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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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AlJindan R, Mahmoud N, AlEraky DM, Almandil NB, AbdulAzeez S, Borgio JF. Phenomics and genomic features of Enterococcus avium IRMC1622a isolated from a clinical sample of hospitalized patient. J Infect Public Health 2024; 17:102463. [PMID: 38833914 DOI: 10.1016/j.jiph.2024.05.051] [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: 12/08/2023] [Revised: 05/16/2024] [Accepted: 05/26/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Enterococcus avium (E. avium) is a Gram-positive nosocomial pathogen that is commonly isolated from the alimentary tract. The objective of this functional genomics study was to identify the resistant genes by analyzing the genome of E. avium IRMC1622a, a type of bacteria found in feces collected from a patient at a Saudi Arabian tertiary hospital. METHODS The bacterial strain IRMC1622a was identified by 16 S rRNA sequencing as Enterococcus sp. The resistance phenomics were performed using VITEK® 2, and morphological analysis was achieved using a scanning electron microscope (SEM). Finally, the whole bacterial genome of the bacterial strain IRMC1622a was subjected to sequencing during October 2023 using Oxford Nanopore long-read sequencing technology, and mining for resistant genes. RESULTS The results of antimicrobial resistant phenomics indicated that the IRMC1622a strain was sensitive to all tested antimicrobial agents except for erythromycin, and the same result was confirmed by genomic analysis in addition to other classes of antibiotics. SEM showed E. avium IRMC1622a is ovoid shape, in single cells (L 1.2797 ± 0.1490 µm), in pairs (L 1.7333 ± 0.1054 µm), and in chains (L 2.44033 ± 0.1978 µm). The E. avium IRMC1622a genome has 14 (in CARD) antimicrobial resistance genes that were identified with several mechanisms of antimicrobial resistance, such as the efflux pump and conferring antibiotic resistance. The present study revealed that the E. avium IRMC1622a genome contains a high number of genes associated with virulence factors, and 14 matched pathogenic protein families and predicted as human pathogen (probability score 0.855). We report two (ISEnfa4 and ISEfa5) mobile genetic elements for the first time in the E. avium genome. CONCLUSIONS The study concludes that E. avium IRMC1622a is susceptible to all tested antibacterials except erythromycin. The IRMC1622a has 14 genes encoding antimicrobial resistance mechanisms, including the efflux pump and conferring antibiotic resistance. This could indicate a potential rise in E. avium resistance in healthcare facilities. These observations may raise concerns regarding E. avium resistance in healthcare. We need more research to understand the pathophysiology of E. avium, which leads to hospital-acquired infections.
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Affiliation(s)
- Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Nehal Mahmoud
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Doaa M AlEraky
- Department of Biomedical Sciences, College of Medicine, Gulf Medical University, Ajman 4184, United Arab Emirates
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
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Harmer CJ, Hall RM. IS 26 and the IS 26 family: versatile resistance gene movers and genome reorganizers. Microbiol Mol Biol Rev 2024; 88:e0011922. [PMID: 38436262 DOI: 10.1128/mmbr.00119-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Abstract
SUMMARYIn Gram-negative bacteria, the insertion sequence IS26 is highly active in disseminating antibiotic resistance genes. IS26 can recruit a gene or group of genes into the mobile gene pool and support their continued dissemination to new locations by creating pseudo-compound transposons (PCTs) that can be further mobilized by the insertion sequence (IS). IS26 can also enhance expression of adjacent potential resistance genes. IS26 encodes a DDE transposase but has unique properties. It forms cointegrates between two separate DNA molecules using two mechanisms. The well-known copy-in (replicative) route generates an additional IS copy and duplicates the target site. The recently discovered and more efficient and targeted conservative mechanism requires an IS in both participating molecules and does not generate any new sequence. The unit of movement for PCTs, known as a translocatable unit or TU, includes only one IS26. TU formed by homologous recombination between the bounding IS26s can be reincorporated via either cointegration route. However, the targeted conservative reaction is key to generation of arrays of overlapping PCTs seen in resistant pathogens. Using the copy-in route, IS26 can also act on a site in the same DNA molecule, either inverting adjacent DNA or generating an adjacent deletion plus a circular molecule carrying the DNA segment lost and an IS copy. If reincorporated, these circular molecules create a new PCT. IS26 is the best characterized IS in the IS26 family, which includes IS257/IS431, ISSau10, IS1216, IS1006, and IS1008 that are also implicated in spreading resistance genes in Gram-positive and Gram-negative pathogens.
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Affiliation(s)
- Christopher J Harmer
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Wei Y, Palacios Araya D, Palmer KL. Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01058-6. [PMID: 38890478 DOI: 10.1038/s41579-024-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
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Affiliation(s)
- Yahan Wei
- School of Podiatric Medicine, The University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, 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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Yang Y, Xie S, He F, Xu Y, Wang Z, Ihsan A, Wang X. Recent development and fighting strategies for lincosamide antibiotic resistance. Clin Microbiol Rev 2024; 37:e0016123. [PMID: 38634634 DOI: 10.1128/cmr.00161-23] [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] [Indexed: 04/19/2024] Open
Abstract
SUMMARYLincosamides constitute an important class of antibiotics used against a wide range of pathogens, including methicillin-resistant Staphylococcus aureus. However, due to the misuse of lincosamide and co-selection pressure, the resistance to lincosamide has become a serious concern. It is urgently needed to carefully understand the phenomenon and mechanism of lincosamide resistance to effectively prevent and control lincosamide resistance. To date, six mobile lincosamide resistance classes, including lnu, cfr, erm, vga, lsa, and sal, have been identified. These lincosamide resistance genes are frequently found on mobile genetic elements (MGEs), such as plasmids, transposons, integrative and conjugative elements, genomic islands, and prophages. Additionally, MGEs harbor the genes that confer resistance not only to antimicrobial agents of other classes but also to metals and biocides. The ultimate purpose of discovering and summarizing bacterial resistance is to prevent, control, and combat resistance effectively. This review highlights four promising strategies, including chemical modification of antibiotics, the development of antimicrobial peptides, the initiation of bacterial self-destruct program, and antimicrobial stewardship, to fight against resistance and safeguard global health.
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Affiliation(s)
- Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shiyu Xie
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fangjing He
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yindi Xu
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Zhifang Wang
- Institute of Animal Husbandry Research, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal campus, Islamabad, Pakistan
| | - Xu Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, Hubei, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei, China
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Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01054-w. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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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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10
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Singh G, Rana A, Smriti. Decoding antimicrobial resistance: unraveling molecular mechanisms and targeted strategies. Arch Microbiol 2024; 206:280. [PMID: 38805035 DOI: 10.1007/s00203-024-03998-2] [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: 03/31/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Antimicrobial resistance poses a significant global health threat, necessitating innovative approaches for combatting it. This review explores various mechanisms of antimicrobial resistance observed in various strains of bacteria. We examine various strategies, including antimicrobial peptides (AMPs), novel antimicrobial materials, drug delivery systems, vaccines, antibody therapies, and non-traditional antibiotic treatments. Through a comprehensive literature review, the efficacy and challenges of these strategies are evaluated. Findings reveal the potential of AMPs in combating resistance due to their unique mechanisms and lower propensity for resistance development. Additionally, novel drug delivery systems, such as nanoparticles, show promise in enhancing antibiotic efficacy and overcoming resistance mechanisms. Vaccines and antibody therapies offer preventive measures, although challenges exist in their development. Non-traditional antibiotic treatments, including CRISPR-Cas systems, present alternative approaches to combat resistance. Overall, this review underscores the importance of multifaceted strategies and coordinated global efforts to address antimicrobial resistance effectively.
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Affiliation(s)
- Gagandeep Singh
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
| | - Anita Rana
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India.
| | - Smriti
- Department of Biosciences (UIBT), Chandigarh University, Punjab, 140413, India
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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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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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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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Fukuda A, Nakajima C, Suzuki Y, Usui M. Transferable linezolid resistance genes (optrA and poxtA) in enterococci derived from livestock compost at Japanese farms. J Glob Antimicrob Resist 2024; 36:336-344. [PMID: 38336229 DOI: 10.1016/j.jgar.2024.01.022] [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: 08/05/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
OBJECTIVES Linezolid is a last-resort antimicrobial in human clinical settings to treat multidrug-resistant Gram-positive bacterial infections. Mobile linezolid resistance genes (optrA, poxtA, and cfr) have been detected in various sources worldwide. However, the presence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in Japan remains uncertain. Therefore, we clarified the existence of linezolid-not-susceptible bacteria and mobile linezolid resistance genes in farm environments in Japan. METHODS Enterococci isolates from faeces compost collected from 10 pig and 11 cattle farms in Japan in 2021 were tested for antimicrobial susceptibility and possession of mobile linezolid resistance genes. Whole-genome sequencing of optrA and/or poxtA genes positive-enterococci was performed. RESULTS Of 103 enterococci isolates, 12 from pig farm compost were not-susceptible (2 resistant and 10 intermediate) to linezolid. These 12 isolates carried mobile linezolid resistance genes on plasmids or chromosomes (5 optrA-positive Enterococcus faecalis, 6 poxtA-positive E. hirae or E. thailandicus, and 1 optrA- and poxtA-positive E. faecium). The genetic structures of optrA- and poxA-carrying plasmids were almost identical to those reported in other countries. These plasmids were capable of transferring among E. faecium and E. faecalis strains. The optrA- and poxtA-positive E. faecium belonged to ST324 (clade A2), a high-risk multidrug-resistant clone. The E. faecalis carrying optrA gene on its chromosome was identified as ST593. CONCLUSIONS Although linezolid is not used in livestock, linezolid-not-susceptible enterococci could be indirectly selected by frequently used antimicrobials, such as phenicols. Moreover, various enterococci species derived from livestock compost may serve as reservoirs of linezolid resistance genes carried on globally disseminated plasmids and multidrug-resistant high-risk clones.
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Affiliation(s)
- Akira Fukuda
- Department of Health and Environmental Sciences, Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan; Division of Research Support, Hokkaido University Institute for Vaccine Research and Development, Sapporo, Japan
| | - Masaru Usui
- Department of Health and Environmental Sciences, Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan.
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Cuny C, Layer-Nicolaou F, Werner G, Witte W. A look at staphylococci from the one health perspective. Int J Med Microbiol 2024; 314:151604. [PMID: 38367509 DOI: 10.1016/j.ijmm.2024.151604] [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: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 02/19/2024] Open
Abstract
Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.
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Affiliation(s)
- Christiane Cuny
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany.
| | - Franziska Layer-Nicolaou
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, National Reference Centre for Staphylococci and Enterococci, Wernigerode Branch, 38855 Wernigerode, Germany
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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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Kim E, Yang SM, Kwak HS, Moon BY, Lim SK, Kim HY. Genomic characteristics of cfr and fexA carrying Staphylococcus aureus isolated from pig carcasses in Korea. Vet Res 2024; 55:21. [PMID: 38365748 PMCID: PMC10874063 DOI: 10.1186/s13567-024-01278-x] [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] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
The emergence of transferable linezolid resistance genes poses significant challenges to public health, as it does not only confer linezolid resistance but also reduces susceptibility to florfenicol, which is widely used in the veterinary field. This study evaluated the genetic characteristics of linezolid-resistant Staphylococcus aureus strains isolated from pig carcasses and further clarified potential resistance and virulence mechanisms in a newly identified sequence type. Of more than 2500 strains isolated in a prior study, 15 isolated from pig carcasses exhibited linezolid resistance (minimum inhibitory concentration ≥ 8 mg/L). The strains were characterized in detail by genomic analysis. Linezolid-resistant S. aureus strains exhibited a high degree of genetic lineage diversity, with one strain (LNZ_R_SAU_64) belonging to ST8004, which has not been reported previously. The 15 strains carried a total of 21 antibiotic resistance genes, and five carried mecA associated with methicillin resistance. All strains harbored cfr and fexA, which mediate resistance to linezolid, phenicol, and other antibiotics. Moreover, the strains carried enterotoxin gene clusters, including the hemolysin, leukotoxin, and protease genes, which are associated with humans or livestock. Some genes were predicted to be carried in plasmids or flanked by ISSau9 and the transposon Tn554, thus being transmittable between staphylococci. Strains carrying the plasmid replicon repUS5 displayed high sequence similarity (99%) to the previously reported strain pSA737 in human clinical samples in the United States. The results illustrate the need for continuous monitoring of the prevalence and transmission of linezolid-resistant S. aureus isolated from animals and their products.
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Affiliation(s)
- Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Seung-Min Yang
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Hyo-Sun Kwak
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Bo-Youn Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin, 17104, Republic of Korea.
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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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Bender JK, Fleige C, Funk F, Moretó-Castellsagué C, Fischer MA, Werner G. Linezolid Resistance Genes and Mutations among Linezolid-Susceptible Enterococcus spp.-A Loose Cannon? Antibiotics (Basel) 2024; 13:101. [PMID: 38275330 PMCID: PMC10812394 DOI: 10.3390/antibiotics13010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
The National Reference Centre for Enterococci receives an increasing number of linezolid-resistant Enterococcus isolates. Linezolid (LIN) resistance is mediated by G2576T 23S rDNA gene mutations and/or acquisition of resistance genes (cfr, optrA, poxtA). There are anecdotal reports that those resistance traits may be present in phenotypically linezolid-susceptible isolates. We aimed to determine the prevalence of LIN resistance genes and mutations in enterococci with a LIN MIC of 4 mg/L in broth microdilution (EUCAST = susceptible) isolated from German hospital patients 2019-2021. LIN MICs were additionally determined by ETEST® and VITEK2. Selected strains were subjected to LIN selective pressure and growth was monitored with increasing antibiotic concentrations. We received 195 isolates (LIN MIC = 4 mg/L). In total, 78/195 (40%) isolates contained either a putative resistance gene, the G2576T mutation, or a combination thereof. Very major error was high for broth microdilution. The ability to predict phenotypic resistance from genotypic profile was highest for G2576T-mediated resistance. Selection experiments revealed that, in particular, E. faecium isolates with resistance gene mutations or poxtA rapidly adapt to MICs above the clinical breakpoint. In conclusion, LIN resistance genes and mutations can be observed in phenotypically linezolid-susceptible enterococci. Those isolates may rapidly develop resistance under LIN selective pressure potentially leading to treatment failure.
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Affiliation(s)
- Jennifer K. Bender
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Carola Fleige
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Finn Funk
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Clara Moretó-Castellsagué
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
- Department of Microbiology and Parasitology, University Hospital of Bellvitge, 08907 Barcelona, Spain
| | - Martin A. Fischer
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
| | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, Robert Koch Institute, 38855 Wernigerode, Germany (F.F.); (C.M.-C.); (M.A.F.); (G.W.)
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21
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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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22
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Nandivarmane SB, Manoharan M, Sugumar M, Sistla S. Evaluation of different linezolid susceptibility testing methods and detection of linezolid resistance gene (cfr) in staphylococcal isolates. Indian J Med Microbiol 2024; 47:100516. [PMID: 38000621 DOI: 10.1016/j.ijmmb.2023.100516] [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: 09/16/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Linezolid is an effective oxazolidinone antibiotic against multi resistant Gram-positive organisms. Linezolid resistance is an emerging problem and some controversy exists about the reliability of different phenotypic methods of linezolid susceptibility testing. Fifty isolates each of methicillin resistant S. aureus (MRSA) and Staphylococcus haemolyticus were tested for linezolid susceptibility using Kirby-Bauer disc diffusion, E-test, automated system VITEK2, Broth micro-dilution (reference method) and PCR for the cfr gene. Six resistant isolates were identified, three each in MRSA and S. haemolyticus, all carrying the cfr gene. E-test and VITEK2 were found to be more accurate than disc diffusion test.
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Affiliation(s)
- Sudarsan Bagavane Nandivarmane
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India.
| | - Meerabai Manoharan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India.
| | - Madhan Sugumar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India.
| | - Sujatha Sistla
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India.
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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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24
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Wang J, Jiang Y, Tian YQ, Qin YY, Jiao X, Pan ZM. Detection of cfr in Klebsiella pneumoniae from pig feed in China. J Antimicrob Chemother 2023; 78:2774-2776. [PMID: 37610381 DOI: 10.1093/jac/dkad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Affiliation(s)
- Jing Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Yue Jiang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yu-Qi Tian
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yan-Ying Qin
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Zhi-Ming Pan
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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Yao H, Xing H, Wang N, Zhang L, Schwarz S, Li C, Cai C, Xu C, Du XD. IS257-mediated amplification of tet(L) variant as a novel mechanism of enhanced tigecycline resistance in Staphylococcus cohnii. Res Microbiol 2023; 174:104114. [PMID: 37572822 DOI: 10.1016/j.resmic.2023.104114] [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: 04/03/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The mechanism of enhanced tigecycline MIC in Staphylococcus cohnii after in vitro tigecycline exposure was investigated. S. cohnii 11-B-312 was exposed to incremental concentrations of tigecycline (2-32 mg/L) and the mutants growing at 8, 16 and 32 mg/L were determined by AST and WGS. Copy number and relative transcription level of the tet(L) gene were determined by quantitative PCR. The fitness cost was evaluated by growth kinetics and competition assays. The results revealed that enhanced tigecycline MIC was identified in S. cohnii mutants. Copy number and relative transcription level of tet(L) in the mutants increased 8-, 20-, and 23-fold and 20-, 34-, and 39-fold in the presence of 8, 16, and 32 mg/L tigecycline, respectively. The read-mapping depth ratio analysis indicated that a multidrug resistance region carrying the tet(L) variant has a gradually increased copy number, correlating with the tigecycline selection pressure. S. cohnii strain 11-B-312_32 had a fitness cost, and enhanced tigecycline MIC can revert to the initial level in the absence of tigecycline. In summary, enhanced tigecycline MIC develops with extensive amplification of an IS257-flanked tet(L)-carrying segment in S. cohnii. IS257 seems to play a vital role in the gain and loss of the amplification product.
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Affiliation(s)
- Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Hongjie Xing
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Nannan Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Likuan Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre of Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Chenglong Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Chang Cai
- College of Arts, Business, Law and Social Sciences, Murdoch University, Murdoch, WA, Australia
| | - Chunyan Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China.
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China.
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Wardal E, Żabicka D, Skalski T, Kubiak-Pulkowska J, Hryniewicz W, Sadowy E. Characterization of a Tigecycline-, Linezolid- and Vancomycin-Resistant Clinical Enteroccoccus faecium Isolate, Carrying vanA and vanB Genes. Infect Dis Ther 2023; 12:2545-2565. [PMID: 37821741 PMCID: PMC10651664 DOI: 10.1007/s40121-023-00881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 09/22/2023] [Indexed: 10/13/2023] Open
Abstract
INTRODUCTION Increasing incidence of Enterococcus faecium resistant to key antimicrobials used in therapy of hospitalized patients is a worrisome phenomenon observed worldwide. Our aim was to characterize a tigecycline-, linezolid- and vancomycin-resistant E. faecium isolate with the vanA and vanB genes, originating from a hematoma of a patient hospitalized in an intensive care unit in Poland. METHODS Antimicrobial susceptibility (a broad panel) was tested using gradient tests with predefined antibiotic concentrations. The complete genome sequence was obtained from a mixed assembly of Illumina MiSeq and Oxford Nanopore's MinION reads. The genome was analyzed with appropriate tools available at the Center for Genomic Epidemiology, PubMLST and GenBank. Transferability of oxazolidinone, tigecycline and vancomycin resistance genes was investigated by conjugation, followed by PCR screen of transconjugants for antimicrobial resistance genes and plasmid rep genes characteristic for the donor and genomic sequencing of selected transconjugants. RESULTS The isolate was resistant to most antimicrobials tested; susceptibility to daptomycin, erythromycin and chloramphenicol was significantly reduced, and only oritavancin retained the full activity. The isolate represented sequence type 18 (ST18) and carried vanA, vanB, poxtA, fexB, tet(L), tet(M), aac(6')-aph(2''), ant(6)-Ia and ant(6')-Ii. The vanA, poxtA and tet(M) genes located on ~ 40-kb plasmids were transferable by conjugation yielding transconjugants resistant to vancomycin, linezolid and tigecycline. The substitutions in LiaS, putative histidine kinase, SulP, putative sulfate transporter, RpoB and RpoC were potential determinants of an elevated daptomycin MIC. Comparative analyses of the studied isolate with E. faecium isolates from other countries revealed its similarity to ST18 isolates from Ireland and Uganda from human infections. CONCLUSIONS We provide the detailed characteristics of the genomic determinants of antimicrobial resistance of a clinical E. faecium demonstrating the concomitant presence of both vanA and vanB and resistance to vancomycin, linezolid, tigecycline and several other compounds and decreased daptomycin susceptibility. This isolate is a striking example of an accumulation of resistance determinants involving various mechanisms by a single hospital strain.
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Affiliation(s)
- Ewa Wardal
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Tomasz Skalski
- Department of Clinical Microbiology and Molecular Diagnostics, University Hospital No 2, ul. Ujejskiego 75, Bydgoszcz, Poland
| | - Joanna Kubiak-Pulkowska
- Department of Clinical Microbiology and Molecular Diagnostics, University Hospital No 2, ul. Ujejskiego 75, Bydgoszcz, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland.
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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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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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29
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Kostova V, Hanke D, Schink AK, Kaspar H, Schwarz S, Krüger-Haker H. ICE-borne erm(T)-mediated macrolide resistance in Mannheimia haemolytica. J Antimicrob Chemother 2023; 78:2379-2381. [PMID: 37533327 DOI: 10.1093/jac/dkad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023] Open
Affiliation(s)
- Valeria Kostova
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | | | - Heike Kaspar
- Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Henrike Krüger-Haker
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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30
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Bender JK, Baufeld E, Becker K, Claus H, Dudakova A, Dörre A, Fila N, Fleige C, Hamprecht A, Hoffmann A, Hogardt M, Kaasch AJ, Kola A, Kriebel N, Layer-Nicolaou F, Marschal M, Molitor E, Mutters NT, Liese J, Nelkenbrecher C, Neumann B, Rohde H, Steinmann J, Sörensen M, Thelen P, Weig M, Zautner AE, Werner G. CHROMAgar™ LIN-R as an efficient screening tool to assess the prevalence of linezolid-resistant enterococci in German hospital patients-a multicentre study approach, 2021-2022. J Antimicrob Chemother 2023; 78:2185-2191. [PMID: 37473450 PMCID: PMC10477123 DOI: 10.1093/jac/dkad218] [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: 04/16/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND In recent years, an increasing number of linezolid-resistant enterococci (LRE) was recognized at the German National Reference Centre (NRC) for Enterococci. National guidelines on infection prevention recommend screening for LRE in epidemiologically linked hospital settings without referring to a reliable and rapid diagnostic method. Since 2020, CHROMAgar™ provide a chromogenic linezolid screening agar, LIN-R, suitable to simultaneously screen for linezolid-resistant staphylococci and enterococci. OBJECTIVES To assess the applicability of CHROMAgar™ LIN-R in clinical settings for detecting LRE directly from patient material and to infer prevalence rates of LRE amongst German hospital patients. METHODS During the 3-month trial period, clinical samples were plated on CHROMAgar™ LIN-R. Antimicrobial susceptibility testing was performed using VITEK2 or disc diffusion. At the NRC, linezolid resistance was determined by broth microdilution, multiplex-PCR for cfr/optrA/poxtA and by a restriction-based assay for 23S rDNA mutations. RESULTS The 12 participating study sites used 13 963 CHROMAgar™ LIN-R plates during the study period. Of 442 presumptive LRE, 192 were confirmed by phenotypic methods. Of these, 161 were received by the NRC and 121 (75%) were verified as LRE. Most of LR-E. faecium 53/81 (65%) exhibited a 23S rRNA gene mutation as the sole resistance-mediating mechanism, whereas optrA constituted the dominant resistance trait in LR-E. faecalis [39/40 (98%)]. Prevalence of LRE across sites was estimated as 1% (ranging 0.18%-3.7% between sites). CONCLUSIONS CHROMAgar™ LIN-R represents a simple and efficient LRE screening tool in hospital settings. A high proportion of false-positive results demands validation of linezolid resistance by a reference method.
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Affiliation(s)
- Jennifer K Bender
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Elsa Baufeld
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Heike Claus
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Anna Dudakova
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Achim Dörre
- Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Nikoletta Fila
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Carola Fleige
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg and Klinikum Oldenburg, Oldenburg, Germany
| | - Armin Hoffmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Hogardt
- Institute of Medical Microbiology and Infection Control, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Achim J Kaasch
- Faculty of Medicine, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke-University, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nancy Kriebel
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Franziska Layer-Nicolaou
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
| | - Matthias Marschal
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Ernst Molitor
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Nico T Mutters
- Institute for Hygiene and Public Health, University Hospital Bonn, Bonn, Germany
| | - Jan Liese
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Claudia Nelkenbrecher
- Institute of Hospital Hygiene, Medical Microbiology and Infectious Diseases, Nuremberg General Hospital, Paracelsus Medical University, Nuremberg, Germany
| | - Bernd Neumann
- Institute of Hospital Hygiene, Medical Microbiology and Infectious Diseases, Nuremberg General Hospital, Paracelsus Medical University, Nuremberg, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jörg Steinmann
- Institute of Hospital Hygiene, Medical Microbiology and Infectious Diseases, Nuremberg General Hospital, Paracelsus Medical University, Nuremberg, Germany
| | - Michael Sörensen
- Laboratory Prof. Gisela Enders and Colleagues, Stuttgart, Germany
| | - Philipp Thelen
- Institute for Medical Microbiology and Virology, Carl von Ossietzky University Oldenburg and Klinikum Oldenburg, Oldenburg, Germany
| | - Michael Weig
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
| | - Andreas E Zautner
- Faculty of Medicine, Institute of Medical Microbiology and Hospital Hygiene, Otto-von-Guericke-University, Magdeburg, Germany
- Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Guido Werner
- Nosocomial Pathogens and Antibiotic Resistances Unit, Department of Infectious Diseases, National Reference Centre for Staphylococci and Enterococci, Robert Koch Institute, Wernigerode, Germany
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Cinthi M, Coccitto SN, Simoni S, Vignaroli C, Brenciani A, Giovanetti E. An Enterococcus faecium Isolated from Bovine Feces in Italy Shares optrA- and poxtA-Carrying Plasmids with Enterococci from Switzerland. Microb Drug Resist 2023; 29:438-442. [PMID: 37523292 DOI: 10.1089/mdr.2023.0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023] Open
Abstract
To investigate the occurrence of oxazolidinone resistance genes, 18 florfenicol-resistant enterococci were isolated from 66 fecal samples collected from several cattle farms in central Italy. The PCR screening indicated that only a bovine florfenicol-resistant isolate, Enterococcus faecium 249031-C, was positive for the presence of optrA and poxtA genes. The strain was tested for its susceptibility to florfenicol, chloramphenicol, linezolid, tedizolid, tetracycline, erythromycin, and vancomycin. Whole Genome Sequencing analysis showed that E. faecium 249031-C, belonging to the ST22 lineage, harbored two plasmids: the optrA-carrying p249031-S (179 kb) and the poxtA-carrying p1818-c (23 kb). p249031-S, containing a new optrA-carrying Tn7695 transposon, was closely related to the plasmid pF88_1 of E. faecium F88, whereas p1818-c had already been detected in a human E. faecium, both enterococci were from Switzerland. The linezolid resistance genes were cotransferred to the E. faecium 64/3 recipient. Circular forms from both optrA- and poxtA-carrying genetic contexts were obtained. The occurrence of oxazolidinone resistance genes in a bovine E. faecium isolate and their localization on conjugative and mobilizable plasmids pose a risk for public health.
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Affiliation(s)
- Marzia Cinthi
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
| | - Sonia Nina Coccitto
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Serena Simoni
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences and Polytechnic University of Marche, Ancona, Italy
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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: 0] [Impact Index Per Article: 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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Krüger-Haker H, Ji X, Hanke D, Fiedler S, Feßler AT, Jiang N, Kaspar H, Wang Y, Wu C, Schwarz S. Genomic Diversity of Methicillin-Resistant Staphylococcus aureus CC398 Isolates Collected from Diseased Swine in the German National Resistance Monitoring Program GE RM-Vet from 2007 to 2019. Microbiol Spectr 2023; 11:e0077023. [PMID: 37154741 PMCID: PMC10269607 DOI: 10.1128/spectrum.00770-23] [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: 02/20/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023] Open
Abstract
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 (CC398) isolates (n = 178) collected in the national resistance monitoring program GERM-Vet from diseased swine in Germany from 2007 to 2019 were investigated for their genomic diversity with a focus on virulence and antimicrobial resistance (AMR) traits. Whole-genome sequencing was followed by molecular typing and sequence analysis. A minimum spanning tree based on core-genome multilocus sequence typing was constructed, and antimicrobial susceptibility testing was performed. Most isolates were assigned to nine clusters. They displayed close phylogenetic relationships but a wide molecular variety, including 13 spa types and 19 known and four novel dru types. Several toxin-encoding genes, including eta, seb, sek, sep, and seq, were detected. The isolates harbored a wide range of AMR properties mirroring the proportions of the classes of antimicrobial agents applied in veterinary medicine in Germany. Multiple novel or rare AMR genes were identified, including the phenicol-lincosamide-oxazolidinone-pleuromutilin-streptogramin A resistance gene cfr, the lincosamide-pleuromutilin-streptogramin A resistance gene vga(C), and the novel macrolide-lincosamide-streptogramin B resistance gene erm(54). Many AMR genes were part of small transposons or plasmids. Clonal and geographical correlations of molecular characteristics and resistance and virulence genes were more frequently observed than temporal relations. In conclusion, this study provides insight into population dynamics of the main epidemic porcine LA-MRSA lineage in Germany over a 13-year-period. The observed comprehensive AMR and virulence properties, most likely resulting from the exchange of genetic material between bacteria, highlighted the importance of LA-MRSA surveillance to prevent further dissemination among swine husbandry facilities and entry into the human community. IMPORTANCE The LA-MRSA-CC398 lineage is known for its low host specificity and frequent multiresistance to antimicrobial agents. Colonized swine and their related surroundings represent a considerable risk of LA-MRSA-CC398 colonization or infection for occupationally exposed people through which such isolates might be further disseminated within the human community. This study provides insight into the diversity of the porcine LA-MRSA-CC398 lineage in Germany. Clonal and geographical correlations of molecular characteristics and resistance and virulence traits were detected and may be associated with the spread of specific isolates through livestock trade, human occupational exposure, or dust emission. The demonstrated genetic variability underlines the lineage's ability to horizontally acquire foreign genetic material. Thus, LA-MRSA-CC398 isolates have the potential to become even more dangerous for various host species, including humans, due to increased virulence and/or limited therapeutic options for infection control. Full-scale LA-MRSA monitoring at the farm, community, and hospital level is therefore essential.
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Affiliation(s)
- Henrike Krüger-Haker
- 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
| | - Xing Ji
- Jiangsu Key Laboratory for Food Quality and Safety, State Key Laboratory, Cultivation Base of Ministry of Science and Technology, Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Dennis Hanke
- 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
| | - Stefan Fiedler
- Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Andrea T. Feßler
- 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
| | - Nansong Jiang
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, MARA, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Heike Kaspar
- Federal Office of Consumer Protection and Food Safety (BVL), Berlin, Germany
| | - Yang Wang
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, MARA, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Congming Wu
- Key Laboratory of Animal Antimicrobial Resistance Surveillance, MARA, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - 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, 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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Werner G, Abu Sin M, Bahrs C, Brogden S, Feßler AT, Hagel S, Kaspar H, Köck R, Kreienbrock L, Krüger-Haker H, Maechler F, Noll I, Pletz MW, Tenhagen BA, Schwarz S, Walther B, Mielke M. [Therapy-relevant antibiotic resistances in a One Health context]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023:10.1007/s00103-023-03713-4. [PMID: 37184673 DOI: 10.1007/s00103-023-03713-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023]
Abstract
One Health refers to a concept that links human, animal, and environmental health. In Germany, there is extensive data on antibiotic resistance (AMR) and multidrug-resistant (micro)organisms (MDRO) in human and veterinary medicine, as well as from studies in various environmental compartments (soil, water, wastewater). All these activities are conducted according to different specifications and standards, which makes it difficult to compare data. A focus on AMR and MDRO of human therapeutic importance is helpful to provide some guidance. Most data are available across sectors on methicillin-resistant Staphylococcus aureus (MRSA) and multiresistant Enterobacterales such as Escherichia coli and Klebsiella pneumoniae. Here, the trends of resistance are heterogeneous. Antibiotic use leads to MRE selection, which is well documented. Success in minimizing antibiotic use has also been demonstrated in recent years in several sectors and could be correlated with success in containing AMR and MDRO (e.g., decrease in MRSA in human medicine). Sector-specific measures to reduce the burden of MDRO and AMR are also necessary, as not all resistance problems are linked to other sectors. Carbapenem resistance is still rare, but most apparent in human pathogens. Colistin resistance occurs in different sectors but shows different mechanisms in each. Resistance to antibiotics of last resort such as linezolid is rare in Germany, but shows a specific One Health correlation. Efforts to harmonize methods, for example in the field of antimicrobial susceptibility testing and genome-based pathogen and AMR surveillance, are an important first step towards a better comparability of the different data collections.
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Affiliation(s)
- Guido Werner
- Robert Koch Institut, Berlin, Deutschland.
- Abt. Infektionskrankheiten, Fachgebiet Nosokomiale Infektionserreger und Antibiotikaresistenzen, Robert Koch-Institut, Außenstelle Wernigerode, Burgstr. 37, 38855, Wernigerode, Deutschland.
| | - Muna Abu Sin
- Robert Koch Institut, Berlin, Deutschland
- WHO Collaborating Centre for Antimicrobial Resistance, Consumption and Healthcare-Associated Infections, Berlin, Deutschland
| | - Christina Bahrs
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - Sandra Brogden
- Institut für Biometrie, Epidemiologie und Informationsverarbeitung, Stiftung Tierärztliche Hochschule Hannover, Hannover, Deutschland
- WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, Hannover, Deutschland
| | - Andrea T Feßler
- Institut für Mikrobiologie und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
- Tiermedizinisches Zentrum für Resistenzforschung (TZR), Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
| | - Stefan Hagel
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - Heike Kaspar
- Bundesamt für Verbraucherschutz und Lebensmittelsicherheit, Berlin, Deutschland
| | - Robin Köck
- Bereich Hygiene und Umweltmedizin, Universitätsmedizin Essen, Essen, Deutschland
- Institut für Hygiene, Universitätsklinikum Münster, Münster, Deutschland
| | - Lothar Kreienbrock
- Institut für Biometrie, Epidemiologie und Informationsverarbeitung, Stiftung Tierärztliche Hochschule Hannover, Hannover, Deutschland
- WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, Hannover, Deutschland
| | - Henrike Krüger-Haker
- Institut für Mikrobiologie und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
- Tiermedizinisches Zentrum für Resistenzforschung (TZR), Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
| | - Frederike Maechler
- Institut für Hygiene und Umweltmedizin, Charité - Universitätsmedizin Berlin, Berlin, Deutschland
| | - Ines Noll
- Robert Koch Institut, Berlin, Deutschland
- WHO Collaborating Centre for Antimicrobial Resistance, Consumption and Healthcare-Associated Infections, Berlin, Deutschland
| | - Mathias W Pletz
- Institut für Infektionsmedizin und Krankenhaushygiene, Universitätsklinikum Jena, Jena, Deutschland
| | - Bernd-Alois Tenhagen
- Fachbereich Epidemiologie, Zoonosen und Antibiotikaresistenz, Abteilung Biologische Sicherheit, Bundesinstitut für Risikobewertung BfR, Berlin, Deutschland
| | - Stefan Schwarz
- Institut für Mikrobiologie und Tierseuchen, Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
- Tiermedizinisches Zentrum für Resistenzforschung (TZR), Fachbereich Veterinärmedizin, Freie Universität Berlin, Berlin, Deutschland
| | - Birgit Walther
- Robert Koch Institut, Berlin, Deutschland
- Fachgebiet Mikrobiologische Risiken, Abteilung Umwelthygiene, Umweltbundesamt, Berlin, Deutschland
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 195] [Impact Index Per Article: 195.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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Han N, Li J, Wan P, Pan Y, Xu T, Xiong W, Zeng Z. Co-Existence of Oxazolidinone Resistance Genes cfr(D) and optrA on Two Streptococcus parasuis Isolates from Swine. Antibiotics (Basel) 2023; 12:antibiotics12050825. [PMID: 37237728 DOI: 10.3390/antibiotics12050825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
This study was performed to investigate the presence and characteristics of the oxazolidinone resistance genes optrA and cfr(D) in Streptococcus parasuis. In total, 36 Streptococcus isolates (30 Streptococcus suis isolates, 6 Streptococcus parasuis isolates) were collected from pig farms in China in 2020-2021, using PCR to determine the presence of optrA and cfr. Then, 2 of the 36 Streptococcus isolates were further processed as follows. Whole-genome sequencing and de novo assembly were employed to analyze the genetic environment of the optrA and cfr(D) genes. Conjugation and inverse PCR were employed to verify the transferability of optrA and cfr(D). The optrA and cfr(D) genes were identified in two S. parasuis strains named SS17 and SS20, respectively. The optrA of the two isolates was located on chromosomes invariably associated with the araC gene and Tn554, which carry the resistance genes erm(A) and ant(9). The two plasmids that carry cfr(D), pSS17 (7550 bp) and pSS20-1 (7550 bp) have 100% nucleotide sequence identity. The cfr(D) was flanked by GMP synthase and IS1202. The findings of this study extend the current knowledge of the genetic background of optrA and cfr(D) and indicate that Tn554 and IS1202 may play an important role in the transmission of optrA and cfr(D), respectively.
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Affiliation(s)
- Ning Han
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Peng Wan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Yu Pan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Tiantian Xu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wenguang Xiong
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhenling Zeng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
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Coccitto SN, Cinthi M, Simoni S, Vignaroli C, Massacci FR, Albini E, Garofalo C, Aquilanti L, Magistrali CF, Brenciani A, Giovanetti E. Identification of plasmids co-carrying cfr(D)/optrA and cfr(D2)/poxtA linezolid resistance genes in two Enterococcus avium isolates from swine brain. Vet Microbiol 2023; 282:109749. [PMID: 37116421 DOI: 10.1016/j.vetmic.2023.109749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 04/30/2023]
Abstract
Oxazolidinones are critically important antibiotics to treat human infections caused by multidrug-resistant bacteria, therefore the occurrence of linezolid-resistant enterococci from food-producing animals poses a serious risk to human health. In this study, Enterococcus avium 38157 and 44917 strains, isolated from the brain of two unrelated piglets, were found to carry the linezolid resistance genes cfr(D)-optrA, and cfr(D2)-poxtA, respectively. Whole genome sequencing analysis of E. avium 38157 revealed that the genes were co-located on the 36.5-kb pEa_cfr(D)-optrA plasmid showing high identity with the pAT02-c of Enterococcus faecium AT02 from pet food. The optrA region, was 99% identical to the one of the pAv-optrA plasmid from a bovine Aerococcus viridans strain, whereas the cfr(D) genetic context was identical to that of the plasmid 2 of E. faecium 15-307.1. pEa_cfr(D)-optrA was not transferable to enterococcal recipients. In E. avium 44917 a cfr(D)-like gene, named cfr(D2), and the poxtA gene were co-located on the transferable 42.6-kb pEa-cfr(D2)-poxtA plasmid 97% identical to the Tn6349 transposon of the human MRSA AOUC-0915. The cfr(D2) genetic context, fully replaced the Tn6644 that in S. aureus AOUC-0915 harbor the cfr gene. In conclusion, this is, the best of our knowledge, the first report of the new cfr(D2) gene variant. The occurrence of plasmids co-carrying two linezolid resistance genes in enterococci from food-producing animals needs close surveillance to prevent their spread to human pathogens.
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Affiliation(s)
- Sonia Nina Coccitto
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marzia Cinthi
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Serena Simoni
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesca Romana Massacci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) 'Togo Rosati', Perugia, Italy
| | - Elisa Albini
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM) 'Togo Rosati', Perugia, Italy
| | - Cristiana Garofalo
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Lucia Aquilanti
- Department of Agricultural, Food and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy.
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Deng L, Zhen W, Wang J, Lin D. Bile Carriage of optrA-Positive Enterococcus faecium in a Patient with Choledocholith. Microbiol Spectr 2023; 11:e0285222. [PMID: 36976027 PMCID: PMC10101025 DOI: 10.1128/spectrum.02852-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
We isolated one Enterococcus faecium isolate SZ21B15 from a bile sample of a patient with choledocholith in Shenzhen, China in 2021. It was positive for oxazolidinone resistance gene optrA and was intermediate to linezolid. The whole genome of E. faecium SZ21B15 was sequenced by Illumina Hiseq. It belonged to ST533 within the clonal complex 17. The optrA gene and additional two resistance genes fexA and erm(A) were located within a 25,777-bp multiresistance region, which was inserted into the chromosomal radC gene, being chromosomal intrinsic resistance genes. The chromosomal optrA gene cluster found in E. faecium SZ21B15 was closely related to the corresponding regions of multiple optrA-carrying plasmids or chromosomes from Enterococcus, Listeria, Staphylococcus, and Lactococcus strains. It further highlights the ability of the optrA cluster that transfers between plasmids and chromosomes and evolves by a series of molecular recombination events. IMPORTANCE Oxazolidinone are effective antimicrobial agents for the treatment of infections caused by multidrug-resistant Gram-positive bacteria, including vancomycin-resistant enterococci. The emergence and global spread of transferable oxazolidinone resistance genes such as optrA is worrisome. Enterococcus spp. can become causes of hospital-associated infections and are also widely distributed in the gastrointestinal tracts of animals and the natural environment. In this study, one E. faecium isolate from bile sample carried chromosomal optrA, being intrinsic resistance gene. optrA-positive E. faecium in bile not only makes the treatment of gallstones difficult, but also may become a reservoir of resistance genes in the body.
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Affiliation(s)
- Li Deng
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Wendong Zhen
- Department of Laboratory Medicine, Shenzhen University General Hospital, Shenzhen University, Shenzhen, China
| | - Jing Wang
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Dachuan Lin
- Guangdong Key Laboratory of Regional Immunity and Diseases, Shenzhen University School of Medicine, Shenzhen University, Shenzhen, China
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Yuan S, Shen DD, Bai YR, Zhang M, Zhou T, Sun C, Zhou L, Wang SQ, Liu HM. Oxazolidinone: A promising scaffold for the development of antibacterial drugs. Eur J Med Chem 2023; 250:115239. [PMID: 36893700 DOI: 10.1016/j.ejmech.2023.115239] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023]
Abstract
Due to the long-term and widespread use of antibiotics in clinic, the problem of bacterial resistance is increasingly serious, and the development of new drugs to treat drug-resistant bacteria has gradually become the mainstream direction of antibiotic research. The oxazolidinone-containing drugs linezolid, tedizolid phosphate and contezolid have been approved to the market, which are effective against a variety of Gram-positive bacterium infections. Moreover, there are also many antibiotics containing oxazolidinone fragment under clinical investigation that show good pharmacokinetic and pharmacodynamic properties with unique mechanism of action against resistant bacteria. In this review, we summarized the oxazolidinone-based antibiotics already on the market or in clinical trials and the representative bioactive molecules, and mainly focused on their structural optimizations, development strategies and structure-activity relationships in hope of insight into the reasonable design for medical chemists to develop new oxazolidinone antibiotics with highly potency and fewer side effects.
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Affiliation(s)
- Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
| | - Dan-Dan Shen
- Department of Obstetrics and Gynecology, Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment Zhengzhou China, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yi-Ru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Miao Zhang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Tian Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Chong Sun
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Li Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Sai-Qi Wang
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer, Zhengzhou Key Laboratory of Precision Therapy of Gastrointestinal Cancer, Zhengzhou, 450008, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
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Abdullahi IN, Lozano C, Juárez-Fernández G, Höfle U, Simón C, Rueda S, Martínez A, Álvarez-Martínez S, Eguizábal P, Martínez-Cámara B, Zarazaga M, Torres C. Nasotracheal enterococcal carriage and resistomes: detection of optrA-, poxtA- and cfrD-carrying strains in migratory birds, livestock, pets, and in-contact humans in Spain. Eur J Clin Microbiol Infect Dis 2023; 42:569-581. [PMID: 36890281 PMCID: PMC10105672 DOI: 10.1007/s10096-023-04579-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/16/2023] [Indexed: 03/10/2023]
Abstract
This study determined the carriage rates and antimicrobial resistance (AMR) genes of enterococci from nasotracheal samples of three healthy animal species and in-contact humans. Nasal samples were collected from 27 dog-owning households (34 dogs, 41 humans) and 4 pig-farms (40 pigs, 10 pig-farmers), and they were processed for enterococci recovery (MALDI-TOF-MS identification). Also, a collection of 144 enterococci previously recovered of tracheal/nasal samples from 87 white stork nestlings were characterized. The AMR phenotypes were determined in all enterococci and AMR genes were studied by PCR/sequencing. MultiLocus-Sequence-Typing was performed for selected isolates. About 72.5% and 60% of the pigs and pig-farmers, and 29.4% and 4.9%, of healthy dogs and owners were enterococci nasal carriers, respectively. In storks, 43.5% of tracheal and 69.2% of nasal samples had enterococci carriages. Enterococci carrying multidrug-resistance phenotype was identified in 72.5%/40.0%/50.0%/23.5%/1.1% of pigs/pig-farmers/dogs/dogs' owners/storks, respectively. Of special relevance was the detection of linezolid-resistant enterococci (LRE) in (a) 33.3% of pigs (E. faecalis-carrying optrA and/or cfrD of ST59, ST330 or ST474 lineages; E. casseliflavus-carrying optrA and cfrD); (b) 10% of pig farmers (E. faecalis-ST330-carrying optrA); (c) 2.9% of dogs (E. faecalis-ST585-carrying optrA); and (d) 1.7% of storks (E. faecium-ST1736-carrying poxtA). The fexA gene was found in all optrA-positive E. faecalis and E. casseliflavus isolates, while fexB was detected in the poxtA-positive E. faecium isolate. The enterococci diversity and AMR rates from the four hosts reflect differences in antimicrobial selection pressure. The detection of LRE carrying acquired and transferable genes in all the hosts emphasizes the need to monitor LRE using a One-Health approach.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Guillermo Juárez-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Ursula Höfle
- Spanish Wildlife Research Institute IREC (CSIC-UCLM-JCCM), SaBio (Health and Biotechnology) Research Group, Ciudad Real, Spain
| | - Carmen Simón
- Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
| | - Silvia Rueda
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Angela Martínez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Sandra Álvarez-Martínez
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Paula Eguizábal
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Beatriz Martínez-Cámara
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, Logroño, 26006, Spain.
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Iurescia M, Diaconu EL, Alba P, Feltrin F, Buccella C, Onorati R, Giacomi A, Caprioli A, Franco A, Battisti A, Carfora V. Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings. Antibiotics (Basel) 2023; 12:antibiotics12030530. [PMID: 36978397 PMCID: PMC10044604 DOI: 10.3390/antibiotics12030530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023] Open
Abstract
The cfr genes encode for a 23S rRNA methyltransferase, conferring a multiresistance phenotype to phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A antibiotics. These genes have been described in staphylococci, including methicillin-resistant Staphylococcus aureus (MRSA). In this study, we retrospectively performed an in-depth genomic characterisation of three cfr-positive, multidrug-resistant (MDR) livestock-associated (LA) MRSA clonal complexes (CCs) 1 and 398 detected in different Italian pig holdings (2008–2011) during population studies on Italian livestock (2008–2014). We used a combined Illumina and Oxford Nanopore Technologies (ONT) whole genome sequencing (WGS) approach on two isolates (the 2008 CC1 and the 2010 CC398 isolates, but not the 2011 CC1 isolate). Interestingly, the three isolates presented different cfr variants, with only one displaying a linezolid-resistant phenotype. In isolate 2008 CC1, the cfr gene was identified within a Tn558 composite transposon-like structure flanked by IS elements located on a novel 44,826 bp plasmid. This represents the first report of CC1 LA-MRSA harbouring the cfr gene in its functional variant. Differently, cfr was chromosomally located in isolate 2010 CC398. Our findings have significant public health implications, confirm the need for the continuous genomic surveillance of cfr-positive zoonotic LA-MRSA, and backdate cfr presence in LA-MRSA from Italian pigs to at least 2008.
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Nüesch-Inderbinen M, Heyvaert L, Treier A, Zurfluh K, Cernela N, Biggel M, Stephan R. High occurrence of Enterococcus faecalis, Enterococcus faecium, and Vagococcus lutrae harbouring oxazolidinone resistance genes in raw meat-based diets for companion animals - a public health issue, Switzerland, September 2018 to May 2020. Euro Surveill 2023; 28:2200496. [PMID: 36757316 PMCID: PMC9912375 DOI: 10.2807/1560-7917.es.2023.28.6.2200496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
IntroductionEnterococci harbouring genes encoding resistance to florfenicol and the oxazolidinone antimicrobial linezolid have emerged among food-producing animals and meat thereof, but few studies have analysed their occurrence in raw meat-based diets (RMBDs) for pets.AimWe aimed to examine how far RMBDs may represent a source of bacteria with oxazolidinone resistance genes.MethodsFifty-nine samples of different types of RMBDs from 10 suppliers (three based in Germany, seven in Switzerland) were screened for florfenicol-resistant Gram-positive bacteria using a selective culture medium. Isolates were phenotypically and genotypically characterised.ResultsA total of 27 Enterococcus faecalis, Enterococcus faecium, and Vagococcus lutrae isolates were obtained from 24 of the 59 samples. The optrA, poxtA, and cfr genes were identified in 24/27, 6/27 and 5/27 isolates, respectively. Chloramphenicol and linezolid minimum inhibitory concentrations (MICs) ranged from 24.0 mg/L-256.0 mg/L, and 1.5 mg/L-8.0 mg/L, respectively. According to the Clinical and Laboratory Standards Institute (CLSI) breakpoints, 26 of 27 isolates were resistant to chloramphenicol (MICs ≥ 32 mg/L), and two were resistant to linezolid (MICs ≥ 8 mg/L). Multilocus sequence typing analysis of the 17 E. faecalis isolates identified 10 different sequence types (ST)s, with ST593 (n = 4 isolates) and ST207 (n = 2 isolates) occurring more than once, and two novel STs (n = 2 isolates). E. faecium isolates belonged to four different STs (168, 264, 822, and 1846).ConclusionThe high occurrence in our sample of Gram-positive bacteria harbouring genes encoding resistance to the critical antimicrobial linezolid is of concern since such bacteria may spread from companion animals to humans upon close contact between pets and their owners.
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Affiliation(s)
| | - Lore Heyvaert
- Department Veterinary and Biosciences, Faculty Veterinary Medicine, University of Ghent, Ghent, Belgium
| | - Andrea Treier
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicole Cernela
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Michael Biggel
- 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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48
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Occurrence of cfr-Positive Linezolid-Susceptible Staphylococcus aureus and Non- aureus Staphylococcal Isolates from Pig Farms. Antibiotics (Basel) 2023; 12:antibiotics12020359. [PMID: 36830270 PMCID: PMC9952267 DOI: 10.3390/antibiotics12020359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/11/2023] Open
Abstract
The emergence and spread of cfr-mediated resistance to linezolid in staphylococci have become a serious global concern. The acquisition of cfr confers multidrug resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A (PhLOPSA phenotype). However, occurrence of cfr-positive and linezolid-susceptible staphylococci has been identified. To investigate the mechanism underlying linezolid susceptibility in cfr-positive Staphylococcus aureus and non-aureus staphylococci (NAS) isolates from pig farms in Korea. Eleven cfr-positive and linezolid-susceptible staphylococci were analyzed for mutations in domain V of 23S rRNA, ribosomal proteins (L3, L4, and L22), cfr open reading frames (ORFs), and cfr promoter regions. The effect of the cfr mutation (Q148K) on the PhLOPSA phenotype was determined using plasmid constructs expressing either the mutated (cfrQ148K) or nonmutated cfr genes. All 11 (six S. aureus and five NAS) cfr-positive and linezolid-susceptible isolates had a point mutation at position 442 in cfr ORFs (C to A) that resulted in the Q148K mutation. No mutations were detected in 23S rRNA, L3, L4, or L22. The Q148K mutation in Cfr is responsible for phenotypes susceptible to PhLOPSA antimicrobial agents. To our knowledge, this is the first study to report the causal role of a single nucleotide mutation (Q148K) in cfr of S. aureus and NAS isolates in PhLOPSA resistance. Continued nationwide surveillance is necessary to monitor the occurrence and dissemination of mutations in cfr that affect resistance phenotypes in staphylococci of human and animal origin.
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49
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Xuan H, Xia L, Schwarz S, Jia H, Yao X, Wang S, Li R, Wei J, Li Z, Shao D, Liu K, Qiu Y, Ma Z, Li B. Various mobile genetic elements carrying optrA in Enterococcus faecium and Enterococcus faecalis isolates from swine within the same farm. J Antimicrob Chemother 2023; 78:504-511. [PMID: 36508313 DOI: 10.1093/jac/dkac421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/20/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES In this study, the distribution of the oxazolidinone/phenicol resistance gene optrA and the mobile genetic elements involved in its dissemination were analysed among enterococcal isolates from a farrow-to-finish swine farm. METHODS Enterococcus faecium and Enterococcus faecalis isolates were obtained from all pig production stages in the farm. The optrA-carrying E. faecium and E. faecalis isolates were subjected to PFGE and antimicrobial susceptibility testing. Complete sequences of the genetically unrelated optrA-carrying E. faecium and E. faecalis isolates were determined using Illumina HiSeq and MinION platforms. RESULTS The optrA gene was present in 12.2% (23/188) of the E. faecium and E. faecalis isolates, most of which originated from nursery and finishing stages. The 23 optrA-positive Enterococcus isolates represented 15 PFGE types. WGS of representative isolates of the 15 PFGE types showed that optrA was carried by diverse genetic elements either located in the chromosomal DNA or on plasmids. A novel optrA-bearing genetic element was identified on two distinct multi-resistance plasmids from E. faecium. Two new hybrid plasmids carrying several resistance genes were found in two E. faecalis isolates. pC25-1-like plasmids and chromosomally integrated Tn6674 and Tn6823-like transposons were prevalent in the remaining Enterococcus isolates. CONCLUSIONS The gene optrA was found in genetically unrelated E. faecium and E. faecalis isolates from the same farm. Analysis of the genetic contexts of optrA suggested that horizontal transfer including different plasmids and transposons played a key role in the dissemination of optrA in this farm.
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Affiliation(s)
- Huiyong Xuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Stefan Schwarz
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany.,Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Haiyan Jia
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xiaohui Yao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Shufeng Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.,College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
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50
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Youenou B, Martins Simoes P, Tristan A, Farfour E, Beauruelle C, Kolenda C, Ranc AG, Vandenesch F, Laurent F, Dupieux C. Linezolid resistance: detection of the cfr(B) gene in French clinical MRSA strains. J Antimicrob Chemother 2023; 78:445-449. [PMID: 36509546 DOI: 10.1093/jac/dkac411] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To describe two linezolid-resistant MRSA strains carrying the cfr(B) gene detected in the French National Reference Centre for staphylococci. METHODS Two linezolid-resistant MRSA strains isolated from cystic fibrosis patients in two different French hospitals in 2017 and 2019 were examined to explore the mechanisms of linezolid resistance. Antimicrobial susceptibility was tested using broth microdilution and gradient strips. The genetic determinants of linezolid resistance were assessed by a multiplex PCR targeting cfr/cfr(B), optrA and poxtA genes, by amplification and sequencing of individual 23S rRNA genes and by WGS using both Illumina and Nanopore technologies. RESULTS The two MRSA strains were resistant to linezolid but susceptible to tedizolid, and PCR-positive for cfr/cfr(B). The WGS analysis indicated that they belonged to two different STs (ST8-MRSA-IV and ST5382-MRSA-IV) and that they both harboured the cfr(B) gene on the same 9.7 kb Tn6218-like chromosomal transposon, a finding only previously reported in Enterococcus sp. and Clostridioides difficile. CONCLUSIONS To the best of our knowledge, this is the first description of the presence of cfr(B) in staphylococci, more specifically in linezolid-resistant MRSA strains. This finding illustrates the risk of horizontal intergenus transfer of oxazolidinone resistance genes in Staphylococcus aureus and highlights the need to monitor such emergence in this species.
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Affiliation(s)
- Benjamin Youenou
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France
| | - Patricia Martins Simoes
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France.,Equipe Pathogénie des staphylocoques, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, France
| | - Anne Tristan
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France.,Equipe Pathogénie des staphylocoques, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, France
| | - Eric Farfour
- Hôpital Foch, Service de Biologie clinique, Suresnes F-92150, France
| | - Clémence Beauruelle
- University Brest, INSERM, EFS, UMR 1078, GGB, Brest F-29200, France.,Department of Bacteriology, Virology, Brest University Hospital, Hospital Hygiene, and Parasitology-Mycology, Brest F-29200, France
| | - Camille Kolenda
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France.,Equipe Pathogénie des staphylocoques, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, France
| | - Anne-Gaëlle Ranc
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France.,Equipe Pathogénie des staphylocoques, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, France
| | - François Vandenesch
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France.,Equipe Pathogénie des staphylocoques, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, France
| | - Frédéric Laurent
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France.,Equipe Pathogénie des staphylocoques, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, France
| | - Céline Dupieux
- Hospices Civils de Lyon, Centre National de Référence des Staphylocoques, Institut des Agents Infectieux, Lyon F-69004, France.,Equipe Pathogénie des staphylocoques, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, France
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