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Chanchaithong P, Chueahiran S, Pinpimai K, Sroithongkham P, Leelapsawas C, Indra R, Yindee J, Chuanchuen R. Chromosomal and plasmid localization of ileS2 in high-level mupirocin-resistant Staphylococcus pseudintermedius and Staphylococcus aureus isolated from canine and feline origins. J Antimicrob Chemother 2024:dkae172. [PMID: 38863334 DOI: 10.1093/jac/dkae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/11/2024] [Indexed: 06/13/2024] Open
Abstract
OBJECTIVES To characterize the mobile genetic elements and genetic localization of ileS2 in high-level mupirocin-resistant (Hi-MupR) methicillin-resistant Staphylococcus pseudintermedius (MRSP) and MRSA isolates recovered from canine and feline clinical samples. METHODS The identification of bacterial species and presence of mecA and ileS2 genes in MRSP and MRSA isolates were performed using MALDI-TOF MS and PCR, respectively. Antimicrobial resistance (AMR) phenotypes were determined by broth microdilution assays. The genome characteristics, ileS2-containing elements and staphylococcal cassette chromosome mec (SCCmec) were illustrated using complete circular genomes obtained from hybrid assembly of Illumina short-reads and Oxford Nanopore Technologies long-reads. These were analysed through phylogenetic and bioinformatics approaches. RESULTS A total of 18 MRSP clinical isolates and four MRSA clinical isolates exhibited the Hi-MupR phenotype and carried multiple AMR genes, including mecA and ileS2 genes. MRSP ST182-SCCmec V (n = 6) and ST282-ΨSCCmec57395-t10 (n = 4) contained the ileS2 transposable unit associated with IS257 on the chromosome. Three MRSA ST398-SCCmec V-t034/t4652 isolates carried ∼42 kb pSK41-like ileS2 plasmids, whereas similar ileS2 plasmids lacking tra genes were found in MRSP ST282-ΨSCCmec57395-t72/t21 isolates. Furthermore, a new group of ileS2 plasmids, carried by MRSP ST45-ΨSCCmec57395, ST433-ΨSCCmecKW21-t05 and ST2165-SCCmec IV-t06, and by one MRSA ST398-SCCmec V-t034 strain, shared the plasmid backbone with the cfr/fexA-carrying plasmid pM084526_1 in MRSA ST398. CONCLUSIONS This study provides the first evidence of ileS2 integration into the S. pseudintermedius chromosome, which is a rare occurrence in staphylococcal species, and plasmids played a pivotal role in dissemination of ileS2 in both staphylococcal species.
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Affiliation(s)
- Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Surawit Chueahiran
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Komkiew Pinpimai
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Parinya Sroithongkham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chavin Leelapsawas
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rusmin Indra
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rungtip Chuanchuen
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Nyasinga J, Munshi Z, Kigen C, Nyerere A, Musila L, Whitelaw A, Ziebuhr W, Revathi G. Displacement of Hospital-Acquired, Methicillin-Resistant Staphylococcus aureus Clones by Heterogeneous Community Strains in Kenya over a 13-Year Period. Microorganisms 2024; 12:1171. [PMID: 38930553 PMCID: PMC11205442 DOI: 10.3390/microorganisms12061171] [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: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/28/2024] Open
Abstract
We determined antibiotic susceptibility and employed Oxford Nanopore whole-genome sequencing to explore strain diversity, resistance, and virulence gene carriage among methicillin-resistant Staphylococcus aureus (MRSA) strains from different infection sites and timepoints in a tertiary Kenyan hospital. Ninety-six nonduplicate clinical isolates recovered between 2010 and 2023, identified and tested for antibiotic susceptibility on the VITEK ID/AST platform, were sequenced. Molecular typing, antibiotic resistance, and virulence determinant screening were performed using the relevant bioinformatics tools. The strains, alongside those from previous studies, were stratified into two periods covering 2010-2017 and 2018-2023 and comparisons were made. Mirroring phenotypic profiles, aac(6')-aph(2″) [aminoglycosides]; gyrA (S84L) and grlA (S80Y) [fluoroquinolones]; dfrG [anti-folates]; and tet(K) [tetracycline] resistance determinants dominated the collection. While the proportion of ST239/241-t037-SCCmec III among MRSA reduced from 37.7% to 0% over the investigated period, ST4803-t1476-SCCmec IV and ST152-t355-SCCmec IV were pre-eminent. The prevalence of Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) genes was 38% (33/87) and 6.8% (6/87), respectively. We observed the displacement of HA-MRSA ST239/241-t037-SCCmec III with the emergence of ST152-t355-SCCmec IV and a greater clonal heterogeneity. The occurrence of PVL+/ACME+ CA-MRSA in recent years warrants further investigations into their role in the CA-MRSA virulence landscape, in a setting of high PVL prevalence.
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Affiliation(s)
- Justin Nyasinga
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
- Department of Biomedical Sciences and Technology, Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Zubair Munshi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
| | - Collins Kigen
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Nyerere
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Lillian Musila
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Whitelaw
- Division of Medical Microbiology and Immunology, Stellenbosch University, Matieland, Stellenbosch 7602, South Africa;
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, Josef-Schneider Str. 2D/15, D-97080 Wurzburg, Germany;
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
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Roy S, Aung MS, Paul SK, Nasreen SA, Haque N, Mazid R, Khan MS, Barman TK, Arafa P, Sathi FA, Nila SS, Jahan A, Urushibara N, Kawaguchiya M, Ohashi N, Kobayashi N. Genetic characterization of methicillin-resistant / susceptible Staphylococcus aureus (MRSA/MSSA) and Staphylococcus argenteus clinical isolates in Bangladesh: Dominance of ST6-MRSA-IV/t304 and detection of cfr/ fexA in ST8-MSSA/t008. IJID REGIONS 2024; 10:132-139. [PMID: 38283056 PMCID: PMC10819717 DOI: 10.1016/j.ijregi.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Objectives Coagulase-positive staphylococcus (CoPS), represented by Staphylococcus aureus, is a major cause of infections in humans. This study aimed to investigate molecular epidemiological characteristics, antimicrobial resistance, and their trends of CoPS in Bangladesh. Methods Clinical isolates of CoPS were collected from two medical institutions in Bangladesh for a 2-year period and analyzed for their species, genotypes, virulence factors, antimicrobial susceptibility, and resistance determinants. Results 172 CoPS isolates collected were identified as S. aureus or S. argenteus (170 and two, respectively). Methicillin-resistant S. aureus (MRSA) accounted for 36% (n = 61), having Staphylococcal cassette chromosome mec (SCCmec)-IV (82%) or V (18%). Panton-Valentine leukocidin (PVL) genes were detected at higher rate in methicillin-susceptible S. aureus (MSSA) (62%) than MRSA (26%). MRSA comprised 11 STs, including a dominant type ST6 (46%) associated with mostly SCCmec-IVa/spa-t304, and one isolate had genetic features of the USA300 clone (ST8/SCCmec-IVa/coa-IIIa/spa-t008/ACME-I/ΦSa2USA). STs of CC1, CC88, and CC398 were common in MSSA, with CC88 showing the highest PVL-positive rate. One MSSA isolate (ST8/spa-t008) harbored fexA and cfr showing susceptibility to linezolid. S. argenteus was methicillin-susceptible and belonged to ST2250/coa-XId. Conclusions Genetic characteristics of current MRSA/MSSA in Bangladesh were revealed, with first identification of S. argenteus at low prevalence.
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Affiliation(s)
- Sangjukta Roy
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | | | - Nazia Haque
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | - Rummana Mazid
- Department of Microbiology, Bangladesh Institute of Health Sciences (BIHS) General Hospital, Dhaka, Bangladesh
| | - Md. Shahed Khan
- Department of Oral Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | | | - Parvez Arafa
- Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh
| | | | | | - Afsana Jahan
- Microbiology Department, Pabna Medical College, Pabna, Bangladesh
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Nobuhide Ohashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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Abdullahi IN, Latorre-Fernández J, Reuben RC, Trabelsi I, González-Azcona C, Arfaoui A, Usman Y, Lozano C, Zarazaga M, Torres C. Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non- aureus Staphylococci and Mammaliicocci. Microorganisms 2023; 12:66. [PMID: 38257893 PMCID: PMC10818522 DOI: 10.3390/microorganisms12010066] [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: 12/05/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of which the mecC has evolutionary been associated with methicillin-resistant Staphylococcus aureus (MRSA) in wild animals, thus loosely referred to as the wild MRSA. In this study, we present an epidemiological review and genomic analysis of non-aureus staphylococci and mammaliicocci that carry the mecC-mediated methicillin resistance trait and determine whether this trait has any relevant link with the One Health niches. All previous studies (2007 till 2023) that described the mecC gene in non-aureus staphylococci and mammaliicocci were obtained from bibliometric databases, reviewed, and systematically analyzed to obtain the antimicrobial resistance (AMR) and virulence determinants, mobilome, and other genetic contents. Moreover, core genome single-nucleotide polymorphism analysis was used to assess the relatedness of these strains. Of the 533 articles analyzed, only 16 studies (on livestock, environmental samples, milk bulk tanks, and wild animals) were eligible for inclusion, of which 17 genomes from 6 studies were used for various in silico genetic analyses. Findings from this systematic review show that all mecC-carrying non-aureus staphylococci were resistant to only beta-lactam antibiotics and associated with the classical SCCmec XI of S. aureusLGA251. Similarly, two studies on wild animals reported mecC-carrying Mammaliicoccus stepanovicii associated with SCCmec XI. Nevertheless, most of the mecC-carrying Mammaliicoccus species presented an MDR phenotype (including linezolid) and carried the SCCmec-mecC hybrid associated with mecA. The phylogenetic analysis of the 17 genomes revealed close relatedness (<20 SNPs) and potential transmission of M. sciuri and M. lentus strains in livestock farms in Algeria, Tunisia, and Brazil. Furthermore, closely related M. sciuri strains from Austria, Brazil, and Tunisia (<40 SNPs) were identified. This systematic review enhances our comprehension of the epidemiology and genetic organization of mecC within the non-aureus staphylococci and mammaliicocci. It could be hypothesized that the mecC-carrying non-aureus staphylococci are evolutionarily related to the wild MRSA-mecC. The potential implications of clonal development of a lineage of mecA/mecC carrying strains across multiple dairy farms in a vast geographical region with the dissemination of MDR phenotype is envisaged. It was observed that most mecC-carrying non-aureus staphylococci and mammaliicocci were reported in mastitis cases. Therefore, veterinarians and veterinary microbiology laboratories must remain vigilant regarding the potential existence of mecA/mecC strains originating from mastitis as a potential niche for this resistance trait.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Javier Latorre-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Islem Trabelsi
- Bioresources, Environment and Biotechnology Laboratory, Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia;
| | - Carmen González-Azcona
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Ameni Arfaoui
- Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1068, Tunisia;
| | - Yahaya Usman
- Department of Medical Laboratory Science, Ahmadu Bello University, Zaria 810107, Nigeria;
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
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Zheng L, Jiang Z, Wang Z, Li Y, Jiao X, Li Q, Tang Y. The prevalence of Staphylococcus aureus and the emergence of livestock-associated MRSA CC398 in pig production in eastern China. Front Microbiol 2023; 14:1267885. [PMID: 38163065 PMCID: PMC10755019 DOI: 10.3389/fmicb.2023.1267885] [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: 07/27/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024] Open
Abstract
Livestock-associated Staphylococcus aureus (LA-MRSA) has been of increasing concern due to its potential risk to humans. This study investigated the prevalence of MRSA in pig production in Eastern China and determined the genomic characteristics of pig-associated MRSA isolates by whole-genome sequencing (WGS). A total of 1,318 samples were collected from pig farms and pig slaughterhouses, and 150 S. aureus were identified, including 63 MRSA isolates and 87 MSSA isolates. MRSA was detected in all pig farms and pig slaughterhouses. The antimicrobial susceptibility test revealed that all MRSA isolates were multidrug-resistant. The WGS and MLST analysis demonstrated that 56 MRSA isolates belonged to clonal complex (CC) 398, and seven MRSA isolates belonged to CC9. All LA-MRSA isolates were absent of phiSa3 phage containing immune evasion cluster (IEC) and possessed an intact hlb gene. In addition, genes associated with Panton-Valentine leukocidin, typically indicative of human adaptation, were not detected. The analysis of antibiotic resistance genes (ARGs) demonstrated that all MRSA isolates contained multiple ARGs. All MRSA isolates had Plthe mecA gene and at least one tetracycline resistance gene. Both tetM and tetK were detected in all MRSA CC398 isolates, while tetL was detected in all MRSA CC9 isolates. The phenicol resistance gene fexA was detected in 51 MRSA isolates, while the linezolid resistance gene cfr was detected in 60 MRSA isolates. The emergence of LA-MRSA CC398 in four pig farms and one slaughterhouse in this study indicates the spread of this clonal complex in the pig production sector in Eastern China. Further investigations are required to understand the potential transmission routes of LA-MRSA CC398 within the pork production chain in China and to assess the potential risks to humans.
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Affiliation(s)
- Lina Zheng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhongyi Jiang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhenyu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yang Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, 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, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiuchun Li
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yuanyue Tang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, Jiangsu, China
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Schouls LM, Witteveen S, van Santen-Verheuvel M, de Haan A, Landman F, van der Heide H, Kuijper EJ, Notermans DW, Bosch T, Hendrickx APA. Molecular characterization of MRSA collected during national surveillance between 2008 and 2019 in the Netherlands. COMMUNICATIONS MEDICINE 2023; 3:123. [PMID: 37700016 PMCID: PMC10497500 DOI: 10.1038/s43856-023-00348-z] [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: 05/03/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Although the Netherlands is a country with a low endemic level, methicillin-resistant Staphylococcus aureus (MRSA) poses a significant health care problem. Therefore, high coverage national MRSA surveillance has been in place since 1989. To monitor possible changes in the type-distribution and emergence of resistance and virulence, MRSA isolates are molecularly characterized. METHODS All 43,321 isolates from 36,520 persons, collected 2008-2019, were typed by multiple-locus variable number tandem repeats analysis (MLVA) with simultaneous PCR detection of the mecA, mecC and lukF-PV genes, indicative for PVL. Next-generation sequencing data of 4991 isolates from 4798 persons were used for whole genome multi-locus sequence typing (wgMLST) and identification of resistance and virulence genes. RESULTS We show temporal change in the molecular characteristics of the MRSA population with the proportion of PVL-positive isolates increasing from 15% in 2008-2010 to 25% in 2017-2019. In livestock-associated MRSA obtained from humans, PVL-positivity increases to 6% in 2017-2019 with isolates predominantly from regions with few pig farms. wgMLST reveals the presence of 35 genogroups with distinct resistance, virulence gene profiles and specimen origin. Typing shows prolonged persistent MRSA carriage with a mean carriage period of 407 days. There is a clear spatial and a weak temporal relationship between isolates that clustered in wgMLST, indicative for regional spread of MRSA strains. CONCLUSIONS Using molecular characterization, this exceptionally large study shows genomic changes in the MRSA population at the national level. It reveals waxing and waning of types and genogroups and an increasing proportion of PVL-positive MRSA.
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Affiliation(s)
- Leo M Schouls
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - Sandra Witteveen
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marga van Santen-Verheuvel
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Angela de Haan
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Fabian Landman
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Han van der Heide
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology and Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daan W Notermans
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Antoni P A Hendrickx
- Centre for Infectious Disease Control. National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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7
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Apostolakos I, Skarlatoudi T, Vatavali K, Giannouli A, Bosnea L, Mataragas M. Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep's Milk. Int J Mol Sci 2023; 24:13883. [PMID: 37762186 PMCID: PMC10530712 DOI: 10.3390/ijms241813883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Dairy products play a crucial role in human nutrition as they provide essential nutrients. However, the presence of diverse microorganisms in these products can pose challenges to food safety and quality. Here, we provide a comprehensive molecular characterization of a diverse collection of lactic acid bacteria (LAB) and staphylococci isolated from raw sheep's milk. Whole-genome sequencing, phenotypic characterization, and bioinformatics were employed to gain insight into the genetic composition and functional attributes of these bacteria. Bioinformatics analysis revealed the presence of various genetic elements. Important toxin-related genes in staphylococci that contribute to their pathogenic potential were identified and confirmed using phenotypic assays, while adherence-related genes, which are essential for attachment to host tissues, surfaces in the dairy environment, and the creation of biofilms, were also present. Interestingly, the Staphylococcus aureus isolates belonged to sequence type 5, which largely consists of methicillin-susceptible isolates that have been involved in severe nosocomial infections. Although genes encoding methicillin resistance were not identified, multiple resistance genes (RGs) conferring resistance to aminoglycosides, macrolides, and fluroquinolones were found. In contrast, LAB had few inherently present RGs and no virulence genes, suggesting their likely safe status as food additives in dairy products. LAB were also richer in bacteriocins and carbohydrate-active enzymes, indicating their potential to suppress pathogens and effectively utilize carbohydrate substrates, respectively. Additionally, mobile genetic elements, present in both LAB and staphylococci, may facilitate the acquisition and dissemination of genetic traits, including RGs, virulence genes, and metabolic factors, with implications for food quality and public health. The molecular and phenotypic characterization presented herein contributes to the effort to mitigate risks and infections (e.g., mastitis) and enhance the safety and quality of milk and products thereof.
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Affiliation(s)
| | | | | | | | | | - Marios Mataragas
- Department of Dairy Research, Institution of Technology of Agricultural Products, Hellenic Agricultural Organization “DIMITRA”, 3rd Ethnikis Antistaseos St., 45221 Ioannina, Greece; (I.A.); (T.S.); (K.V.); (A.G.); (L.B.)
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8
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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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