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Musher DM, Elisarraras FX. Is it time to retire the term 'bloodstream infection'? (Submitted as Letter to the Editor). J Infect 2024; 89:106184. [PMID: 38744377 DOI: 10.1016/j.jinf.2024.106184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Affiliation(s)
- Daniel M Musher
- Departments of Medicine and Molecular Virology and Immunology Baylor College of Medicine, Houston, TX 77030, USA; Medical Care Line, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA.
| | - Francisco X Elisarraras
- Departments of Medicine and Molecular Virology and Immunology Baylor College of Medicine, Houston, TX 77030, USA
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2
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Hofstetter KS, Jacko NF, Shumaker MJ, Talbot BM, Petit RA, Read TD, David MZ. Strain Differences in Bloodstream and Skin Infection: Methicillin-Resistant Staphylococcus aureus Isolated in 2018-2021 in a Single Health System. Open Forum Infect Dis 2024; 11:ofae261. [PMID: 38854395 PMCID: PMC11160326 DOI: 10.1093/ofid/ofae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Staphylococcus aureus is a common cause of skin and soft-tissue infections (SSTIs) and has become the most common cause of bloodstream infections (BSIs) in recent years, but whether the strains causing these two clinical syndromes overlap has not been studied adequately. USA300/500 (clonal complex [CC] 8-sequence type [ST] 8) and USA100 (CC5-ST5) have dominated among methicillin-resistant S aureus (MRSA) strains in the United States since the early 2000s. We compared the genomes of unselected MRSA isolates from 131 SSTIs with those from 145 BSIs at a single US center in overlapping periods in 2018-2021. CC8 MRSA was more common among SSTIs, and CC5 was more common among BSIs, consistent with prior literature. Based on clustering genomes with a threshold of 15 single-nucleotide polymorphisms, we identified clusters limited to patients with SSTI and separate clusters exclusively comprising patients with BSIs. However, we also identified eight clusters that included at least one SSTI and one BSI isolate. This suggests that virulent MRSA strains are transmitted from person to person locally in the healthcare setting or the community and that single lineages are often capable of causing both SSTIs and BSIs.
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Affiliation(s)
- Katrina S Hofstetter
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Natasia F Jacko
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Margot J Shumaker
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brooke M Talbot
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Robert A Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael Z David
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Costa FG, Mills KB, Crosby HA, Horswill AR. The Staphylococcus aureus regulatory program in a human skin-like environment. mBio 2024; 15:e0045324. [PMID: 38546267 PMCID: PMC11077960 DOI: 10.1128/mbio.00453-24] [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: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 04/09/2024] Open
Abstract
Staphylococcus aureus is a Gram-positive pathogen responsible for the majority of skin and soft tissue infections (SSTIs). S. aureus colonizes the anterior nares of approximately 20%-30% of the population and transiently colonizes the skin, thereby increasing the risk of developing SSTIs and more serious infections. Current laboratory models that mimic the skin surface environment are expensive, require substantial infrastructure, and limit the scope of bacterial physiology studies under human skin conditions. To overcome these limitations, we developed a cost-effective, open-source, chemically defined media recipe termed skin-like medium (SLM) that incorporates key aspects of the human skin surface environment and supports growth of several staphylococcal species. We utilized SLM to investigate the transcriptional response of methicillin-resistant Staphylococcus aureus (MRSA) following growth in SLM compared to a commonly used laboratory media. Through RNA-seq analysis, we observed the upregulation of several virulence factors, including genes encoding functions involved in adhesion, proteolysis, and cytotoxicity. To further explore these findings, we conducted quantitative reverse transcription-PCR (qRT-PCR) experiments to determine the influence of media composition, pH, and temperature on the transcriptional response of key factors involved in adhesion and virulence. We also demonstrated that MRSA primed in SLM adhered better to human corneocytes and demonstrated adhesin-specific phenotypes that previously required genetic manipulation. This improved adherence to corneocytes was dependent on both acidic pH and growth in SLM. These results support the potential utility of SLM as an in vitro model for assessing staphylococcal physiology and metabolism on human skin. IMPORTANCE Staphylococcus aureus is the major cause of skin diseases, and its increased prevalence in skin colonization and infections present a need to understand its physiology in this environment. The work presented here outlines S. aureus upregulation of colonization and virulence factors using a newly developed medium that strives to replicate the human skin surface environment and demonstrates roles for adhesins clumping factor A (ClfA), serine-rich repeat glycoprotein adhesin (SraP), and the fibronectin binding proteins (Fnbps) in human corneocyte adherence.
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Affiliation(s)
- Flavia G. Costa
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Krista B. Mills
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Heidi A. Crosby
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alexander R. Horswill
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Veterans Affairs, Eastern Colorado Healthcare System, Aurora, Colorado, USA
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Souza SSR, Smith JT, Marcovici MM, Eckhardt EM, Hansel NB, Martin IW, Andam CP. Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance. NPJ ANTIMICROBIALS AND RESISTANCE 2024; 2:14. [PMID: 38725655 PMCID: PMC11076216 DOI: 10.1038/s44259-024-00032-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Joshua T. Smith
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Michael M. Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
| | - Elissa M. Eckhardt
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Nicole B. Hansel
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Isabella W. Martin
- Dartmouth-Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, NY USA
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Simon SJ, Sater M, Herriott I, Huntley M, Briars E, Hollenbeck BL. Staphylococcus epidermidis joint isolates: Whole-genome sequencing demonstrates evidence of hospital transmission and common antimicrobial resistance. Infect Control Hosp Epidemiol 2024; 45:150-156. [PMID: 38099465 DOI: 10.1017/ice.2023.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
OBJECTIVE We investigated genetic, epidemiologic, and environmental factors contributing to positive Staphylococcus epidermidis joint cultures. DESIGN Retrospective cohort study with whole-genome sequencing (WGS). PATIENTS We identified S. epidermidis isolates from hip or knee cultures in patients with 1 or more prior corresponding intra-articular procedure at our hospital. METHODS WGS and single-nucleotide polymorphism-based clonality analyses were performed, including species identification, in silico multilocus sequence typing (MLST), phylogenomic analysis, and genotypic assessment of the prevalence of specific antibiotic resistance and virulence genes. Epidemiologic review was performed to compare cluster and noncluster cases. RESULTS In total, 60 phenotypically distinct S. epidermidis isolates were identified. After removal of duplicates and impure samples, 48 isolates were used for the phylogenomic analysis, and 45 (93.7%) isolates were included in the clonality analysis. Notably, 5 S. epidermidis strains (10.4%) showed phenotypic susceptibility to oxacillin yet harbored mecA, and 3 (6.2%) strains showed phenotypic resistance despite not having mecA. Smr was found in all isolates, and mupA positivity was not observed. We also identified 6 clonal clusters from the clonality analysis, which accounted for 14 (31.1%) of the 45 S. epidermidis isolates. Our epidemiologic investigation revealed ties to common aspirations or operative procedures, although no specific common source was identified. CONCLUSIONS Most S. epidermidis isolates from clinical joint samples are diverse in origin, but we identified an important subset of 31.1% that belonged to subclinical healthcare-associated clusters. Clusters appeared to resolve spontaneously over time, suggesting the benefit of routine hospital infection control and disinfection practices.
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Affiliation(s)
- Samantha J Simon
- Research Department, New England Baptist Hospital, Boston, Massachusetts
| | | | | | | | | | - Brian L Hollenbeck
- Research Department, New England Baptist Hospital, Boston, Massachusetts
- Infectious Diseases, New England Baptist Hospital, Boston, Massachusetts
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Raghuram V, Gunoskey JJ, Hofstetter KS, Jacko NF, Shumaker MJ, Hu YJ, Read TD, David MZ. Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures. Microb Genom 2023; 9:001111. [PMID: 37934072 PMCID: PMC10711313 DOI: 10.1099/mgen.0.001111] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/21/2023] [Indexed: 11/08/2023] Open
Abstract
The most common approach to sampling the bacterial populations within an infected or colonized host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. Sequencing a mixture of several colonies (pool-seq) is a better approach to detect population heterogeneity, but it is more complex to analyse due to different types of heterogeneity, such as within-clone polymorphisms, multi-strain mixtures, multi-species mixtures and contamination. Here, we compared 8 single-colony isolates (singles) and pool-seq on a set of 2286 Staphylococcus aureus culture samples to identify features that can distinguish pure samples, samples undergoing intraclonal variation and mixed strain samples. The samples were obtained by swabbing 3 body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to those for the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of intra-clonal polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.
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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
| | - Jessica J. Gunoskey
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Katrina S. Hofstetter
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Natasia F. Jacko
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Margot J. Shumaker
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael Z. David
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, USA
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Costa FG, Mills KB, Crosby HA, Horswill AR. The Staphylococcus aureus regulatory program in a human skin-like environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563767. [PMID: 37961268 PMCID: PMC10634794 DOI: 10.1101/2023.10.24.563767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Staphylococcus aureus is a Gram-positive pathogen responsible for the majority of skin and soft tissue infections (SSTIs). S. aureus colonizes the anterior nares of approximately 20-30% of the population and transiently colonizes the skin, thereby increasing the risk of developing SSTIs and more serious infections. Current laboratory models that mimic the skin surface environment are expensive, require substantial infrastructure, and limit the scope of bacterial physiology studies under human skin conditions. To overcome these limitations, we developed a cost-effective, open-source, chemically defined media recipe termed skin-like media (SLM) that incorporates key aspects of the human skin surface environment and supports growth of several Staphylococcal species. We utilized SLM to investigate the transcriptional response of methicillin-resistant S. aureus (MRSA) following growth in SLM compared to a commonly used laboratory media. Through RNA-seq analysis, we observed the upregulation of several virulence factors, including genes encoding functions involved in adhesion, proteolysis, and cytotoxicity. To further explore these findings, we conducted qRT-PCR experiments to determine the influence of media composition, pH, and temperature on the transcriptional response of key factors involved in adhesion and virulence. We also demonstrated that MRSA primed in SLM adhered better to human corneocytes and demonstrated adhesin-specific phenotypes that previously required genetic manipulation. These results support the potential utility of SLM as an in vitro model for assessing Staphylococcal physiology and metabolism on human skin. Importance Staphylococcus aureus is the major cause of skin diseases, and its increased prevalence in skin colonization and infections present a need to understand its physiology in this environment. The work presented here outlines S. aureus upregulation of colonization and virulence factors using a newly developed media that strives to replicate the human skin surface environment, and demonstrates roles for adhesins ClfA, SraP, and Fnbps in human corneocyte adherence.
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8
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Raghuram V, Gunoskey JJ, Hofstetter KS, Jacko NF, Shumaker MJ, Hu YJ, Read TD, David MZ. Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonisation cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544959. [PMID: 37397999 PMCID: PMC10312683 DOI: 10.1101/2023.06.14.544959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The most common approach to sampling the bacterial populations within an infected or colonised host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. An alternative is to sequence a mixture containing multiple colonies ("pool-seq"), but this has the disadvantage that it is a non-homogeneous sample, making it difficult to perform specific experiments. We compared differences in measures of genetic diversity between eight single-colony isolates (singles) and pool-seq on a set of 2286 S. aureus culture samples. The samples were obtained by swabbing three body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple Multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.
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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
| | - Jessica J. Gunoskey
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katrina S. Hofstetter
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Natasia F. Jacko
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Margot J. Shumaker
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Michael Z. David
- Division of Infectious Diseases, Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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