BackgroundHealth care–associated Staphylococcus aureus infections are declining but remain common. Conversely, rates of community-associated infections have not decreased because of the inadequacy of public health mechanisms to control transmission in a community setting. Our long-term goal is to use risk-based information from empirical socio-cultural-biological evidence of carriage and transmission to inform intervention strategies that reduce S aureus transmission in the community. Broad differences in social interactions because of cultural affiliation, travel, and residency patterns may impact S aureus carriage and transmission, either as risk or as protective factors.ObjectiveThis study aims to (1) characterize S aureus carriage rates and compare circulating pathogen genotypes with those associated with disease isolated from local clinical specimens across resident groups and across Hispanic and non-Hispanic white ethnic groups and (2) evaluate social network relationships and social determinants of health-based risk factors for their impact on carriage and transmission of S aureus.MethodsWe combine sociocultural survey approaches to population health sampling with S aureus carriage and pathogen genomic analysis to infer transmission patterns. Whole genome sequences of S aureus from community and clinical sampling will be phylogenetically compared to determine if strains that cause disease (clinical samples) are representative of community genotypes. Phylogenetic comparisons of strains collected from participants within social groups can indicate possible transmission within the group. We can therefore combine transmission data with social determinants of health variables (socioeconomic status, health history, etc) and social network variables (both egocentric and relational) to determine the extent to which social relationships are associated with S aureus transmission.ResultsWe conducted a first year pilot test and feasibility test of survey and biological data collection and analytic procedures based on the original funded design for this project (#NIH U54MD012388). That design resulted in survey data collection from 336 groups and 1337 individuals. The protocol, described below, is a revision based on data assessment, new findings for statistical power analyses, and refined data monitoring procedures.ConclusionsThis study is designed to evaluate ethnic-specific prevalence of S aureus carriage in a US border community. The study will also examine the extent to which kin and nonkin social relationships are concordant with carriage prevalence in social groups. Genetic analysis of S aureus strains will further distinguish putative transmission pathways across social relationship contexts and inform our understanding of the correspondence of S aureus reservoirs across clinical and community settings. Basic community-engaged nonprobabilistic sampling procedures provide a rigorous framework for completion of this 5-year study of the social and cultural parameters of S aureus carriage and transmission.

Background Molecular assays are important tools for pathogen detection but need to be periodically re-evaluated with the discovery of additional genetic diversity that may cause assays to exclude target taxa or include non-target taxa. A single well-developed assay can find broad application across research, clinical, and industrial settings. Pathogen prevalence within a population is estimated using such assays and accurate results are critical for formulating effective public health policies and guiding future research. A variety of assays for the detection of Staphylococcus aureus are currently available. The utility of commercial assays for research is limited, given proprietary signatures and lack of transparent validation. Results In silico testing of existing peer-reviewed assays show that most suffer from a lack of sensitivity and specificity. We found no assays that were specifically designed and validated for quantitative use. Here we present a qPCR assay, SaQuant, for the detection and quantification of S. aureus as might be collected on sampling swabs. Sensitivity and specificity of the assay was 95.6 and 99.9 %, respectively, with a limit of detection of between 3 and 5 genome equivalents and a limit of quantification of 8.27 genome equivalents. The presence of DNA from non-target species likely to be found in a swab sample, did not impact qualitative or quantitative abilities of the assay. Conclusions This assay has the potential to serve as a valuable tool for the accurate detection and quantification of S. aureus collected from human body sites in order to better understand the dynamics of prevalence and transmission in community settings.

Disease control relies on pathogen identification and understanding reservoirs. Staphylococcus aureus infection prevention is based upon decades of research on colonization and infection, but diminishing returns from mitigation efforts suggest significant knowledge gaps. Existing knowledge and mitigation protocols are founded upon culture-based detection, with almost no information about pathogen quantities. We employed a qPCR assay on samples from three body sites to characterize colonization more comprehensively than previous studies by describing both prevalence and pathogen quantity. We show a much higher overall prevalence (65.9%) than previously documented, with higher quantities and prevalence associated with the nares, non-Hispanic males (86.9%), and correlating with colonization in other body sites. These results suggest that research and clinical practices likely misclassify over half of colonized persons, limiting mitigation measures and their impact. This work begins the process of rebuilding foundational knowledge of S. aureus carriage with more accurate and wholistic approaches.

Aims To understand the impact of storage temperature on recovery of Staphylococcus aureus on sampling swabs. S. aureus is a common cause of skin and soft tissue infections, but also causes a variety of life-threatening diseases. With a large pool of asymptomatic carriers and transmission that can occur even through indirect contact, mitigation efforts have had limited success. Swab sampling, followed by culturing, is a cornerstone of epidemiological studies, however S. aureus viability on swabs stored at different temperatures has not been characterized. Methods and Results We determined survival rates on swabs stored at five different temperatures. Samples stored at-70°C had no decay over time while samples stored at higher temperatures showed an exponential decay in viability. Mortality rates were greatest for swabs stored at 37°C. Survival at intermediate temperatures (-20°C-20.5°C) did not differ significantly, however we observed more variation at higher temperatures. Conclusions To maximize recovery of S. aureus cells, samples should be stored at-70°C or processed for culturing without delay. Significance and Impact of Study Epidemiological studies of bacterial diseases are typically limited to determination of pathogen presence/absence, yet quantitative assessments of pathogen load and genetic diversity can provide insights into disease progression and severity, likelihood of transmission, and adaptive evolutionary potential. For studies of S. aureus where time or access to a microbiology laboratory may delay culturing, deep freezing or timely culturing will maximize the degree to which sampling results reflect source status.

Staphylococcus aureus exists as a pathogen and commensal. Individuals with asymptomatic carriage serve as a reservoir for transmission and are at increased risk of infecting themselves. In order to characterize the genomic diversity of S. aureus circulating in the community, we sequenced 166 genomes collected from individuals in Yuma, AZ.