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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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2
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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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3
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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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Ali Alghamdi B, Al-Johani I, Al-Shamrani JM, Musamed Alshamrani H, Al-Otaibi BG, Almazmomi K, Yusnoraini Yusof N. Antimicrobial resistance in methicillin-resistant staphylococcus aureus. Saudi J Biol Sci 2023; 30:103604. [PMID: 36936699 PMCID: PMC10018568 DOI: 10.1016/j.sjbs.2023.103604] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/02/2023] [Accepted: 02/19/2023] [Indexed: 03/02/2023] Open
Abstract
In the medical community, antibiotics are revered as a miracle because they stop diseases brought on by pathogenic bacteria. Antibiotics have become the cornerstone of contemporary medical advancements ever since penicillin was discovered. Antibiotic resistance developed among germs quickly, placing a strain in the medical field. Methicillin-resistant Staphylococcus aureus (MRSA), Since 1961, has emerged as the major general antimicrobial resistant bacteria (AMR) worldwide. MRSA can easily transmit across the hospital system and has mostly gained resistance to medications called beta-lactamases. This enzyme destroys the cell wall of beta-lactam antibiotics resulting in resistance against that respective antibiotic. Daptomycin, linezolid and vancomycin were previously used to treat MRSA infections. However, due to mutations and Single nucleotide polymorphisms (SNPs) in Open reading frames (ORFs) and SCCmec machinery of respective antibody, MRSA developed resistance against those antibiotics. The MRSA strains (USA300, CC398, CC130 etc.), when their pan-genomes were analyzed were found the genes involved in invoking resistance against the antibiotics as well as the epidemiology of that respective strain. PENC (penicillin plus potassium clavulanate) is the new antibiotic showing potential in treatment of MRSA though it is itself resistant against penicillin alone. In this review, our main focus is on mechanism of development of AMR in MRSA, how different ORFs are involved in evoking resistance in MRSA and what is the core-genome of different antimicrobial resistant MRSA.
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Affiliation(s)
- Bandar Ali Alghamdi
- Department of Cardiac Surgery, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Intisar Al-Johani
- Department of Biotechnology, Taif University, Taif City, Saudi Arabia
| | | | - Hussein Musamed Alshamrani
- Directorate of Health Affairs in Qunfudah Center (Namerah Primary Health care) Pharmacy Department, Saudi Arabia
| | | | - Kholod Almazmomi
- Department of Biotechnology, Taif University, Taif City, Saudi Arabia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Corresponding author at.: Institute for Research in Molecular Medicine (INFORMM) Universiti Sains Malaysia Kubang Kerian, Kelantan 16150, Malaysia.
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Pountain AW, Jiang P, Yao T, Homaee E, Guan Y, Podkowik M, Shopsin B, Torres VJ, Golding I, Yanai I. Transcription-replication interactions reveal principles of bacterial genome regulation. RESEARCH SQUARE 2023:rs.3.rs-2724389. [PMID: 37034646 PMCID: PMC10081379 DOI: 10.21203/rs.3.rs-2724389/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Organisms determine the transcription rates of thousands of genes through a few modes of regulation that recur across the genome1. These modes interact with a changing cellular environment to yield highly dynamic expression patterns2. In bacteria, the relationship between a gene's regulatory architecture and its expression is well understood for individual model gene circuits3,4. However, a broader perspective of these dynamics at the genome-scale is lacking, in part because bacterial transcriptomics have hitherto captured only a static snapshot of expression averaged across millions of cells5. As a result, the full diversity of gene expression dynamics and their relation to regulatory architecture remains unknown. Here we present a novel genome-wide classification of regulatory modes based on each gene's transcriptional response to its own replication, which we term the Transcription-Replication Interaction Profile (TRIP). We found that the response to the universal perturbation of chromosomal replication integrates biological regulatory factors with biophysical molecular events on the chromosome to reveal a gene's local regulatory context. While the TRIPs of many genes conform to a gene dosage-dependent pattern, others diverge in distinct ways, including altered timing or amplitude of expression, and this is shaped by factors such as intra-operon position, repression state, or presence on mobile genetic elements. Our transcriptome analysis also simultaneously captures global properties, such as the rates of replication and transcription, as well as the nestedness of replication patterns. This work challenges previous notions of the drivers of expression heterogeneity within a population of cells, and unearths a previously unseen world of gene transcription dynamics.
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Affiliation(s)
- Andrew W. Pountain
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY USA
| | - Peien Jiang
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY USA
- Department of Biology, New York University, New York, NY, USA
| | - Tianyou Yao
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL USA
| | - Ehsan Homaee
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Yichao Guan
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL USA
| | - Magdalena Podkowik
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
| | - Bo Shopsin
- Department of Medicine, Division of Infectious Diseases, NYU Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY USA
| | - Victor J. Torres
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY USA
| | - Ido Golding
- Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL USA
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana,IL USA
| | - Itai Yanai
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
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Bonn CM, Rafiqullah IM, Crawford JA, Qian YM, Guthrie JL, Matuszewska M, Robinson DA, McGavin MJ. Repeated Emergence of Variant TetR Family Regulator, FarR, and Increased Resistance to Antimicrobial Unsaturated Fatty Acid among Clonal Complex 5 Methicillin-Resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0074922. [PMID: 36744906 PMCID: PMC10019231 DOI: 10.1128/aac.00749-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Resistance-nodulation-division (RND) superfamily efflux pumps promote antibiotic resistance in Gram-negative pathogens, but their role in Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA) is undocumented. However, recent in vitro selections for resistance of S. aureus to an antimicrobial fatty acid, linoleic acid, and an antibiotic, rhodomyrtone, identified H121Y and C116R substitution variants, respectively, in a TetR family regulator, FarR, promoting increased expression of the RND pump FarE. Hypothesizing that in vivo selection pressures have also promoted the emergence of FarR variants, we searched available genome data and found that strains with FarRH121Y from human and bovine hosts have emerged sporadically in clonal complexes (CCs) CC1, CC30, CC8, CC22, and CC97, whereas multiple FarR variants have occurred within CC5 hospital-associated (HA)-MRSA. Of these, FarRE160G and FarRE93EE were exclusive to CC5, while FarRC116Y, FarRP165L, and FarRG166D also occurred in nonrelated CCs, primarily from bovine hosts. Within CC5, FarRC116Y and FarRG166D strains were polyphyletic, each exhibiting two emergence events. FarRC116Y and FarRE160G were individually sufficient to confer increased expression of FarE and enhanced resistance to linoleic acid (LA). Isolates with FarRE93EE were most closely related to S. aureus N315 MRSA and exhibited increased resistance independently of FarRE93EE. Accumulation of pseudogenes and additional polymorphisms in FarRE93EE strains contributed to a multiresistance phenotype which included fosfomycin and fusidic acid resistance in addition to increased linoleic acid resistance. These findings underscore the remarkable adaptive capacity of CC5 MRSA, which includes the polyphyletic USA100 lineage of HA-MRSA that is endemic in the Western hemisphere and known for the acquisition of multiple resistance phenotypes.
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Affiliation(s)
- Camryn M. Bonn
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Iftekhar M. Rafiqullah
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - John A. Crawford
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Yi Meng Qian
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
| | - Jennifer L. Guthrie
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Marta Matuszewska
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Martin J. McGavin
- Department of Microbiology, University of Western Ontario, London, Ontario, Canada
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
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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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Anti-Restriction Gene Homologs Are Highly Represented in Methicillin-Resistant and Multidrug-Resistant Staphylococcus aureus ST239 and ST398: Implications for Resistance Gene Acquisitions. Antibiotics (Basel) 2022; 11:antibiotics11091217. [PMID: 36139996 PMCID: PMC9495042 DOI: 10.3390/antibiotics11091217] [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: 08/10/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 11/17/2022] Open
Abstract
Multidrug resistance is commonly acquired by transferring DNA from one bacterium to another. However, the mechanisms that enhance the acquisitions of foreign genes are poorly understood, as well as the dynamics of their transmission between hosts in different environments. Here, genomic approaches were applied to evaluate the enrichment of the S. aureus chromosome with resistance traits in groups of genomes with or without anti-restriction genes and to analyze some evolutionary aspects of these acquisitions. Furthermore, the role played by an anti-restriction gene in improving multiresistance in MRSA was investigated by molecular cloning. A strong association was observed between the presence of anti-restriction gene homologs and patterns of multidrug resistance. Human isolates, mainly ST239-SCCmecIII, carry ardA-H1, and from animal sources, mainly CC398, carry ardA-H2. Increased DNA transfer was observed for clones that express the ardA-H1 allele, corroborating its role in promoting gene transfer. In addition, ardA-H1 was expressed in the dsDNA format in the BMB9393 strain. The evolution of successful multidrug-resistant MRSA lineages of the ST239 and ST398 was initiated not only by the entry of the mec cassette but also by the acquisition of anti-restriction gene homologs. Understanding the mechanisms that affect DNA transfer may provide new tools to control the spread of drug resistance.
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Abstract
Staphylococcus aureus causes a variety of debilitating and life-threatening diseases, and thus remains a challenging global health threat. S. aureus is remarkably diverse, yet only a minority of methicillin-resistant S. aureus (MRSA) clones have caused pandemic proportions of diseases. The genetic drivers of the successful dissemination of some clones across wide geographical expanses remain poorly understood. We analyzed 386 recently published MRSA genomes from bloodstream infections sampled in North, Central, and South America from 2011 to 2018. Here, we show that MRSA-associated bloodstream infections were attributable to two genetically distinct lineages. One lineage consisted almost exclusively of sequence type (ST) 8, which emerged in 1964. A second lineage emerged in 1986 and consisted of STs 5, 105, and 231. The two lineages have simultaneously disseminated across geographically distant sites. Sublineages rapidly diverged within locations in the early 2000s. Their diversification was associated with independent acquisitions of unique variants of the mobile mecA-carrying chromosomal cassette and distinct repertoires of antimicrobial resistance genes. We show that the evolution and spread of invasive multidrug-resistant MRSA in the Americas was driven by transcontinental dissemination, followed by more recent establishment and divergence of local pathogen populations. Our study highlights the need for continued international surveillance of high-risk clones to control the global health threat of multidrug resistance. IMPORTANCE Bloodstream infections due to S. aureus cause significant patient morbidity and mortality worldwide, exacerbated by the emergence and spread of methicillin resistant S. aureus (MRSA). This study provides important insights on the evolution and long-distance geographic expansion of two distinct MRSA lineages that predominate in bloodstream infections in the past 5 decades. The success of these two lineages partly lies on their acquisition of a diverse set of antimicrobial resistance genes and of unique variants of the mobile genetic element SCCmec that carries the gene mecA conferring resistance to beta-lactams. High-risk antimicrobial resistant clones can therefore rapidly disseminate across long distances and establish within local communities within a short period of time. These results have important implications for global initiatives and local epidemiological efforts to monitor and control invasive MRSA infections and transcontinental spread of multidrug resistance.
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10
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Smith JT, Eckhardt EM, Hansel NB, Eliato TR, Martin IW, Andam CP. Genomic epidemiology of methicillin-resistant and -susceptible Staphylococcus aureus from bloodstream infections. BMC Infect Dis 2021; 21:589. [PMID: 34154550 PMCID: PMC8215799 DOI: 10.1186/s12879-021-06293-3] [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: 02/04/2021] [Accepted: 06/01/2021] [Indexed: 01/13/2023] Open
Abstract
Background Bloodstream infections due to Staphylococcus aureus cause significant patient morbidity and mortality worldwide. Of major concern is the emergence and spread of methicillin-resistant S. aureus (MRSA) in bloodstream infections, which are associated with therapeutic failure and increased mortality. Methods We generated high quality draft genomes from 323 S. aureus blood culture isolates from patients diagnosed with bloodstream infection at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA in 2010–2018. Results In silico detection of antimicrobial resistance genes revealed that 133/323 isolates (41.18%) carry horizontally acquired genes conferring resistance to at least three antimicrobial classes, with resistance determinants for aminoglycosides, beta-lactams and macrolides being the most prevalent. The most common resistance genes were blaZ and mecA, which were found in 262/323 (81.11%) and 104/323 (32.20%) isolates, respectively. Majority of the MRSA (102/105 isolates or 97.14%) identified using in vitro screening were related to two clonal complexes (CC) 5 and 8. The two CCs emerged in the New Hampshire population at separate times. We estimated that the time to the most recent common ancestor of CC5 was 1973 (95% highest posterior density (HPD) intervals: 1966–1979) and 1946 for CC8 (95% HPD intervals: 1924–1959). The effective population size of CC8 increased until the late 1960s when it started to level off until late 2000s. The levelling off of CC8 in 1968 coincided with the acquisition of SCCmec Type IV in majority of the strains. The plateau in CC8 also coincided with the acceleration in the population growth of CC5 carrying SCCmec Type II in the early 1970s, which eventually leveled off in the early 1990s. Lastly, we found evidence for frequent recombination in the two clones during their recent clonal expansion, which has likely contributed to their success in the population. Conclusions We conclude that the S. aureus population was shaped mainly by the clonal expansion, recombination and co-dominance of two major MRSA clones in the last five decades in New Hampshire, USA. These results have important implications on the development of effective and robust strategies for intervention, control and treatment of life-threatening bloodstream infections. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06293-3.
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Affiliation(s)
- Joshua T Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Elissa M Eckhardt
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, 03756, USA
| | - Nicole B Hansel
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, 03756, USA
| | | | - Isabella W Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, 03756, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, 12222, USA.
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11
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Wirth T, Wong V, Vandenesch F, Rasigade JP. Applied phyloepidemiology: Detecting drivers of pathogen transmission from genomic signatures using density measures. Evol Appl 2020; 13:1513-1525. [PMID: 32684973 PMCID: PMC7359849 DOI: 10.1111/eva.12991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/04/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the driving forces of an epidemic is key to inform intervention strategies against it. Correlating measures of the epidemic success of a pathogen with ancillary parameters such as its drug resistance profile provides a flexible tool to identify such driving forces. The recently described time‐scaled haplotypic density (THD) method facilitates the inference of a pathogen's epidemic success from genetic data. Contrary to demogenetic approaches that define success in an aggregated fashion, the THD computes an independent index of success for each isolate in a collection. Modeling this index using multivariate regression, thus, allows us to control for various sources of bias and to identify independent predictors of success. We illustrate the use of THD to address key questions regarding three exemplary epidemics of multidrug‐resistant (MDR) bacterial lineages, namely Mycobacterium tuberculosis Beijing, Salmonella Typhi H58, and Staphylococcus aureus ST8 (including ST8‐USA300 MRSA), based on previously published, international genetic datasets. In each case, THD analysis allowed to identify the impact, or lack thereof, of various factors on the epidemic success, independent of confounding by population structure and geographic distribution. Our results suggest that rifampicin resistance drives the MDR Beijing epidemic and that fluoroquinolone resistance drives the S. aureus ST8/USA300 epidemic, in line with previous evidence of a lack of resistance‐associated fitness cost in these pathogens. Conversely, fluoroquinolone resistance measurably hampered the success of S. Typhi H58 and non‐H58. These findings illustrate how THD can help leverage the massive genomic datasets generated by molecular epidemiology studies to address new questions. THD implementation for the R platform is available at https://github.com/rasigadelab/thd.
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Affiliation(s)
- Thierry Wirth
- Institut de Systématique, Evolution, Biodiversité UMR-CNRS 7205 Muséum National d'Histoire Naturelle Université Pierre et Marie Curie Université des Antilles Ecole Pratique des Hautes Etudes Sorbonne Universités Paris France.,EPHE PSL University Paris France
| | - Vanessa Wong
- Cambridge Institute for Medical Research Welcome Trust Center Cambridge UK
| | - François Vandenesch
- CIRI INSERM U1111 CNRS UMR5308 ENS Lyon University of Lyon Lyon France.,Institut des Agents Infectieux Hospices Civils de Lyon Lyon France
| | - Jean-Philippe Rasigade
- CIRI INSERM U1111 CNRS UMR5308 ENS Lyon University of Lyon Lyon France.,Institut des Agents Infectieux Hospices Civils de Lyon Lyon France
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12
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Chamon RC, Marques LM, Timenetsky J, da Costa Rachid CT, Ferreira RB, de Oliveira TL, Glatthardt T, de Oliveira Moreira L, dos Santos KR. Genome Sequence of a Highly Virulent pvl-positive Vancomycin intermediate- resistant Staphylococcus aureus Sequence Type 30. Curr Genomics 2020; 21:128-137. [PMID: 32655307 PMCID: PMC7324871 DOI: 10.2174/1389202921666200327105756] [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: 02/14/2020] [Revised: 03/16/2020] [Accepted: 03/16/2020] [Indexed: 11/22/2022] Open
Abstract
Background:
Staphylococcus aureus isolates expressing the Panton-Valentine Leukocidin
(PVL) have been related to a wide range of diseases. Recently, pvl-positive community-associated
methicillin-resistant S. aureus belonging to USA1100 (ST30/CC30/SCCmec IV) lineage has emerged
in Brazilian hospitals.
Objective:
The aim of this work was to sequence the genome of a pvl-positive USA1100 Vancomycin-
Intermediate-Resistant S. aureus (VISA) isolate from Rio de Janeiro, Brazil.
Methods:
The 13420 genome was sequenced using the HiSeq 2500 platform. The draft genome, plasmids
annotation, and genome analysis were performed using RAST. Comparison of the relative pvl
gene expression of six S. aureus isolates was performed by qRT-PCR.
Results:
The isolate presented the ϕPVL phage codifying for the H2b PVL protein isoform, and another
prophage carrying a PVL variant named lukF and lukS-PV.2. The 13420 genome presented a
high number of virulence determinants, such as genes codifying for serine-protease proteins, enterotoxins
(egc), the immune evasion cluster (IEC), adhesion proteins, spermine/spermidine acetyltransferase
gene (blt), superantigen-like proteins, as well as the ica operon. Point mutations at vraS, tcaA,
and tcaB genes were detected. Moreover, the PVL mRNA relative expression of the 13420 isolate was
five times higher than mRNA PVL levels of the USA300/ST8 reference strain.
Conclusion:
We described for the first time the genome sequence of a VISA isolate harboring two
pvl-associated genes and other virulence factors that may improve the USA1100/ST30 lineage fitness
and impact its pathogenicity and spreading at Brazilian hospitals.
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Affiliation(s)
- Raiane C. Chamon
- Laboratorio de Infeccao Hospitalar, Departamento de Microbiologia Medica, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas M. Marques
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Bahia, Brazil
| | - Jorge Timenetsky
- Instituto de Ciencias Biomedicas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Caio T.C. da Costa Rachid
- Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rosana B.R. Ferreira
- Laboratorio de Infeccao Hospitalar, Departamento de Microbiologia Medica, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tamara L.R. de Oliveira
- Laboratorio de Infeccao Hospitalar, Departamento de Microbiologia Medica, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thais Glatthardt
- Laboratorio de Infeccao Hospitalar, Departamento de Microbiologia Medica, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lilian de Oliveira Moreira
- Laboratorio de Bacteriologia e Imunologia Clinica, Departamento de Analises Clínicas e Toxicologicas, Faculdade de Farmacia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kátia R.N. dos Santos
- Laboratorio de Infeccao Hospitalar, Departamento de Microbiologia Medica, Instituto de Microbiologia Paulo de Goes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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13
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Genovese C, La Fauci V, D'Amato S, Squeri A, Anzalone C, Costa GB, Fedele F, Squeri R. Molecular epidemiology of antimicrobial resistant microorganisms in the 21th century: a review of the literature. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:256-273. [PMID: 32420962 PMCID: PMC7569612 DOI: 10.23750/abm.v91i2.9176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/26/2022]
Abstract
Healthcare-associated infections (HAIs) are the most frequent and severe complication acquired in healthcare settings with high impact in terms of morbidity, mortality and costs. Many bacteria could be implicated in these infections, but, expecially multidrug resistance bacteria could play an important role. Many microbial typing technologies have been developed until to the the bacterial whole-genome sequencing and the choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. In several studies the molecular investigation of pathogens involved in HAIs was performed with many microorganisms identified as causative agents such as Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Clostridium difficile, Acinetobacter spp., Enterobacter spp., Enterococcus spp., Staphylococcus aureus and several more minor species. Here, we will describe the most and least frequently reported clonal complex, sequence types and ribotypes with their worldwide geographic distribution for the most important species involved in HAIs.
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Affiliation(s)
- Cristina Genovese
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Vincenza La Fauci
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Smeralda D'Amato
- Postgraduate Medical School in Hygiene and Preventive Medicine, University of Messina, Italy.
| | - Andrea Squeri
- Department of Human Pathology of the adult and developmental age Gaetano Barresi, University of Messina, Messina, Italy.
| | - Carmelina Anzalone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Gaetano Bruno Costa
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Francesco Fedele
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
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14
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Wu K, Conly J, McClure JA, Kurwa HA, Zhang K. Arginine Catabolic Mobile Element in Evolution and Pathogenicity of the Community-Associated Methicillin-Resistant Staphylococcus aureus Strain USA300. Microorganisms 2020; 8:microorganisms8020275. [PMID: 32085445 PMCID: PMC7074830 DOI: 10.3390/microorganisms8020275] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 02/14/2020] [Indexed: 01/11/2023] Open
Abstract
USA300 is a predominant community-associated methicillin-resistant Staphylococcus aureus strain which carries an arginine catabolic mobile element (ACME). ACME contains potential virulence factors including an arginine deiminase (arc) pathway and an oligopeptide permease (opp-3) system, which are proposed to play a role in bacterial virulence and transmission. However, the role of ACME in evolution and pathogenicity of USA300 remains to be elucidated. ACME and arcA deletion mutants were created by allelic replacement from a USA300 clinical isolate. By comparing wild type and isogenic ACME deletion USA300 strains, ACME was shown not to contribute to bacterial survival on plastic surfaces, and mouse skin surfaces. ACME did not contribute to bacterial virulence in cell invasion and cytotoxicity assays, invertebrate killing assays and a mouse skin infection model. Wild-type ACME negative USA300 clinical isolates showed similar associations with invasive anatomic sites as ACME positive isolates. Our experiments also demonstrated that ACME can spontaneously excise from the bacterial chromosome to generate an ACME deletion strain at a low frequency. Our results do not support that the ACME element alone is a significant factor in the transmission and virulence of USA300 strain, and ACME may have been coincidently incorporated into the genome of USA300.
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Affiliation(s)
- Kaiyu Wu
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AL T2N 4N1, Canada; (K.W.); (J.C.)
| | - John Conly
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AL T2N 4N1, Canada; (K.W.); (J.C.)
- Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, AL T2N 4N1, Canada
- Department of Medicine, University of Calgary, Calgary, AL T2N 4N1, Canada;
- The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AL T2N 4N1, Canada
- Centre for Antimicrobial Resistance, Alberta Health Services/Alberta Public Laboratories/University of Calgary, Calgary, AL T2N 4N1, Canada;
| | - Jo-Ann McClure
- Centre for Antimicrobial Resistance, Alberta Health Services/Alberta Public Laboratories/University of Calgary, Calgary, AL T2N 4N1, Canada;
| | - Habib A. Kurwa
- Department of Medicine, University of Calgary, Calgary, AL T2N 4N1, Canada;
| | - Kunyan Zhang
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, AL T2N 4N1, Canada; (K.W.); (J.C.)
- Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, AL T2N 4N1, Canada
- Department of Medicine, University of Calgary, Calgary, AL T2N 4N1, Canada;
- The Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AL T2N 4N1, Canada
- Centre for Antimicrobial Resistance, Alberta Health Services/Alberta Public Laboratories/University of Calgary, Calgary, AL T2N 4N1, Canada;
- Correspondence: ; Tel.: +1-403-210-8484
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15
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Macori G, Bellio A, Bianchi DM, Chiesa F, Gallina S, Romano A, Zuccon F, Cabrera-Rubio R, Cauquil A, Merda D, Auvray F, Decastelli L. Genome-Wide Profiling of Enterotoxigenic Staphylococcus aureus Strains Used for the Production of Naturally Contaminated Cheeses. Genes (Basel) 2019; 11:E33. [PMID: 31892220 PMCID: PMC7016664 DOI: 10.3390/genes11010033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/19/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and an important cause of livestock infections. More than 20 staphylococcal enterotoxins with emetic activity can be produced by specific strains responsible for staphylococcal food poisoning, one of the most common food-borne diseases. Whole genome sequencing provides a comprehensive view of the genome structure and gene content that have largely been applied in outbreak investigations and genomic comparisons. In this study, six enterotoxigenic S. aureus strains were characterised using a combination of molecular, phenotypical and computational methods. The genomes were analysed for the presence of virulence factors (VFs), where we identified 110 genes and classified them into five categories: adherence (n = 31), exoenzymes (n = 28), genes involved in host immune system evasion (n = 7); iron uptake regulatory system (n = 8); secretion machinery factors and toxins' genes (n = 36), and 39 genes coding for transcriptional regulators related to staphylococcal VFs. Each group of VFs revealed correlations among the six enterotoxigenic strains, and further analysis revealed their accessory genomic content, including mobile genetic elements. The plasmids pLUH02 and pSK67 were detected in the strain ProNaCC1 and ProNaCC7, respectively, carrying out the genes sed, ser, and selj. The genes carried out by prophages were detected in the strain ProNaCC2 (see), ProNaCC4, and ProNaCC7 (both positive for sea). The strain ProNaCC5 resulted positive for the genes seg, sei, sem, sen, seo grouped in an exotoxin gene cluster, and the strain ProNaCC6 resulted positive for seh, a transposon-associated gene. The six strains were used for the production of naturally contaminated cheeses which were tested with the European Screening Method for staphylococcal enterotoxins. The results obtained from the analysis of toxins produced in cheese, combined with the genomic features represent a portrait of the strains that can be used for the production of staphylococcal enterotoxin-positive cheese as reference material.
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Affiliation(s)
- Guerrino Macori
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Alberto Bellio
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Daniela Manila Bianchi
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Francesco Chiesa
- Dipartimento di Scienze Veterinarie, Università di Torino, 10095 Grugliasco, Italy;
| | - Silvia Gallina
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Angelo Romano
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Fabio Zuccon
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
| | - Raúl Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996, Ireland-APC Microbiome Ireland, University College Cork, T12YT20 Cork, Ireland;
| | - Alexandra Cauquil
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Déborah Merda
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Fréderic Auvray
- European Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Laboratory for Food Safety, ANSES, Université Paris-Est, F-94700 Maisons-Alfort, France; (A.C.); (D.M.); (F.A.)
| | - Lucia Decastelli
- National Reference Laboratory for Coagulase-Positive Staphylococci including Staphylococcus aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (A.B.); (D.M.B.); (S.G.); (A.R.); (F.Z.); (L.D.)
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16
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Harrison EM, Ba X, Coll F, Blane B, Restif O, Carvell H, Köser CU, Jamrozy D, Reuter S, Lovering A, Gleadall N, Bellis KL, Uhlemann AC, Lowy FD, Massey RC, Grilo IR, Sobral R, Larsen J, Rhod Larsen A, Vingsbo Lundberg C, Parkhill J, Paterson GK, Holden MTG, Peacock SJ, Holmes MA. Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus. Nat Microbiol 2019; 4:1680-1691. [PMID: 31235959 PMCID: PMC7611363 DOI: 10.1038/s41564-019-0471-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/26/2019] [Indexed: 01/04/2023]
Abstract
Antibiotic resistance in bacterial pathogens threatens the future of modern medicine. One such resistant pathogen is methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to nearly all β-lactam antibiotics, limiting treatment options. Here, we show that a significant proportion of MRSA isolates from different lineages, including the epidemic USA300 lineage, are susceptible to penicillins when used in combination with β-lactamase inhibitors such as clavulanic acid. Susceptibility is mediated by a combination of two different mutations in the mecA promoter region that lowers mecA-encoded penicillin-binding protein 2a (PBP2a) expression, and in the majority of isolates by either one of two substitutions in PBP2a (E246G or M122I) that increase the affinity of PBP2a for penicillin in the presence of clavulanic acid. Treatment of S. aureus infections in wax moth and mouse models shows that penicillin/β-lactamase inhibitor susceptibility can be exploited as an effective therapeutic choice for 'susceptible' MRSA infection. Finally, we show that isolates with the PBP2a E246G substitution have a growth advantage in the presence of penicillin but the absence of clavulanic acid, which suggests that penicillin/β-lactamase susceptibility is an example of collateral sensitivity (resistance to one antibiotic increases sensitivity to another). Our findings suggest that widely available and currently disregarded antibiotics could be effective in a significant proportion of MRSA infections.
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Affiliation(s)
- Ewan M Harrison
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Francesc Coll
- London School of Hygiene and Tropical Medicine, London, UK
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Henry Carvell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Sandra Reuter
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Andrew Lovering
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Franklin D Lowy
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Inês R Grilo
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Rita Sobral
- UCIBIO@REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jesper Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Gavin K Paterson
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | | | - Sharon J Peacock
- Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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17
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Immunofluorescence Microscopy for the Detection of Surface Antigens in Methicillin Resistant Staphylococcus aureus (MRSA). Methods Mol Biol 2019. [PMID: 31523764 DOI: 10.1007/978-1-4939-9849-4_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Immunofluorescence microscopy is a widely used laboratory method which allows detection and visualization of specific antigens. The method employs the specificity of antibodies to deliver fluorophore to a specific target and then visualize it with a microscope. The power of the technique is that it requires relatively little manipulation and relatively few bacterial cells, enabling the detection of antigen expression where other methods cannot, such as during an actual infection in an animal. Here, we apply the method to follow antigen expression on the surface of MRSA cells over time in in vivo infection models.
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18
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Jamrozy D, Misra R, Xu Z, Ter-Stepanyan MM, Kocharyan KS, Cave R, Hambardzumyan AD, Mkrtchyan HV. Novel Methicillin-Resistant Staphylococcus aureus CC8 Clone Identified in a Hospital Setting in Armenia. Front Microbiol 2019; 10:1592. [PMID: 31354680 PMCID: PMC6635598 DOI: 10.3389/fmicb.2019.01592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/26/2019] [Indexed: 11/17/2022] Open
Abstract
Whole-genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) has been sparse in low- and middle-income countries, therefore, its population structure is unknown for many regions. We conducted a pilot surveillance of MRSA in the maternity ward of a teaching hospital in Armenia, to characterize the genotypes of circulating MRSA clones. In total, 10 MRSA isolates from a hospital environment (n = 4) and patients (n = 6) were recovered between March and May 2015 and April and May 2016, respectively. WGS analysis showed that the isolates belonged to two clonal complexes (CCs): CC8 (n = 8) and CC30 (n = 2). MRSA CC30 isolates carried staphylococcal cassette chromosome mec (SCCmec) type IVa, whereas MRSA CC8 revealed a type-VT-related SCCmec, which contained a CRISPR/Cas array and showed a high similarity to SCCmec found in coagulase-negative staphylococci. All but one MRSA CC8 isolates carried a plasmid identical to the pSK67 and four also carried a pathogenicity island similar to SaPI5. Phylogenetic analysis showed that the MRSA CC8 isolates formed a monophyletic cluster, which emerged around 1995 and was distinct from representatives of globally-distributed MRSA CC8 lineages. WGS characterization of MRSA in countries with no previous S. aureus genomic surveillance can therefore reveal an unrecognized diversity of MRSA lineages.
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Affiliation(s)
- Dorota Jamrozy
- Wellcome Sanger Institute, Saffron Walden, United Kingdom
| | - Raju Misra
- Core Research Laboratories, Molecular Biology, Natural History Museum, London, United Kingdom
| | - Zhen Xu
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Tianjin, China
- Department of Toxicology and Sanitary Chemistry, Tianjin Medical University, Tianjin, China
| | | | - Karine S. Kocharyan
- Department of Epidemiology, Yerevan State Medical University, Yerevan, Armenia
| | - Rory Cave
- School of Health, Sport and Bioscience, University of East London, London, United Kingdom
| | | | - Hermine V. Mkrtchyan
- School of Health, Sport and Bioscience, University of East London, London, United Kingdom
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19
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Complete Genome Sequences of Two Methicillin-Susceptible Staphylococcus aureus Clinical Strains Closely Related to Community-Associated Methicillin-Resistant S. aureus USA300. Microbiol Resour Announc 2019; 8:8/17/e00356-19. [PMID: 31023802 PMCID: PMC6486259 DOI: 10.1128/mra.00356-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Predominant community-associated methicillin-resistant Staphylococcus aureus strain USA300 is believed to have originated from an ancestral methicillin-susceptible strain, although the details of that evolution remain unknown. To help understand the emergence of this highly successful strain, we sequenced the genomes of two methicillin-susceptible Staphylococcus aureus clinical strains that are very closely related to USA300. Predominant community-associated methicillin-resistant Staphylococcus aureus strain USA300 is believed to have originated from an ancestral methicillin-susceptible strain, although the details of that evolution remain unknown. To help understand the emergence of this highly successful strain, we sequenced the genomes of two methicillin-susceptible Staphylococcus aureus clinical strains that are very closely related to USA300.
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20
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Mohamed N, Timofeyeva Y, Jamrozy D, Rojas E, Hao L, Silmon de Monerri NC, Hawkins J, Singh G, Cai B, Liberator P, Sebastian S, Donald RGK, Scully IL, Jones CH, Creech CB, Thomsen I, Parkhill J, Peacock SJ, Jansen KU, Holden MTG, Anderson AS. Molecular epidemiology and expression of capsular polysaccharides in Staphylococcus aureus clinical isolates in the United States. PLoS One 2019; 14:e0208356. [PMID: 30641545 PMCID: PMC6331205 DOI: 10.1371/journal.pone.0208356] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus capsular polysaccharides (CP) are important virulence factors under evaluation as vaccine antigens. Clinical S. aureus isolates have the biosynthetic capability to express either CP5 or CP8 and an understanding of the relationship between CP genotype/phenotype and S. aureus epidemiology is valuable. Using whole genome sequencing, the clonal relatedness and CP genotype were evaluated for disease-associated S. aureus isolates selected from the Tigecycline Evaluation and Surveillance Trial (T.E.S.T) to represent different geographic regions in the United States (US) during 2004 and 2009–10. Thirteen prominent clonal complexes (CC) were identified, with CC5, 8, 30 and 45 representing >80% of disease isolates. CC5 and CC8 isolates were CP type 5 and, CC30 and CC45 isolates were CP type 8. Representative isolates from prevalent CC were susceptible to in vitro opsonophagocytic killing elicited by anti-CP antibodies, demonstrating that susceptibility to opsonic killing is not linked to the genetic lineage. However, as not all S. aureus isolates may express CP, isolates representing the diversity of disease isolates were assessed for CP production. While approximately 35% of isolates (primarily CC8) did not express CP in vitro, CP expression could be clearly demonstrated in vivo for 77% of a subset of these isolates (n = 20) despite the presence of mutations within the capsule operon. CP expression in vivo was also confirmed indirectly by measuring an increase in CP specific antibodies in mice infected with CP5 or CP8 isolates. Detection of antigen expression in vivo in relevant disease states is important to support the inclusion of these antigens in vaccines. Our findings confirm the validity of CP as vaccine targets and the potential of CP-based vaccines to contribute to S. aureus disease prevention.
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Affiliation(s)
- Naglaa Mohamed
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Yekaterina Timofeyeva
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Dorota Jamrozy
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Eduardo Rojas
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Li Hao
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | | | - Julio Hawkins
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Guy Singh
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Bing Cai
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Paul Liberator
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Shite Sebastian
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Robert G. K. Donald
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - Ingrid L. Scully
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - C. Hal Jones
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | - C. Buddy Creech
- Vanderbilt Vaccine Research Program, Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Isaac Thomsen
- Vanderbilt Vaccine Research Program, Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Sharon J. Peacock
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kathrin U. Jansen
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
| | | | - Annaliesa S. Anderson
- Pfizer Vaccine Research and Development, Pearl River, New York, United States of America
- * E-mail:
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Blaustein RA, McFarland AG, Ben Maamar S, Lopez A, Castro-Wallace S, Hartmann EM. Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil. mSystems 2019; 4:e00281-18. [PMID: 30637341 PMCID: PMC6325168 DOI: 10.1128/msystems.00281-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/07/2018] [Indexed: 12/11/2022] Open
Abstract
Understanding underlying mechanisms involved in microbial persistence in the built environment (BE) is essential for strategically mitigating potential health risks. To test the hypothesis that BEs impose selective pressures resulting in characteristic adaptive responses, we performed a pangenomics meta-analysis leveraging 189 genomes (accessed from GenBank) of two epidemiologically important taxa, Bacillus cereus and Staphylococcus aureus, isolated from various origins: the International Space Station (ISS; a model BE), Earth-based BEs, soil, and humans. Our objectives were to (i) identify differences in the pangenomic composition of generalist and host-associated organisms, (ii) characterize genes and functions involved in BE-associated selection, and (iii) identify genomic signatures of ISS-derived strains of potential relevance for astronaut health. The pangenome of B. cereus was more expansive than that of S. aureus, which had a dominant core component. Genomic contents of both taxa significantly correlated with isolate origin, demonstrating an importance for biogeography and potential niche adaptations. ISS/BE-enriched functions were often involved in biosynthesis, catabolism, materials transport, metabolism, and stress response. Multiple origin-enriched functions also overlapped across taxa, suggesting conserved adaptive processes. We further characterized two mobile genetic elements with local neighborhood genes encoding biosynthesis and stress response functions that distinctively associated with B. cereus from the ISS. Although antibiotic resistance genes were present in ISS/BE isolates, they were also common in counterparts elsewhere. Overall, despite differences in microbial lifestyle, some functions appear common to remaining viable in the BE, and those functions are not typically associated with direct impacts on human health. IMPORTANCE The built environment contains a variety of microorganisms, some of which pose critical human health risks (e.g., hospital-acquired infection, antibiotic resistance dissemination). We uncovered a combination of complex biological functions that may play a role in bacterial survival under the presumed selective pressures in a model built environment-the International Space Station-by using an approach to compare pangenomes of bacterial strains from two clinically relevant species (B. cereus and S. aureus) isolated from both built environments and humans. Our findings suggest that the most crucial bacterial functions involved in this potential adaptive response are specific to bacterial lifestyle and do not appear to have direct impacts on human health.
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Affiliation(s)
- Ryan A. Blaustein
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Alexander G. McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
| | - Alberto Lopez
- Department of Microbiology-Immunology, Northwestern University, Evanston, Illinois, USA
| | - Sarah Castro-Wallace
- Biomedical Research and Environmental Sciences Division, NASA Johnson Space Center, Houston, Texas, USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, USA
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Read TD, Petit RA, Yin Z, Montgomery T, McNulty MC, David MZ. USA300 Staphylococcus aureus persists on multiple body sites following an infection. BMC Microbiol 2018; 18:206. [PMID: 30518317 PMCID: PMC6282268 DOI: 10.1186/s12866-018-1336-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/12/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND USA300 methicillin-resistant Staphylococcus aureus (MRSA) is a community- and hospital-acquired pathogen that frequently causes infections but also can survive on the human body asymptomatically as a part of the normal microbiota. We devised a comparative genomic strategy to track colonizing USA300 at different body sites after an initial infection. We sampled ST8 S. aureus from subjects at the site of a first known MRSA infection. Within 60 days of this infection and again 12 months later, each subject was tested for asymptomatic colonization in the nose, throat and perirectal region. 93 S. aureus strains underwent whole genome shotgun sequencing. RESULTS Among 28 subjects at the initial sampling time, we isolated S. aureus from the nose, throat and perirectal sites from 15, 11 and 15 of them, respectively. Twelve months later we isolated S. aureus from 9 subjects, with 6, 3 and 3 strains from the nose, throat and perirectal area, respectively. Genome sequencing revealed that 23 patients (ages 0-66 years) carried USA300 intra-subject lineages (ISLs), defined as having an index infection isolate and closely related colonizing strains. Pairwise distance between strains in different ISLs was 48 to 162 single nucleotide polymorphisms (SNPs) across the core regions of the chromosome, whereas within the same ISL it was 0 to 26 SNPs. Strains in ISLs from the same subject differed in plasmid and prophage content, and contained deletions that removed the mecA-containing SCCmec and ACME regions. Five strains contained frameshift mutations in agr toxin-regulating genes. Persistence of an ISL was not associated with clinical or demographic subject characteristics. We inferred that colonization with the ISL occurred about 18 weeks before the first assessment of asymptomatic colonization. CONCLUSIONS Clonal lineages of USA300 may continue to colonize people at one or more anatomic sites up to a year after an initial infection and experience loss of the SCCmec, loss and gain of other mobile genetic elements, and mutations in the agr operon.
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Affiliation(s)
- Timothy D. Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Robert A. Petit
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Zachary Yin
- Department of Pediatrics, Section of Infectious Diseases, University of Chicago, Chicago, IL USA
| | - Tuyaa Montgomery
- Department of Pediatrics, Section of Infectious Diseases, University of Chicago, Chicago, IL USA
| | - Moira C. McNulty
- Department of Medicine, Section of Infectious Diseases and Global Health, University of Chicago, Chicago, IL USA
| | - Michael Z. David
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania, Philadelphia, PA USA
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Improved Subtyping of Staphylococcus aureus Clonal Complex 8 Strains Based on Whole-Genome Phylogenetic Analysis. mSphere 2018; 3:3/3/e00464-17. [PMID: 29720527 PMCID: PMC5932376 DOI: 10.1128/msphere.00464-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/12/2017] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus. Strains of Staphylococcus aureus in clonal complex 8 (CC8), including USA300, USA500, and the Iberian clone, are prevalent pathogens in the United States, both inside and outside health care settings. Methods for typing CC8 strains are becoming obsolete as the strains evolve and diversify, and whole-genome sequencing has shown that some strain types fall into multiple sublineages within CC8. In this study, we attempt to clarify the strain nomenclature of CC8, classifying the major strain types based on whole-genome sequence phylogenetics using both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) genomes. We show that isolates of the Archaic and Iberian clones from decades ago make up the most basal clade of the main CC8 lineages and that at least one successful lineage of CC8, made up mostly of MSSA, diverged before the other well-known strain types USA500 and USA300. We also show that the USA500 type includes two clades separated by the previously described “Canadian epidemic MRSA” strain CMRSA9, that one clade containing USA500 also contains the USA300 clade, and that the USA300-0114 strain type is not a monophyletic group. Additionally, we present a rapid, simple CC8 strain-typing scheme using real-time PCR assays that target single nucleotide polymorphisms (SNPs) derived from our CC8 phylogeny and show the significant benefit of using more stable genomic markers based on evolutionary lineages over traditional S. aureus typing techniques. This more accurate and accessible S. aureus typing system may improve surveillance and better inform the epidemiology of this very important pathogen. IMPORTANCEStaphylococcus aureus is a major human pathogen worldwide in both community and health care settings. Surveillance for S. aureus strains is important to our understanding of their spread and to informing infection prevention and control. Confusion surrounding the strain nomenclature of one of the most prevalent lineages of S. aureus, clonal complex 8 (CC8), and the imprecision of current tools for typing S. aureus make surveillance and source tracing difficult and sometimes misleading. In this study, we clarify the CC8 strain designations and propose a new typing scheme for CC8 isolates that is rapid and easy to use. This typing scheme is based on relatively stable genomic markers, and we demonstrate its superiority over traditional typing techniques. This scheme has the potential to greatly improve epidemiological investigations of S. aureus.
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Frisch MB, Castillo-Ramírez S, Petit RA, Farley MM, Ray SM, Albrecht VS, Limbago BM, Hernandez J, See I, Satola SW, Read TD. Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages. mSphere 2018; 3:e00571-17. [PMID: 29720528 PMCID: PMC5932375 DOI: 10.1128/msphere.00571-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/09/2018] [Indexed: 01/09/2023] Open
Abstract
USA500 isolates are clonal complex 8 (CC8) Staphylococcus aureus strains closely related to the prominent community- and hospital-associated USA300 group. Despite being relatively understudied, USA500 strains cause a significant burden of disease and are the third most common methicillin-resistant S. aureus (MRSA) strains identified in the U.S. Emerging Infections Program (EIP) invasive S. aureus surveillance. To better understand the genetic relationships of the strains, we sequenced the genomes of 539 USA500 MRSA isolates from sterile site infections collected through the EIP between 2005 and 2013 in the United States. USA500 isolates fell into three major clades principally separated by their distribution across different U.S. regions. Clade C1 strains, found principally in the Northeast, were associated with multiple IS256 insertion elements in their genomes and higher levels of antibiotic resistance. C2 was associated with Southern states, and E1 was associated with Western states. C1 and C2 strains all shared a frameshift in the gene encoding AdsA surface-attached surface protein. We propose that the term "USA500" should be used for CC8 strains sharing a recent common ancestor with the C1, C2, and E1 strains but not in the USA300 group.IMPORTANCE In this work, we have removed some of the confusion surrounding the use of the name "USA500," placed USA500 strains in the context of the CC8 group, and developed a strategy for assignment to subclades based on genome sequence. Our new phylogeny of USA300/USA500 will be a reference point for understanding the genetic adaptations that have allowed multiple highly virulent clonal strains to emerge from within CC8 over the past 50 years.
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Affiliation(s)
- M B Frisch
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - R A Petit
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - M M Farley
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Atlanta VA Medical Center, Decatur, Georgia, USA
| | - S M Ray
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - V S Albrecht
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - B M Limbago
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Hernandez
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - I See
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - S W Satola
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - T D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8. Proc Natl Acad Sci U S A 2017; 114:E10596-E10604. [PMID: 29158405 PMCID: PMC5724248 DOI: 10.1073/pnas.1702472114] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
USA300 is a hypervirulent, community-acquired, multidrug-resistant Staphylococcus aureus clone that started to spread in the United States around 17 years ago. Many studies detected it also in South America, Europe, and the Asia-Pacific region. In this study, we show that USA300 is also circulating in sub-Saharan Africa. Locating the temporal and spatial origin of clonal lineages is important with respect to epidemiology and molecular evolution of pathogens. We show that USA300 evolved from a less virulent and less resistant ancestor circulating in Central Europe around 160 years ago. Constant surveillance of pathogen transmission routes is vital to prevent and control potential outbreaks. Whole genome sequencing proved to be a useful tool for epidemiological surveillance. USA300 is a pandemic clonal lineage of hypervirulent, community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) with specific molecular characteristics. Despite its high clinical relevance, the evolutionary origin of USA300 remained unclear. We used comparative genomics of 224 temporal and spatial diverse S. aureus isolates of multilocus sequence type (ST) 8 to reconstruct the molecular evolution and global dissemination of ST8, including USA300. Analyses of core SNP diversity and accessory genome variations showed that the ancestor of all ST8 S. aureus most likely emerged in Central Europe in the mid-19th century. From here, ST8 was exported to North America in the early 20th century and progressively acquired the USA300 characteristics Panton–Valentine leukocidin (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME), and a specific mutation in capsular polysaccharide gene cap5E. Although the PVL-encoding phage ϕSa2USA was introduced into the ST8 background only once, various SCCmec types were introduced to ST8 at different times and places. Starting from North America, USA300 spread globally, including Africa. African USA300 isolates have aberrant spa-types (t112, t121) and form a monophyletic group within the clade of North American USA300. Large parts of ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa represent a symplesiomorphic group of ST8 (i.e., a group representing the characteristics of the ancestor), which are rarely found in other world regions. Isolates previously discussed as USA300 ancestors, including USA500 and a “historic” CA-MRSA from Western Australia, were shown to be only distantly related to recent USA300 clones.
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Sansevere EA, Robinson DA. Staphylococci on ICE: Overlooked agents of horizontal gene transfer. Mob Genet Elements 2017; 7:1-10. [PMID: 28932624 DOI: 10.1080/2159256x.2017.1368433] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 10/19/2022] Open
Abstract
Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus, which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn916 was capable of transfer from Enterococcus to Staphylococcus. However, recent work has begun to thaw this field. To date, 2 families of ICEs have been identified among staphylococci - Tn916 that includes the Tn5801 subfamily, and ICE6013 that includes at least 7 subfamilies. Both Tn5801 and ICE6013 commonly occur in clinical strains of S. aureus. Tn5801 is the most studied of the Tn916 family elements in staphylococci and encodes tetracycline resistance and a protein that, when expressed in Escherichia coli, inhibits restriction barriers to incoming DNA. ICE6013 is among the shortest known ICEs, but it still includes many uncharacterized open reading frames. This element uses an IS30-like transposase as its recombinase, providing some versatility in integration sites. ICE6013 also conjugatively transfers among receptive S. aureus strains at relatively higher frequency than Tn5801. Continued study of these mobile genetic elements may reveal the full extent to which ICEs impact horizontal gene transfer and the evolution of staphylococci.
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Affiliation(s)
- Emily A Sansevere
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
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27
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Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus. J Bacteriol 2017; 199:JB.00629-16. [PMID: 28138100 DOI: 10.1128/jb.00629-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/25/2017] [Indexed: 01/04/2023] Open
Abstract
ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013 A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.
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Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks. Genome Med 2016; 8:102. [PMID: 27716432 PMCID: PMC5048656 DOI: 10.1186/s13073-016-0353-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/13/2016] [Indexed: 01/30/2023] Open
Abstract
Background Long-term care facilities (LTCF) are potential reservoirs for methicillin-resistant Staphylococcus aureus (MRSA), control of which may reduce MRSA transmission and infection elsewhere in the healthcare system. Whole-genome sequencing (WGS) has been used successfully to understand MRSA epidemiology and transmission in hospitals and has the potential to identify transmission between these and LTCF. Methods Two prospective observational studies of MRSA carriage were conducted in LTCF in England and Ireland. MRSA isolates were whole-genome sequenced and analyzed using established methods. Genomic data were available for MRSA isolated in the local healthcare systems (isolates submitted by hospitals and general practitioners). Results We sequenced a total of 181 MRSA isolates from the two study sites. The majority of MRSA were multilocus sequence type (ST)22. WGS identified one likely transmission event between residents in the English LTCF and three putative transmission events in the Irish LTCF. WGS also identified closely related isolates present in colonized Irish residents and their immediate environment. Based on phylogenetic reconstruction, closely related MRSA clades were identified between the LTCF and their healthcare referral network, together with putative MRSA acquisition by LTCF residents during hospital admission. Conclusions These data confirm that MRSA is transmitted between residents of LTCF and is both acquired and transmitted to others in referral hospitals and beyond. Our data present compelling evidence for the importance of environmental contamination in MRSA transmission, reinforcing the importance of environmental cleaning. The use of WGS in this study highlights the need to consider infection control in hospitals and community healthcare facilities as a continuum. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0353-5) contains supplementary material, which is available to authorized users.
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