Genome Sequences of Community Carriage Strains of Staphylococcus aureus from Yuma, Arizona

Pearson, Talima; Hepp, Crystal M.; Trotter, Robert T.; Mbegbu, Mimi; Russakoff, Benjamin; Yagüe, David Panisello; Wood, Colin; Tucker-Morgan, Kara; Ceniceros, Kathya; Padilla, Cristina Rodríguez; Kyman, Shari; Villa, Francisco A.

doi:10.1128/mra.00449-21

Cited by 4 publications

(6 citation statements)

References 21 publications

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“…Details on efforts to prevent false positive results are detailed in Russakoff et al [ 6 ] and include whole genome sequencing and MLST v2.0 and SCC mec Finder v1.2 analyses ( www.genomicepidemiology.org ) of putative S . aureus colonies [ 38 ]. For samples that were culture negative but SaQuant positive, an amplicon sequencing approach was used to verify species designation [ 6 ] as well as extensive validation of the SaQuant assay to ensure accurate classification on samples with low S .…”

Section: Methodsmentioning

confidence: 99%

“…CHROMagar Staph aureus chromogenic media allows for differentiation of S. aureus from other species as S. aureus colonies appear pink to mauve while other bacterial species are inhibited or will appear colorless or blue. Details on efforts to prevent false positive results are detailed in Russakoff et al [6] and include whole genome sequencing and MLST v2.0 and SCCmecFinder v1.2 analyses (www.genomicepidemiology.org) of putative S. aureus colonies [38]. For samples that were culture negative but SaQuant positive, an amplicon sequencing approach was used to verify species designation [6] as well as extensive validation of the SaQuant assay to ensure accurate classification on samples with low S. aureus quantities [6,36].…”

Section: Detection Of S Aureusmentioning

confidence: 99%

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Cross-sectional study of the association of social relationship resources with Staphylococcus aureus colonization in naturally occurring social groups along the US/Mexico border

Barger

Lininger²,

Trotter³

et al. 2023

PLoS ONE

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Asymptomatic carriage of Staphylococcus aureus is a major risk factor for subsequent clinical infection. Diminishing returns from mitigation efforts emphasize the need to better understand colonization, spread, and transmission of this opportunistic pathogen. While contact with other people presents opportunities for pathogen exposure and transmission, diversity of social connections may be protective against pathogens such as the common cold. This study examined whether social relationship resources, including the amount and diversity of social contacts, are associated with S. aureus colonization. Participants were community members (N = 443; 68% Hispanic) in naturally occurring social groups in southwestern Arizona. Four types of social relationships and loneliness were assessed, and samples from the skin, nose and throat were obtained to ascertain S. aureus colonization. Overall S. aureus prevalence was 64.8%. Neither the amount nor the diversity of social contacts were associated with S. aureus colonization. The concurrent validity of the social relationship assessments was supported by their moderate intercorrelations and by their positive association with self-rated health. The results suggest that the association of social network diversity and susceptibility to the common cold does not extend to S. aureus colonization. Conversely, colonization prevalence was not higher among those with more social contacts. The latter pattern suggests that social transmission may be relatively infrequent or that more intimate forms of social interaction may drive transmission and colonization resulting in high community prevalence of S. aureus colonization. These data inform communicable disease control efforts.

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Section: Methodsmentioning

confidence: 99%

Section: Detection Of S Aureusmentioning

confidence: 99%

Cross-sectional study of the association of social relationship resources with Staphylococcus aureus colonization in naturally occurring social groups along the US/Mexico border

Barger

Lininger²,

Trotter³

et al. 2023

PLoS ONE

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“…This study is part of a larger investigation aimed at understanding carriage and transmission within social groups in a population on the US/Mexico border (Pearson et al 2021; Barger et al 2020; Pearson et al 2019). Study staff recruited participants in naturally occurring social groups of two or more persons and supervised the self-collection of swabs from three body sites: the nares, throat, and palm.…”

Section: Methodsmentioning

confidence: 99%

“…To better understand binary and quantitative community-based carriage, we apply a quantitative PCR assay to samples collected from a large cohort of community members in Yuma, Arizona (Barger et al 2020; Pearson et al 2019; 2021). Based on data collected during the validation of a new highly sensitive and specific qPCR assay for the accurate detection and quantification of S. aureus (Wood et al 2021), we expected to achieve higher detection sensitivity compared to culture-based detection.…”

Section: Introductionmentioning

confidence: 99%

A quantitative assessment of Staphylococcus aureus community carriage in Yuma, Arizona

Russakoff

Wood

Lininger

et al. 2022

Preprint

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Staphylococcus aureus is a frequent cause of mild and severe infections that occur when these commensal bacteria penetrate the outer layers of skin or mucosa. As most S. aureus infections are the result of autoinfection, and community-acquired infections are increasingly common, it is important to better understand S. aureus colonization characteristics in the community setting. Using standard culture technique and a quantitative PCR assay (SaQuant), we detected and quantified S. aureus across the nares, throat, and palm of 548 community-dwelling individuals in southwestern Arizona. Using culture-based methods, we detected S. aureus colonization in the nares of 26.3% of individuals (n = 144); however, the combination of two detection methods across multiple body sites resulted in much higher prevalence than has been reported previously. Overall, 65.9% of participants were colonized, with significantly higher prevalence in males (compared to females) and non-Hispanics (compared to Hispanics), with this pattern especially evident in nares and throat samples. Colonizing quantities in the nares were slightly higher in males and significantly greater among non-Hispanics. The clear sex and ethnicity patterns warrant further investigation in order to identify and leverage protective factors that may drive these disparities. In the nares, S. aureus density was the highest, most variable, and correlates with colonization in other body sites such as throat and palm. Our results demonstrate that screening by culture-based methods only can miss individuals colonized by S. aureus and that previous carriage statistics are likely underestimates. By including a highly sensitive quantitative assay, this work provides a roadmap towards more comprehensive and accurate characterization of S. aureus carriage and the potential for more effective mitigation.AUTHOR SUMMARYEffective disease control and prevention is tied to pathogen identification and understanding reservoirs. Staphylococcus aureus infection prevention efforts and protocols are based upon decades of research on colonization patterns and associated links to subsequent infection. Unfortunately, efforts to prevent S. aureus infections have been met with diminishing returns, suggesting significant gaps in fundamental knowledge of colonization. However, this knowledge and resulting protocols, are founded upon culture-based detection. By employing a new quantitative PCR assay on samples from three body sites in 548 individuals, we can characterize colonization more comprehensively than previous studies by describing both prevalence and pathogen quantity. Our highly sensitive detection resulted in an overall prevalence of 65.9%. Higher quantities were associated with the nares and were highest among non-Hispanic males (86.9%). Overall prevalence was much higher than has been previously documented. Common research practices, such as culture-based detection from a single body site, may misclassify over half of colonized persons. Future studies incorporating quantitative data, especially with longitudinal sampling at more body sites will provide a more wholistic understanding of community carriage, colonization dynamics, and likelihood of autoinfection and transmission.

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“…We used samples from an ongoing research project designed to better understand community carriage and transmission among social groups in a population on the United States/Mexico border [25][26][27][28][29]. These samples were part of Project 1116783 that was approved by the Northern Arizona University Institutional Review Board.…”

Section: Empirical Example Of Population Sequencing Of S Aureus To De...mentioning

confidence: 99%

Population sequencing for diversity and transmission analyses

Pearson,

Furstenau,

Wood

et al. 2024

Preprint

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Genomic diversity in a pathogen population is the foundation for evolution and adaptations in virulence, drug resistance, pathogenesis, and immune evasion. Characterizing, analyzing, and understanding population-level diversity is also essential for epidemiological and forensic tracking of sources and revealing detailed pathways of transmission and spread. For bacteria, culturing, isolating, and sequencing the large number of individual colonies required to adequately sample diversity can be prohibitively time-consuming and expensive. While sequencing directly from a mixed population will show variants among reads, they cannot be linked to reveal allele combinations associated with particular traits or phylogenetic inheritance patterns. Here, we describe the theory and method of how population sequencing directly from a mixed sample can be used in conjunction with sequencing a very small number of colonies to describe the phylogenetic diversity of a population without haplotype reconstruction. To demonstrate the utility of population sequencing in capturing phylogenetic diversity, we compared isogenic clones to population sequences ofBurkholderia pseudomalleifrom the sputum of a single patient. We also analyzed population sequences ofStaphylococcus aureusderived from different people and different body sites. Sequencing results confirm our ability to capture and characterize phylogenetic diversity in our samples. Our analyses ofB. pseudomalleipopulations led to the surprising discovery that the pathogen population is highly structured in sputum, suggesting that for some pathogens, sputum sampling may preserve structuring in the lungs and thus present a non-invasive alternative to understanding colonization, movement, and pathogen/host interactions. Our analyses ofS. aureussamples show how comparing phylogenetic diversity across populations can reveal directionality of transmission between hosts and across body sites, demonstrating the power and utility for characterizing the spread of disease and identification of reservoirs at the finest levels. We anticipate that population sequencing and analysis can be broadly applied to accelerate research in a broad range of fields reliant on a foundational understanding of population diversity.Author SummaryThe ability to characterize diversity in a single bacterial population (i.e., a single host or even a single body site) is critical for understanding adaptation and evolution, with far-reaching implications on disease treatment and prevention that include revealing patterns of spread and persistence. While the scientific community has made great strides in sequencing methods to characterize single colonies and entire communities, there is a dearth of studies at the population level. This is because 1) the need to culture and sequence a sufficiently representative number of isogenic colonies is prohibitive, and 2) the theoretical foundation for characterizing a population by sequencing a single sample (as is done for microbiome and metagenomic analyses) has not been developed. Here, we introduce this theoretical foundation and validate its applicability by characterizing a lung infection caused byBurkholderia pseudomallei. We also demonstrate the utility of this method in determining the directionality of spread ofStaphylococcus aureusbetween people and across body sites within the same host (a level of spatial resolution that has not been previously performed). We anticipate that this work will open the door to a host of new studies and discoveries across a diverse set of microbiological fields.

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Genome Sequences of Community Carriage Strains of Staphylococcus aureus from Yuma, Arizona

Cited by 4 publications

References 21 publications

Cross-sectional study of the association of social relationship resources with Staphylococcus aureus colonization in naturally occurring social groups along the US/Mexico border

Cross-sectional study of the association of social relationship resources with Staphylococcus aureus colonization in naturally occurring social groups along the US/Mexico border

A quantitative assessment of Staphylococcus aureus community carriage in Yuma, Arizona

Population sequencing for diversity and transmission analyses

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