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Supriadi IR, Santosaningsih D, Budayanti NS, Zandijk WHA, Rijfkogel A, Klaassen CHW, Severin JA. Identification and characterization of Staphylococcus argenteus from Indonesia. Int J Med Microbiol 2024; 316:151629. [PMID: 39053073 DOI: 10.1016/j.ijmm.2024.151629] [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: 03/15/2024] [Revised: 05/31/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND In 2015, Staphylococcus argenteus was reported for the first time as a novel species of the Staphylococcus aureus complex. While S. argenteus has been found in many countries, its presence in Indonesia has not been reported yet. Our aim is to confirm S. argenteus presence in Indonesia, describe its characteristics and analyze its genomic diversity. METHODS The S. aureus isolates used in this study were collected from patients with skin and soft tissue infections in Indonesia, between July 2009 to February 2010. Randomly selected isolates were recultured from -80 C° stocks and analyzed using matrix-assisted laser desorption/ionization - time of flight (MALDI-TOF). Isolates identified as S. argenteus, S. roterodami, or S. schweitzeri and S. aureus with a low score in the MALDI-TOF analysis were analyzed by a real-time PCR targeting the nucA gene able to identify true S. argenteus. Isolates identified as S. argenteus were further characterized by whole genome sequencing. Vitek®2 (bioMérieux) was used for antimicrobial susceptibility testing. RESULTS Fifteen isolates were identified as S. argenteus, with the majority belonging to ST2250. Two pairs of isolates proved to be identical by core genome multilocus sequence typing analysis. Most isolates were susceptible to all antibiotics tested, except for seven isolates (46.7 %) that were resistant to benzylpenicillin, and one isolate was resistant to tetracycline (6.7 %). The presence of resistance genes blaZ and tet(45) correlated with these findings. Notably, the sey enterotoxin gene was prevalent in 80 % of the isolates. Other virulence factor genes were less prevalent. Plasmid replicon types in S. argenteus were also known to S. aureus. CONCLUSION Our study reveals the occurrence of S. argenteus in Indonesia. The diversity within Indonesian S. argenteus matches the global diversity of S. argenteus. Identical isolates between patients indicate potential transmission events. A lower prevalence of a broad panel of virulence factors suggests that S. argenteus is less virulent than S. aureus.
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Affiliation(s)
- Indri Rooslamiati Supriadi
- National Biomedical and Genome Science Institute, Directorate of Healthcare Services, Ministry of Health of Indonesia, Jakarta, Indonesia; Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Cardiology, University Medical Centre Utrecht, the Netherlands
| | - Dewi Santosaningsih
- Department of Clinical Microbiology, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
| | - Nyoman S Budayanti
- Department of Microbiology, Faculty of Medicine, Universitas Udayana/Udayana University Hospital, Badung, Indonesia
| | - Willemien H A Zandijk
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Amber Rijfkogel
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Corné H W Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Juliëtte A Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands.
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Hetsa BA, Asante J, Mbanga J, Ismail A, Abia ALK, Amoako DG, Essack SY. Genomic Characterization of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Implicated in Bloodstream Infections, KwaZulu-Natal, South Africa: A Pilot Study. Antibiotics (Basel) 2024; 13:796. [PMID: 39334971 PMCID: PMC11429224 DOI: 10.3390/antibiotics13090796] [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: 07/13/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/30/2024] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen and a leading cause of bloodstream infections, with its capacity to acquire antibiotic resistance genes posing significant treatment challenges. This pilot study characterizes the genomic profiles of S. aureus isolates from patients with bloodstream infections in KwaZulu-Natal, South Africa, to gain insights into their resistance mechanisms, virulence factors, and clonal and phylogenetic relationships. Six multidrug-resistant (MDR) S. aureus isolates, comprising three methicillin-resistant S. aureus (MRSA) and three methicillin-susceptible S. aureus (MSSA), underwent whole genome sequencing and bioinformatics analysis. These isolates carried a range of resistance genes, including blaZ, aac(6')-aph(2″), ant(9)-Ia, ant(6)-Ia, and fosB. The mecA gene, which confers methicillin resistance, was detected only in MRSA strains. The isolates exhibited six distinct spa types (t9475, t355, t045, t1265, t1257, and t7888) and varied in virulence gene profiles. Panton-Valentine leukocidin (Luk-PV) was found in one MSSA isolate. Two SCCmec types, IVd(2B) and I(1B), were identified, and the isolates were classified into four multilocus sequence types (MLSTs), with ST5 (n = 3) being the most common. These sequence types clustered into two clonal complexes, CC5 and CC8. Notably, two MRSA clones were identified: ST5-CC5-t045-SCCmec_I(1B) and the human-associated endemic clone ST612-CC8-t1257-SCCmec_IVd(2B). Phylogenomic analysis revealed clustering by MLST, indicating strong genetic relationships within clonal complexes. These findings highlight the value of genomic surveillance in guiding targeted interventions to reduce treatment failures and mortality.
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Affiliation(s)
- Bakoena A. Hetsa
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (J.A.); (J.M.); (A.L.K.A.); (D.G.A.); (S.Y.E.)
| | - Jonathan Asante
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (J.A.); (J.M.); (A.L.K.A.); (D.G.A.); (S.Y.E.)
- School of Pharmacy and Pharmaceutical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (J.A.); (J.M.); (A.L.K.A.); (D.G.A.); (S.Y.E.)
- Department of Applied Biology & Biochemistry, National University of Science and Technology, Corner Cecil Avenue & Gwanda Road, Bulawayo 263, Zimbabwe
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg 2193, South Africa;
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Akebe L. K. Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (J.A.); (J.M.); (A.L.K.A.); (D.G.A.); (S.Y.E.)
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (J.A.); (J.M.); (A.L.K.A.); (D.G.A.); (S.Y.E.)
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (J.A.); (J.M.); (A.L.K.A.); (D.G.A.); (S.Y.E.)
- School of Pharmacy, University of Jordan, Amman 11942, Jordan
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3
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Ndhlovu GON, Javkar KG, Matuvhunye T, Ngondoh F, Jamrozy D, Bentley S, Shittu AO, Dube FS. Investigating genomic diversity of Staphylococcus aureus associated with pediatric atopic dermatitis in South Africa. Front Microbiol 2024; 15:1422902. [PMID: 39224215 PMCID: PMC11366657 DOI: 10.3389/fmicb.2024.1422902] [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: 04/24/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Importance Staphylococcus aureus frequently colonizes the skin and nose of patients with atopic dermatitis (AD), a disease associated with skin barrier dysfunction and chronic cutaneous inflammation. Published genomic studies on AD-associated S. aureus in pediatric populations in sub-Saharan Africa are limited. Objectives To investigate the phenotypic and genomic diversity of S. aureus in children with and without AD during early childhood. Data setting and participants A cross-sectional study of 220 children (aged 9-38 months) with AD (cases) and without AD (controls) from Cape Town and Umtata, South Africa. Main outcomes and measures S. aureus phenotypic and genomic diversity were investigated using whole-genome sequencing, antibiotic susceptibility testing and biofilm microtiter assay. Results Of the 124 S. aureus isolates recovered from 220 children, 96 isolates (79 cases and 17 controls) with high-quality sequences were analyzed. Isolates from cases showed greater phenotypic resistance to gentamicin (10%), rifampicin (4%), chloramphenicol (4%), and exhibited multidrug resistance (9%) than in controls. Furthermore, the isolates from cases formed stronger biofilms than those from controls (76% vs. 35%, p = 0.001), but showed no dominance of any virulence factor gene or mobile genetic elements. There was no significant difference in the distribution of immune evasion cluster types between cases and controls. However, IEC type G was identified only among cases. Conclusion and relevance AD-associated S. aureus has phenotypic and genetic features that are important for successful pathogenic colonization and survival. Further studies are needed to assess the pathological implications of colonization of various S. aureus lineages in vivo to elucidate their pathological contribution to AD pathogenesis and pathophysiology.
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Affiliation(s)
- Gillian O. N. Ndhlovu
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Kiran G. Javkar
- Department of Computer Science, University of Maryland, College Park, MD, United States
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, MD, United States
| | - Takudzwa Matuvhunye
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Froodia Ngondoh
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Dorota Jamrozy
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Stephen Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adebayo O. Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
- Institute of Medical Microbiology, University Hospital Munster, Munster, Germany
| | - Felix S. Dube
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease & Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Jesumirhewe C, Odufuye TO, Ariri JU, Adebiyi AA, Sanusi AT, Stöger A, Daza-Prieto B, Allerberger F, Cabal-Rosel A, Ruppitsch W. Genetic Characterization of Antibiotic-Resistant Staphylococcus spp. and Mammaliicoccus sciuri from Healthy Humans and Poultry in Nigeria. Antibiotics (Basel) 2024; 13:733. [PMID: 39200033 PMCID: PMC11350800 DOI: 10.3390/antibiotics13080733] [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: 06/14/2024] [Revised: 07/18/2024] [Accepted: 07/29/2024] [Indexed: 09/01/2024] Open
Abstract
Staphylococcus spp. poses a significant threat to human and animal health due to their capacity to cause a wide range of infections in both. In this study, resistance genes conferring antibiotic resistance in Staphylococcus spp. and Mammaliicoccus sciuri isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 61 Staphylococcus spp. isolates were obtained from urine, wounds, nasal and chicken fecal samples. Species identification was carried out by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Antimicrobial susceptibility testing was performed using the Kirby-Bauer method for 16 antibiotics. Whole-genome sequencing was used for characterization of the isolates. The 61 investigated isolates included Staphylococcus aureus, S. arlettae, M. sciuri, S. haemolyticus, and S. epidermidis. A total of 47 isolates (77%) belonged to human samples and 14 (23%) isolates were collected from poultry samples. All were phenotypically resistant to at least three antimicrobial(s). Multiple resistance determinants were detected in the human and poultry isolates analyzed. Phylogenetic analysis revealed close relatedness among the isolates within each species for S. arlettae, M. sciuri, and S. haemolyticus, respectively. This study delivered comprehensive genomic insights into antibiotic-resistant Staphylococcus species and M. sciuri isolates from human and poultry sources in Edo state, Nigeria, from a One Health perspective.
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Affiliation(s)
- Christiana Jesumirhewe
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Tolulope Oluwadamilola Odufuye
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Juliana Ukinebo Ariri
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Amdallat Arike Adebiyi
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Amina Tanko Sanusi
- Department of Pharmaceutical Microbiology, College of Pharmacy, Igbinedion University Okada, Okada 302111, Edo State, Nigeria; (T.O.O.); (J.U.A.); (A.A.A.); (A.T.S.)
| | - Anna Stöger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Beatriz Daza-Prieto
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Franz Allerberger
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Adriana Cabal-Rosel
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, 1090 Vienna, Austria; (A.S.); (B.D.-P.); (F.A.); (A.C.-R.); (W.R.)
- Faculty of Food Technology, Food Safety and Ecology, University of Donja Gorica, 81000 Podgorica, Montenegro
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Raghuram V, Petit RA, Karol Z, Mehta R, Weissman DB, Read TD. Average nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. mSystems 2024; 9:e0014324. [PMID: 38934646 PMCID: PMC11265343 DOI: 10.1128/msystems.00143-24] [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: 01/29/2024] [Accepted: 04/16/2024] [Indexed: 06/28/2024] Open
Abstract
Staphylococcus aureus causes both hospital- and community-acquired infections in humans worldwide. Due to the high incidence of infection, S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole-genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of average nucleotide identity revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10%-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location. Notably, strain-diffuse genes were associated with prophages; strain-concentrated genes were associated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic resistance genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core, and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions. IMPORTANCE We analyzed the genomic diversity of Staphylococcus aureus, a globally prevalent bacterial species that causes serious infections in humans. Our goal was to build a genetic picture of the different strains of S. aureus and which genes may be associated with them. We reprocessed >84,000 genomes and subsampled to remove redundancy. We found that individual samples sharing >99.5% of their genome could be grouped into strains. We also showed that a portion of genes that are present in intermediate frequency in the species are strongly associated with some strains but completely absent from others, suggesting a role in strain specificity. This work lays the foundation for understanding individual gene histories of the S. aureus species and also outlines strategies for processing large bacterial genomic data sets.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Robert A. Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Zach Karol
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Rohan Mehta
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | | | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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Chen F, Yin Y, Chen H, Wang R, Wang S, Wang H. Global genetic diversity and Asian clades evolution: a phylogeographic study of Staphylococcus aureus sequence type 5. Antimicrob Agents Chemother 2024; 68:e0117523. [PMID: 38259089 PMCID: PMC10916392 DOI: 10.1128/aac.01175-23] [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: 09/13/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Staphylococcus aureus sequence type (ST) 5 has spread worldwide; however, phylogeographic studies on the evolution of global phylogenetic and Asian clades of ST5 are lacking. This study included 368 ST5 genome sequences, including 111 newly generated sequences. Primary phylogenetic analysis suggested that there are five clades, and geographical clustering of ST5 methicillin-resistant S. aureus (MRSA) was linked to the acquisition of S. aureus pathogenicity islands (SaPIs; enterotoxin gene island) and integration of the prophage φSa3. The most recent common ancestor of global S. aureus ST5 dates back to the mid-1940s, coinciding with the clinical introduction of penicillin. Bayesian phylogeographic inference allowed to ancestrally trace the Asian ST5 MRSA clade to Japan, which may have spread to major cities in China and Korea in the 1990s. Based on a pan-genome-wide association study, the emergence of Asian ST5 clades was attributed to the gain of prophages, SaPIs, and plasmids, as well as the coevolution of resistance genes. Clade IV displayed greater genomic diversity than the Asian MRSA clades. Collectively, our study provides in-depth insights into the global evolution of S. aureus ST5 mainly in China and the United States and reveals that different S. aureus ST5 clades have arisen independently in different parts of the world, with limited geographic dispersal across continents.
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Affiliation(s)
- Fengning Chen
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
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Raghuram V, Petit RA, Karol Z, Mehta R, Weissman DB, Read TD. Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577756. [PMID: 38352482 PMCID: PMC10862745 DOI: 10.1101/2024.01.29.577756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Robert A Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Zach Karol
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Rohan Mehta
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | | | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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Lu C, Xiao W, Yu H, Song W, Zhou Z, Dong N, Fan Z, Li H. Genomic analysis of foodborne Staphylococcus aureus obtained from unannounced food inspections between 2012 and 2021 in East China. FEMS Microbiol Lett 2024; 371:fnae062. [PMID: 39085038 DOI: 10.1093/femsle/fnae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/20/2024] [Accepted: 07/30/2024] [Indexed: 08/02/2024] Open
Abstract
Staphylococcus aureus is a significant cause of foodborne illness in China. Our investigation concentrated on the genetic characterization of foodborne S. aureus identified during unannounced inspections conducted in Suzhou from 2012 to 2021. Dominant clones included clonal complex (CC) 1, CC398, CC188, and CC7, with CC398 notably increasing in 2020-2021. The isolates commonly contained 1-3 plasmids, with rep5a (48.55%) and rep16 (44.51%) predominating. A concerning 24.3% showed multidrug resistance, particularly to penam (blaZ and mecA) and fosfomycin (fosB), with resistance rates rising from 32.7% to 53.3%, potentially linked to the increase in CC types like CC5, CC20, and CC25. Most isolates carried genes for virulence factors such as aureolysin, hemolysin, staphylokinase, and staphylococcal complement inhibitor. A significant increase in virulence genes, especially the enterotoxin gene sea, was observed, possibly associated with shifts in CC1 and CC7 prevalence. This underscores the necessity for ongoing surveillance to understand the genomic traits of S. aureus in ensuring food safety.
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Affiliation(s)
- Chu Lu
- Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Wenjie Xiao
- Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
- Department of Orthopedics, The Second Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215004, China
| | - Haoyun Yu
- Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Weiyi Song
- Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Zhemin Zhou
- Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Ning Dong
- Department of Clinical Laboratory, Second Affiliated Hospital, Department of Epidemiology and Biostatistics, School of Public Health, The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zhihai Fan
- Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
- Department of Orthopedics, The Second Affiliated Hospital of Soochow University, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215004, China
| | - Heng Li
- Department of Microbiology, School of Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123, China
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Vasconcelos PC, Leite EL, Saraiva MMS, Ferrari RG, Cibulski SP, Silva NMV, Freitas Neto OC, Givisiez PEN, Vieira RFC, Oliveira CJB. Genomic Analysis of a Community-Acquired Methicillin-Resistant Staphylococcus aureus Sequence Type 1 Associated with Caprine Mastitis. Pathogens 2023; 13:23. [PMID: 38251331 PMCID: PMC10819347 DOI: 10.3390/pathogens13010023] [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: 11/03/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.
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Affiliation(s)
- Priscylla C. Vasconcelos
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Elma L. Leite
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Mauro M. S. Saraiva
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
- School of Agricultural and Veterinarian Sciences, Department of Pathology, Reproduction, and One Health, São Paulo State University (Unesp), Jaboticabal 14884-900, SP, Brazil
| | - Rafaela G. Ferrari
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Samuel P. Cibulski
- Center for Biotechnology (CBiotec), Federal University of Paraiba (CBiotec/UFPB), João Pessoa 58051-900, PB, Brazil;
| | - Nubia M. V. Silva
- Animal Production Center, National Institute of Semiarid (INSA), Campina Grande 58434-700, PB, Brazil;
| | - Oliveiro C. Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, MG, Brazil;
| | - Patrícia E. N. Givisiez
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
| | - Rafael F. C. Vieira
- Department of Public Health Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Center for Computational Intelligence to Predict Health and Environmental Risks (CIPHER), The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Celso J. B. Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia 58051-900, PB, Brazil; (P.C.V.); (E.L.L.); (M.M.S.S.); (R.G.F.); (P.E.N.G.)
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10
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Jiang JH, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev 2023; 36:e0014822. [PMID: 37982596 PMCID: PMC10732075 DOI: 10.1128/cmr.00148-22] [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: 11/21/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.
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Affiliation(s)
- Jhih-Hang Jiang
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - David R. Cameron
- Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Cara Nethercott
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Marta Aires-de-Sousa
- Laboratory of Molecular Genetics, Institutode Tecnologia Químicae Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Escola Superior de Saúde da Cruz Vermelha Portuguesa-Lisboa (ESSCVP-Lisboa), Lisbon, Portugal
| | - Anton Y. Peleg
- Department of Microbiology, Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, Melbourne, Victoria, Australia
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11
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Houtak G, Bouras G, Nepal R, Shaghayegh G, Cooksley C, Psaltis AJ, Wormald PJ, Vreugde S. The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis. Microb Genom 2023; 9:001128. [PMID: 38010322 PMCID: PMC10711304 DOI: 10.1099/mgen.0.001128] [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: 08/11/2023] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.
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Affiliation(s)
- Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Gohar Shaghayegh
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Clare Cooksley
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Alkis James Psaltis
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Peter-John Wormald
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
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12
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Mehta RS, Petit RA, Read TD, Weissman DB. Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes. BMC Bioinformatics 2023; 24:243. [PMID: 37296404 PMCID: PMC10251594 DOI: 10.1186/s12859-023-05363-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.
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Affiliation(s)
- Rohan S Mehta
- Department of Physics, Emory University, Atlanta, GA, USA.
| | - Robert A Petit
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
- Wyoming Public Health Laboratory, Cheyenne, WY, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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13
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Rodrigues IC, Ribeiro-Almeida M, Ribeiro J, Silveira L, Prata JC, Pista A, Martins da Costa P. Occurrence of Multidrug-Resistant Bacteria Resulting from the Selective Pressure of Antibiotics: A Comprehensive Analysis of ESBL K. pneumoniae and MRSP Isolated in a Dog with Rhinorrhea. Vet Sci 2023; 10:vetsci10050326. [PMID: 37235409 DOI: 10.3390/vetsci10050326] [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: 03/31/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Because of public health concerns, much greater scrutiny is now placed on antibiotic use in pets, especially for antimicrobial agents that have human analogs. Therefore, this study aimed to characterize the phenotypic and genotypic profiles of multidrug-resistant bacteria isolated from nasal swabs samples taken from a one-year-old male Serra da Estrela dog with rhinorrhea that was treated with amikacin. An extended-spectrum β-lactamases (ESBL) Klebsiella pneumoniae was isolated in the first sample taken from the left nasal cavity of the dog. Seven days later, methicillin-resistant (MRSP) Staphylococcus pseudintermedius was also isolated. Nevertheless, no alterations to the therapeutic protocol were performed. Once the inhibitory action of the antibiotic disappeared, the competitive advantage of the amikacin-resistant MRSP was lost, and only commensal flora was observed on both nasal cavities. The genotypic profile of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae revealed the same characteristics and close relation to other strains, mainly from Estonia, Slovakia and Romania. Regarding MRSP isolates, although resistance to aminoglycosides was present in the first MRSP, the second isolate carried aac(6')-aph(2″), which enhanced its resistance to amikacin. However, the veterinary action was focused on the treatment of the primary agent (ESBL K. pneumoniae), and the antibiotic applied was according to its phenotypic profile, which may have led to the resolution of the infectious process. Therefore, this study highlights the importance of targeted therapy, proper clinical practice and laboratory-hospital communication to safeguard animal, human and environmental health.
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Affiliation(s)
- Inês C Rodrigues
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Marisa Ribeiro-Almeida
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Rede de Química e Tecnologia (REQUIMTE), Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Jorge Ribeiro
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Leonor Silveira
- Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1600-609 Lisbon, Portugal
| | - Joana C Prata
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- TOXRUN-Toxicology Research Unit, University Institute of Health Sciences, Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), 4585-116 Gandra, Portugal
| | - Angela Pista
- Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1600-609 Lisbon, Portugal
| | - Paulo Martins da Costa
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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14
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Snoussi M, Noumi E, Bouali N, Bazaid AS, Alreshidi MM, Altayb HN, Chaieb K. Antibiotic Susceptibility Profiling of Human Pathogenic Staphylococcus aureus Strains Using Whole Genome Sequencing and Genome-Scale Annotation Approaches. Microorganisms 2023; 11:1124. [PMID: 37317098 DOI: 10.3390/microorganisms11051124] [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: 04/01/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
Staphylococcus species are major pathogens with increasing importance due to the rise in antibiotic resistance. Whole genome sequencing and genome-scale annotation are promising approaches to study the pathogenicity and dissemination of virulence factors in nosocomial methicillin-resistant and multidrug-resistant bacteria in intensive care units. Draft genome sequences of eight clinical S. aureus strains were assembled and annotated for the prediction of antimicrobial resistance genes, virulence factors, and phylogenetic analysis. Most of the studied S. aureus strains displayed multi-resistance toward the tested drugs, reaching more than seven drugs up to 12 in isolate S22. The mecA gene was detected in three isolates (S14, S21, and S23), mecC was identified in S8 and S9, and blaZ was commonly identified in all isolates except strain S23. Additionally, two complete mobile genomic islands coding for methicillin resistance SCCmec Iva (2B) were identified in strains S21 and S23. Numerous antimicrobial resistance genes (norA, norC, MgrA, tet(45), APH(3')-IIIa, and AAC(6')-APH(2″)) were identified in chromosomes of different strains. Plasmid analysis revealed the presence of blaZ, tetK, and ermC in different plasmid types, located in gene cassettes containing plasmid replicons (rep) and insertion sequences (IS). Additionally, the aminoglycoside-resistant determinants were identified in S1 (APH(3')-IIIa), while AAC(6)-APH(2″) was detected in strains S8 and S14. The trimethoprim (dfrC) resistance gene was detected in S. aureus S21, and the fosfomycin (fosB) resistance gene was detected only in S. aureus S14. We also noted that S. aureus S1 belongs to ST1-t127, which has been reported as one of the most frequent human pathogen types. Additionally, we noted the presence of rare plasmid-mediated mecC-MRSA in some of our isolates.
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Affiliation(s)
- Mejdi Snoussi
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Emira Noumi
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Nouha Bouali
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Abdulrahman S Bazaid
- Department of Medical, Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Ha'il 55476, Saudi Arabia
| | - Mousa M Alreshidi
- Department of Biology, College of Science, University of Ha'il, Ha'il P.O. Box 2440, Saudi Arabia
- Medical and Diagnostic Research Centre, University of Ha'il, Ha'il 55473, Saudi Arabia
| | - Hisham N Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environmental and Products, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
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15
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Al-Trad EI, Chew CH, Che Hamzah AM, Suhaili Z, Rahman NIA, Ismail S, Puah SM, Chua KH, Kwong SM, Yeo CC. The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia. Antibiotics (Basel) 2023; 12:antibiotics12040733. [PMID: 37107095 PMCID: PMC10135026 DOI: 10.3390/antibiotics12040733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a priority nosocomial pathogen with plasmids playing a crucial role in its genetic adaptability, particularly in the acquisition and spread of antimicrobial resistance. In this study, the genome sequences of 79 MSRA clinical isolates from Terengganu, Malaysia, (obtained between 2016 and 2020) along with an additional 15 Malaysian MRSA genomes from GenBank were analyzed for their plasmid content. The majority (90%, 85/94) of the Malaysian MRSA isolates harbored 1-4 plasmids each. In total, 189 plasmid sequences were identified ranging in size from 2.3 kb to ca. 58 kb, spanning all seven distinctive plasmid replication initiator (replicase) types. Resistance genes (either to antimicrobials, heavy metals, and/or biocides) were found in 74% (140/189) of these plasmids. Small plasmids (<5 kb) were predominant (63.5%, 120/189) with a RepL replicase plasmid harboring the ermC gene that confers resistance to macrolides, lincosamides, and streptogramin B (MLSB) identified in 63 MRSA isolates. A low carriage of conjugative plasmids was observed (n = 2), but the majority (64.5%, 122/189) of the non-conjugative plasmids have mobilizable potential. The results obtained enabled us to gain a rare view of the plasmidomic landscape of Malaysian MRSA isolates and reinforces their importance in the evolution of this pathogen.
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Affiliation(s)
- Esra'a I Al-Trad
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Nerus 21300, Malaysia
| | | | - Zarizal Suhaili
- Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut 22200, Malaysia
| | - Nor Iza A Rahman
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
| | - Salwani Ismail
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
| | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Stephen M Kwong
- Infectious Diseases & Microbiology, School of Medicine, Western Sydney University, Campbelltown 2560, Australia
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
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16
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Al-Trad EI, Che Hamzah AM, Puah SM, Chua KH, Hanifah MZ, Ayub Q, Palittapongarnpim P, Kwong SM, Chew CH, Yeo CC. Complete Genome Sequence and Analysis of a ST573 Multidrug-Resistant Methicillin-Resistant Staphylococcus aureus SauR3 Clinical Isolate from Terengganu, Malaysia. Pathogens 2023; 12:pathogens12030502. [PMID: 36986424 PMCID: PMC10053073 DOI: 10.3390/pathogens12030502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a World Health Organization-listed priority pathogen. Scarce genomic data are available for MRSA isolates from Malaysia. Here, we present the complete genome sequence of a multidrug-resistant MRSA strain SauR3, isolated from the blood of a 6-year-old patient hospitalized in Terengganu, Malaysia, in 2016. S. aureus SauR3 was resistant to five antimicrobial classes comprising nine antibiotics. The genome was sequenced on the Illumina and Oxford Nanopore platforms and hybrid assembly was performed to obtain its complete genome sequence. The SauR3 genome consists of a circular chromosome of 2,800,017 bp and three plasmids designated pSauR3-1 (42,928 bp), pSauR3-2 (3011 bp), and pSauR3-3 (2473 bp). SauR3 belongs to sequence type 573 (ST573), a rarely reported sequence type of the staphylococcal clonal complex 1 (CC1) lineage, and harbors a variant of the staphylococcal cassette chromosome mec (SCCmec) type V (5C2&5) element which also contains the aac(6')-aph(2″) aminoglycoside-resistance genes. pSauR3-1 harbors several antibiotic resistance genes in a 14,095 bp genomic island (GI), previously reported in the chromosome of other staphylococci. pSauR3-2 is cryptic, whereas pSauR3-3 encodes the ermC gene that mediates inducible resistance to macrolide-lincosamide-streptogramin B (iMLSB). The SauR3 genome can potentially be used as a reference genome for other ST573 isolates.
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Affiliation(s)
- Esra'a I Al-Trad
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
| | | | - Suat Moi Puah
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Muhamad Zarul Hanifah
- Monash University Malaysia Genomics Facility, School of Science, Monash University, Bandar Sunway 47500, Malaysia
| | - Qasim Ayub
- Monash University Malaysia Genomics Facility, School of Science, Monash University, Bandar Sunway 47500, Malaysia
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Mahidol University, Bangkok 10400, Thailand
| | - Stephen M Kwong
- Infectious Diseases & Microbiology, School of Medicine, Western Sydney University, Campbelltown 2560, Australia
| | - Ching Hoong Chew
- Faculty of Health Sciences, Universiti Sultan Zainal Abidin, Kuala Nerus 21300, Malaysia
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu 20400, Malaysia
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17
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Leclerc Q, Clements A, Dunn H, Hatcher J, Lindsay JA, Grandjean L, Knight GM. Quantifying patient- and hospital-level antimicrobial resistance dynamics in Staphylococcus aureus from routinely collected data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.15.23285946. [PMID: 36824943 PMCID: PMC9949191 DOI: 10.1101/2023.02.15.23285946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Antimicrobial resistance (AMR) to all antibiotic classes has been found in the pathogen Staphylococcus aureus . The reported prevalence of these resistances vary, driven by within-host AMR evolution at the patient level, and between-host transmission at the hospital level. Without dense longitudinal sampling, pragmatic analysis of AMR dynamics at multiple levels using routine surveillance data is essential to inform control measures. We explored S. aureus AMR diversity in 70,000 isolates from a UK paediatric hospital between 2000-2020, using electronic datasets containing multiple routinely collected isolates per patient with phenotypic antibiograms, hospitalisation information, and antibiotic consumption. At the hospital-level, the proportion of isolates that were meticillin-resistant (MRSA) increased between 2014-2020 from 25 to 50%, before sharply decreasing to 30%, likely due to a change in inpatient demographics. Temporal trends in the proportion of isolates resistant to different antibiotics were often correlated in MRSA, but independent in meticillin-susceptible S. aureus . Ciprofloxacin resistance in MRSA decreased from 70% to 40% of tested isolates between 2007-2020, likely linked to a national policy to reduce fluoroquinolone usage in 2007. At the patient level, we identified frequent AMR diversity, with 4% of patients ever positive for S. aureus simultaneously carrying, at some point, multiple isolates with different resistances. We detected changes over time in AMR diversity in 3% of patients ever positive for S. aureus . These changes equally represented gain and loss of resistance. Within this routinely collected dataset, we found that 65% of changes in resistance within a patient’s S. aureus population could not be explained by antibiotic exposure or between-patient transmission of bacteria, suggesting that within-host evolution via frequent gain and loss of AMR genes may be responsible for these changing AMR profiles. Our study highlights the value of exploring existing routine surveillance data to determine underlying mechanisms of AMR. These insights may substantially improve our understanding of the importance of antibiotic exposure variation, and the success of single S. aureus clones.
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Affiliation(s)
- Quentin Leclerc
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology & Public Health, London School of Hygiene & Tropical Medicine, UK
- Antimicrobial Resistance Centre, London School of Hygiene & Tropical Medicine, UK
- Institute for Infection & Immunity, St George’s University of London, UK
| | - Alastair Clements
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology & Public Health, London School of Hygiene & Tropical Medicine, UK
- Institute for Infection & Immunity, St George’s University of London, UK
| | | | | | - Jodi A Lindsay
- Institute for Infection & Immunity, St George’s University of London, UK
| | - Louis Grandjean
- Department of Infection, Immunity & Inflammation, Institute of Child Health, University College London, UK
| | - Gwenan M Knight
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, Faculty of Epidemiology & Public Health, London School of Hygiene & Tropical Medicine, UK
- Antimicrobial Resistance Centre, London School of Hygiene & Tropical Medicine, UK
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18
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Haidari H, Vasilev K, Cowin AJ, Kopecki Z. Bacteria-Activated Dual pH- and Temperature-Responsive Hydrogel for Targeted Elimination of Infection and Improved Wound Healing. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51744-51762. [PMID: 36356210 DOI: 10.1021/acsami.2c15659] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antibacterial treatment that provides on-demand release of therapeutics that can kill a broad spectrum of pathogens while maintaining long-term efficacy and without developing resistance or causing side effects is urgently required in clinical practice. Here, we demonstrate the development of a multistimuli-responsive hydrogel, prepared by cross-linking N-isopropylacrylamide with acrylic acid and loaded with ultrasmall silver nanoparticles (AgNPs), offering the on-demand release of Ag+ ions triggered by changes in the wound microenvironment. We demonstrate that this dual-responsive hydrogel is highly sensitive to a typical wound pH and temperature change, evidenced by the restricted release of Ag+ ions at acidic pH (<5.5) while significantly promoting the release in alkaline pH (>7.4) (>90% release). The pH-dependent release and antibacterial effect show minimal killing at pH 4 or 5.5 but dramatically activated at pH 7.4 and 10, eliminating >95% of the pathogens. The in vivo antibacterial efficacy and safety showed a high potency to clear Staphylococcus aureus wound infection while significantly accelerating the wound healing rate. This multifunctional hydrogel presents a promising bacteria-responsive delivery platform that serves as an on-demand carrier to not only reduce side effects but also significantly boost the antibacterial efficiency based on physiological needs. It offers great potential to improve the way wound infections are treated with direct clinical implications, providing a single platform for long-lasting application in wound management.
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Affiliation(s)
- Hanif Haidari
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Krasimir Vasilev
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Allison J Cowin
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Zlatko Kopecki
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
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Comparative Genomic Analysis of a Multidrug-Resistant Staphylococcus hominis ShoR14 Clinical Isolate from Terengganu, Malaysia, Led to the Discovery of Novel Mobile Genetic Elements. Pathogens 2022; 11:pathogens11121406. [PMID: 36558739 PMCID: PMC9782665 DOI: 10.3390/pathogens11121406] [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: 10/29/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus hominis is a coagulase-negative Staphylococcus (CoNS) commensal capable of causing serious systemic infections in humans. The emergence of multidrug-resistant S. hominis strains is of concern but little is known about the characteristics of this organism, particularly from Malaysia. Here, we present the comparative genome analysis of S. hominis ShoR14, a multidrug-resistant, methicillin-resistant blood isolate from Terengganu, Malaysia. Genomic DNA of S. hominis ShoR14 was sequenced on the Illumina platform and assembled using Unicycler v0.4.8. ShoR14 belonged to sequence type (ST) 1 which is the most prevalent ST of the S. hominis subsp. hominis. Comparative genomic analysis with closely related strains in the database with complete genome sequences, led to the discovery of a novel variant of the staphylococcal chromosome cassette mec (SCCmec) type VIII element harboring the mecA methicillin-resistance gene in ShoR14 and its possible carriage of a SCCfus element that encodes the fusidic acid resistance gene (fusC). Up to seven possible ShoR14 plasmid contigs were identified, three of which harbored resistance genes for tetracycline (tetK), chloramphenicol (catA7), macrolides, lincosamides, and streptogramin B (ermC). Additionally, we report the discovery of a novel mercury-resistant transposon, Tn7456, other genomic islands, and prophages which make up the S. hominis mobilome.
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20
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Pennone V, Prieto M, Álvarez-Ordóñez A, Cobo-Diaz JF. Antimicrobial Resistance Genes Analysis of Publicly Available Staphylococcus aureus Genomes. Antibiotics (Basel) 2022; 11:1632. [PMID: 36421276 PMCID: PMC9686812 DOI: 10.3390/antibiotics11111632] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 07/30/2023] Open
Abstract
Staphylococcus aureus is a pathogen that can cause severe illness and express resistance to multiple antimicrobial agents. It is part of the ESKAPE organisms and it has been included by the Centers for Disease Control and Prevention (CDC) of USA in the list of serious threats to humans. Many antimicrobial mechanisms have been identified, and, in particular, antimicrobial resistance genes (ARGs) can be determined by whole genome sequencing. Mobile genetic elements (MGEs) can determine the spread of these ARGs between strains and species and can be identified with bioinformatic analyses. The scope of this work was to analyse publicly available genomes of S. aureus to characterise the occurrence of ARGs present in chromosomes and plasmids in relation to their geographical distribution, isolation sources, clonal complexes, and changes over time. The results showed that from a total of 29,679 S. aureus genomes, 24,765 chromosomes containing 73 different ARGs, and 21,006 plasmidic contigs containing 47 different ARGs were identified. The most abundant ARG in chromosomes was mecA (84%), while blaZ was the most abundant in plasmidic contigs (30%), although it was also abundant in chromosomes (42%). A total of 13 clonal complexes were assigned and differences in ARGs and CC distribution were highlighted among continents. Temporal changes during the past 20 years (from 2001 to 2020) showed that, in plasmids, MRSA and macrolide resistance occurrence decreased, while the occurrence of ARGs associated with aminoglycosides resistance increased. Despite the lack of metadata information in around half of the genomes analysed, the results obtained enable an in-depth analysis of the distribution of ARGs and MGEs throughout different categories to be undertaken through the design and implementation of a relatively simple pipeline, which can be also applied in future works with other pathogens, for surveillance and screening purposes.
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Affiliation(s)
- Vincenzo Pennone
- Department of Food and Drug, Università degli Studi di Parma, 43121 Parma, Italy
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Institute of Food Science and Technology, Universidad de León, 24071 León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
- Institute of Food Science and Technology, Universidad de León, 24071 León, Spain
| | - José F. Cobo-Diaz
- Department of Food Hygiene and Technology, Universidad de León, 24071 León, Spain
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21
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Labuschagne C, Karzis J, Britz H, Petzer IM. Characterisation of Staphylococci Isolated from Milk Samples of a Water Buffalo Herd. Antibiotics (Basel) 2022; 11:antibiotics11111609. [PMID: 36421253 PMCID: PMC9686803 DOI: 10.3390/antibiotics11111609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Water buffalo produce a tenth of milk for global human consumption. Non-aureus staphylococci (NAS) are among the most commonly isolated bacteria from mastitis in water buffalo and dairy cows. These results described the initial characterisation of 17 NAS—15 Staphylococcus simulans and two Staphylococcus chromogenes from a water buffalo herd (n = 44) in South Africa. The isolates were identified by classical microbiology, MALDI-TOF, and 16S rRNA, and the disc diffusion method determined the antibiotic susceptibility. A multi-locus sequence typing scheme (MLST) was developed to determine S. simulans sequence types (ST), by defining and comparing seven housekeeping gene fragment sequences. Sequence typing confirmed all 15 S. simulans isolates from water buffalo which belonged to a single ST, genetically distant from the six bovine STs isolated from adjacent farms, which also varied, indicating no current bacterial transfer between species. The antibiotic resistance patterns of S. simulans varied between beta-lactams. The mean milk somatic cell count (SCC) for the water buffalo milk samples was 166,500 cells/mL milk. This information offers insights into the epidemiology and comparison among isolates from various origins, which leads to effective proactive mastitis strategies resulting in safe, high-quality dairy products from water buffalo and dairy cows for human consumption.
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Affiliation(s)
| | - Joanne Karzis
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
- Correspondence: ; Tel.: +27-012-529-8405
| | - Hans Britz
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
| | - Inge-Marié Petzer
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort 0110, South Africa
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22
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Gerlach D, Sieber RN, Larsen J, Krusche J, De Castro C, Baumann J, Molinaro A, Peschel A. Horizontal transfer and phylogenetic distribution of the immune evasion factor tarP. Front Microbiol 2022; 13:951333. [PMID: 36386695 PMCID: PMC9650247 DOI: 10.3389/fmicb.2022.951333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/12/2022] [Indexed: 11/29/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a major human pathogen, uses the prophage-encoded tarP gene as an important immune evasion factor. TarP glycosylates wall teichoic acid (WTA) polymers, major S. aureus surface antigens, to impair WTA immunogenicity and impede host defence. However, tarP phages appear to be restricted to only a few MRSA clonal lineages, including clonal complexes (CC) 5 and 398, for unknown reasons. We demonstrate here that tarP-encoding prophages can be mobilized to lysogenize other S. aureus strains. However, transfer is largely restricted to closely related clones. Most of the non-transducible clones encode tarM, which generates a WTA glycosylation pattern distinct from that mediated by TarP. However, tarM does not interfere with infection by tarP phages. Clonal complex-specific Type I restriction-modification systems were the major reasons for resistance to tarP phage infection. Nevertheless, tarP phages were found also in unrelated S. aureus clones indicating that tarP has the potential to spread to distant clonal lineages and contribute to the evolution of new MRSA clones.
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Affiliation(s)
- David Gerlach
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | | | - Janes Krusche
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | - Juliane Baumann
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples, Naples, Italy
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Section, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
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Marami LM, Berhanu G, Tekle M, Agga GE, Beyene TJ, Tufa TB, Beyi AF, Edao BM. Antimicrobial Resistance of Staphylococci at Animal Human Interface in Smallholders and Dairy Farms in Central Oromia, Ethiopia. Infect Drug Resist 2022; 15:3767-3777. [PMID: 35859913 PMCID: PMC9291660 DOI: 10.2147/idr.s370592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/06/2022] [Indexed: 12/04/2022] Open
Abstract
Purpose Staphylococcus species come from a variety of sources and can contaminate milk during milking, cause mastitis and other diseases in animals and humans. The enterotoxins they produce cause food poisoning. Our objectives were to isolate, biochemically characterize, and determine antimicrobial susceptibility profiles of Staphylococcus species from dairy farms in central Oromia, Ethiopia. Methods A total of 339 samples (n = 135 [raw milk], n = 135 [udders’ swabs], n = 25 [milkers’ hands swabs], n = 44 [pooled milking utensils’ swabs]) were collected from smallholders and dairy farms. Bacteriological culture and biochemical tests were performed to isolate and identify Staphylococcus species, and the Kirby Bauer disk diffusion method was used for antimicrobial susceptibility testing. Results Across all sample types and dairy farms, 247 (72.9%) Staphylococcus isolates were obtained which comprised of 101 (74.8%) isolates from raw milk, 98 (72.6%) from udder swabs, 30 (68.2%) from pooled utensil swabs, and 18 (72%) from milkers’ hand swabs. Fifty coagulase-positive Staphylococcus isolates (20 S. aureus, 20 S. hyicus and 10 S. intermedius) subjected to antimicrobial susceptibility tests have shown various degrees of resistance. All S. aureus isolates were 100% resistant to ampicillin and penicillin. Out of 20 S. hyicus isolates, 90% were resistant to ampicillin and 85% to penicillin. S. intermedius isolates (n=10) were 70% resistant to nalidixic acid and penicillin whilst remaining 100% resistant to ampicillin. Five S. aureus, three S. intermedius and two S. hyicus isolates from raw milk, milk utensil swabs and milkers’ hand swabs were multidrug-resistant (resistance to at least three classes of antimicrobials). Conclusion This study revealed a high prevalence of staphylococci in the dairy cattle, milkers and milking utensils with multidrug-resistant coagulase-positive Staphylococcus species suggesting the significance of pasteurization. Further research is encouraged on the factors leading to antibiotic resistance in Staphylococcus species.
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Affiliation(s)
- Lencho Megersa Marami
- Department of Veterinary Laboratory Technology, School of Veterinary Medicine, Ambo University, Ambo, Oromia, Ethiopia
| | - Gemechu Berhanu
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Dambi Dollo University, Dambi Dollo, Oromia, Ethiopia
| | - Muluken Tekle
- Department of Microbiology, Immunology and Veterinary Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Oromia, Ethiopia
| | - Getahun Ejeta Agga
- US Department of Agriculture, Agricultural Research Service, Food Animal Environmental Systems Research Unit, Bowling Green, KY, USA
| | - Tariku Jibat Beyene
- Centre for Surgical Outcomes Research, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Takele Beyene Tufa
- Department of Microbiology, Immunology and Veterinary Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Oromia, Ethiopia
| | - Ashenafi Feyisa Beyi
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA
| | - Bedaso Mammo Edao
- Department of Microbiology, Immunology and Veterinary Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Oromia, Ethiopia
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Antimicrobial resistance and genomic analysis of staphylococci isolated from livestock and farm attendants in Northern Ghana. BMC Microbiol 2022; 22:180. [PMID: 35864456 PMCID: PMC9306040 DOI: 10.1186/s12866-022-02589-9] [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: 08/02/2021] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
Background The emergence of antimicrobial resistant bacteria in food producing animals is of growing concern to food safety and health. Staphylococci are common inhabitants of skin and mucous membranes in humans and animals. Infections involving antibiotic resistant staphylococci are associated with increased morbidity and mortality, with notable economic consequences. Livestock farms may enable cross-species transfer of antibiotic resistant staphylococci. The aim of the study was to investigate antimicrobial resistance patterns of staphylococci isolated from livestock and farm attendants in Northern Ghana using phenotypic and genotypic methods. Antimicrobial susceptibility testing was performed on staphylococci recovered from livestock and farm attendants and isolates resistant to cefoxitin were investigated using whole genome sequencing. Results One hundred and fifty-two staphylococci comprising S. sciuri (80%; n = 121), S. simulans (5%; n = 8), S. epidermidis (4%; n = 6), S. chromogens (3%; n = 4), S. aureus (2%; n = 3), S. haemolyticus (1%; n = 2), S. xylosus (1%; n = 2), S. cohnii (1%; n = 2), S. condimenti (1%; n = 2), S. hominis (1%; n = 1) and S. arlettae (1%; n = 1) were identified. The isolates showed resistance to penicillin (89%; n = 135), clindamycin (67%; n = 102), cefoxitin (19%; n = 29), tetracycline (15%; n = 22) and erythromycin (11%; n = 16) but showed high susceptibility to gentamicin (96%; n = 146), sulphamethoxazole/trimethoprim (98%; n = 149) and rifampicin (99%; n = 151). All staphylococci were susceptible to linezolid and amikacin. Carriage of multiple resistance genes was common among the staphylococcal isolates. Genome sequencing of methicillin (cefoxitin) resistant staphylococci (MRS) isolates revealed majority of S. sciuri (93%, n = 27) carrying mecA1 (which encodes for beta-lactam resistance) and the sal(A) gene, responsible for resistance to lincosamide and streptogramin. Most of the MRS isolates were recovered from livestock. Conclusion The study provides insights into the genomic content of MRS from farm attendants and livestock in Ghana and highlights the importance of using whole-genome sequencing to investigate such opportunistic pathogens. The finding of multi-drug resistant staphylococci such as S. sciuri carrying multiple resistant genes is of public health concern as they could pose a challenge for treatment of life-threatening infections that they may cause.
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Kim H, Park S, Seo H, Chung H, Kim ES, Sung H, Kim MN, Bae S, Jung J, Kim MJ, Kim SH, Lee SO, Choi SH, Kim YS, Chong YP. Clinical impact of and microbiological risk factors for qacA/B positivity in ICU-acquired ST5-methicillin-resistant SCCmec type II Staphylococcus aureus bacteremia. Sci Rep 2022; 12:11413. [PMID: 35794229 PMCID: PMC9259651 DOI: 10.1038/s41598-022-15546-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/24/2022] [Indexed: 12/14/2022] Open
Abstract
Concern about resistance to chlorhexidine has increased due to the wide use of the latter. The impact of the qacA/B and smr chlorhexidine tolerance genes on the outcome of methicillin-resistant Staphylococcus aureus (MRSA) infections is unclear. We evaluated the prevalence and clinical impact of, and microbiological risk factors for, qacA/B tolerance in MRSA bacteremia. MRSA bacteremia that occurred more than two days after intensive care unit admission between January 2009 and December 2018 was identified from a prospective cohort of S. aureus bacteremia in a tertiary-care hospital from South Korea. A total of 183 MRSA blood isolates was identified, and the major genotype found was ST5-MRSA-II (87.4%). The prevalences of qacA/B and smr were 67.2% and 3.8%, respectively. qacA/B-positive isolates were predominantly ST5-MRSA-II (96.7% [119/123]), the dominant hospital clone. In a homogenous ST5-MRSA-II background, qacA/B positivity was independently associated with septic shock (aOR, 4.85), gentamicin resistance (aOR, 74.43), and non-t002 spa type (aOR, 74.12). qacA/B positivity was found to have decreased significantly in ST5-MRSA-II in association with a decline in qacA/B-positive t2460, despite the increasing use of chlorhexidine since 2010 (P < 0.001 for trend). Continuous surveillance of the qac genes, and molecular characterization of their plasmids, are needed to understand their role in MRSA epidemiology.
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Affiliation(s)
- Haein Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Sunghee Park
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Hyeonji Seo
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Hyemin Chung
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Eun Sil Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
- Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seongman Bae
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Jiwon Jung
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Min Jae Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Sang-Oh Lee
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Sang-Ho Choi
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Yang Soo Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Yong Pil Chong
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro-43-gil, Songpa-gu, Seoul, 05505, South Korea.
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Staphylococcus aureus Causing Skin and Soft Tissue Infections in Companion Animals: Antimicrobial Resistance Profiles and Clonal Lineages. Antibiotics (Basel) 2022; 11:antibiotics11050599. [PMID: 35625243 PMCID: PMC9137735 DOI: 10.3390/antibiotics11050599] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is a relevant agent of skin and soft tissue infections (SSTIs) in animals. Fifty-five S. aureus comprising all SSTI-related isolates in companion animals, collected between 1999 and 2018 (Lab 1) or 2017 and 2018 (Lab 2), were characterized regarding susceptibility to antibiotics and heavy metals and carriage of antimicrobial resistance determinants. Clonal lineages were established by PFGE, MLST and agr typing. Over half of the isolates (56.4%, 31/55) were methicillin-resistant S. aureus (MRSA), and 14.5% showed a multidrug resistance (MDR) phenotype. Resistance was most frequently observed for beta-lactams (81.8%, related to blaZ and/or mecA), fluoroquinolones (56.4%) and macrolides/lincosamides (14.5%, related to erm(A) or erm(C)). The distributions of heavy-metal MICs allowed the detection of non-wild-type populations associated with several resistance genes. The collection showed genetic diversity, with prevalence of clonal lineage ST22-agrI (45.5%, 25/55), comprising only MRSA isolates, and several less frequently detected clones, including ST5-agrII (14.6%, 8/55), ST398-agrI (9.1%, 5/55) and ST72-agrI (7.3%, 4/55). This work highlights the high frequency of SSTI-related MRSA strains that reflect the clonal lineages circulating both in companion animals and humans in Portugal, reinforcing the need for a One Health approach when studying staphylococci causing infections in companion animals.
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Li IC, Yu GY, Huang JF, Chen ZW, Chou CH. Comparison of Reference-Based Assembly and De Novo Assembly for Bacterial Plasmid Reconstruction and AMR Gene Localization in Salmonella enterica Serovar Schwarzengrund Isolates. Microorganisms 2022; 10:227. [PMID: 35208682 PMCID: PMC8874696 DOI: 10.3390/microorganisms10020227] [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: 12/28/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/02/2022] Open
Abstract
It is well established that plasmids carrying multiple antimicrobial resistance (AMR) genes can be easily transferred among bacterial isolates by horizontal gene transfer. Previous studies have shown that a combination of short- and long-read approaches is effective in reconstructing accurate plasmids. However, high-quality Illumina short reads mapped onto the long reads in the context of an AMR hybrid monitoring strategy have not yet been explored. Hence, this study aimed to improve the reconstruction of plasmids, including the localization of AMR genes, using the above-described parameters on whole-genome sequencing (WGS) results. To the best of our knowledge, this study is the first to use S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) to confirm the number and sizes of plasmids detected by in silico-based predictions in Salmonella strains. Our results showed that de novo assembly did not detect the number of bacterial plasmids more accurately than reference-based assembly did. As this new hybrid mapping strategy surpassed de novo assembly in bacterial reconstruction, it was further used to identify the presence and genomic location of AMR genes among three Salmonella enterica serovar Schwarzengrund isolates. The AMR genes identified in the bacterial chromosome among the three Salmonella enterica serovar Schwarzengrund isolates included: AAC(3)-IV, AAC(6')-Iy, aadA2, APH(4)-Ia, cmlA1, golS, mdsA, mdsB, mdsC, mdtK, qacH, sdiA, sul2, sul3, and TEM-1 genes. Moreover, the presence of TEM-1, AAC(3)-IV, aadA2, APH(4)-Ia, cmlA1, dfrA12, floR, sul1, sul3, and tet(A) genes found within three IncFIB plasmids and one IncX1 plasmid highlight their possible transmission into the environment, which is a public health risk. In conclusion, the generated data using this new hybrid mapping strategy will contribute to the improvement of AMR monitoring and support the risk assessment of AMR dissemination.
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Affiliation(s)
- I-Chen Li
- Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 106, Taiwan;
| | - Gine-Ye Yu
- Animal Technology Research Center, Agricultural Technology Research Institute, No. 52, Kedong 2nd Rd., Zhunan Township, Miaoli County 350, Taiwan; (G.-Y.Y.); (J.-F.H.)
| | - Jing-Fang Huang
- Animal Technology Research Center, Agricultural Technology Research Institute, No. 52, Kedong 2nd Rd., Zhunan Township, Miaoli County 350, Taiwan; (G.-Y.Y.); (J.-F.H.)
| | - Zeng-Weng Chen
- Animal Technology Research Center, Agricultural Technology Research Institute, No. 52, Kedong 2nd Rd., Zhunan Township, Miaoli County 350, Taiwan; (G.-Y.Y.); (J.-F.H.)
| | - Chung-Hsi Chou
- Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei City 106, Taiwan;
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Montelongo Hernandez C, Putonti C, Wolfe AJ. Characterizing Plasmids in Bacteria Species Relevant to Urinary Health. Microbiol Spectr 2021; 9:e0094221. [PMID: 34937183 PMCID: PMC8694116 DOI: 10.1128/spectrum.00942-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022] Open
Abstract
The urinary tract has a microbial community (the urinary microbiota or urobiota) that has been associated with human health. Whole genome sequencing of bacteria is a powerful tool, allowing investigation of the genomic content of the urobiota, also called the urinary microbiome (urobiome). Bacterial plasmids are a significant component of the urobiome yet are understudied. Because plasmids can be vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. In this project, we sought plasmids in 11 clinically relevant urinary species: Aerococcus urinae, Corynebacterium amycolatum, Enterococcus faecalis, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Lactobacillus gasseri, Lactobacillus jensenii, Staphylococcus epidermidis, Streptococcus anginosus, and Streptococcus mitis. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in other species sequenced thus far. Some identified plasmidic assemblies were predicted to have putative virulence and/or antibiotic resistance genes, although the majority of their annotated coding regions were of unknown predicted function. In this study, we report on plasmids from urinary species as a first step to understanding the role of plasmids in the bacterial urobiota. IMPORTANCE The microbial community of the urinary tract (urobiota) has been associated with human health. Whole genome sequencing of bacteria permits examination of urobiota genomes, including plasmids. Because plasmids are vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. Currently, urobiota plasmids are understudied. Here, we sought plasmids in 11 clinically relevant urinary species. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in the other 6 species. We identified putative virulence and/or antibiotic resistance genes in some of the plasmidic assemblies, but most of their annotated coding regions were of unknown function. This is a first step to understanding the role of plasmids in the bacterial urobiota.
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Affiliation(s)
- Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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Staphylococcal phages and pathogenicity islands drive plasmid evolution. Nat Commun 2021; 12:5845. [PMID: 34615859 PMCID: PMC8494744 DOI: 10.1038/s41467-021-26101-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
Conjugation has classically been considered the main mechanism driving plasmid transfer in nature. Yet bacteria frequently carry so-called non-transmissible plasmids, raising questions about how these plasmids spread. Interestingly, the size of many mobilisable and non-transmissible plasmids coincides with the average size of phages (~40 kb) or that of a family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs, ~11 kb). Here, we show that phages and PICIs from Staphylococcus aureus can mediate intra- and inter-species plasmid transfer via generalised transduction, potentially contributing to non-transmissible plasmid spread in nature. Further, staphylococcal PICIs enhance plasmid packaging efficiency, and phages and PICIs exert selective pressures on plasmids via the physical capacity of their capsids, explaining the bimodal size distribution observed for non-conjugative plasmids. Our results highlight that transducing agents (phages, PICIs) have important roles in bacterial plasmid evolution and, potentially, in antimicrobial resistance transmission.
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Amirsoleimani A, Brion G, Francois P. Co-Carriage of Metal and Antibiotic Resistance Genes in Sewage Associated Staphylococci. Genes (Basel) 2021; 12:genes12101473. [PMID: 34680871 PMCID: PMC8535820 DOI: 10.3390/genes12101473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Controlling spread of resistance genes from wastewater to aquatic systems requires more knowledge on how resistance genes are acquired and transmitted. Whole genomic sequences from sewage-associated staphylococcus isolates (20 S. aureus, 2 Staphylococcus warneri, and 2 Staphylococcus delphini) were analyzed for the presence of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Plasmid sequences were identified in each isolate to investigate co-carriage of ARGs and MRGs within. BLASTN analysis showed that 67% of the isolates carried more than one ARG. The carriage of multiple plasmids was observed more in CC5 than CC8 S. aureus strains. Plasmid exchange was observed in all staphylococcus species except the two S. delphini isolates that carried multiple MRGs, no ARGs, and no plasmids. 85% of S. aureus isolates carried the blaZ gene, 76% co-carried blaZ with cadD and cadX, with 62% of these isolates carrying blaZ, cadD, and cadX on the same plasmid. The co-carriage of ARGs and MRGs in S. warneri isolates, and carriage of MRGs in S. delphini, without plasmids suggests non-conjugative transmission routes for gene acquisition. More studies are required that focus on the transduction and transformation routes of transmission to prevent interspecies exchange of ARGs and MRGs in sewage-associated systems.
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Affiliation(s)
- Atena Amirsoleimani
- Department of Civil Engineering, University of Kentucky, Lexington, KY 40506, USA;
- Correspondence: ; Tel.: +1-(859)257-4467
| | - Gail Brion
- Department of Civil Engineering, University of Kentucky, Lexington, KY 40506, USA;
| | - Patrice Francois
- Genomic Research Laboratory, Infectious Diseases Department, University Medical Center, 364-8501 Geneva, Switzerland;
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Rumpf C, Lange J, Schwartbeck B, Kahl BC. Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies? Pathogens 2021; 10:1177. [PMID: 34578208 PMCID: PMC8466686 DOI: 10.3390/pathogens10091177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.
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Affiliation(s)
| | | | | | - Barbara C. Kahl
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (C.R.); (J.L.); (B.S.)
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Karampatakis T, Papadopoulos P, Tsergouli K, Angelidis AS, Melidou A, Sergelidis D, Papa A. Genetic characterization of livestock-associated methicillin-resistant Staphylococcus aureus isolated in Greece. Braz J Microbiol 2021; 52:2091-2096. [PMID: 34387854 DOI: 10.1007/s42770-021-00587-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/31/2021] [Indexed: 11/26/2022] Open
Abstract
The interest in livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) strains is increasing due to their wide distribution and transmission even in persons without previous contact with livestock, and these strains pose a public health threat. The aim of the study was the genetic characterization of the whole genome of two epidemiologically unrelated t034 LA-MRSA strains previously isolated from the nasal cavities of a goat and a farmer in Greece. Both strains were assigned to the ST398-Vc-t034 type and they were carrying a single transposon identical to Tn6133. They harbored genes conferring resistance to several antibiotics (aminoglycosides, β-lactams, macrolides, streptogramin B, tetracycline, and trimethoprim), and genes associated with virulence (enterotoxins, γ-hemolysins, and aureolysin). The present study can serve as baseline for further LA-MRSA epidemiological and evolutionary studies in Greece, while awareness and increased surveillance are needed to avoid their spread.
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Affiliation(s)
- Theodoros Karampatakis
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece.
| | - Panagiotis Papadopoulos
- Laboratory of Food Hygiene-Veterinary Public Health, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Katerina Tsergouli
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Apostolos S Angelidis
- Laboratory of Safety and Quality of Milk and Dairy Products, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Angeliki Melidou
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
| | - Daniel Sergelidis
- Laboratory of Food Hygiene-Veterinary Public Health, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anna Papa
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, 541 24, Thessaloniki, Greece
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Ward-specific clustering of methicillin-resistant Staphylococcus aureus spa-type t037 and t045 in two hospitals in South Africa: 2013 to 2017. PLoS One 2021; 16:e0253883. [PMID: 34185791 PMCID: PMC8241065 DOI: 10.1371/journal.pone.0253883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/14/2021] [Indexed: 12/02/2022] Open
Abstract
Introduction Methicillin-resistant Staphylococcus aureus (MRSA) is a highly clonal pathogen causing infections in various settings. The aim of this study was to determine if healthcare-associated (HA) MRSA isolates with the same spa-type originating from two geographically distinct hospitals in South Africa were genetically related based on PFGE. Furthermore, a small subset of MRSA isolates were characterised with WGS and then compared to PFGE to determine if PFGE is still a reliable method to define outbreaks and/or transmission chains. Methods Staphylococcus aureus isolated from blood cultures (BC) were submitted to the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses (CHARM) as part of a laboratory-based surveillance programme (GERMS-SA). The identified HA-MRSA isolates underwent molecular characterisation [Staphylococcal Chromosome Cassette (SCC) mec and spa-typing]. Pulsed-field gel electrophoresis (PFGE) was performed on selected isolates with the same spa-type. Twenty-one MRSA isolates were selected for whole-genome sequencing (WGS) based on spa-type, PFGE clustering, time and place of isolation. Results Eighteen percent (n = 95/529) and 33% (n = 234/710) of isolates collected, from two public tertiary academic hospitals in the Gauteng (GAU) and the Western Cape (WC) provinces, were identified as MRSA, respectively. The most dominant clone in the GAU hospital was t037-III-MRSA (43.2%; n = 41/95). The most dominant clones in the WC hospital was t037-III-MRSA (23.9%, n = 56/234) and t045-I-MRSA (23.5%, n = 55/234). The GAU-t037-III-MRSA cases and WC-t045-I-MRSA cases occurred in the paediatric patient population, whereas the WC-t037-III-MRSA cases occurred in the adult patient population. A novel spa-type (t19935) was detected in the GAU hospital. PFGE showed that the GAU- and WC-t037-III-MRSA isolates were genetically indistinguishable, as well as most of the WC-t045-I-MRSA isolates. The Vienna/Hungarian/Brazilian clone and British EMRSA-3 clone were in circulation and a low frequency of single nucleotide polymorphisms (SNP) (≤20) differences was observed among isolates with the same spa-type. Conclusion The low number of SNP differences is suggestive of uninterrupted strain transmission and the persistence of t037-III-MRSA and t045-I-MRSA from 2013 to 2017 in the two studied hospitals. Alternative infection prevention and control strategies should be considered to supplement control efforts.
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Mores CR, Montelongo C, Putonti C, Wolfe AJ, Abouelfetouh A. Investigation of Plasmids Among Clinical Staphylococcus aureus and Staphylococcus haemolyticus Isolates From Egypt. Front Microbiol 2021; 12:659116. [PMID: 34149648 PMCID: PMC8213342 DOI: 10.3389/fmicb.2021.659116] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Staphylococci can cause a wide array of infections that can be life threatening. These infections become more deadly when the isolates are antibiotic resistant and thus harder to treat. Many resistance determinants are plasmid-mediated; however, staphylococcal plasmids have not yet been fully characterized. In particular, plasmids and their contributions to antibiotic resistance have not been investigated within the Arab states, where antibiotic use is not universally regulated. Here, we characterized the putative plasmid content among 56 Staphylococcus aureus and 10 Staphylococcus haemolyticus clinical isolates from Alexandria, Egypt. Putative plasmid sequences were detected in over half of our collection. In total, we identified 72 putative plasmid sequences in 27 S. aureus and 1 S. haemolyticus isolates. While these isolates typically carried one or two plasmids, we identified one isolate-S. aureus AA53-with 11 putative plasmids. The plasmid sequences most frequently encoded a Rep_1, RepL, or PriCT_1 type replication protein. As expected, antibiotic resistance genes were widespread among the identified plasmid sequences. Related plasmids were identified amongst our clinical isolates; homologous plasmids present in multiple isolates clustered into 11 groups based upon sequence similarity. Plasmids from the same cluster often shared antibiotic resistance genes, including blaZ, which is associated with β-lactam resistance. Our analyses suggest that plasmids are a key factor in the pathology and epidemiology of S. aureus in Egypt. A better characterization of plasmids and the role they contribute to the success of Staphylococci as pathogens will guide the design of effective control strategies to limit their spread.
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Affiliation(s)
- Carine R. Mores
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
| | - Cesar Montelongo
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
| | - Catherine Putonti
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
| | - Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alalamein University, Alalamein, Egypt
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Sato'o Y, Omoe K, Aikawa Y, Kano M, Ono HK, Hu DL, Nakane A, Sugai M. Investigation of Staphylococcus aureus positive for Staphylococcal enterotoxin S and T genes. J Vet Med Sci 2021; 83:1120-1127. [PMID: 34039784 PMCID: PMC8349821 DOI: 10.1292/jvms.20-0662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus produces staphylococcal enterotoxins (SEs) and causes food poisoning. It is known that almost all SE-encoding genes are present on various types of mobile genetic elements and can mobilize among S. aureus populations. Further, plasmids comprise one of SE gene carriers. Previously, we reported novel SEs, SES and SET, harbored by the plasmid pF5 from Fukuoka5. In the present study, we analyzed the distribution of these SEs in various S. aureus isolates in Japan. We used 526 S. aureus strains and found 311 strains positive for at least one SE/SE-like toxin gene, but only two strains (Fukuoka5 and Hiroshima3) were positive for ses and set among the specimens. We analyzed two plasmids (pF5 and pH3) from these strains and found that they were different. Whereas these plasmids partially shared similar sequences involved in the ser/selj/set/ses gene cluster, other sequences were different. A comparison of these plasmids with those deposited in the NCBI database revealed that only one plasmid had the ser/selj/set/ses cluster with a stop mutation in set similar to that in pH3. In addition, the chromosomes of Fukuoka5 and Hiroshima3, positive for ses and set, were classified into different genotypes. Despite the low rate of gene positivity for these SEs, it is suggested that there is diversity in plasmids and strains carrying these two SEs. Consequently, regarding the entire feature of SE prevalence, we improved the multiplex PCR detection method for the SE superfamily to obtain further insight.
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Affiliation(s)
- Yusuke Sato'o
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima-shi, Hiroshima 734-8551, Japan.,Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu 501-1193, Japan.,Present address: Division of Bacteriology, Department of infection and immunity, School of Medicine, Jichi Medical University, Shimotsuke, Tochigi 323-0498, Japan
| | - Katsuhiko Omoe
- Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu 501-1193, Japan
| | - Yasuko Aikawa
- Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan
| | - Mayuko Kano
- Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan
| | - Hisaya K Ono
- Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu 501-1193, Japan.,Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8560, Japan.,Laboratory of Zoonoses, Kitasato University School of Veterinary Medicine, Towada, Aomori 034-8628, Japan
| | - Dong-Liang Hu
- Laboratory of Zoonoses, Kitasato University School of Veterinary Medicine, Towada, Aomori 034-8628, Japan
| | - Akio Nakane
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8560, Japan
| | - Motoyuki Sugai
- Department of Bacteriology, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima-shi, Hiroshima 734-8551, Japan.,Present address: Antimicrobial Resistance Research Center, National Institute of Infectious Diseases (NIID), Murayama, Tokyo 189-0002, Japan
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Park S, Ronholm J. Staphylococcus aureus in Agriculture: Lessons in Evolution from a Multispecies Pathogen. Clin Microbiol Rev 2021; 34:e00182-20. [PMID: 33568553 PMCID: PMC7950364 DOI: 10.1128/cmr.00182-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is a formidable bacterial pathogen that is responsible for infections in humans and various species of wild, companion, and agricultural animals. The ability of S. aureus to move between humans and livestock is due to specific characteristics of this bacterium as well as modern agricultural practices. Pathoadaptive clonal lineages of S. aureus have emerged and caused significant economic losses in the agricultural sector. While humans appear to be a primary reservoir for S. aureus, the continued expansion of the livestock industry, globalization, and ubiquitous use of antibiotics has increased the dissemination of pathoadaptive S. aureus in this environment. This review comprehensively summarizes the available literature on the epidemiology, pathophysiology, genomics, antibiotic resistance (ABR), and clinical manifestations of S. aureus infections in domesticated livestock. The availability of S. aureus whole-genome sequence data has provided insight into the mechanisms of host adaptation and host specificity. Several lineages of S. aureus are specifically adapted to a narrow host range on a short evolutionary time scale. However, on a longer evolutionary time scale, host-specific S. aureus has jumped the species barrier between livestock and humans in both directions several times. S. aureus illustrates how close contact between humans and animals in high-density environments can drive evolution. The use of antibiotics in agriculture also drives the emergence of antibiotic-resistant strains, making the possible emergence of human-adapted ABR strains from agricultural practices concerning. Addressing the concerns of ABR S. aureus, without negatively affecting agricultural productivity, is a challenging priority.
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Affiliation(s)
- Soyoun Park
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
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Di Gregorio S, Haim MS, Vielma Vallenilla J, Cohen V, Rago L, Gulone L, Aanensen DM, Argimón S, Mollerach M. Genomic Epidemiology of CC30 Methicillin-Resistant Staphylococcus aureus Strains from Argentina Reveals Four Major Clades with Distinctive Genetic Features. mSphere 2021; 6:e01297-20. [PMID: 33692199 PMCID: PMC8546718 DOI: 10.1128/msphere.01297-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus clonal complex 30 (CC30) has given rise to epidemics worldwide and is one of the most prevalent lineages in Argentina, represented by sequence type 30 methicillin-resistant S. aureus SCCmec type IV (ST30-MRSA-IV). ST30-MRSA-IV has displaced previous prevalent clones in the country and demonstrated increased virulence. Despite the burden of infections caused by ST30-MRSA-IV both in hospitals and in communities in Argentina, no detailed genome-based characterization of this clone is available to date. In this study, we used whole-genome sequencing (WGS) to evaluate the genetic diversity, population structure, and genomic characteristics of 190 CC30-MRSA strains circulating in Argentina between 2004 and 2015. Phylogenetic analysis revealed the existence of 4 major clades: ARG-1 (CC30-MRSA-IVc-spa t012), ARG-2 (ST30-MRSA-IVc-spa t021 related), ARG-3 (ST30-MRSA-IVh/j-spa t021 and related), and ARG-4 (CC30-MRSA-IVc-spa t019 and related). The clades were characterized by different distributions of antimicrobial resistance determinants, virulence genes, and mobile genetic elements (MGEs). While ARG-1 and ARG-4 were related to global epidemic MRSA-16 (EMRSA-16) and South West Pacific (SWP) clones, respectively, ARG-3 was phylogenetically distinct from previously defined CC30 epidemic clones. ARG-4, the most prevalent and geographically disseminated in the collection (N = 164), was characterized by specific MGEs and chromosomal mutations that might have contributed to its virulence and success. To our knowledge, this is the first genomic epidemiology study of CC30-MRSA in Argentina, which will serve as baseline genomic data going forward to inform public health measures for infection prevention and control.IMPORTANCE The rise in prevalence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is of public health concern. In Argentina, several studies documented a shift in the epidemiology of CA-MRSA since 2009, with clonal complex 30 (CC30) and, in particular, sequence type 30 MRSA SCCmec type IV (ST30-MRSA-IV) replacing other clones both in communities and in hospitals and possibly displaying increased virulence. By sequencing the whole genomes of 190 CC30 MRSA isolates recovered from Argentina between 2005 and 2015, we showed that they represented a diverse population composed of 4 major clades. The predominant clade evolved from the South West Pacific clone but has acquired a distinct repertoire of mobile genetic elements, virulence genes, and chromosomal mutations that might play a role in its success. Our work is the first extensive genomic study of CC30 S. aureus in Argentina and will contribute not only to the development of genomic surveillance in the region but also to our understanding of the global epidemiology of this pathogen.
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Affiliation(s)
- Sabrina Di Gregorio
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - María Sol Haim
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jesús Vielma Vallenilla
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - Victoria Cohen
- The Centre for Genomic Pathogen Surveillance (CGPS), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Lucía Rago
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
| | - Lucía Gulone
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - David M Aanensen
- The Centre for Genomic Pathogen Surveillance (CGPS), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Argimón
- The Centre for Genomic Pathogen Surveillance (CGPS), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Marta Mollerach
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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38
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Abstract
Plasmids have largely contributed to the spread of antimicrobial resistance genes among Staphylococcus strains. Knowledge about the fitness cost that plasmids confer on clinical staphylococcal isolates and the coevolutionary dynamics that drive plasmid maintenance is still scarce. In this study, we aimed to analyze the initial fitness cost of plasmids in the bacterial pathogen Staphylococcus aureus and the plasmid-host adaptations that occur over time. For that, we first designed a CRISPR (clustered regularly interspaced palindromic repeats)-based tool that enables the removal of native S. aureus plasmids and then transferred three different plasmids isolated from clinical S. aureus strains to the same-background clinical cured strain. One of the plasmids, pUR2940, obtained from a livestock-associated methicillin-resistant S. aureus (LA-MRSA) ST398 strain, imposed a significant fitness cost on both its native and the new host. Experimental evolution in a nonselective medium resulted in a high rate pUR2940 loss and selected for clones with an alleviated fitness cost in which compensatory adaptation occurred via deletion of a 12.8-kb plasmid fragment, contained between two ISSau10 insertion sequences and harboring several antimicrobial resistance genes. Overall, our results describe the relevance of plasmid-borne insertion sequences in plasmid rearrangement and maintenance and suggest the potential benefits of reducing the use of antibiotics both in animal and clinical settings for the loss of clinical multidrug resistance plasmids.
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Naorem RS, Blom J, Fekete C. Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary. PeerJ 2021; 9:e10185. [PMID: 33520430 PMCID: PMC7811285 DOI: 10.7717/peerj.10185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/24/2020] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered together, which suggests that these strains are highly alike; however, comparative genome analysis exposed that the acquisition of phage elements, and plasmids through the events of MGEs transfer contribute to differences in their phenotypic characters. This comparative genome analysis would improve the knowledge about the pathogenic S. aureus strain’s characterization, and responsible for clinically important phenotypic differences among the S. aureus strains.
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Affiliation(s)
- Romen Singh Naorem
- Department of General and Environmental Microbiology, University of Pécs, Pécs, Hungary
| | - Jochen Blom
- Bioinformatics & Systems Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Csaba Fekete
- Department of General and Environmental Microbiology, University of Pécs, Pécs, Hungary
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40
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Frosini SM, Bond R, McCarthy AJ, Feudi C, Schwarz S, Lindsay JA, Loeffler A. Genes on the Move: In Vitro Transduction of Antimicrobial Resistance Genes between Human and Canine Staphylococcal Pathogens. Microorganisms 2020; 8:E2031. [PMID: 33353175 PMCID: PMC7766859 DOI: 10.3390/microorganisms8122031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 01/09/2023] Open
Abstract
Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) between people and pets, and their co-carriage, are well-described. Potential exchange of antimicrobial resistance (AMR) genes amongst these staphylococci was investigated in vitro through endogenous bacteriophage-mediated transduction. Bacteriophages were UV-induced from seven donor isolates of canine (MRSP) and human (MRSA) origin, containing tet(M), tet(K), fusB or fusC, and lysates filtered. Twenty-seven tetracycline- and fusidic acid- (FA-) susceptible recipients were used in 122 donor-recipient combinations (22 tetracycline, 100 FA) across 415 assays (115 tetracycline, 300 FA). Bacteriophage lysates were incubated with recipients and presumed transductants quantified on antimicrobial-supplemented agar plates. Tetracycline resistance transduction from MRSP and MRSA to methicillin-susceptible S. pseudintermedius (MSSP) was confirmed by PCR in 15/115 assays. No FA-resistance transfer occurred, confirmed by negative fusB/fusC PCR, but colonies resulting from FA assays had high MICs (≥32 mg/L) and showed mutations in fusA, two at a novel position (F88L), nine at H457[Y/N/L]. Horizontal gene transfer of tetracycline-resistance confirms that resistance genes can be shared between coagulase-positive staphylococci from different hosts. Cross-species AMR transmission highlights the importance of good antimicrobial stewardship across humans and veterinary species to support One Health.
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Affiliation(s)
- Sian Marie Frosini
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
| | - Ross Bond
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
| | - Alex J. McCarthy
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK;
| | - Claudia Feudi
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14195 Berlin, Germany; (C.F.); (S.S.)
| | - Stefan Schwarz
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14195 Berlin, Germany; (C.F.); (S.S.)
| | - Jodi A. Lindsay
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK;
| | - Anette Loeffler
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
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41
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Karki AB, Neyaz L, Fakhr MK. Comparative Genomics of Plasmid-Bearing Staphylococcus aureus Strains Isolated From Various Retail Meats. Front Microbiol 2020; 11:574923. [PMID: 33193185 PMCID: PMC7644949 DOI: 10.3389/fmicb.2020.574923] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/06/2020] [Indexed: 01/19/2023] Open
Abstract
Food poisoning due to the consumption of Staphylococcus aureus contaminated food is a major health problem worldwide. In this study, we sequenced the genomes of ten plasmid-bearing S. aureus strains isolated from retail beef, chicken, turkey, and pork. The chromosomes of the strains varied in size from 2,654,842 to 2,807,514 bp, and a total of 25 plasmids were identified ranging from 1.4 to 118 kb. Comparative genomic analysis revealed similarities between strains isolated from the same retail meat source, indicating an origin-specific genomic composition. Genes known to modulate attachment, invasion, and toxin production were identified in the 10 genomes. Strains from retail chicken resembled human clinical isolates with respect to virulence factors and genomic islands, and retail turkey and pork isolates shared similarity with S. aureus from livestock. Most chromosomes contained antimicrobial resistance, heavy metal resistance, and stress response genes, and several plasmids contained genes involved in antimicrobial resistance and virulence. In conclusion, the genomes of S. aureus strains isolated from retail meats showed an origin-specific composition and contained virulence and antimicrobial resistance genes similar to those present in human clinical isolates.
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Affiliation(s)
| | | | - Mohamed K. Fakhr
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
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42
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Ogundipe FO, Ojo OE, Feßler AT, Hanke D, Awoyomi OJ, Ojo DA, Akintokun AK, Schwarz S, Maurischat S. Antimicrobial Resistance and Virulence of Methicillin-Resistant Staphylococcus aureus from Human, Chicken and Environmental Samples within Live Bird Markets in Three Nigerian Cities. Antibiotics (Basel) 2020; 9:antibiotics9090588. [PMID: 32911712 PMCID: PMC7558163 DOI: 10.3390/antibiotics9090588] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 11/16/2022] Open
Abstract
Background: Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a major threat to public health. This study investigated the occurrence of MRSA in humans, chickens, chicken meat and environmental samples within poultry farms and live bird markets in southwestern Nigeria. Methods: MRSA were isolated using selective culture and tested for antimicrobial susceptibility by broth microdilution. Selected isolates were characterized by whole genome sequencing (WGS). From WGS data, spa, dru, multilocus sequence typing (MLST) and SCCmec types, but also virulence and antimicrobial resistance genes, were identified. Results: Fifty-six MRSA isolates were detected in 734 samples. They showed resistance to β-lactams (100%), tetracycline (60.7%), ciprofloxacin (33.9%), erythromycin (28.6%), gentamicin (32.1%), and trimethoprim/sulfamethoxazole (10.7%). All 30 isolates investigated by WGS carried mecA, dfrG, and tet(38) genes. Other resistance genes detected were blaZ (83.3%), fosB (73.3%), tet(K) (60.0%), aacA-aphD (36.6%), aphA3 (33.3%), msr(A) (30.0%), mph(C) (30.0%), dfrS1 (3.3%), and sat4 (3.3%). Seven spa types (t091, t314, t657, t1476, t2331, t4690 and t12236), four known (dt9aw, dt10ao, dt10cj, and dt11a) and two novel (dt10dr and dt11dw) dru types, as well as five sequence types (ST8, ST121, ST152, ST772 and ST789) were found among the MRSA isolates. All ST121 isolates carried an SCCmec type IV cassette and were not dru-typeable. ST152 and ST121 were found only in specific sample categories within defined locations, while ST8 and ST772 were distributed across most sample categories and locations. Three SCCmec types, IVa, V and Vc, were identified. All MRSA isolates possessed virulence genes including aur, clpP, coa, fnbA, esaA, hly, hla, ica, isdA, srtB, sspA, and vWbp, among others. The toxic shock syndrome toxin gene (tst) was not detected in any isolate, whereas the Pantone-Valentine leukocidin genes lukF-PV/lukS-PV were present in all ST121, all ST772, and all but one ST152 isolates. Conclusion: The results of this study (i) showed that chicken meat is contaminated by MRSA and (ii) suggested that live bird markets may serve as focal points for the dissemination of MRSA within the community.
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Affiliation(s)
- Flora Olubunmi Ogundipe
- Department of Microbiology, College of Biosciences, Federal University of Agriculture, Abeokuta 110124, Nigeria; (F.O.O.); (D.A.O.); (A.K.A.)
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (D.H.)
| | - Olufemi Ernest Ojo
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (D.H.)
- Department of Veterinary Microbiology, College of Veterinary Medicine, Federal University of Agriculture, Abeokuta 110124, Nigeria;
| | - Andrea T. Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (D.H.)
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (D.H.)
| | - Olajoju Jokotola Awoyomi
- Department of Veterinary Public Health and Preventive Medicine, College of Veterinary Medicine, Federal University of Agriculture, Abeokuta 110124, Nigeria;
| | - David Ajiboye Ojo
- Department of Microbiology, College of Biosciences, Federal University of Agriculture, Abeokuta 110124, Nigeria; (F.O.O.); (D.A.O.); (A.K.A.)
| | - Aderonke Kofoworola Akintokun
- Department of Microbiology, College of Biosciences, Federal University of Agriculture, Abeokuta 110124, Nigeria; (F.O.O.); (D.A.O.); (A.K.A.)
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (D.H.)
- Correspondence:
| | - Sven Maurischat
- Department Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany;
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43
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Naorem RS, Urban P, Goswami G, Fekete C. Characterization of methicillin-resistant Staphylococcus aureus through genomics approach. 3 Biotech 2020; 10:401. [PMID: 32864286 PMCID: PMC7441129 DOI: 10.1007/s13205-020-02387-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/10/2020] [Indexed: 01/09/2023] Open
Abstract
In the present study, a total of 35 S. aureus isolates collected from two different geographical locations viz., Germany and Hungary were tested for their methicillin-resistant phenotype which revealed a high incidence of methicillin-resistant S. aureus. The quantitative test for biofilm production revealed that 73.3% of isolates were biofilm producers. The isolates were further characterized using a set of biochemical and genotypic methods such as amplification and analysis of S. aureus species-specific sequence and mecA gene. The 33 mecA positive isolates were then characterized by the amplification of SCCmec and pvl toxin genes. Further, based on the biofilm-forming phenotype, 15 isolates were selected and characterized through PCR–RFLP of coa gene, polymorphism of spa gene and amplification of biofilm-associated genes. The dendrogram prepared from the results of both biochemical and genotypic analyses of the 15 isolates showed that except for the isolates SA G5 and SA H29, the rest of the isolates grouped themselves according to their locations. Thus, the two isolates were selected for further characterization through whole-genome sequencing. Comparative genome analysis revealed that SA G5 and SA H29 have 97.20% ANI values with 2344 gene clusters (core-genome) of which 16 genes were related to antibiotic resistance genes and 57 genes encode virulence factors. The highest numbers of singleton genes were found in SA H29 that encodes proteins for virulence, resistance, mobile elements, and lanthionine biosynthesis. The high-resolution phylogenetic trees generated based on shared proteins and SNPs revealed a clear difference between the two strains and can be useful in distinguishing closely related genomes. The present study demonstrated that the whole-genome sequence analysis technique is required to get a better insight into the MRSA strains which would be helpful in improving diagnostic investigations in real-time to improve patient care.
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Affiliation(s)
- Romen Singh Naorem
- Department of General and Environmental Microbiology, Institute of Biology, University of Pécs, Pécs, 7624 Hungary
| | - Peter Urban
- Department of General and Environmental Microbiology, Institute of Biology, University of Pécs, Pécs, 7624 Hungary
- Microbial Biotechnology Research Group, Szentágothai Research Centre, Pécs, 7624 Hungary
| | - Gunajit Goswami
- Department of Life Sciences, Dibrugarh University, Dibrugarh, 786004 Assam India
| | - Csaba Fekete
- Department of General and Environmental Microbiology, Institute of Biology, University of Pécs, Pécs, 7624 Hungary
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44
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Sousa M, Silva N, Borges V, P Gomes J, Vieira L, Caniça M, Torres C, Igrejas G, Poeta P. MRSA CC398 recovered from wild boar harboring new SCCmec type IV J3 variant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137845. [PMID: 32199375 DOI: 10.1016/j.scitotenv.2020.137845] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/02/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
A methicillin-resistant Staphylococcus aureus CC398 was recovered from a wild female boar (Sus scrofa) in the north of Portugal, in 2013 (Sousa et al. 2017). Whole genome sequencing (WGS) revealed this strain carries a new variant of a mecA-containing staphylococcal chromosomal gene cassette (SCCmec) type IV with an uncommon J3 region. WGS studies can facilitate surveillance and provide more detailed characterization of bacterial clones circulating in the wild, reinforcing the need for a one health perspective to better understand and control antimicrobial resistance.
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Affiliation(s)
- Margarida Sousa
- MicroART - Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Veterinary and Animal Science Research Center (CECAV), UTAD, Vila Real, Portugal; Functional Genomics and Proteomics Unit, UTAD, Vila Real, Portugal; National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AR-HAI), National Institute of Health Dr. Ricardo Jorge (NIH), Lisbon, Portugal; Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Nuno Silva
- Moredun Research Institute (MRI), Pentlands Science Park, Bush Loan, Penicuik, Scotland, UK
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - João P Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AR-HAI), National Institute of Health Dr. Ricardo Jorge (NIH), Lisbon, Portugal; Centre for the Study of Animal Sciences (CECA/ICETA), University of Oporto, Oporto, Portugal
| | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Gilberto Igrejas
- Functional Genomics and Proteomics Unit, UTAD, Vila Real, Portugal; Department of Genetics and Biotechnology, UTAD, Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Caparica, Portugal
| | - Patrícia Poeta
- MicroART - Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, Lisboa, Caparica, Portugal.
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45
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LaBreck PT, Rice GK, Paskey AC, Elassal EM, Cer RZ, Law NN, Schlett CD, Bennett JW, Millar EV, Ellis MW, Hamilton T, Bishop-Lilly KA, Merrell DS. Corrigendum: Conjugative Transfer of a Novel Staphylococcal Plasmid Encoding the Biocide Resistance Gene, qacA. Front Microbiol 2020; 11:877. [PMID: 32477301 PMCID: PMC7241116 DOI: 10.3389/fmicb.2020.00877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/15/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Patrick T LaBreck
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Gregory K Rice
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Emad M Elassal
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Regina Z Cer
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Natasha N Law
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Martin Army Community Hospital, Fort Benning, GA, United States
| | - Carey D Schlett
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Jason W Bennett
- Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Eugene V Millar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, MD, United States.,Infectious Diseases Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Michael W Ellis
- University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Theron Hamilton
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - Kimberly A Bishop-Lilly
- Naval Medical Research Center, Biological Defense Research Directorate, Fort Detrick, MD, United States
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.,Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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46
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Chieffi D, Fanelli F, Cho GS, Schubert J, Blaiotta G, Franz CMAP, Bania J, Fusco V. Novel insights into the enterotoxigenic potential and genomic background of Staphylococcus aureus isolated from raw milk. Food Microbiol 2020; 90:103482. [PMID: 32336356 DOI: 10.1016/j.fm.2020.103482] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/27/2020] [Accepted: 02/29/2020] [Indexed: 11/17/2022]
Abstract
In this study, 53 Staphylococcus (S.) aureus strains were typed by 16S-23S rDNA intergenic spacer region (ISR) typing and staphylococcal enterotoxin gene (SEg) typing for all the staphylococcal enterotoxin (se) and staphylococcal enterotoxin-like toxin (sel) genes known to date, revealing a higher discriminatory power than that of multi locus sequence typing. Six strains, one of each ISR- and SEg-type, were genome sequenced and the ability to produce some classical and new SEs when growing in milk was investigated. The manual analysis of the six genomes allowed us to confirm, correct and expand the results of common available genomic data pipelines such as VirulenceFinder. Moreover, it enabled us to (i) investigate the actual location of se and sel genes, even for genes such as selY, whose location (in the core genome) was so far unknown, (ii) find novel allelic variants of se and sel genes and pseudogenes, (iii) correctly annotate se and sel genes and pseudogenes, and (iv) discover a novel type of enterotoxin gene cluster (egc), i.e. the egc type 5 in strains 356P and 364P, while S. argenteus MSHR1132 harbored the egc type 6. Four of the six S. aureus strains produced sufficient amounts of SEA, SEC, SED and SEH in milk to cause staphylococcal food poisoning (SFP), with S. aureus 372 P being the highest producer of SED in milk found to date, producing as much as ca. 47,300 ng/mL and 49,200 ng/mL of SED, after 24 and 48 h of incubation in milk at 37 °C, respectively. S. aureus 372 P released a low amount of SER in milk, most likely because the seR gene was present as a pseudogene, putatively encoding only 51 amino acids. These findings confirm that not only the classical SEs, but also the new ones can represent a potential hazard for the consumers' health if produced in foods in sufficient amounts. Therefore, the detection of SEs in foods, especially if involved in SFP cases, should focus not only on classical, but also on all the new SEs and SEls known to date. Where reference methods are unavailable, the presence of the relevant genes, by using the conventional and real time PCR protocols we exhaustively provided herein, and their nucleotide sequences, should be investigated.
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Affiliation(s)
- Daniele Chieffi
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Francesca Fanelli
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy
| | - Gyu-Sung Cho
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Justyna Schubert
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Giuseppe Blaiotta
- Department of Agricultural Sciences, Division of Vine and Wine Sciences, University of Naples Federico II, Viale Italia, 83100, Avellino, Italy
| | - Charles M A P Franz
- Max Rubner-Institut, Department of Microbiology and Biotechnology, Hermann-Weigmann-Straße 1, 24103, Kiel, Germany
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Vincenzina Fusco
- National Research Council of Italy, Institute of Sciences of Food Production (CNR-ISPA), Bari, Italy.
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Neyaz L, Rajagopal N, Wells H, Fakhr MK. Molecular Characterization of Staphylococcus aureus Plasmids Associated With Strains Isolated From Various Retail Meats. Front Microbiol 2020; 11:223. [PMID: 32140145 PMCID: PMC7042431 DOI: 10.3389/fmicb.2020.00223] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/30/2020] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus is considered one of the most important foodborne bacterial pathogens causing food poisoning and related illnesses. S. aureus strains harbor plasmids encoding genes for virulence and antimicrobial resistance, but few studies have investigated S. aureus plasmids, especially megaplasmids, in isolates from retail meats. Furthermore, knowledge about the distribution of genes encoding replication (rep) initiation proteins in food isolates is lacking. In this study, the prevalence of plasmids in S. aureus strains isolated from retail meats purchased in Oklahoma was investigated; furthermore, we evaluated associations between rep families, selected virulence and antimicrobial resistance genes, and food source origin. Two hundred and twenty-two S. aureus isolates from chicken (n = 55), beef liver (n = 43), pork (n = 42), chicken liver (n = 29), beef (n = 24), turkey (n = 22), and chicken gizzards (n = 7) were subjected to plasmid screening with alkaline lysis and PFGE to detect small-to-medium sized and large plasmids, respectively. The S. aureus isolates contained variable sizes of plasmids, and PFGE was superior to alkaline lysis in detecting large megaplasmids. A total of 26 rep families were identified by PCR, and the most dominant rep families were rep10 and rep7 in 164 isolates (89%), rep21 in 124 isolates (56%), and rep12 in 99 isolates (45%). Relationships between selected rep genes, antimicrobial resistance and virulence genes, and meat sources were detected. In conclusion, S. aureus strains isolated from retail meats harbor plasmids with various sizes and there is an association between rep genes on these plasmids and the meat source or the antimicrobial resistance of the strains harboring them.
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Affiliation(s)
- Leena Neyaz
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Nisha Rajagopal
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Harrington Wells
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Mohamed K Fakhr
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
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LaBreck PT, Merrell DS. Fitness costs associated with carriage of a large staphylococcal plasmid are reduced by subinhibitory concentrations of antiseptics. Microbiologyopen 2020; 9:e1005. [PMID: 32053737 PMCID: PMC7142362 DOI: 10.1002/mbo3.1005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/23/2023] Open
Abstract
Staphylococcus aureus carries a collection of mobile genetic elements that often harbor virulence and antimicrobial resistance genes. Since the introduction of antibiotics, plasmids have become a major genetic element responsible for the distribution of antimicrobial resistance. Under antimicrobial selection, resistance plasmids are maintained within bacterial populations as a means to ensure survival. However, in the absence of selection, large plasmids can be lost due to the fitness costs associated with harboring these genetic elements. pC02 is a previously identified multidrug resistance, conjugative plasmid that is found in S. aureus. In addition to antibiotic resistance, pC02 also carries genes known to be associated with antiseptic resistance. Among these, we previously characterized the contribution of qacA to pC02 mediated reduced chlorhexidine susceptibility. Herein, we demonstrate that pC02 also mediates triclosan resistance, likely due to the presence of fabI, a known triclosan resistance gene. Moreover, we demonstrate that conjugative transfer of pC02 increases triclosan resistance in recipient cells. Competition assays demonstrated a fitness cost associated with carriage of the large pC02 plasmid. However, subinhibitory concentrations of either chlorhexidine or triclosan abrogated this fitness cost. Given the widespread use of these antiseptics, both of which accumulate in wastewater and other environmental reservoirs, indiscriminate use of antiseptics likely imposes a constant selective pressure that promotes maintenance of antimicrobial resistance factors within S. aureus.
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Affiliation(s)
- Patrick T LaBreck
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland.,Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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Systematic Analysis of Efflux Pump-Mediated Antiseptic Resistance in Staphylococcus aureus Suggests a Need for Greater Antiseptic Stewardship. mSphere 2020; 5:5/1/e00959-19. [PMID: 31941819 PMCID: PMC6968660 DOI: 10.1128/msphere.00959-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
S. aureus remains a significant cause of disease within hospitals and communities. To reduce the burden of S. aureus infections, antiseptics are ubiquitously used in our daily lives. Furthermore, many antiseptic compounds are dual purpose and are found in household products. The increased abundance of antiseptic compounds has selected for S. aureus strains that carry efflux pumps that increase resistance to antiseptic compounds; however, the effect of carrying multiple pumps within S. aureus is unclear. We demonstrated that an isogenic strain carrying multiple efflux pumps had an additive resistance phenotype to cetrimide. Moreover, in a strain carrying qacA and norA, increased chlorhexidine tolerance was observed after the strain was preexposed to subinhibitory concentrations of a different common-use antiseptic. Taken together, our findings demonstrate cooperation between antiseptic resistance efflux pumps and suggest that their protective phenotype may be exacerbated by priming with subinhibitory concentrations of household antiseptics. Staphylococcus aureus-associated infections can be difficult to treat due to multidrug resistance. Thus, infection prevention is critical. Cationic antiseptics, such as chlorhexidine (CHX) and benzalkonium chloride (BKC), are liberally used in health care and community settings to prevent infection. However, increased administration of antiseptics has selected for S. aureus strains that show reduced susceptibilities to cationic antiseptics. This increased resistance has been associated with carriage of specific efflux pumps (QacA, QacC, and NorA). Since prior published studies focused on different strains and on strains carrying only a single efflux gene, the relative importance of these various systems to antiseptic resistance is difficult to ascertain. To overcome this, we engineered a collection of isogenic S. aureus strains that harbored norA, qacA, and qacC, individually or in combination. MIC assays showed that qacA was associated with increased resistance to CHX, cetrimide (CT), and BKC, qacC was associated with resistance to CT and BKC, and norA was necessary for basal-level resistance to the majority of tested antiseptics. When all three pumps were present in a single strain, an additive effect was observed in the MIC for CT. Transcriptional analysis revealed that expression of qacA and norA was significantly induced following exposure to BKC. Alarmingly, in a strain carrying qacA and norA, preexposure to BKC increased CHX tolerance. Overall, our results reveal increased antiseptic resistance in strains carrying multiple efflux pumps and indicate that preexposure to BKC, which is found in numerous daily-use products, can increase CHX tolerance. IMPORTANCES. aureus remains a significant cause of disease within hospitals and communities. To reduce the burden of S. aureus infections, antiseptics are ubiquitously used in our daily lives. Furthermore, many antiseptic compounds are dual purpose and are found in household products. The increased abundance of antiseptic compounds has selected for S. aureus strains that carry efflux pumps that increase resistance to antiseptic compounds; however, the effect of carrying multiple pumps within S. aureus is unclear. We demonstrated that an isogenic strain carrying multiple efflux pumps had an additive resistance phenotype to cetrimide. Moreover, in a strain carrying qacA and norA, increased chlorhexidine tolerance was observed after the strain was preexposed to subinhibitory concentrations of a different common-use antiseptic. Taken together, our findings demonstrate cooperation between antiseptic resistance efflux pumps and suggest that their protective phenotype may be exacerbated by priming with subinhibitory concentrations of household antiseptics.
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50
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Abstract
Staphylococci, and in particular Staphylococcus aureus, cause an extensive variety of infections in a range of hosts. The comprehensive analysis of staphylococcal genomes reveals mechanisms controlling the organism's biology, pathobiology, and dissemination. Whole-genome sequencing technologies led to a quantum leap in our understanding of bacterial genomes. The recent cost reduction of sequencing has resulted in unprecedented volumes of genomic information about S. aureus, one of the most sequenced bacterial species. Collecting, comparing, and interpreting big data is challenging, but fascinating insights have emerged. For example, it is becoming clearer which selective pressures staphylococci face in their habitats and which mechanisms allow this pathogen to adapt, survive, and spread. A key theme is the constant evolution of staphylococci as they alter their genome, exchange DNA, and adapt to new environments, leading to the emergence of increasingly successful, antibiotic-resistant, immune-evading, and host-adapted colonizers and pathogens. This article introduces the structure of staphylococcal genomes, details how genomes vary between strains, outlines the mechanisms of genetic variation, and describes the features of successful clones.
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Affiliation(s)
- Jodi A Lindsay
- St. George's, University of London, Institute of Infection and Immunity, London, United Kingdom
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