHB18, forming the novel ICESsuHB18-1. CONCLUSIONS This is the first report demonstrating the functionally active UCS-optrA + lsa(E) excising from ICESsuHB18 and inserting into the erm(B)-positive GISsuHB18 during the conjugation process. The location of optrA and lsa(E) on a multiresistance UCS enhances its persistence and dissemination.
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Affiliation(s)
- Qin Yang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Luxin Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Guanzheng Zhao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Qingpo Cui
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaowei Gong
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Luyu Ying
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Tingting Yang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Mengjiao Fu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhangqi Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Song X, Zhong Z, Bai J, Pu T, Wang X, He H, Chen Y, Yang C, Zhang Q. Emergence of genetic diversity and multi-drug resistant Clostridium perfringens from wild birds. BMC Vet Res 2024; 20:300. [PMID: 38971814 PMCID: PMC11227187 DOI: 10.1186/s12917-024-04168-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Clostridium perfringens (C. perfringens) is an important zoonotic microorganism that can cause animal and human infections, however information about the prevalence status in wild birds of this pathogenic bacterium is currently limited. RESULT In this study, 57 strains of C. perfringens were isolated from 328 fecal samples of wild birds. All the isolates were identified as type A and 70.18% of the isolates carried the cpb2 gene. Antimicrobial susceptibility testing showed that and 22.80% of the isolates were classified as multidrug-resistant strains. The MLST analysis of the 57 isolates from wild birds was categorized into 55 different sequence types (STs) and clustered into eight clonal complexes (CCs) with an average of 20.1 alleles and the Simpson Diversity index (Ds) of 0.9812, and revealed a high level of genetic diversity within the C. perfringens populations. Interestingly, the isolates from swan goose were clustered in the same CC while isolates from other bird species were more scattered suggesting that a potential difference in genetic diversity among the C. perfringens populations associated with different bird species. CONCLUSION C. perfringens exhibits a wide range of host adaptations, varying degrees of antimicrobial resistance, and a high degree of genetic diversity in wild birds. Understanding the prevalence, toxin type, antimicrobial resistance, and genetic diversity of C. perfringens in wildlife populations is essential for developing effective strategies for disease control and management.
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Affiliation(s)
- Xinglong Song
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Beijing Milu Ecological Research Center, Beijing Academy of Science and Technology, Beijing, China
| | - Zhenyu Zhong
- Beijing Milu Ecological Research Center, Beijing Academy of Science and Technology, Beijing, China
| | - Jiade Bai
- Beijing Milu Ecological Research Center, Beijing Academy of Science and Technology, Beijing, China
| | - Tianchun Pu
- Beijing Key Laboratory of Captive Wildlife Technologies in Beijing Zoo, Beijing, China
| | - Xuehan Wang
- School of Biomedicine, Beijing City University, Beijing, China
| | - Hongxuan He
- National Research Center for Wildlife-Born Diseases, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yaqian Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Congshan Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.
| | - Qingxun Zhang
- Beijing Milu Ecological Research Center, Beijing Academy of Science and Technology, Beijing, China.
- School of Biomedicine, Beijing City University, Beijing, China.
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing. Nucleic Acids Res 2024:gkae528. [PMID: 38909293 DOI: 10.1093/nar/gkae528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Melanie B Prentice
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Gene S Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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Abdullahi IN, Lozano C, Zarazaga M, Latorre-Fernández J, Hallstrøm S, Rasmussen A, Stegger M, Torres C. Genomic Characterization and Phylogenetic Analysis of Linezolid-Resistant Enterococcus from the Nostrils of Healthy Hosts Identifies Zoonotic Transmission. Curr Microbiol 2024; 81:225. [PMID: 38877167 PMCID: PMC11178607 DOI: 10.1007/s00284-024-03737-2] [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: 02/13/2024] [Accepted: 05/08/2024] [Indexed: 06/16/2024]
Abstract
Linezolid resistance in Enterococcus spp. is increasingly considered critically important and a public health threat which mandates the need to understand their genomic contents and dissemination patterns. Here, we used whole-genome sequencing to characterize the resistome, virulome and mobile genetic elements of nine linezolid-resistant (LZDR) enterococci (seven optrA-E. faecalis, one poxtA-E. faecium and one optrA-E. casseliflavus) previously obtained from the nares of healthy dogs, pigs, pig farmers and tracheal samples of nestling storks in Spain. Also, the relatedness of the isolates with publicly available genomes was accessed by core-genome single nucleotide polymorphism (SNP) analysis. The optrA gene of the E. faecalis and E. casseliflavus isolates was located downstream of the fexA gene. The optrA gene in the E. casseliflavus isolate was carried in a plasmid (pURX4962), while those in the seven E. faecalis isolates were chromosomally located. The OptrA proteins were mostly variants of wild type (DP-2: Y176D/T481P; RDK: I104R/Y176D/E256K; DD-3: Y176D/G393D; and EDD: K3E/Y176D/G393D), except two that were wild type (one E. faecalis and one E. casseliflavus). The poxtA gene in the E. faecium isolate was found alone within its contig. The cfrD was upstream of ermB gene in the E. casseliflavus isolate and flanked by ISNCY and IS1216. All the LZDR enterococci carried plasmid rep genes (2-3) containing tetracycline, chloramphenicol and aminoglycoside resistance genes. All isolates except E. casseliflavus carried at least one intact prophage, of which E. faecalis-ST330 (X4957) from a pig carried the highest (n = 5). Tn6260 was associated with lnuG in E. faecalis-ST330 while Tn554 was with fexA in E. feaecalis-ST59 isolates. All except E. casseliflavus (n = 0) carried at least two metal resistance genes (MRGs), of which poxtA-carrying E. faecium-ST1739 isolate contained the most (arsA, copA, fief, ziaA, znuA, zosA, zupT, and zur). SNP-based analyses identified closely related optrA-E. faecalis isolates from a pig and a pig farmer on the same farm (SNP = 4). Moreover, optrA- carrying E. faecalis-ST32, -ST59, and -ST474 isolates from pigs were related to those previously described from humans (sick and healthy) and cattle in Spain, Belgium, and Switzerland (SNP range 43-86). These findings strongly suggest the transmission of LZDR-E. faecalis between a pig and a pig farmer and potential inter-country dissemination. These highlight the need to strengthen molecular surveillance of LZDR enterococci in all ecological niches and body parts to direct appropriate control strategies.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, College of Medical Sciences, Ahmadu Bello University, PMB 05 , Zaria, Nigeria
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| | - Javier Latorre-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
| | - Søren Hallstrøm
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute, Copenhagen, Denmark
| | - Astrid Rasmussen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institute, Copenhagen, Denmark
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, Australia
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
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Fujii A, Kawada-Matsuo M, Nguyen-Tra Le M, Masuda K, Tadera K, Suzuki Y, Nishihama S, Hisatsune J, Sugawara Y, Kashiyama S, Shiba H, Aikawa T, Ohge H, Sugai M, Komatsuzawa H. Antibiotic susceptibility and genome analysis of Enterococcus species isolated from inpatients in one hospital with no apparent outbreak of vancomycin-resistant Enterococcus in Japan. Microbiol Immunol 2024. [PMID: 38873884 DOI: 10.1111/1348-0421.13155] [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: 01/17/2024] [Revised: 05/02/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
To prevent nosocomial infection, it is important to screen for potential vancomycin-resistant Enterococcus (VRE) among patients. In this study, we analyzed enterococcal isolates from inpatients in one hospital without any apparent outbreak of VRE. Enterococcal isolates were collected from inpatients at Hiroshima University Hospital from April 1 to June 30, 2021 using selective medium for Enterococci. Multilocus sequence typing, antimicrobial susceptibility testing, and whole-genome sequencing were performed. A total of 164 isolates, including Enterococcus faecium (41 isolates), Enterococcus faecalis (80 isolates), Enterococcus raffinosus (11 isolates), Enterococcus casseliflavus (nine isolates), Enterococcus avium (12 isolates), Enterococcus lactis (eight isolates), Enterococcus gallinarum (two isolates), and Enterococcus malodoratus (one isolate), were analyzed. We found one vanA-positive E. faecium, which was already informed when the patient was transferred to the hospital, nine vanC-positive E. casseliflavus, and two vanC-positive E. gallinarum. E. faecium isolates showed resistance to ampicillin (95.1%), imipenem (95.1%), and levofloxacin (87.8%), and E. faecalis isolates showed resistance to minocycline (49.4%). Ampicillin- and levofloxacin-resistant E. faecium had multiple mutations in penicillin-binding protein 5 (PBP5) (39/39 isolates) and ParC/GyrA (21/36 isolates), respectively. E. raffinosus showed resistance to ampicillin (81.8%), imipenem (45.5%), and levofloxacin (45.5%), and E. lactis showed resistance to ampicillin (37.5%) and imipenem (50.0%). The linezolid resistance genes optrA and cfr(B) were found only in one isolate of E. faecalis and E. raffinosus, respectively. This study, showing the status of enterococci infection in hospitalized patients, is one of the important information when considering nosocomial infection control of VRE.
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Affiliation(s)
- Ayumi Fujii
- Department of Oral and Maxillofacial Surgery, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Miki Kawada-Matsuo
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Mi Nguyen-Tra Le
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Kanako Masuda
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Kayoko Tadera
- Section of Clinical Laboratory, Division of Clinical Support, Hiroshima University Hospital, Hiroshima, Japan
| | - Yujin Suzuki
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Saki Nishihama
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Junzo Hisatsune
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashi Murayama, Japan
| | - Yo Sugawara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashi Murayama, Japan
| | - Seiya Kashiyama
- Section of Clinical Laboratory, Division of Clinical Support, Hiroshima University Hospital, Hiroshima, Japan
| | - Hideki Shiba
- Department of Biological Endodontics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomonao Aikawa
- Department of Oral and Maxillofacial Surgery, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashi Murayama, Japan
| | - Hitoshi Komatsuzawa
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
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9
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Mullally CA, Fahriani M, Mowlaboccus S, Coombs GW. Non- faecium non- faecalis enterococci: a review of clinical manifestations, virulence factors, and antimicrobial resistance. Clin Microbiol Rev 2024; 37:e0012123. [PMID: 38466110 PMCID: PMC11237509 DOI: 10.1128/cmr.00121-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
SUMMARYEnterococci are a diverse group of Gram-positive bacteria that are typically found as commensals in humans, animals, and the environment. Occasionally, they may cause clinically relevant diseases such as endocarditis, septicemia, urinary tract infections, and wound infections. The majority of clinical infections in humans are caused by two species: Enterococcus faecium and Enterococcus faecalis. However, there is an increasing number of clinical infections caused by non-faecium non-faecalis (NFF) enterococci. Although NFF enterococcal species are often overlooked, studies have shown that they may harbor antimicrobial resistance (AMR) genes and virulence factors that are found in E. faecium and E. faecalis. In this review, we present an overview of the NFF enterococci with a particular focus on human clinical manifestations, epidemiology, virulence genes, and AMR genes.
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Affiliation(s)
- Christopher A Mullally
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Marhami Fahriani
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
| | - Shakeel Mowlaboccus
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Geoffrey W Coombs
- Antimicrobial Resistance and Infectious Diseases (AMRID) Research Laboratory, Murdoch University, Murdoch, Western Australia, Australia
- The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- PathWest Laboratory Medicine-WA, Department of Microbiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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10
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Hou J, Xu Q, Zhou L, Chai J, Lin L, Ma C, Zhu Y, Zhang W. Identification of an Enterococcus faecium strain isolated from raw bovine milk co-harbouring the oxazolidinone resistance genes optrA and poxtA in China. Vet Microbiol 2024; 293:110103. [PMID: 38718528 DOI: 10.1016/j.vetmic.2024.110103] [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: 02/05/2024] [Revised: 04/23/2024] [Accepted: 05/01/2024] [Indexed: 05/15/2024]
Abstract
Oxazolidinones are potent antimicrobial agents used to treat human infections caused by multidrug-resistant Gram-positive bacteria. The growing resistance to oxazolidinones poses a significant threat to public health. In August 2021, a linezolid-resistant Enterococcus faecium BN83 was isolated from a raw milk sample of cow in Inner Mongolia, China. This isolate exhibited a multidrug resistance phenotype and was resistant to most of drugs tested including linezolid and tedizolid. PCR detection showed that two mobile oxazolidinones resistance genes, optrA and poxtA, were present in this isolate. Whole genome sequencing analysis revealed that the genes optrA and poxtA were located on two different plasmids, designated as pBN83-1 and pBN83-2, belonging to RepA_N and Inc18 families respectively. Genetic context analysis suggested that optrA gene on plasmid pBN83-1 was located in transposon Tn6261 initially found in E. faecalis. Comprehensive analysis revealed that Tn6261 act as an important horizontal transmission vector for the spread of optrA in E. faecium. Additionally, poxtA-bearing pBN83-2 displayed high similarity to numerous plasmids from Enterococcus of different origin and pBN83-2-like plasmid represented a key mobile genetic element involved in movement of poxtA in enterococcal species. The presence of optrA- and poxtA-carrying E. faecium in raw bovine milk represents a public health concern and active surveillance is urgently warranted to investigate the prevalence of oxazolidinone resistance genes in animal-derived food products.
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Affiliation(s)
- Jie Hou
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Qiu Xu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Longyu Zhou
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jiyun Chai
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Longhua Lin
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Caiping Ma
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Yao Zhu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Wanjiang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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11
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Wang L, Li F, Liu T, Ouyang C, Wang X, Li M, Huang Z, Huang J, Wang L, Wang X. Identification of a multidrug resistance genomic island harboring a nonfunctional optrA gene in Campylobacter coli of chicken origin. Vet Microbiol 2024; 293:110083. [PMID: 38593623 DOI: 10.1016/j.vetmic.2024.110083] [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: 10/26/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
Campylobacter spp., such as Campylobacter jejuni and Campylobacter coli, are important zoonotic Gram-negative pathogens that cause acute intestinal diseases in humans. In this study, a retrospective analysis was conducted on previously collected Campylobacter isolates from antimicrobial resistance surveillance. A total of 29 optrA-positive C. coli strains were identified and subjected to second-generation sequencing. Multilocus sequence typing and single nucleotide polymorphism analyses demonstrated that the 29 optrA-positive isolates were genetically homogeneous. Notably, among the 29 isolated strains, the ΔoptrA variants exhibit a nonsense mutation at position 979 where the base C is substituted by T, leading to the formation of a premature termination codon. The alignment of sequences and genetic environmental characteristics suggested that ΔoptrA located on a chromosomally carried multidrug-resistant genomic island. There are other resistant genes on the multidrug resistance genomic island, such as aph(2'')-If, aph(3')-III, aadE, tet(O), tet(L), cat, erm(A), optrA and blaOXA-61. As a result, the 29 ΔoptrA-positive strains displayed susceptibility to both florfenicol and linezolid. The ΔoptrA gene is linked to the erm(A) gene, resulting in the formation of translocatable unit (TU) that are encompassed by two copies of IS1216 mobile elements. Multiple occurrences of similar TUs have been documented in numerous C. coli and provided evidence for the significance of TUs in facilitating the transfer of drug resistance genes in C. coli.
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Affiliation(s)
- Liangliang Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Fan Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Chen Ouyang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyue Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Meifang Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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12
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Chen C, Li D, Shang Y, Lin Z, Wen Z, Li P, Yu Z, Chen Z, Liu X. Antibacterial Activity and Mechanism of Candesartan Cilexetil against Enterococcus faecalis. ACS OMEGA 2024; 9:21510-21519. [PMID: 38764675 PMCID: PMC11097336 DOI: 10.1021/acsomega.4c02153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
Enterococcus faecalis infections pose a significant clinical challenge due to their multidrug resistance and propensity for biofilm formation. Exploring alternative treatment options, such as repurposing existing drugs, is crucial in addressing this issue. This study investigates the antibacterial activity of candesartan cilexetil against E. faecalis and elucidates its mechanism of action. Candesartan cilexetil exhibited notable antibacterial activity against both E. faecalis and Enterococcus faecium, with minimum inhibitory concentration (MIC) of ≤25 μM. Time-kill curves demonstrated concentration-dependent bactericidal effects. Candesartan cilexetil could significantly inhibited biofilm formation at the concentration of 1/4× MIC and induced alterations in biofilm structure. Permeability assays revealed compromised bacterial membranes, accompanied by the dissipation of membrane potential in E. faecalis cells after treatment with candesartan cilexetil. Checkerboard analysis showed that bacterial membrane phospholipids phosphatidylglycerol and cardiolipin could neutralize the antibacterial activity of candesartan cilexetil in a dose-dependent manner. Biolayer interferometry (BLI) assay indicated specific interactions between candesartan cilexetil and phosphatidylglycerol or cardiolipin. This study demonstrates the promising antibacterial and antibiofilm activities of candesartan cilexetil against multidrug-resistant E. faecalis. The mechanism of action involves disruption of bacterial membranes, possibly by interacting with membrane phospholipids. These findings underscore the potential utility of candesartan cilexetil as an effective therapeutic agent for combating E. faecalis infections, offering a valuable strategy in the battle against antibiotic-resistant pathogens.
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Affiliation(s)
| | | | | | | | - Zewen Wen
- Department of Infectious
Diseases and Shenzhen Key Laboratory for Endogenous Infections, Huazhong University of Science and Technology Union
Shenzhen Hospital, No. 89 Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Peiyu Li
- Department of Infectious
Diseases and Shenzhen Key Laboratory for Endogenous Infections, Huazhong University of Science and Technology Union
Shenzhen Hospital, No. 89 Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Zhijian Yu
- Department of Infectious
Diseases and Shenzhen Key Laboratory for Endogenous Infections, Huazhong University of Science and Technology Union
Shenzhen Hospital, No. 89 Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Zhong Chen
- Department of Infectious
Diseases and Shenzhen Key Laboratory for Endogenous Infections, Huazhong University of Science and Technology Union
Shenzhen Hospital, No. 89 Taoyuan Road, Nanshan District, Shenzhen 518052, China
| | - Xiaoju Liu
- Department of Infectious
Diseases and Shenzhen Key Laboratory for Endogenous Infections, Huazhong University of Science and Technology Union
Shenzhen Hospital, No. 89 Taoyuan Road, Nanshan District, Shenzhen 518052, China
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13
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Wang Z, Liu D, Zhang J, Liu L, Zhang Z, Liu C, Hu S, Wu L, He Z, Sun H. Genomic epidemiology reveals multiple mechanisms of linezolid resistance in clinical enterococci in China. Ann Clin Microbiol Antimicrob 2024; 23:41. [PMID: 38704577 PMCID: PMC11070108 DOI: 10.1186/s12941-024-00689-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/21/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Infections caused by linezolid-resistant enterococci (LRE) are clinically difficult to treat and threaten patient health. However, there is a lack of studies on long time-span LRE strains in China. For this reason, our study comprehensively revealed the resistance mechanisms of LRE strains collected in a Chinese tertiary care hospital from 2011 to 2022. METHODS Enterococcal strains were screened and verified after retrospective analysis of microbial data. Subsequently, 65 LRE strains (61 Enterococcus faecalis and 4 Enterococcus faecium, MIC ≥ 8 µg/ml), 1 linezolid-intermediate Enterococcus faecium (MIC = 4 µg/ml) and 1 linezolid-susceptible Enterococcus faecium (MIC = 1.5 µg/ml) were submitted for whole-genome sequencing (WGS) analysis and bioinformatics analysis. RESULTS The optrA gene was found to be the most common linezolid resistance mechanism in our study. We identified the wild-type OptrA and various OptrA variants in 98.5% of LRE strains (61 Enterococcus faecalis and 3 Enterococcus faecium). We also found one linezolid-resistant Enterococcus faecium strain carried both optrA and cfr(D) gene, while one linezolid-resistant Enterococcus faecium only harbored the poxtA gene. Most optrA genes (55/64) were located on plasmids, with impB-fexA-optrA, impB-fexA-optrA-erm(A), fexA-optrA-erm(A), and fexA-optrA segments. A minority of optrA genes (9/64) were found on chromosomes with the Tn6674-like platform. Besides, other possible linezolid resistance-associated mechanisms (mutations in the rplC and rplD genes) were also found in 26 enterococcal strains. CONCLUSIONS Our study suggested that multiple mechanisms of linezolid resistance exist among clinical LRE strains in China.
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Affiliation(s)
- Ziran Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China
| | - Danping Liu
- School of Engineering Medicine, Beihang University, Rd37, xueyuan, Haidian, Beijing, 100191, P.R. China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People's Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China
| | - Lingli Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China
| | - Zeming Zhang
- School of Engineering Medicine, Beihang University, Rd37, xueyuan, Haidian, Beijing, 100191, P.R. China
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People's Republic of China, Beijing, China
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China
| | - Chang Liu
- Department of Clinical Laboratory, Beijing Huaxin Hospital, The First Hospital of Tsinghua University, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Linhuan Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zilong He
- School of Engineering Medicine, Beihang University, Rd37, xueyuan, Haidian, Beijing, 100191, P.R. China.
- Key Laboratory of Big Data-Based Precision Medicine, Beihang University, Ministry of Industry and Information Technology of the People's Republic of China, Beijing, China.
- Key Laboratory of Biomechanics and Mechanobiology, Beihang University, Ministry of Education, Beijing, China.
| | - Hongli Sun
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing, Dongcheng, Beijing, 100730, P.R. China.
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14
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Cai Y, Chen C, Sun T, Li G, Wang W, Zhao H, An T. Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome. ENVIRONMENT INTERNATIONAL 2024; 187:108704. [PMID: 38692150 DOI: 10.1016/j.envint.2024.108704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
With the rapid growth of aquaculture globally, large amounts of antibiotics have been used to treat aquatic disease, which may accelerate induction and spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquaculture environments. Herein, metagenomic and 16S rRNA analyses were used to analyze the potentials and co-occurrence patterns of pathogenome (culturable and unculturable pathogens), antibiotic resistome (ARGs), and mobilome (mobile genetic elements (MGEs)) from mariculture waters near 5000 km coast of South China. Total 207 species of pathogens were identified, with only 10 culturable species. Furthermore, more pathogen species were detected in mariculture waters than those in coastal waters, and mariculture waters were prone to become reservoirs of unculturable pathogens. In addition, 913 subtypes of 21 ARG types were also identified, with multidrug resistance genes as the majority. MGEs including plasmids, integrons, transposons, and insertion sequences were abundantly present in mariculture waters. The co-occurrence network pattern between pathogenome, antibiotic resistome, and mobilome suggested that most of pathogens may be potential multidrug resistant hosts, possibly due to high frequency of horizontal gene transfer. These findings increase our understanding of mariculture waters as reservoirs of antibiotic resistome and mobilome, and as yet another hotbed for creation and transfer of new antibiotic-resistant pathogenome.
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Affiliation(s)
- Yiwei Cai
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Chunliang Chen
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Tong Sun
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guiying Li
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wanjun Wang
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Huijun Zhao
- Centre for Clean Environment and Energy, and Griffith School of Environment, Gold Coast Campus, Griffith University, Queensland 4222, Australia
| | - Taicheng An
- Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Key Laboratory of City Cluster Environmental Safety and Green Development (Department of Education), School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
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15
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Yang Q, Wang X, Schwarz S, Zhu Y, Zhang W. Identification of ISVlu1-derived translocatable units containing optrA and/or fexA genes generated by homologous or illegitimate recombination in Lactococcus garvieae of porcine origin. Vet Microbiol 2024; 292:110048. [PMID: 38479301 DOI: 10.1016/j.vetmic.2024.110048] [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: 01/30/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/10/2024]
Abstract
The optrA gene encodes an ABC-F protein which confers cross-resistance to oxazolidinones and phenicols. Insertion sequence ISVlu1, a novel ISL3-family member, was recently reported to be involved in the transmission of optrA in Vagococcus lutrae. However, the role of ISVlu1 in mobilizing resistance genes has not yet fully explored. In this study, two complete and three truncated copies of ISVlu1 were found on plasmid pBN62-optrA from Lactococcus garvieae. Analysis of the genetic context showed that both optrA and the phenicols resistance gene fexA were flanked by the complete or truncated ISVlu1 copies. Moreover, three different-sized ISVlu1-based translocatable units (TUs) carrying optrA and/or fexA, were detected from pBN62-optrA. Sequence analysis revealed that the TU-optrA was generated by homologous recombination while TU-fexA and TU-optrA+fexA were the products of illegitimate recombinations. Importantly, conjugation assays confirmed that pBN62-optrA was able to successfully transfer into the recipient Enterococcus faecalis JH2-2. To our knowledge, this is the first report about an optrA-carrying plasmid in L. garvieae which could horizontally transfer into other species. More importantly, the ISVlu1-flanked genetic structures containing optrA and/or fexA were also observed in bacteria of different species, which underlines that ISVlu1 is highly active and plays a vital role in the transfer of some important resistance genes, such as optrA and fexA.
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Affiliation(s)
- Qin Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiumei Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany; Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Berlin 14163, Germany
| | - Yao Zhu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
| | - Wanjiang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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16
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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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Rani V, Aye NK, Saksena R, Dabi KC, Mannan MAU, Gaind R. Risk factors and outcome associated with the acquisition of MDR linezolid-resistant Enterococcus faecium: a report from tertiary care centre. Eur J Clin Microbiol Infect Dis 2024; 43:767-775. [PMID: 38372832 DOI: 10.1007/s10096-024-04784-0] [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: 01/07/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
OBJECTIVE The aim of the study was to determine the resistance profile of linezolid-resistant Enterococcus faecium (LREfm) and to investigate risk factors and outcomes associated with LREfm infections. MATERIAL AND METHODS A prospective case-control study was undertaken (2019 to 2022) and included 202 patients with LREfm infections (cases) and 200 controls with LSEfm infections. Clinical data was prospectively collected and analysed for risk factors and outcomes. Antimicrobial susceptibility was performed, and resistance profile was studied using WHOnet. RESULTS Risk factors associated with LREfm infection were site of infection UTI (OR 5.87, 95% CI 2.59-13.29, p ≤ 0.001), prior use of carbapenem (OR 2.85 95% CI 1.62-5.02, p ≤ 0.001) and linezolid (OR 10.13, 95% CI 4.13-24.82, p ≤ 0.001), use of central line (OR 5.54, 95% CI 2.35-13.09, p ≤ 0.001), urinary catheter (OR 0.29, 95% CI 0.12-0.70, p ≤ 0.001) and ventilation (OR 14.87, 95% CI 7.86-28.11, p ≤ 0.007). The hospital stay 8-14 days (< 0.001) prior to infection and the mortality rate (p = 0.003) were also significantly high among patients with LREfm infections. Linezolid and vancomycin resistance coexisted; further, MDR, XDR and PDR phenotypes were significantly higher among LREfm. CONCLUSION This study provided insight into epidemiology of MDR LREfm in a setting where linezolid use is high. The main drivers of infections with LREfm are multiple, including use of carbapenems and linezolid. Invasive procedures and increased hospital stay facilitate spread through breach in infection control practises. As therapeutic options are limited, ongoing surveillance of LREfm and VRE is critical to guide appropriate use of linezolid and infection control policies.
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Affiliation(s)
- Vandana Rani
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, 110029, India
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144422, India
| | - N Kitoi Aye
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, 110029, India
| | - Rushika Saksena
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, 110029, India
| | - Kailash Chandra Dabi
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, 110029, India
| | - Mohammad Amin-Ul Mannan
- Department of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144422, India.
- Division of Infectious Disease, The Lundquist Institute, UCLA Harbor Medical Center, Los Angeles, CA, 90502, USA.
| | - Rajni Gaind
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, 110029, India.
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Kardos G, Laczkó L, Kaszab E, Timmer B, Szarka K, Prépost E, Bányai K. Phylogeny of Transferable Oxazolidinone Resistance Genes and Homologs. Antibiotics (Basel) 2024; 13:311. [PMID: 38666987 PMCID: PMC11047308 DOI: 10.3390/antibiotics13040311] [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: 02/07/2024] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/29/2024] Open
Abstract
Oxazolidinone resistance, especially transmissible resistance, is a major public health concern, and the origin of this resistance mechanism is not yet resolved. This study aims to delve into the phylogenetic origin of the transmissible oxazolidinone resistance mechanisms conferring cross-resistance to other drugs of human and veterinary importance. The amino acid sequences of the five cfr ribosomal methylases and optrA and poxtA were used as queries in searches against 219,549 bacterial proteomes in the NCBI RefSeq database. Hits with >40% amino acid identity and >80% query coverage were aligned, and phylogenetic trees were reconstructed. All five cfr genes yielded highly similar trees, with rlmN housekeeping ribosomal methylases located basal to the sister groups of S-adenosyl-methionine-dependent methyltransferases from various Deltaproteobacteria and Actinomycetia, including antibiotic-producing Streptomyces species, and the monophyletic group of cfr genes. The basal branches of the latter contained paenibacilli and other soil bacteria; they then could be split into the clades [cfr(C):cfr(E)] and [[cfr:cfr(B)]:cfr(D)], always with different Bacillaceae in their stems. Lachnospiraceae were encountered in the basal branches of both optrA and poxtA trees. The ultimate origin of the cfr genes is the rlmN housekeeping ribosomal methylases, which evolved into a suicide-avoiding methylase in antibiotic producers; a soil organism (Lachnospiraceae, Paenibacilli) probably acted as a transfer organism into pathogenic bacteria. In the case of optrA, the porcine pathogenic Streptococcus suis was present in all branches, while the proteins closest to poxtA originated from Clostridia.
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Affiliation(s)
- Gábor Kardos
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
| | - Levente Laczkó
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
- HUN-REN-DE Conservation Biology Research Group, H-4032 Debrecen, Hungary
| | - Eszter Kaszab
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, H-1078 Budapest, Hungary
| | - Bálint Timmer
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- Department of Medical Microbiology and Immunology, University of Pécs, H-7624 Pécs, Hungary
| | - Krisztina Szarka
- Institute of Metagenomics, University of Debrecen, H-4032 Debrecen, Hungary; (B.T.); (K.S.)
- One Health Institute, Faculty of Health Sciences, University of Debrecen, H-4032 Debrecen, Hungary; (L.L.); (E.K.)
| | - Eszter Prépost
- Department of Health Industry, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Krisztián Bányai
- Pathogen Discovery Group, HUN-REN Veterinary Medical Research Institute, H-1143 Budapest, Hungary
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, H-1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, H-1078 Budapest, Hungary
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Xu J, Wang H, Xu R, Li Q, Li L, Su Y, Liu J, Zhu W. Daily fluctuation of Lactobacillus species and their antibiotic resistome in the colon of growing pigs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170821. [PMID: 38336077 DOI: 10.1016/j.scitotenv.2024.170821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
There are various types of bacteria inhabiting the intestine that help maintain the balance of the intestinal microbiota. Lactobacillus is one of the important beneficial bacteria and is widely used as a food starter and probiotic. In this study, we investigated the daily fluctuation of the colonic Lactobacillus species and their distribution of antibiotic resistance genes (ARGs) as well as antibiotic susceptibility in pigs. Metagenomic analysis revealed that genus Lactobacillus was one of the most dominant genera in the colon of growing pigs. Rhythmicity analysis revealed that 84 out of 285 Lactobacillus species exhibited rhythmic patterns. Lactobacillus johnsonii and Lactobacillus reuteri were the two most abundant lactobacilli with circadian oscillation, which increased during the day and decreased at night. The profile of the antibiotic resistome was modified over time within 24-h period. Elfamycin resistance genes were the most enriched class found in Lactobacillus. Furthermore, the seven strains of Lactobacillus isolated from the pig intestine mainly exhibited resistance to gentamicin, erythromycin, and lincomycin. The whole genome annotation of four Lactobacillus strains indicated the presence of multiple ARGs, including elfamycin resistance genes, however, the most abundant ARG was optrA in genome of four strains. These results indicate the presence of various Lactobacillus species harboring a large number of ARGs in the swine intestine. This implies that when using animal-derived lactobacilli, it is essential to assess antibiotic resistance to prevent further transmission between animals and the environment.
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Affiliation(s)
- Jianjian Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongyu Wang
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongying Xu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiuke Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Lian Li
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong Su
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jinxin Liu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China
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20
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Baciu AP, Baciu C, Baciu G, Gurau G. The burden of antibiotic resistance of the main microorganisms causing infections in humans - review of the literature. J Med Life 2024; 17:246-260. [PMID: 39044924 PMCID: PMC11262613 DOI: 10.25122/jml-2023-0404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 02/21/2024] [Indexed: 07/25/2024] Open
Abstract
One of the biggest threats to human well-being and public health is antibiotic resistance. If allowed to spread unchecked, it might become a major health risk and trigger another pandemic. This proves the need to develop antibiotic resistance-related global health solutions that take into consideration microdata from various global locations. Establishing positive social norms, guiding individual and group behavioral habits that support global human health, and ultimately raising public awareness of the need for such action could all have a positive impact. Antibiotic resistance is not just a growing clinical concern but also complicates therapy, making adherence to current guidelines for managing antibiotic resistance extremely difficult. Numerous genetic components have been connected to the development of resistance; some of these components have intricate paths of transfer between microorganisms. Beyond this, the subject of antibiotic resistance is becoming increasingly significant in medical microbiology as new mechanisms underpinning its development are identified. In addition to genetic factors, behaviors such as misdiagnosis, exposure to broad-spectrum antibiotics, and delayed diagnosis contribute to the development of resistance. However, advancements in bioinformatics and DNA sequencing technology have completely transformed the diagnostic sector, enabling real-time identification of the components and causes of antibiotic resistance. This information is crucial for developing effective control and prevention strategies to counter the threat.
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Key Words
- AOM, acute otitis media
- CDC, Centers for Disease Control and Prevention
- CRE, carbapenem-resistant Enterobacterales
- ESBL, extended-spectrum beta-lactamase
- Hib, Haemophilus influenzae type b
- LVRE, linezolid/vancomycin -resistant enterococci
- MBC, minimum bactericidal concentration
- MBL, metallo-beta-lactamases
- MDR, multidrug-resistant
- MIC, minimum inhibitor concentration
- MRSA, methicillin-resistant Staphylococcus aureus
- PBP, penicillin-binding protein
- SCCmec staphylococcal chromosomal cassette mec
- VRE, vancomycin-resistant enterococci
- XDR, extensively drug-resistant
- antibiotic resistance
- antibiotics
- beta-lactamase
- cIAI, complicated intra-abdominal infection
- cUTI, complicated urinary tract infection
- carbapenems
- methicillin-resistant Staphylococcus aureus
- vancomycin
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Affiliation(s)
| | - Carmen Baciu
- MedLife Hyperclinic Nicolae Balcescu, Galati, Romania
| | - Ginel Baciu
- Sf. Ioan Emergency Clinical Hospital for Children, Galati, Romania
- Faculty of Medicine and Pharmacy, Dunarea de Jos University, Galati, Romania
| | - Gabriela Gurau
- Sf. Ioan Emergency Clinical Hospital for Children, Galati, Romania
- Faculty of Medicine and Pharmacy, Dunarea de Jos University, Galati, Romania
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21
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Lin C, Feng Y, Xie X, Zhang H, Wu J, Zhu Y, Yu J, Feng J, Su W, Lai S, Zhang A. Antimicrobial resistance characteristics and phylogenetic relationships of pleuromutilin-resistant Enterococcus isolates from different environmental samples along a laying hen production chain. J Environ Sci (China) 2024; 137:195-205. [PMID: 37980008 DOI: 10.1016/j.jes.2023.01.012] [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: 10/17/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 11/20/2023]
Abstract
Antimicrobial resistance in the laying hen production industry has become a serious public health problem. The antimicrobial resistance and phylogenetic relationships of the common conditional pathogen Enterococcus along the laying hen production chain have not been systematically clarified. 105 Enterococcus isolates were obtained from 115 environmental samples (air, dust, feces, flies, sewage, and soil) collected along the laying hen production chain (breeding chicken, chick, young chicken, and commercial laying hen). These Enterococcus isolates exhibited resistance to some clinically relevant antibiotics, such as tetracycline (92.4%), streptomycin (92.4%), and erythromycin (91.4%), and all strains had multidrug resistance phenotypes. Whole genome sequencing characterized 29 acquired antibiotic resistance genes (ARGs) that conferred resistance to 11 classes of antibiotics in 51 pleuromutilin-resistant Enterococcus isolates, and lsa(E), which mediates resistance to pleuromutilins, always co-occurred with lnu(B). Alignments with the Mobile Genetic Elements database identified four transposons (Tn554, Tn558, Tn6261, and Tn6674) with several ARGs (erm(A), ant(9)-la, fex(A), and optrA) that mediated resistance to many clinically important antibiotics. Moreover, we identified two new transposons that carried ARGs in the Tn554 family designated as Tn7508 and Tn7492. A complementary approach based on conventional multi-locus sequence typing and whole genome single nucleotide polymorphism analysis showed that phylogenetically related pleuromutilin-resistant Enterococcus isolates were widely distributed in various environments on different production farms. Our results indicate that environmental contamination by antimicrobial-resistant Enterococcus requires greater attention, and they highlight the risk of pleuromutilin-resistant Enterococcus and ARGs disseminating along the laying hen production chain, thereby warranting effective disinfection.
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Affiliation(s)
- Cong Lin
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuxuan Feng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xianjun Xie
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haoyu Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jie Wu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yixiao Zhu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jing Yu
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jingyi Feng
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wen Su
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shanming Lai
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Anyun Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.
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Chen W, Wang Q, Wu H, Xia P, Tian R, Li R, Xia L. Molecular epidemiology, phenotypic and genomic characterization of antibiotic-resistant enterococcal isolates from diverse farm animals in Xinjiang, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168683. [PMID: 37996027 DOI: 10.1016/j.scitotenv.2023.168683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Multidrug-resistant (MDR) bacteria in farm environments can be transferred to humans through the food chain and occupational exposure. Enterococcus infections caused by linezolid resistant enterococci (LRE) are becoming more challenging to treat as their resistance to antibiotics intensifies. Therefore, this study investigated the molecular epidemiology, phenotypic and genomic characterization of enterococci in seven species of farm animals (sheep, chicken, swine, camel, cattle, equine, pigeon) anal swab from Xinjiang, China by agar dilution method, polymerase chain reaction (PCR), whole-genome sequencing (WGS) and bioinformatics analysis. A total of 771 samples were collected, 599 (78 %) were contaminated with Enterococcus spp., among which Enterococcus faecalis (350/599) was dominant. Antimicrobial susceptibility testing showed that high resistance was observed in rifampicin (80 %), tetracycline (71 %), doxycycline (71 %), and erythromycin (69 %). The results of PCR showed the highest prevalent antibiotic resistance genes (ARGs) were aac(6')-aph(2″) (85 %), followed by tet(M) (73 %), erm(B) (62 %), and aph(3')-IIIa (61 %). Besides, 29 optrA-carrying E. faecalis isolates belonging to 13 STs (including 3 new alleles) were detected, with ST714 (31 %, 9/29) being the dominant ST type. The phylogenetic tree showed that optrA-carrying E. faecalis prevalent in the intensive swine farm is mainly caused by clonal transmission. Notably, optrA gene in Enterococcus spp. isolate from camel was first characterized here. WGS of E. faecalis F109 isolate from camel confirmed the colocalization of optrA with other five ARGs in the same plasmid (pAFL-109F). The optrA-harboring genetic context is IS1216E-fexA-optrA-erm(A)-IS1216E. This study highlights the prevalence of MDR Enterococcus (≥88 %) and four ARGs (≥75 %) in swine (intensive farming), cattle (commercial farming), and chickens (backyard farming) are high and also highlights that optrA-carrying E. faecalis of farm animals incur a transmission risk to humans through environment, food consumption and others. Therefore, antibiotic-resistant bacteria (ARB) monitoring and effective control measures should be strengthened and implemented in diverse animals.
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Affiliation(s)
- Wanzhao Chen
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Herbivore Drug Research and Creation, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Huimin Wu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Panpan Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Rui Tian
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, 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.
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; Xinjiang Key Laboratory of Herbivore Drug Research and Creation, Xinjiang Agricultural University, Urumqi 830052, China.
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23
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Wu M, Kang J, Tao J, Yang Y, Li G, Jia W. Clinical Characteristics and Drug Resistance Mechanisms of Linezolid-Non-Susceptible Enterococcus in a Tertiary Hospital in Northwest China. Infect Drug Resist 2024; 17:485-494. [PMID: 38348228 PMCID: PMC10860515 DOI: 10.2147/idr.s442105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
Purpose To understand the detection rate and distribution characteristics of Linezolid-nonsusceptible Enterococcus (LNSE) and analyze the molecular typing and main drug resistance mechanisms of LNSE, providing a theoretical basis for the precision prevention and control of LNSE hospital infections. Methods A total of 40 LNSE strains isolated from clinical specimens between January 1, 2012, and December 31, 2022, were collected. The LNSE isolates identified by instrument detection were confirmed using a microbroth dilution method. The WHONET 5.0 software was used for statistical analysis of LNSE detection rate, and the LNSE judgment was based on the 2022 CLSI criteria. PCR methods were used to detect 23S rRNA, cfr, optrA, and L3, L4 ribosomal RNA sites for linezolid resistance genes, and gene sequencing was used to verify the amplified PCR products. Multiple locus sequence typing (MLST) was performed to analyze the homology of LNSE strains. Results A total of 6924 Enterococcus isolates were separated and identified from January 1, 2012, to December 31, 2022, of which 40 were LNSE strains (26 Enterococcus faecalis, 14 Enterococcus faecium), with a detection rate of 0.58% (40/6924). Among them, 28 Linezolid-intermediated Enterococcus(LIE) were detected, accounting for 0.4% (28/6924), and 12 Linezolid-resistant Enterococcus(LRE) were detected, with a detection rate of 0.17% (12/6924). Among the LNSE strains, 23 were resistant to genes. The 40 LNSE strains could be divided into 20 different ST types, with ST16 being the main type, accounting for 12.5% (5/40). Conclusion The detection of LNSE strains was dominated by Enterococcus faecalis, and the main resistance mechanism of LRE strains was carrying the optrA gene, with 23S rRNA gene mutations also contributing to resistance. New resistance gene phenotypes (optrA +/23S rRNA+) emerged. Most LRE cases were sporadic, and clonal dissemination was observed in some strains.
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Affiliation(s)
- Mengying Wu
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Jia Kang
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Jia Tao
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Yanwen Yang
- Department of Neurology, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Gang Li
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Wei Jia
- Medical Experimental Center, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
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Ocejo M, Mugica M, Oporto B, Lavín JL, Hurtado A. Whole-genome long-read sequencing to unveil Enterococcus antimicrobial resistance in dairy cattle farms exposed a widespread occurrence of Enterococcus lactis. Microbiol Spectr 2024; 12:e0367223. [PMID: 38230937 PMCID: PMC10846211 DOI: 10.1128/spectrum.03672-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
Enterococcus faecalis (Efs) and Enterococcus faecium (Efm) are major causes of multiresistant healthcare-associated or nosocomial infections. Efm has been traditionally divided into clades A (healthcare associated) and B (community associated) but clade B has been recently reassigned to Enterococcus lactis (Elc). However, identification techniques do not routinely differentiate Elc from Efm. As part of a longitudinal study to investigate the antimicrobial resistance of Enterococcus in dairy cattle, isolates initially identified as Efm were confirmed as Elc after Oxford-Nanopore long-fragment whole-genome sequencing and genome comparisons. An Efm-specific PCR assay was developed and used to identify isolates recovered from animal feces on five farms, resulting in 44 Efs, 23 Efm, and 59 Elc. Resistance, determined by broth microdilution, was more frequent in Efs than in Efm and Elc but all isolates were susceptible to ampicillin, daptomycin, teicoplanin, tigecycline, and vancomycin. Genome sequencing analysis of 32 isolates identified 23 antimicrobial resistance genes (ARGs, mostly plasmid-located) and 2 single nucleotide polymorphisms associated with resistance to 10 antimicrobial classes, showing high concordance with phenotypic resistance. Notably, linezolid resistance in Efm was encoded by the optrA gene, located in plasmids downstream of the fexA gene. Although most Elc lacked virulence factors and genetic determinants of resistance, one isolate carried a plasmid with eight ARGs. This study showed that Elc is more prevalent than Efm in dairy cattle but carries fewer ARGs and virulence genes. However, Elc can carry multi-drug-resistant plasmids like those harbored by Efm and could act as a donor of ARGs for other pathogenic enterococcal species.IMPORTANCEEnterococcus species identification is crucial due to differences in pathogenicity and antibiotic resistance profiles. The failure of traditional methods or whole-genome sequencing-based taxonomic classifiers to distinguish Enterococcus lactis (Elc) from Enterococcus faecium (Efm) results in a biased interpretation of Efm epidemiology. The Efm species-specific real-time PCR assay developed here will help to properly identify Efm (only the formerly known clade A) in future studies. Here, we showed that Elc is prevalent in dairy cattle, and although this species carries fewer genetic determinants of resistance (GDRs) than Enterococcus faecalis (Efs) and Efm, it can carry multi-drug-resistant (MDR) plasmids and could act as a donor of resistance genes for other pathogenic enterococcal species. Although all isolates (Efs, Efm, and Elc) were susceptible to critically or highly important antibiotics like daptomycin, teicoplanin, tigecycline, and vancomycin, the presence of GDRs in MDR-plasmids is a concern since antimicrobials commonly used in livestock could co-select and confer resistance to critically important antimicrobials not used in food-producing animals.
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Affiliation(s)
- Medelin Ocejo
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Maitane Mugica
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Beatriz Oporto
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - José Luis Lavín
- Applied Mathematics Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ana Hurtado
- Animal Health Department, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
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Lysitsas M, Triantafillou E, Spyrou V, Billinis C, Valiakos G. Phenotypic Investigation of Florfenicol Resistance and Molecular Detection of floR Gene in Canine and Feline MDR Enterobacterales. Vet Sci 2024; 11:71. [PMID: 38393089 PMCID: PMC10892669 DOI: 10.3390/vetsci11020071] [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: 11/27/2023] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Florfenicol is a promising antibiotic for use in companion animals, especially as an alternative agent for infections caused by MDR bacteria. However, the emergence of resistant strains could hinder this potential. In this study, florfenicol resistance was investigated in a total of 246 MDR Enterobacterales obtained from canine and feline clinical samples in Greece over a two-year period (October 2020 to December 2022); a total of 44 (17,9%) florfenicol-resistant strains were recognized and further investigated. Most of these isolates originated from urine (41.9%) and soft tissue (37.2%) samples; E. coli (n = 14) and Enterobacter cloacae (n = 12) were the predominant species. The strains were examined for the presence of specific florfenicol-related resistance genes floR and cfr. In the majority of the isolates (31/44, 70.5%), the floR gene was detected, whereas none carried cfr. This finding creates concerns of co-acquisition of plasmid-mediated florfenicol-specific ARGs through horizontal transfer, along with several other resistance genes. The florfenicol resistance rates in MDR isolates seem relatively low but considerable for a second-line antibiotic; thus, in order to evaluate the potential of florfenicol to constitute an alternative antibiotic in companion animals, continuous monitoring of antibiotic resistance profiles is needed in order to investigate the distribution of florfenicol resistance under pressure of administration of commonly used agents.
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Affiliation(s)
- Marios Lysitsas
- Faculty of Veterinary Science, University of Thessaly, 431 00 Karditsa, Greece; (M.L.); (C.B.)
| | | | - Vassiliki Spyrou
- Department of Animal Science, University of Thessaly, 413 34 Larissa, Greece;
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 431 00 Karditsa, Greece; (M.L.); (C.B.)
| | - George Valiakos
- Faculty of Veterinary Science, University of Thessaly, 431 00 Karditsa, Greece; (M.L.); (C.B.)
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Liu P, Zeng B, Wu X, Zheng F, Zhang Y, Liao X. Risk exploration and prediction model construction for linezolid-resistant Enterococcus faecalis based on big data in a province in southern China. Eur J Clin Microbiol Infect Dis 2024; 43:259-268. [PMID: 38032514 PMCID: PMC10821975 DOI: 10.1007/s10096-023-04717-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Enterococcus faecalis is a common cause of healthcare-associated infections. Its resistance to linezolid, the antibiotic of last resort for vancomycin-resistant enterococci, has become a growing threat in healthcare settings. METHODS We analyzed the data of E. faecalis isolates from 26 medical institutions between 2018 and 2020 and performed univariate and multivariate logistic regression analyses to determine the independent predictors for linezolid-resistant E. faecalis (LREFs). Then, we used the artificial neural network (ANN) and logistic regression (LR) to build a prediction model for linezolid resistance and performed a performance evaluation and comparison. RESULTS Of 12,089 E. faecalis strains, 755 (6.25%) were resistant to linezolid. Among vancomycin-resistant E. faecalis, the linezolid-resistant rate was 24.44%, higher than that of vancomycin-susceptible E. faecalis (p < 0.0001). Univariate and multivariate regression analyses showed that gender, age, specimen type, length of stay before culture, season, region, GDP (gross domestic product), number of beds, and hospital level were predictors of linezolid resistance. Both the ANN and LR models constructed in the study performed well in predicting linezolid resistance in E. faecalis, with AUCs of 0.754 and 0.741 in the validation set, respectively. However, synthetic minority oversampling technique (SMOTE) did not improve the prediction ability of the models. CONCLUSION E. faecalis linezolid-resistant rates varied by specimen site, geographic region, GDP level, facility level, and the number of beds. At the same time, community-acquired E. faecalis with linezolid resistance should be monitored closely. We can use the prediction model to guide clinical medication and take timely prevention and control measures.
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Affiliation(s)
- Peijun Liu
- Administration Department of Nosocomial Infection, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China
| | - Bangwei Zeng
- Administration Department of Nosocomial Infection, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China.
| | - Xiaoyan Wu
- Administration Department of Nosocomial Infection, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China
| | - Feng Zheng
- Information Department, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China
| | - Yangmei Zhang
- Administration Department of Nosocomial Infection, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China
| | - Xiaohua Liao
- Administration Department of Nosocomial Infection, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China
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Panchal J, Patel A, Patel S, Goswami D. Understanding mastitis: Microbiome, control strategies, and prevalence - A comprehensive review. Microb Pathog 2024; 187:106533. [PMID: 38171428 DOI: 10.1016/j.micpath.2023.106533] [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: 10/30/2023] [Revised: 12/12/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
Mastitis significantly affects the udder tissue in dairy cattle, leading to inflammation, discomfort, and a decline in both milk yield and quality. The condition can be attributed to an array of microbial agents that access the mammary gland through multiple pathways. The ramifications of this ailment are not merely confined to animal welfare but extend to the financial viability of the livestock industry. This review offers a historical lens on mastitis, tracing its documentation back to 1851, and examines its global distribution with a focus on regional differences in prevalence and antimicrobial resistance (AMR) patterns. Specific microbial genes and communities implicated in both mastitis and AMR are explored, including Staphylococcus aureus, Streptococcus agalactiae,Streptococcus dysagalactiae, Streptococcus uberis Escherichia coli, Klebsiella pneumoniae, Mycoplasma bovis, Corynebacterium bovis, among others. These microorganisms have evolved diverse strategies to elude host immune responses and neutralize commonly administered antibiotics, complicating management efforts. The review aims a comprehensive overview of the current knowledge and research gaps on mastitis and AMR, and to highlight the need for a One Health approach to address this global health issue. Such an approach entails multi-disciplinary cooperation to foster judicious antibiotic use, enhance preventive measures against mastitis, and bolster surveillance and monitoring of AMR in pathogens responsible for mastitis.
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Affiliation(s)
- Janki Panchal
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Arun Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
| | - Sandip Patel
- Department of Veterinary Microbiology, College of Veterinary Sciences & Animal Husbandry, Sardarkrushinagar, 385505, Kamdhenu University, Gujarat, India
| | - Dweipayan Goswami
- Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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28
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Zhao M, He S, Wen R, Li C, Chen X, Lin X, Wang H, Tang Y. Membrane vesicles derived from Enterococcus faecalis promote the co-transfer of important antibiotic resistance genes located on both plasmids and chromosomes. J Antimicrob Chemother 2024; 79:320-326. [PMID: 38109479 DOI: 10.1093/jac/dkad381] [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: 07/20/2023] [Accepted: 11/28/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Bacterial membrane vesicles (BMVs) are novel vehicles of antibiotic resistance gene (ARG) transfer in Gram-negative bacteria, but their role in the spread of ARGs in Gram-positive bacteria has not been defined. The purpose of this study was to evaluate the role of MVs in the transmission of antimicrobial resistance in Gram-positive bacteria. METHODS A linezolid-resistant Enterococcus faecalis CQ20 of swine origin was selected as the donor strain. Linezolid-susceptible E. faecalis SC032 of human origin, Enterococcus faecium BM4105 and Escherichia coli were selected as recipient strains. The presence of plasmids (pCQ20-1 and pCQ20-2) and an optrA-carrying transposon Tn6674 in CQ20, MVs and vesiculants was verified by WGS or PCR. MVs were isolated with density gradient centrifugation, and MV-mediated transformation was performed to assess the horizontal transferability of MVs. The MICs for CQ20 and its vesiculants were determined by the broth microdilution method. RESULTS CQ20-derived MVs (CQ20-MV) were isolated, and PCR identified the presence of two plasmids and the optrA gene in the CQ20-MVs. MV-mediated transformation to E. faecalis SC032 and E. faecium BM4105 was successfully performed, and the WGS data also showed that both plasmids pCQ20-1 and pCQ20-2 and optrA-carrying transposon Tn6674 were transferred to E. faecalis SC032 and E. faecium BM4105, but failed for E. coli. Additionally, vesiculants that had acquired ARGs still had the ability to spread these genes via MVs. CONCLUSIONS To our knowledge, this is the first report of MV-mediated co-transfer of ARG-carrying plasmids and transposons in the Gram-positive bacterium E. faecium.
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Affiliation(s)
- Mengyu Zhao
- 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, College of Life Science, Sichuan University, Chengdu, China
| | - Shuang He
- 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, College of Life Science, Sichuan University, Chengdu, China
| | - Renqiao Wen
- 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, College of Life Science, Sichuan University, Chengdu, China
| | - Chao 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, College of Life Science, Sichuan University, Chengdu, China
| | - Xinggui Chen
- 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, College of Life Science, Sichuan University, Chengdu, China
| | - Xiaolong Lin
- 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, College of Life Science, Sichuan University, Chengdu, China
| | - Hongning 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, College of Life Science, Sichuan University, Chengdu, China
| | - Yizhi Tang
- 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, College of Life Science, Sichuan University, Chengdu, China
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Dai X, Sun J, Zhao W, Wang J, Zhang X, Liu X, Li A, Zhao J, Han P, Wang X, Wang L, Huang J. Emergence of a novel ISS1N-optrA-carrying transposon within an integrative and conjugative element from Streptococcus parasuis. J Antimicrob Chemother 2024; 79:61-65. [PMID: 37965874 DOI: 10.1093/jac/dkad347] [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: 06/19/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
OBJECTIVES To investigate the genetic context and transferability of the oxazolidinone resistance gene optrA in a Streptococcus parasuis isolate. METHODS The optrA-carrying S. parasuis isolate SFJ45 was characterized by PCR, antimicrobial susceptibility testing, complete genome sequencing and bioinformatic analysis. The transferability of optrA was verified by conjugation, followed by SmaI-PFGE and Southern blotting. RESULTS The S. parasuis isolate SFJ45 was positive for optrA, mef(A), msr(D), erm(B), tetAB(P)', tet(M), aadE, aphA3, catQ, dfrG and mdt(A), conferring an MDR phenotype. The optrA gene was flanked by ISS1N at both termini in the same orientation, representing a novel 8750 bp pseudo-compound transposon, organized as the ISS1N-hth-clb-4hp-optrA-2hp-ISS1N structure. The ISS1N-optrA-carrying transposon was further inserted within an integrative and conjugative element, ICESpsuSFJ45, at 3' end of the fda gene. Conjugative transfer of the ISS1N-optrA-carrying transposon with ICESpsuSFJ45 was observed from S. parasuis to Streptococcus suis at a frequency of (1.01 ± 3.12) × 10-7. CONCLUSIONS ISS1N was found to be associated with optrA spreading for the first time. Integration of the ISS1N-optrA transposon within ICESpsuSFJ45 may lead to the co-selection of optrA with other antimicrobial resistance genes, contributing to its horizontal transfer from S. parasuis to clinically more important bacterial pathogens.
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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 210095, China
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenbin Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianzhong Wang
- Agricultural Technology Integrated Service Center, Agricultural and Rural Bureau of Xiangcheng District of Suzhou City, Suzhou 215131, China
| | - Xiaohui Zhang
- Department of Veterinary Medicine, College of Animal Science and Technology, Hainan University, Haikou 570228, China
| | - Xiao Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Aijuan Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaqi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Peizhao Han
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing 210095, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing 210095, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing 210095, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing 210095, China
- Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing 210095, China
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Gagetti P, Faccone D, Ceriana P, Lucero C, Menocal A, Argentina GL, Corso A. Emergence of optrA-mediated linezolid resistance in clinical isolates of Enterococcus faecalis from Argentina. J Glob Antimicrob Resist 2023; 35:335-341. [PMID: 37923130 DOI: 10.1016/j.jgar.2023.10.014] [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: 09/02/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023] Open
Abstract
OBJECTIVES The aim of this study was to characterize the first 14 optrA-carrying linezolid resistant E. faecalis clinical isolates recovered in seven Argentinian hospitals between 2016 and 2021. The epidemiology of optrA-carrying isolates and the optrA genetic context were determined. METHODS The isolates were phenotypically and genotypically characterized. Susceptibility to 13 antimicrobial agents was performed; clonal relationship was assessed by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Data provided by the whole-genome sequencing were used for identification of sequence types, antimicrobial resistance genes, optrA variants, phylogenetic tree, and mobile genetic elements responsible to the dissemination of these strains. RESULTS All the optrA-carrying E. faecalis isolates were multidrug-resistant and harboured several antimicrobial resistance genes. They carried three optrA variants and belonged to different lineages; however, three of them belonged to the hyperepidemic CC16. Mobile genetic elements were detected in all the isolates. The analysis of the optrA flanking region suggests the plasmidic localization in most of the isolates. CONCLUSIONS To the best of our knowledge, this is the first report of optrA-mediated linezolid resistance in Argentina. The emergence and dissemination of the optrA genes in clinical E. faecalis isolates are of concern and highlights the importance of initiating the antimicrobial surveillance of Enterococcus spp. under a One Health strategy.
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Affiliation(s)
- Paula Gagetti
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Diego Faccone
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Paola Ceriana
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Celeste Lucero
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Alejandra Menocal
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Grupo Lre Argentina
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Alejandra Corso
- Antimicrobial Agents Division, National and Regional Reference Laboratory in Antimicrobial Resistance, National Institute of Infectious Diseases - ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina.
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Xu CW, Zhou X, Zhang XL, Zhou Q, Qi HX, Li YX, Liu SC, Zhang AY. Whole genome sequence of Streptococcus pluranimalium SP21-2, a porcine strain harbouring optrA and lsa(E) with chromosomal location. J Glob Antimicrob Resist 2023; 35:101-103. [PMID: 37709136 DOI: 10.1016/j.jgar.2023.09.007] [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: 03/30/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVES The aim of this study was to characterise the whole genome sequence of multidrug-resistant Streptococcus pluranimalium strain SP21-2 of swine origin in China. METHODS Illumina Miseq (200X coverage) and Nanopore PromethION platform (100X coverage) were used for genome sequencing. Rapid Annotation using Subsystem Technology (RAST) was used to annotate the genome of SP21-2. The antimicrobial resistance genes (ARGs) were identified using ResFinder-4.1. RESULTS The assembled circular genome of S. pluranimalium SP21-2 was 1,987,058 bp in length with a GC content of 39.54%, and no plasmid sequence was detected. A total of 2086 coding sequences were predicted by RAST. Oxazolidinone-phenicol resistance gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), are both located on chromosomes, associated with IS1216 and ISS1S, respectively. In addition, SP21-2 harbours lnu(B) (lincosamide), ant (6)-Ia and aac(6')-aph(2") (aminoglycoside), erm(B) (macrolide), and tet(O) (tetracycline). CONCLUSION We firstly report the oxazolidinone-phenicol gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), in S. pluranimalium. In this strain, we firstly identified ISS1S and IS1216 carrying ARGs in S. pluranimalium, which will provide a valuable reference to understanding potential transfer mechanisms of ARGs in S. pluranimalium.
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Affiliation(s)
- Chang-Wen Xu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China; Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Xue Zhou
- Chongqing Academy of Annimal Sciences, Chongqing, China
| | - Xia-Lan Zhang
- Central Agricultural Broadcasting and Television School (Banan, Chongqing), Chongqing, China
| | - Quan Zhou
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Hao-Xuan Qi
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Yun-Xia Li
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Shi-Chun Liu
- Guanghan Orthopedic Hospital, Guanghan, Sichuan, China
| | - An-Yun Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan University; Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China.
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Agyirifo DS, Mensah TA, Senya ASY, Hounkpe A, Dornyoh CD, Otwe EP. Dynamics of antimicrobial resistance and virulence of staphylococcal species isolated from foods traded in the Cape Coast metropolitan and Elmina municipality of Ghana. Heliyon 2023; 9:e21584. [PMID: 38027608 PMCID: PMC10663863 DOI: 10.1016/j.heliyon.2023.e21584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
The impact of staphylococci on food poisoning and infections could be higher than previously reported. In this study, we characterised the occurrence and coexistence of antimicrobial resistance and virulence genes of staphylococci isolates in foods. Staphylococci were isolated from 236 samples of selected street-vended foods and identified. The pattern of antimicrobial resistance and virulence genes in the staphylococci were assessed using disc diffusion, PCR and analysis of next-generation sequencing data. The food samples (70.76 %) showed a high prevalence of staphylococci and differed among the food categories. Forty-five Staphylococcus species were identified and comprised coagulase-negative and positive species. Staphylococcus sciuri (now Mammaliicoccus sciuri), S. aureus, S. kloosii, S. xylosus, S. saprophyticus, S. haemolyticus and S. succinus were the most abundant species. The staphylococcal isolates exhibited resistance to tetracycline, levofloxacin, ciprofloxacin, norfloxacin, gentamicin and amikacin and susceptibility to nitrofurantoin. Antimicrobial susceptibilities were also reported for cefoperazone, ceftriaxone, cefotaxime, nalidixic acid and piperacillin-tazobactam. The antimicrobial resistance and virulence genes commonly detected consisted of tet, arl, macB, van, gyr, nor, optrA, bcrA, blaZ, taeA and S. aureus lmrS. The isolates frequently exhibited multiple resistance (30.42 %) of up to eight antimicrobial drug classes. The isolates predominantly harboured genes that express efflux pump proteins (50.53 %) for antibiotic resistance compared with inactivation (10.05 %), target alteration (26.72 %), protection (7.67 %) and replacement (3.17 %). The virulence determinants comprised genes of pyrogenic toxin superantigens (eta, etb, tst), adhesions (clf, fnbA, fnbB, cna, map, ebp, spA, vWbp, coa) and genes that express exoproteins (nuclease, metalloprotease, γ-hemolysin, hyaluronate lyase). There was a statistically significant difference in the prevalence of staphylococci isolates and their antimicrobial resistance and virulence profile as revealed by the phenotypic, PCR and next-generation sequencing techniques. The findings suggest a higher health risk for consumers. We recommend a critical need for awareness and antimicrobial susceptibility and anti-virulence strategies to ensure food safety and counteract the spread of this clinically relevant genus.
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Affiliation(s)
- Daniel Sakyi Agyirifo
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Theophilus Abonyi Mensah
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Andrews Senyenam Yao Senya
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Alphonse Hounkpe
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Cindy Deladem Dornyoh
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Emmanuel Plas Otwe
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast, Ghana
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Sordo M, Grilo T, Freire S, Rodrigues B, Bouvier M, Poirel L, Aires-de-Sousa M. Rapid culture-based LNZ test for detection of linezolid susceptibility/resistance in staphylococci and enterococci. Diagn Microbiol Infect Dis 2023; 107:116058. [PMID: 37657232 DOI: 10.1016/j.diagmicrobio.2023.116058] [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: 06/21/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
A rapid, easy-to-handle, cost-effective and universal culture-based test was developed for the identification of linezolid resistance among the most clinically relevant enterococcal and staphylococcal species. Our technique was tested using linezolid-resistant (n = 50) and linezolid-susceptible (n = 67) Gram-positive isolates: 34 Enterococcus faecium, 20 Enterococcus faecalis, 20 Staphylococcus aureus, 38 Staphylococcus epidermidis, and 5 Staphylococcus capitis. The susceptibility/resistance phenotype of E. faecium, E. faecalis, S. aureus, and S. epidermidis to linezolid was detected within 4.5 hours, while an extended timeframe was actually required for S. capitis (6.5 hours). The Rapid LNZ test showed a full agreement with the standard broth microdilution method, independently of the molecular resistance mechanism and MIC values, with sensitivities and specificities of 100% for all species.
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Affiliation(s)
- Miguel Sordo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Teresa Grilo
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Samanta Freire
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal; Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Bruna Rodrigues
- Laboratory of Molecular Biology, Portuguese Red Cross, Lisboa, Portugal
| | - Maxime Bouvier
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Marta Aires-de-Sousa
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisboa, Portugal; Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal.
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Abdullahi IN, Lozano C, Simón C, Zarazaga M, Torres C. Within-Host Diversity of Coagulase-Negative Staphylococci Resistome from Healthy Pigs and Pig Farmers, with the Detection of cfr-Carrying Strains and MDR- S. borealis. Antibiotics (Basel) 2023; 12:1505. [PMID: 37887206 PMCID: PMC10604674 DOI: 10.3390/antibiotics12101505] [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: 09/08/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
The ecology and diversity of resistome in coagulase-negative staphylococci (CoNS) from healthy pigs and pig farmers are rarely available as most studies focused on the livestock-associated methicillin-resistant S. aureus. This study aims to characterize the antimicrobial resistance (AMR) mechanisms, intra-host species diversity (more than one species in a host), and intra-species AMR diversity (same species with more than one AMR profile) in CoNS recovered from the nasal cavities of healthy pigs and pig farmers. One-hundred-and-one CoNS strains previously recovered from 40 pigs and 10 pig farmers from four Spanish pig farms were tested to determine their AMR profiles. Non-repetitive strains were selected (n = 75) and their AMR genes, SCCmec types, and genetic lineages were analyzed by PCR/sequencing. Of the non-repetitive strains, 92% showed a multidrug resistance (MDR) phenotype, and 52% were mecA-positive, which were associated with SCCmec types V (46.2%), IVb (20.5%), and IVc (5.1%). A total of 28% of the pigs and pig farmers had intra-host species diversity, while 26% had intra-species AMR diversity. High repertoires of AMR genes were detected, including unusual ones such as tetO, ermT, erm43, and cfr. Most important was the detection of cfr (in S. saprophyticus and S. epidermidis-ST16) in pigs and pig farmers; whereas MDR-S. borealis strains were identified in pig farmers. Pig-to-pig transmission of CoNS with similar AMR genes and SCCmec types was detected in 42.5% of pigs. The high level of multidrug, within-host, and intra-species resistome diversity in the nasal CoNS highlights their ability to be AMR gene reservoirs in healthy pigs and pig farmers. The detection of MDR-S. borealis and linezolid-resistant strains underscore the need for comprehensive and continuous surveillance of MDR-CoNS at the pig farm level.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
| | - Carmen Simón
- Faculty of Veterinary Medicine, University of Zaragoza, 50001 Zaragoza, Spain;
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (C.L.); (M.Z.)
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Wang Q, Peng K, Liu Z, Li Y, Xiao X, Du XD, Li R, Wang Z. Genomic insights into linezolid-resistant Enterococci revealed its evolutionary diversity and poxtA copy number heterogeneity. Int J Antimicrob Agents 2023; 62:106929. [PMID: 37487950 DOI: 10.1016/j.ijantimicag.2023.106929] [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: 04/12/2023] [Revised: 07/03/2023] [Accepted: 07/15/2023] [Indexed: 07/26/2023]
Abstract
OBJECTIVES This study aimed to determine the molecular mechanisms of linezolid-resistant enterococci (LRE) in swine slaughterhouses in China and apply the "One Health" perspective to analyse the evolutionary dynamics of poxtA-positive E. faecium in clinical and non-clinical settings worldwide. METHODS The phenotypic and genomic characteristics of multiple LRE isolates were systematically investigated using antimicrobial susceptibility testing, transfer assays, evolutionary experiments, quantitative RT-PCR assays, whole-genome sequencing, and bioinformatics analyses. RESULTS Swine faeces served as a significant reservoir for LRE isolates, and optrA and poxtA were the primary contributors to linezolid resistance. Co-occurrence network analysis revealed a significant interconnection between optrA and several other ARGs. The poxtA copy number heterogeneity and polymorphism were initially observed in E. faecium parental and evolved isolates. The poxtA-carrying tandem repeat region exhibits high mobility and has undergone extensive duplication owing to linezolid pressure. The poxtA copy number varies from four copies on the plasmid of E. faecium IC25 to 11 copies on the plasmid and six copies on the chromosome in the evolved isolate IC25-50_poxtA. Furthermore, phylogenetic analysis of 185 poxtA-positive E. faecium strains worldwide found that one isolate from a French patient in 2018 shared only two SNPs with CC17 E. faecium isolates IC25 and IC7-2 from this study, highlighting the potential global transmission of CC17 poxtA-positive E. faecium between humans and animals. CONCLUSION This study identified amplification of poxtA as a response of E. faecium to linezolid pressure. Phylogenetic analysis shed light on the potential global transmission of hospital-associated CC17 poxtA-positive E. faecium in clinical and non-clinical settings.
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Affiliation(s)
- Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Xia Xiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, P. R. China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, P.R. China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, P. R. China.
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Carcione D, Intra J, Andriani L, Campanile F, Gona F, Carletti S, Mancini N, Brigante G, Cattaneo D, Baldelli S, Chisari M, Piccirilli A, Di Bella S, Principe L. New Antimicrobials for Gram-Positive Sustained Infections: A Comprehensive Guide for Clinicians. Pharmaceuticals (Basel) 2023; 16:1304. [PMID: 37765112 PMCID: PMC10536666 DOI: 10.3390/ph16091304] [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: 08/08/2023] [Revised: 08/30/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic resistance is a public health problem with increasingly alarming data being reported. Gram-positive bacteria are among the protagonists of severe nosocomial and community infections. The objective of this review is to conduct an extensive examination of emerging treatments for Gram-positive infections including ceftobiprole, ceftaroline, dalbavancin, oritavancin, omadacycline, tedizolid, and delafloxacin. From a methodological standpoint, a comprehensive analysis on clinical trials, molecular structure, mechanism of action, microbiological targeting, clinical use, pharmacokinetic/pharmacodynamic features, and potential for therapeutic drug monitoring will be addressed. Each antibiotic paragraph is divided into specialized microbiological, clinical, and pharmacological sections, including detailed and appropriate tables. A better understanding of the latest promising advances in the field of therapeutic options could lead to the development of a better approach in managing antimicrobial therapy for multidrug-resistant Gram-positive pathogens, which increasingly needs to be better stratified and targeted.
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Affiliation(s)
- Davide Carcione
- Laboratory of Medicine and Microbiology, Busto Arsizio Hospital—ASST Valle Olona, 21052 Busto Arsizio, VA, Italy; (D.C.); (G.B.)
| | - Jari Intra
- Clinical Chemistry Laboratory, Fondazione IRCCS San Gerardo Dei Tintori, 20900 Monza, MB, Italy;
| | - Lilia Andriani
- Clinical Pathology and Microbiology Unit, Hospital of Sondrio, 23100 Sondrio, Italy;
| | - Floriana Campanile
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123 Catania, Italy;
| | - Floriana Gona
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (F.G.); (S.C.)
| | - Silvia Carletti
- Laboratory of Microbiology and Virology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (F.G.); (S.C.)
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy;
- Laboratory of Medical Microbiology and Virology, Fondazione Macchi University Hospital, 21100 Varese, Italy
| | - Gioconda Brigante
- Laboratory of Medicine and Microbiology, Busto Arsizio Hospital—ASST Valle Olona, 21052 Busto Arsizio, VA, Italy; (D.C.); (G.B.)
| | - Dario Cattaneo
- Department of Infectious Diseases ASST Fatebenefratelli Sacco, 20157 Milan, Italy;
| | - Sara Baldelli
- Pharmacology Laboratory, Clinical Chemistry Laboratory, Diagnostic Department, ASST Spedali Civili, 25123 Brescia, Italy;
| | - Mattia Chisari
- Microbiology and Virology Unit, Great Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89100 Reggio Calabria, Italy;
| | - Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Stefano Di Bella
- Clinical Department of Medical, Surgical, and Health Sciences, Trieste University, 34129 Trieste, Italy;
| | - Luigi Principe
- Microbiology and Virology Unit, Great Metropolitan Hospital “Bianchi-Melacrino-Morelli”, 89100 Reggio Calabria, Italy;
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Ngbede EO, Sy I, Akwuobu CA, Nanven MA, Adikwu AA, Abba PO, Adah MI, Becker SL. Carriage of linezolid-resistant enterococci (LRE) among humans and animals in Nigeria: coexistence of the cfr, optrA, and poxtA genes in Enterococcus faecium of animal origin. J Glob Antimicrob Resist 2023; 34:234-239. [PMID: 37516354 DOI: 10.1016/j.jgar.2023.07.016] [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: 03/10/2023] [Revised: 07/09/2023] [Accepted: 07/25/2023] [Indexed: 07/31/2023] Open
Abstract
OBJECTIVES In contrast to increasing reports of the emergence of linezolid-resistant enterococci (LRE) emanating from many countries in Europe, Asia, and North America, data on its status and dissemination from the African continent remain scarce, with the information available limited to countries in North Africa. This study investigated the carriage of LRE and the genetic mechanism of resistance among Enterococcus faecium and Enterococcus faecalis strains recovered from humans and animals in Makurdi, Nigeria. METHODS We conducted a cross-sectional study between June 2020 and July 2021 during which 630 non-duplicate human and animal faecal samples were collected and processed for the recovery of LRE. The genetic mechanisms for resistance were investigated using polymerase chain reaction (PCR) and Sanger sequencing. RESULTS Linezolid-resistant enterococci were recovered from 5.87% (37/630; 95% CI: 4.17-8.00) of the samples, with the prevalence in animals and humans being 6.22% [(28/450); 95% CI: 4.17-8.87] and 5.00% [(9/180); 95% CI: 2.31-9.28], respectively. All isolates remained susceptible to vancomycin. No known point mutation mediating linezolid resistance was detected in the 23S rRNA and ribosomal protein genes; however, acquisition of one or more potentially transferable genes (cfr, optrA, and poxtA) was observed in 26 of the 37 LRE isolates. Co-existence of all three transferable genes in a single isolate was found in four E. faecium strains of animal origin. CONCLUSION This study provides baseline evidence for the emergence and active circulation of LRE driven majorly by the acquisition of the optrA gene in Nigeria. To the best of our knowledge, our study is the first to report a co-carriage of all three transferable linezolid resistance determinants in E. faecium. Active LRE surveillance is urgently required to understand the extent of LRE spread across sub-Saharan Africa and to develop tailored mitigation strategies.
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Affiliation(s)
- Emmanuel O Ngbede
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Gebäude 43D-66421 Homburg/Saar, Germany; Department of Veterinary Microbiology, Federal University of Agriculture, Makurdi, Nigeria; Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany.
| | - Issa Sy
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Gebäude 43D-66421 Homburg/Saar, Germany
| | - Chinedu A Akwuobu
- Department of Veterinary Microbiology, Federal University of Agriculture, Makurdi, Nigeria; Amadu Ali Centre for Public Health and Comparative Medicine, Federal University of Agriculture, Makurdi, Nigeria
| | - Maurice A Nanven
- National Veterinary Research Institute, Vom, Plateau State, Nigeria
| | - Alex A Adikwu
- Department of Veterinary Public Health and Preventive Medicine, Federal University of Agriculture, Makurdi, Nigeria
| | - Paul O Abba
- Department of Medical Microbiology and Parasitology, Benue State University Teaching Hospital, Makurdi, Nigeria
| | - Mohammed I Adah
- Amadu Ali Centre for Public Health and Comparative Medicine, Federal University of Agriculture, Makurdi, Nigeria; Department of Veterinary Medicine, Federal University of Agriculture, Makurdi, Nigeria
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße, Gebäude 43D-66421 Homburg/Saar, Germany; Swiss Tropical and Public Health Institute, CH-4002 Allschwil, Switzerland; University of Basel, CH-4003 Basel, Switzerland.
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Douglas EJ, Laabei M. Staph wars: the antibiotic pipeline strikes back. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001387. [PMID: 37656158 PMCID: PMC10569064 DOI: 10.1099/mic.0.001387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Antibiotic chemotherapy is widely regarded as one of the most significant medical advancements in history. However, the continued misuse of antibiotics has contributed to the rapid rise of antimicrobial resistance (AMR) globally. Staphylococcus aureus, a major human pathogen, has become synonymous with multidrug resistance and is a leading antimicrobial-resistant pathogen causing significant morbidity and mortality worldwide. This review focuses on (1) the targets of current anti-staphylococcal antibiotics and the specific mechanisms that confirm resistance; (2) an in-depth analysis of recently licensed antibiotics approved for the treatment of S. aureus infections; and (3) an examination of the pre-clinical pipeline of anti-staphylococcal compounds. In addition, we examine the molecular mechanism of action of novel antimicrobials and derivatives of existing classes of antibiotics, collate data on the emergence of resistance to new compounds and provide an overview of key data from clinical trials evaluating anti-staphylococcal compounds. We present several successful cases in the development of alternative forms of existing antibiotics that have activity against multidrug-resistant S. aureus. Pre-clinical antimicrobials show promise, but more focus and funding are required to develop novel classes of compounds that can curtail the spread of and sustainably control antimicrobial-resistant S. aureus infections.
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Affiliation(s)
| | - Maisem Laabei
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
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Zhang J, Yang Y, Sun H, Luo X, Cui X, Miao Q, He D, Zhao J, Yan F, Pan Y, Zhai Y, Hu G. Prevalence of the optrA gene among Streptococcus suis isolates from diseased pigs and identification of a novel integrative conjugative element ICESsu988S. Res Microbiol 2023; 174:104078. [PMID: 37149078 DOI: 10.1016/j.resmic.2023.104078] [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: 12/10/2022] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/08/2023]
Abstract
Aim of this study was to investigate the prevalence and genetic environment of the oxazolidinone resistance gene optrA in Streptococcus suis (S. suis) isolates from diseased pigs in China. A total of 178 S. suis isolates were screened for the optrA gene by PCR. The phenotypes and genotypes of optrA-positive isolates were investigated by antimicrobial susceptibility testing, core genome Multilocus Sequence Typing (cgMLST), capsular serotypes determination and whole-genome sequencing (WGS). Fifty-one (28.7%) S. suis isolates were positive for optrA. Phylogenetic analysis indicated that the spread of the optrA among S. suis isolates was primarily due to horizontal transfer. Analysis of S. suis serotypes from diseased pigs revealed substantial diversity. The genetic environment of optrA was complex and diverse and could be divided into 12 different types. Interestingly, we identified a novel integrative and conjugative element ICESsu988S, carrying optrA and erm(T) genes. This is to the best of our knowledge the first report of the optrA and erm(T) co-located on an ICE in S. suis. Our results showed a high prevalence of optrA gene in S. suis isolates in China. Further research is needed to evaluate the importance of ICEs, as they horizontally propagate important clinical resistance genes.
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Affiliation(s)
- Junkai Zhang
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China.
| | - Huarun Sun
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China.
| | - Xingwei Luo
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Xiaodie Cui
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Qingqing Miao
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Dandan He
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Jinfeng Zhao
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Fengbin Yan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yushan Pan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yajun Zhai
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Gongzheng Hu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
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Wu K, Li Z, Fang M, Yuan Y, Fox EM, Liu Y, Li R, Bai L, Zhang W, Zhang WM, Yang Q, Chang L, Li P, Wang X, Wang J, Yang Z. Genome characteristics of the optrA-positive Clostridium perfringens strain QHY-2 carrying a novel plasmid type. mSystems 2023; 8:e0053523. [PMID: 37458450 PMCID: PMC10469678 DOI: 10.1128/msystems.00535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/04/2023] [Indexed: 09/01/2023] Open
Abstract
Clostridium perfringens is a bacterial species of importance to both public and animal health. The gene optrA is the first gene that confers resistance to the tedizolid, a last-resort antimicrobial agent in human medicine. Herein, we whole-genome sequenced and analyzed one optrA-positive C. perfringens strain QHY-2 from Tibetan sheep in Qinghai province and identified one optrA plasmid pQHY-2. The plasmid shared similar structure with the optrA-positive plasmids p2C45 and p21-D-5b previously identified in C. perfringens, demonstrating the potential horizontal transmission of the optrA plasmids among C. perfringens strains. Annotation of the optrA-positive plasmids showed optrA and erm(A) located on a segment flanked by IS element IS1216E, and fexA, optrA, and erm(A) located on a segment flanked by IS element ISVlu1, which revealed the possible dissemination mechanism. Additionally, a Tn6218-like transposon carrying aac(6')-aph(2″) and erm(B) was also detected on pQHY-2, demonstrating the transposition of Tn6218 and spread of antibiotic resistance among Clostridium bacteria. Molecular analysis indicated the optrA-positive plasmids belonged to a plasmid type distinct from the pCW3-like plasmids, pCP13-like plasmids, or pIP404-like plasmids. Further structure analysis showed they might be formed by inserting segments into plasmid pCPCPI53k-r1_1, which coexist with two pCW3-like plasmids and one pCP13-like plasmid in C. perfringens strain CPI 53k-r1 isolated from a healthy human in Finland. IMPORTANCE Antimicrobial resistance is now a global concern posing threats to food safety and public health. The pCW3-like plasmids can encode several main toxin genes and three antibiotic resistance genes (ARGs), including tetA(P), tetB(P), and erm(B), which used to be considered as the main carrier of ARGs in Clostridium perfringens. In this study, we found the optrA plasmids, which belonged to a novel plasmid type, could also harbor many other ARGs, indicating this type of plasmid might be the potential repository of ARGs in C. perfringens. Additionally, this type of plasmid could coexist with the pCW3-like plasmids and pCP13-like plasmids that encoded toxin genes associated with gastrointestinal diseases, which showed the potential threat to public health.
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Affiliation(s)
- Ke Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Zhe Li
- Bureau of Agriculture and Rural Affairs, Junan, China
| | - Mingjin Fang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Yuan Yuan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Edward M. Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Yingqiu Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Ruichao Li
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Li Bai
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing, China
| | - Wen Zhang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan, Ningxia, China
| | - Wei-Min Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qi Yang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan, Ningxia, China
| | - Lingling Chang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Pu Li
- Department of Critical Care Medicine, the Second Affiliated Hospital of Air Force Medical University, Shaanxi, China
| | - Xinglong Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Juan Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing, China
| | - Zengqi Yang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
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Paredes-Amaya CC, Ulloa MT, García-Angulo VA. Fierce poison to others: the phenomenon of bacterial dependence on antibiotics. J Biomed Sci 2023; 30:67. [PMID: 37574554 PMCID: PMC10424368 DOI: 10.1186/s12929-023-00963-x] [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: 04/25/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023] Open
Abstract
Beyond the development of resistance, the effects of antibiotics on bacteria and microbial communities are complex and far from exhaustively studied. In the context of the current global antimicrobial resistance crisis, understanding the adaptive and physiological responses of bacteria to antimicrobials is of paramount importance along with the development of new therapies. Bacterial dependence on antibiotics is a phenomenon in which antimicrobials instead of eliminating the pathogens actually provide a boost for their growth. This trait comprises an extreme example of the complexities of responses elicited by microorganisms to these drugs. This compelling evolutionary trait was readily described along with the first wave of antibiotics use and dependence to various antimicrobials has been reported. Nevertheless, current molecular characterizations have been focused on dependence on vancomycin, linezolid and colistin, three critically important antibiotics frequently used as last resource therapy for multi resistant pathogens. Outstanding advances have been made in understanding the molecular basis for the dependence to vancomycin, including specific mutations involved. Regarding linezolid and colistin, the general physiological components affected by the dependence, namely ribosomes and membrane function respectively, have been established. Nonetheless the implications of antibiotic dependence in clinically relevant features, such as virulence, epidemics, relationship with development of resistance, diagnostics and therapy effectiveness require clarification. This review presents a brief introduction of the phenomenon of bacterial dependence to antibiotics and a summary on early and current research concerning the basis for this trait. Furthermore, the available information on the effect of dependence in key clinical aspects is discussed. The studies performed so far underline the need to fully disclose the biological and clinical significance of this trait in pathogens to successfully assess its role in resistance and to design adjusted therapies.
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Affiliation(s)
- Claudia C Paredes-Amaya
- Microbiology Department, Escuela de Ciencias Básicas, Facultad de Salud, Universidad del Valle, Cali, Colombia
| | - María Teresa Ulloa
- Microbiology and Micology Program, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Independencia 1027, Independencia, RM, Santiago, Chile
- Vertebral I+D+i - Corporation for Assistance for Burned Children (Coaniquem), Santiago, Chile
| | - Víctor Antonio García-Angulo
- Microbiology and Micology Program, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Independencia 1027, Independencia, RM, Santiago, Chile.
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Baker M, Zhang X, Maciel-Guerra A, Dong Y, Wang W, Hu Y, Renney D, Hu Y, Liu L, Li H, Tong Z, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China. NATURE FOOD 2023; 4:707-720. [PMID: 37563495 PMCID: PMC10444626 DOI: 10.1038/s43016-023-00814-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.
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Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, People's Republic of China
| | | | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - David Renney
- Nimrod Veterinary Products Ltd., Moreton-in-Marsh, UK
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Longhai Liu
- Shandong Kaijia Food Co., Weifang, People's Republic of China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, Luoyang City, People's Republic of China
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, Luoyang City, People's Republic of China
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang City, People's Republic of China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang City, People's Republic of China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao City, People's Republic of China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Beijing City, People's Republic of China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, People's Republic of China.
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Torabi M, Faghri J, Poursina F. Detection of Genes Related to Linezolid Resistance ( poxtA, cfr, and optrA) in Clinical Isolates of Enterococcus spp. from Humans: A First Report from Iran. Adv Biomed Res 2023; 12:205. [PMID: 37694234 PMCID: PMC10492618 DOI: 10.4103/abr.abr_74_23] [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: 02/25/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 09/12/2023] Open
Abstract
Background Enterococci may develop resistance to linezolid through chromosomal mutations that involve specific linezolid resistance genes, such as cfr, optrA, and poxtA. The objective of this study was to evaluate the antibiotic susceptibility of enterococcal isolates and identify cfr, optrA, and poxtA genes in MDR isolates. Materials and Methods Enterococcal isolates were collected from various clinical specimens at Al-Zahra, Amin, and Khorshid Hospitals in Isfahan. The Enterococcus isolates were identified as belonging to the E. faecalis and E. faecium species by using specific gene (D alanine D alanine ligase ddl) sets in PCR. To detect cfr, optrA, and poxtA genes among the species, a multiplex-PCR assay was performed. Results Out of 175 isolates, E. faecalis predominated 129/175 (73.7%). Furthermore, the prevalence of vancomycin-resistant Enterococci (VRE) and linezolid-resistant Enterococci (LRE) was 29.7% and 4%, respectively. The overall prevalence of MDR was 91.1%, 68.9%, and 66.6% of E. faecium, E. faecalis, and other Enterococcus spp., respectively. Interestingly, the frequency of optrA (71.4%) in E. faecium and poxtA and crf (42.8%) in E. faecalis were detected among LRE species. A statistically significant relationship (P < 0.05) was found between the presence of the three genes and the occurrence of LRE. Conclusion This is the first study to report the detection of linezolid resistance genes (cfr, optrA, and poxtA) in clinical Enterococcus spp. isolates from Iran, conducted at Isfahan University of Medical Sciences hospitals. The emergence of enterococcal strains that resist linezolid is concerning as it can lead to the spread of resistant strains among patients, resulting in treatment failure.
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Affiliation(s)
- Majid Torabi
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jamshid Faghri
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farkhondeh Poursina
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Yang Q, Zhu Y, Schwarz S, Zhang W, Wang X. Characterization of an optrA-harbouring unconventional circularizable structure located on a novel ICESa2603 family-like integrative and conjugative element ICESsuHN38 in Streptococcus suis. J Antimicrob Chemother 2023:dkad205. [PMID: 37390381 DOI: 10.1093/jac/dkad205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/14/2023] [Indexed: 07/02/2023] Open
Abstract
OBJECTIVES To identify the novel genetic elements involved in the horizontal transfer of the oxazolidinone/phenicol resistance gene optrA in Streptococcus suis. METHODS Whole-genome DNA of the optrA-positive isolate S. suis HN38 was subjected to WGS via both Illumina HiSeq and Oxford Nanopore platforms. MICs of several antimicrobial agents (erythromycin, linezolid, chloramphenicol, florfenicol, rifampicin and tetracycline) were determined by broth microdilution. PCR assays were performed to identify the circular forms of the novel integrative and conjugative element (ICE) ICESsuHN38, but also the unconventional circularizable structure (UCS) excised from this ICE. The transferability of ICESsuHN38 was evaluated by conjugation assays. RESULTS S. suis isolate HN38 harboured the oxazolidinone/phenicol resistance gene optrA. The optrA gene was flanked by two copies of erm(B) genes in the same orientation, located on a novel ICESa2603 family-like ICE, designated ICESsuHN38. PCR assays revealed that a novel UCS carrying the optrA and one copy of erm(B) could be excised from ICESsuHN38. Conjugation assays confirmed that ICESsuHN38 was able to successfully transfer into the recipient strain S. suis BAA. CONCLUSIONS In this work, a novel optrA-carrying mobile genetic element, a UCS, was identified in S. suis. The optrA gene was flanked by copies of erm(B) and its location on the novel ICESsuHN38 will aid its horizontal dissemination.
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Affiliation(s)
- Qin Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yao Zhu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Wanjiang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xiumei Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, 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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Nüesch-Inderbinen M, Biggel M, Haussmann A, Treier A, Heyvaert L, Cernela N, Stephan R. Oxazolidinone resistance genes in florfenicol-resistant enterococci from beef cattle and veal calves at slaughter. Front Microbiol 2023; 14:1150070. [PMID: 37389336 PMCID: PMC10301837 DOI: 10.3389/fmicb.2023.1150070] [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: 01/23/2023] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
Background Linezolid is a critically important oxazolidinone antibiotic used in human medicine. Although linezolid is not licensed for use in food-producing animals, the use of florfenicol in veterinary medicine co-selects for oxazolidinone resistance genes. Objective This study aimed to assess the occurrence of cfr, optrA, and poxtA in florfenicol-resistant isolates from beef cattle and veal calves from different herds in Switzerland. Methods A total of 618 cecal samples taken from beef cattle and veal calves at slaughter originating from 199 herds were cultured after an enrichment step on a selective medium containing 10 mg/L florfenicol. Isolates were screened by PCR for cfr, optrA, and poxtA which are genes known to confer resistance to oxazolidinones and phenicols. One isolate per PCR-positive species and herd was selected for antimicrobial susceptibility testing (AST) and whole-genome sequencing (WGS). Results Overall, 105 florfenicol-resistant isolates were obtained from 99 (16%) of the samples, corresponding to 4% of the beef cattle herds and 24% of the veal calf herds. Screening by PCR revealed the presence of optrA in 95 (90%) and poxtA in 22 (21%) of the isolates. None of the isolates contained cfr. Isolates included for AST and WGS analysis were Enterococcus (E.) faecalis (n = 14), E. faecium (n = 12), E. dispar (n = 1), E. durans (n = 2), E. gallinarum (n = 1), Vagococcus (V.) lutrae (n = 2), Aerococcus (A.) urinaeequi (n = 1), and Companilactobacillus (C.) farciminis (n = 1). Thirteen isolates exhibited phenotypic linezolid resistance. Three novel OptrA variants were identified. Multilocus sequence typing identified four E. faecium ST18 belonging to hospital-associated clade A1. There was a difference in the replicon profile among optrA- and poxtA-harboring plasmids, with rep9 (RepA_N) plasmids dominating in optrA-harboring E. faecalis and rep2 (Inc18) and rep29 (Rep_3) plasmids in poxtA-carrying E. faecium. Conclusion Beef cattle and veal calves are reservoirs for enterococci with acquired linezolid resistance genes optrA and poxtA. The presence of E. faecium ST18 highlights the zoonotic potential of some bovine isolates. The dispersal of clinically relevant oxazolidinone resistance genes throughout a wide variety of species including Enterococcus spp., V. lutrae, A. urinaeequi, and the probiotic C. farciminis in food-producing animals is a public health concern.
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Affiliation(s)
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Adrian Haussmann
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Andrea Treier
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Lore Heyvaert
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, University of Ghent, Ghent, Belgium
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Dai X, Zhao J, Sun J, Chen L, Han P, Wang X, Huang J, Wang L. ICESpsuAH0906, a novel optrA-carrying element conferring resistance to phenicols and oxazolidinones from Streptococcus parasuis, is transferable to Streptococcus suis. Vet Microbiol 2023; 283:109795. [PMID: 37269713 DOI: 10.1016/j.vetmic.2023.109795] [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: 01/31/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/05/2023]
Abstract
Streptococcus parasuis is a potential opportunistic zoonotic pathogen which is a close relative to Streptococcus suis, which exhibit extensive genetic exchange. The occurrence and dissemination of oxazolidinone resistance poses a severe threat to public health. However, such knowledge about the optrA gene in S. parasuis is limited. Herein, we characterized an optrA-positive multi-resistant S. parasuis isolate AH0906, in which the capsular polysaccharide locus exhibited a hybrid structure of S. suis serotype 11 and S. parasuis serotype 26. The optrA and erm(B) genes were co-located on a novel ICE of the ICESsuYZDH1 family, designated ICESpsuAH0906. IS1216E-optrA-carrying translocatable unit could be formed when excised from ICESpsuAH0906. ICESpsuAH0906 was found to be transferable from isolate AH0906 to Streptococcus suis P1/7RF at a relative high frequency of ∼ 10-5. Nonconservative integrations of ICESpsuAH0906 into the primary site SSU0877 and secondary site SSU1797 with 2-/4-nt imperfect direct repeats in recipient P1/7RF were observed. Upon transfer, the transconjugant displayed elevated MICs of the corresponding antimicrobial agents and performed a weak fitness cost when compared with the recipient strain. To our knowledge, it is the first description of the transfer of optrA in S. prarasuis and the first report of interspecies transfer of ICE with triplet serine integrases (of the ICESsuYZDH1 family). Considering the high transmission frequency of the ICEs and the extensive genetic exchange potential of S. parasuis with other streptococci, attention should be paid to the dissemination of the optrA gene from S. parasuis to clinically more important bacterial pathogens.
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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 210095, China
| | - Jiaqi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Peizhao Han
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing 210095, China; Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing 210095, China; Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing 210095, China.
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; Risk Assessment Center of Veterinary Drug Residue and Antimicrobial Resistance, Nanjing Agricultural University, Nanjing 210095, China; Center for Veterinary Drug Research and Evaluation, Nanjing Agricultural University, Nanjing 210095, China.
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Tian T, Yang X, Liu S, Han Z, Qiao W, Li J, Yang M, Zhang Y. Hyper-thermophilic anaerobic pretreatment enhances the removal of transferable oxazolidinone and phenicol cross-resistance gene optrA in enterococci. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 167:92-102. [PMID: 37245400 DOI: 10.1016/j.wasman.2023.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/08/2023] [Accepted: 05/18/2023] [Indexed: 05/30/2023]
Abstract
The extensive use of florfenicol in poultry industry results in the emergence of optrA gene, which also confers resistance to clinically important antibiotic linezolid. This study investigated the occurrence, genetic environments, and removal of optrA in enterococci in mesophilic (37 °C) and thermophilic (55 °C) anaerobic digestion systems, and a hyper-thermophilic (70 °C) anaerobic pretreatment system for chicken waste. A total of 331 enterococci were isolated and analyzed for antibiotic resistance against linezolid and florfenicol. The optrA gene was frequently detected in enterococci from chicken waste (42.7%) and effluents from mesophilic (72%) and thermophilic (56.8%) reactors, but rarely detected in the hyper-thermophilic (5.8%) effluent. Whole-genome sequencing revealed that optrA-carrying Enterococcus faecalis sequence type (ST) 368 and ST631 were the dominant clones in chicken waste, and they remained dominant in mesophilic and thermophilic effluents, respectively. The plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E was the core genetic element for optrA in ST368, whereas chromosomal Tn554-fexA-optrA was the key one in ST631. IS1216E might play a key role in horizontal transfer of optrA due to its presence in different clones. Hyper-thermophilic pretreatment removed enterococci with plasmid-borne IS1216E-fexA-optrA-erm(A)-IS1216E. A hyper-thermophilic pretreatment is recommended for chicken waste to mitigate dissemination of optrA from animal waste to the environment.
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Affiliation(s)
- Tiantian Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Yang
- Department of Municipal and Environmental Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Shihai Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Qiao
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Jiuyi Li
- Department of Municipal and Environmental Engineering, Beijing Jiaotong University, Beijing 100044, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, 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; University of Chinese Academy of Sciences, Beijing 100049, China.
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50
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Ha HTA, Nguyen PTL, Hung TTM, Tuan LA, Thuy BT, Lien THM, Thai PD, Thanh NH, Bich VTN, Anh TH, Hanh NTH, Minh NT, Thanh DP, Mai SNT, The HC, Trung NV, Thu NH, Duong TN, Anh DD, Ngoc PT, Bañuls AL, Choisy M, van Doorn HR, Suzuki M, Hoang TH. Prevalence and Associated Factors of optrA-Positive- Enterococcus faecalis in Different Reservoirs around Farms in Vietnam. Antibiotics (Basel) 2023; 12:954. [PMID: 37370273 PMCID: PMC10294904 DOI: 10.3390/antibiotics12060954] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Linezolid is an antibiotic of last resort for the treatment of infections caused by Gram-positive bacteria, including vancomycin-resistant enterococci. Enterococcus faecalis, a member of enterococci, is a significant pathogen in nosocomial infections. E. faecalis resistance to linezolid is frequently related to the presence of optrA, which is often co-carried with fex, phenicol exporter genes, and erm genes encoding macrolide resistance. Therefore, the common use of antibiotics in veterinary might promote the occurrence of optrA in livestock settings. This is a cross-sectional study aiming to investigate the prevalence of optrA positive E. faecalis (OPEfs) in 6 reservoirs in farms in Ha Nam province, Vietnam, and its associated factors and to explore genetic relationships of OPEfs isolates. Among 639 collected samples, the prevalence of OPEfs was highest in flies, 46.8% (51/109), followed by chickens 37.3% (72/193), dogs 33.3% (17/51), humans 18.7% (26/139), wastewater 16.4% (11/67) and pigs 11.3%, (14/80). The total feeding area and total livestock unit of the farm were associated with the presence of OPEfs in chickens, flies, and wastewater. Among 186 OPEfs strains, 86% were resistant to linezolid. The presence of optrA was also related to the resistant phenotype against linezolid and levofloxacin of E. faecalis isolates. Close genotypic relationships identified by Pulsed Field Gel Electrophoresis between OPEfs isolates recovered from flies and other reservoirs including chickens, pigs, dogs, and wastewater suggested the role of flies in the transmission of antibiotic-resistant pathogens. These results provided warnings of linezolid resistance although it is not used in livestock.
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Affiliation(s)
- Hoang Thi An Ha
- Hanoi Medical University, Hanoi 100000, Vietnam; (H.T.A.H.); (T.H.A.)
- Department of Microbiology, Vinh Medical University, Vinh 431000, Vietnam
| | - Phuong Thi Lan Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Tran Thi Mai Hung
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Le Anh Tuan
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Bui Thanh Thuy
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Tran Hoang My Lien
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Pham Duy Thai
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Nguyen Ha Thanh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Vu Thi Ngoc Bich
- Oxford University Clinical Research Unit, Hanoi 100000, Vietnam; (V.T.N.B.); (H.R.v.D.)
| | - Tran Hai Anh
- Hanoi Medical University, Hanoi 100000, Vietnam; (H.T.A.H.); (T.H.A.)
| | - Ngo Thi Hong Hanh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Nguyen Thi Minh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Duy Pham Thanh
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
| | - Si-Nguyen T. Mai
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
| | - Hao Chung The
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
| | - Nguyen Vu Trung
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City 700000, Vietnam;
| | | | - Tran Nhu Duong
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
| | - Pham Thi Ngoc
- National Institute of Veterinary Research, Hanoi 100000, Vietnam;
| | - Anne-Laure Bañuls
- MIVEGEC (IRD-CNRS-Université de Montpellier), LMI DRISA, Centre IRD, 34394 Montpellier, France;
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City 700000, Vietnam; (D.P.T.); (S.-N.T.M.); (H.C.T.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - H. Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi 100000, Vietnam; (V.T.N.B.); (H.R.v.D.)
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo 162-0052, Japan;
| | - Tran Huy Hoang
- Hanoi Medical University, Hanoi 100000, Vietnam; (H.T.A.H.); (T.H.A.)
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Vietnam; (P.T.L.N.); (T.T.M.H.); (L.A.T.); (B.T.T.); (T.H.M.L.); (P.D.T.); (N.H.T.); (N.T.H.H.); (N.T.M.); (T.N.D.); (D.D.A.)
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