Dataset Information

Genomic Epidemiology of MRSA During Incarceration at a Large Inner-City Jail.

ABSTRACT:

Background

Congregate settings, such as jails, may be a location where colonized detainees transmit methicillin-resistant Staphylococcus aureus (MRSA). We examined MRSA acquisition during incarceration and characterized the genomic epidemiology of MRSA entering the jail and isolated during incarceration.

Methods

Males incarcerated at the Cook County Jail were enrolled within 72 h of intake and MRSA surveillance cultures collected. Detainees in jail at Day 30 were re-cultured to determine MRSA acquisition. A survey was administered to identify acquisition predictors. Genomic sequencing of surveillance and clinical isolates was integrated with epidemiologic and jail location data to track MRSA transmission pathways.

Results

800 males were enrolled; 19% MRSA colonized at intake. Of 184 who reached Day 30 visit, 12 acquired MRSA. Heroin use before entering (OR 3.67, P = .05) and sharing personal items during incarceration (OR = 4.92, P = .01) were predictors of acquisition. Sequenced clinical USA300 isolates (n = 112) were more genetically similar than diverse intake USA300 strains (P < .001), suggesting jail transmission. Four acquired colonization isolates were within 20 single-nucleotide variant (SNVs) of other isolates; 4 were within 20 SNVs of an intake isolate, 2 for an acquisition isolate, and 1 for a clinical isolate. Individuals with genetically similar isolates were more likely to have had overlapping stays in the same buildings.

Conclusion

There was a high MRSA burden entering jail. Genomic analysis of acquisition and clinical isolates suggests potential spread of incoming strains and networks of spread during incarceration, with spread often occurring among detainees housed in similar locations. Sharing personal items during incarceration is associated with MRSA acquisition and could be a focus for intervention.

SUBMITTER: Popovich KJ

PROVIDER: S-EPMC8664465 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundJails may facilitate spread of methicillin-resistant Staphylococcus aureus (MRSA) in urban areas. We examined MRSA colonization upon entrance to a large urban jail to determine if there are MRSA transmission networks preceding incarceration.MethodsMales incarcerated in Cook County Jail (Chicago) were enrolled, with enrichment for people living with human immunodeficiency virus (PLHIV), within 72 hours of intake. Surveillance cultures assessed prevalence of MRSA colonization. Whole-genome sequencing (WGS) identified preincarceration transmission networks.We examined methicillin-resistant Staphylococcus aureus (MRSA) isolates to determine if there are transmission networks that precede incarceration. A large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to community reservoirs for MRSA.ResultsThere were 718 individuals (800 incarcerations) enrolled; 58% were PLHIV. The prevalence of MRSA colonization at intake was 19%. In multivariate analysis, methamphetamine use, unstable housing, current/recent skin infection, and recent injection drug use were predictors of MRSA. Among PLHIV, recent injection drug use, current skin infection, and HIV care at outpatient clinic A that emphasizes comprehensive care to the lesbian, gay, bisexual, transgender community were predictors of MRSA. Fourteen (45%) of 31 detainees with care at clinic A had colonization. WGS revealed that this prevalence was not due to clonal spread in clinic but rather to an intermingling of distinct community transmission networks. In contrast, genomic analysis supported spread of USA500 strains within a network. Members of this USA500 network were more likely to be PLHIV (P < .01), men who have sex with men (P < .001), and methamphetamine users (P < .001).ConclusionsA large proportion of individuals enter jail colonized with MRSA. Molecular epidemiology and colonization risk factors provide clues to identify colonized detainees entering jail and potential community reservoirs of MRSA.

Project description:Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of health care-associated (HA) and community-associated (CA) infections. USA300 strains are historically CA-MRSA, while USA100 strains are HA-MRSA. Here, we update an antibiotic prediction rule to distinguish these two genotypes based on antibiotic resistance phenotype using whole-genome sequencing (WGS), a more discriminatory methodology than pulsed-field gel electrophoresis (PFGE). MRSA clinical isolates collected from 2007 to 2017 underwent WGS; associated epidemiologic data were ascertained. In developing the rule, we examined MRSA isolates that included a population with a history of incarceration. Performance characteristics of antibiotic susceptibility for predicting USA300 compared to USA100, as defined by WGS, were examined. Phylogenetic analysis was performed to examine resistant USA300 clades. We identified 275 isolates (221 USA300, 54 USA100). Combination susceptibility to clindamycin or levofloxacin performed the best overall (sensitivity 80.7%, specificity 75.9%) to identify USA300. The average number of antibiotic classes with resistance was higher for USA100 (3 versus 2, P < 0.001). Resistance to ≤2 classes was predictive for USA300 (area under the curve (AUC) 0.84, 95% confidence interval 0.78 to 0.90). Phylogenetic analysis identified a cluster of USA300 strains characterized by increased resistance among incarcerated individuals. Using a combination of clindamycin or levofloxacin susceptibility, or resistance to ≤2 antibiotic classes, was predictive of USA300 as defined by WGS. Increased resistance was observed among individuals with incarceration exposure, suggesting circulation of a more resistant USA300 clade among at-risk community networks. Our phenotypic prediction rule could be used as an epidemiologic tool to describe community and nosocomial shifts in USA300 MRSA and quickly identify emergence of lineages with increased resistance. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of health care-associated (HA) and community-associated (CA) infections, but the epidemiology of these strains (USA100 and USA300, respectively) now overlaps in health care settings. Although sequencing technology has become more available, many health care facilities still lack the capabilities to perform these analyses. In this study, we update a simple prediction rule based on antibiotic resistance phenotype with integration of whole-genome sequencing (WGS) to predict strain type based on antibiotic resistance profiles that can be used in settings without access to molecular strain typing methods. This prediction rule has many potential epidemiologic applications, such as analysis of retrospective data sets, regional monitoring, and ongoing surveillance of CA-MRSA infection trends. We demonstrate application of this rule to identify an emerging USA300 strain with increased antibiotic resistance among incarcerated individuals that deviates from the rule.