Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 in a County Jail.

Background: In the coronavirus disease 2019 (COVID-19) pandemic, correctional facilities are potential hotspots for transmission. We examined the genomic epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the pandemic in one of the country's largest urban jails. Methods: Existing SARS-CoV-2 isolates from 131 detainees at the Cook County Jail in Chicago, Illinois, from March 2020 through May 2020 were analyzed by whole-genome sequencing. Contemporaneous isolates from Rush University Medical Center (Chicago, Illinois) and the Global Initiative on Sharing All Influenza Data (GISAID) were used to identify genetic clusters containing only jail isolates. Transmission windows were identified for each pair of detainees using the date of the SARS-CoV-2-positive test and location data to determine if detainees overlapped in the jail, within a specific building, or within particular living units during transmission windows. Results: We identified 29 jail-only clusters that contained 75 of the 132 SARS-CoV-2 isolates from detainees; of these clusters, 17 (58.6%) had individuals who overlapped in the jail during putative transmission windows. Focusing on specific buildings revealed that 2 buildings, a single- and double-cell style of housing. were associated with having detainees infected with similar SARS-CoV-2 genomes during their infectious time period (P < .001). Conclusions: Our findings suggest that there was transmission of SARS-CoV-2 in the jail, in the setting of extensive importation of COVID-19 from the community. Numerous infection control practices at intake and during incarceration were implemented in the jail to limit viral spread. Our study shows the importance of genomic analysis in this type of settings and how it can be utilized within infection control protocols.

Introduction to A Compendium of Strategies to Prevent Healthcare-Associated Infections In Acute-Care Hospitals: 2022 Updates.

Since the initial publication of A Compendium of Strategies to Prevent Healthcare-Associated Infections in Acute Care Hospitals in 2008, the prevention of healthcare-associated infections (HAIs) has continued to be a national priority. Progress in healthcare epidemiology, infection prevention, antimicrobial stewardship, and implementation science research has led to improvements in our understanding of effective strategies for HAI prevention. Despite these advances, HAIs continue to affect ∼1 of every 31 hospitalized patients, leading to substantial morbidity, mortality, and excess healthcare expenditures, and persistent gaps remain between what is recommended and what is practiced.The widespread impact of the coronavirus disease 2019 (COVID-19) pandemic on HAI outcomes in acute-care hospitals has further highlighted the essential role of infection prevention programs and the critical importance of prioritizing efforts that can be sustained even in the face of resource requirements from COVID-19 and future infectious diseases crises.The Compendium: 2022 Updates document provides acute-care hospitals with up-to-date, practical expert guidance to assist in prioritizing and implementing HAI prevention efforts. It is the product of a highly collaborative effort led by the Society for Healthcare Epidemiology of America (SHEA), the Infectious Disease Society of America (IDSA), the Association for Professionals in Infection Control and Epidemiology (APIC), the American Hospital Association (AHA), and The Joint Commission, with major contributions from representatives of organizations and societies with content expertise, including the Centers for Disease Control and Prevention (CDC), the Pediatric Infectious Disease Society (PIDS), the Society for Critical Care Medicine (SCCM), the Society for Hospital Medicine (SHM), the Surgical Infection Society (SIS), and others.

Layered Screening and Contact-Limiting Interventions Are Necessary to Reduce SARS-Cov-2 Outbreak Risks in Large Urban Jails.

Highly transmissible infections with short serial intervals, such as SARS-Cov-2 and influenza, can quickly overwhelm healthcare resources in institutional settings such as jails. We assessed the impact of intake screening measures on the risk of SARS-CoV-2 outbreaks in this setting. We identified which elements of the intake process created the largest reductions in caseload. We implemented an individual-based simulation representative of SARS-Cov-2 transmission in a large urban jail utilizing testing at entry, quarantine, and post-quarantine testing to protect its general population from mass infection. We tracked the caseload under each scenario and quantified the impact of screening steps by varying quarantine duration, removing testing, and using a range of test sensitivities. We repeated the simulations under a range of transmissibility and community prevalence levels to evaluate the sensitivity of our results. We found that brief quarantine of newly incarcerated individuals separate from the existing population of the jail to permit pre-quarantine and end-of-quarantine tests reduced SARS-CoV-2 caseload 30-70% depending on test sensitivity. These results were robust to variation in the transmissibility. Further quarantine (up to 14 days) on average created only a 5% further reduction in caseload. A multilayered intake process is necessary to limit the spread of highly transmissible pathogens with short serial intervals. The pre-symptomatic phase means that no single strategy can be effective. We also show that shorter durations of quarantine combined with testing can be nearly as effective at preventing spread as longer-duration quarantine up to 14 days.

SHEA/IDSA/APIC Practice Recommendation: Strategies to prevent methicillin-resistant Staphylococcus aureus transmission and infection in acute-care hospitals: 2022 Update.

Previously published guidelines have provided comprehensive recommendations for detecting and preventing healthcare-associated infections (HAIs). The intent of this document is to highlight practical recommendations in a concise format designed to assist acute-care hospitals in implementing and prioritizing efforts to prevent methicillin-resistant Staphylococcus aureus (MRSA) transmission and infection. This document updates the "Strategies to Prevent Methicillin-Resistant Staphylococcus aureus Transmission and Infection in Acute Care Hospitals" published in 2014.1 This expert guidance document is sponsored by the Society for Healthcare Epidemiology of America (SHEA). It is the product of a collaborative effort led by SHEA, the Infectious Diseases Society of America (IDSA), the Association for Professionals in Infection Control and Epidemiology (APIC), the American Hospital Association (AHA), and The Joint Commission, with major contributions from representatives of a number of organizations and societies with content expertise.

Genomic Analysis of Community Transmission Networks for MRSA Among Females Entering a Large Inner-city Jail.

BACKGROUND: It is unclear if there are differences in methicillin-resistant Staphylococcus aureus (MRSA) risk between sexes in high-risk populations. METHODS: Females incarcerated at the Cook County Jail were enrolled within 72 hours of intake. Surveillance cultures (nares, throat, groin) were collected to determine the prevalence of MRSA colonization. A survey was administered to identify colonization predictors. Univariate and multivariate analyses were performed to identify predictors of colonization at intake. Genomic sequencing was performed on MRSA colonization and archived clinical isolates. RESULTS: Two hundred fifty women were enrolled (70% African American, 15% Hispanic), with 70% previously in jail. The prevalence of MRSA colonization at intake was 20%, with 42% of those colonized solely in the throat or groin. Univariate predictors of MRSA colonization at entrance were illicit drug use, unstable housing, engaging in anal sex, recent exchange of sex for drugs/money, and a higher number of recent sexual partners. With multivariate adjustment for race/ethnicity, use of needles for illicit drugs was a significant predictor of MRSA. Use of illicit drugs was also associated with inclusion in a genomic cluster. Nares colonization was significantly associated with not being in a genomic cluster (18.8% vs 78.6%; P < .001), whereas exclusive extranasal colonization was associated (odds ratio, 15.89; P < .001). CONCLUSIONS: We found that a high proportion (20%) of females entered jail colonized with MRSA, suggesting that previously reported sex disparities of a lower risk in women may not apply to high-risk populations. Our findings suggest high-risk activities or venues in the community for MRSA, with potential for directing sex-specific interventions.

Genomic Epidemiology Suggests Community Origins of Healthcare-Associated USA300 Methicillin-Resistant Staphylococcus aureus.

BACKGROUND: Hospital-onset (HO) methicillin-resistant Staphylococcus aureus (MRSA) infections have declined over the past decade due to infection control strategies; community-onset (CO) and healthcare-associated community-onset (HACO) MRSA, particularly USA300, has declined less. We examined the role of community strains to explain the difference. METHODS: We performed whole-genome sequencing (WGS) on MRSA clinical isolates from Cook County Health patients during 2011-2014. We defined infections as CO, HO, or HACO epidemiologically. We integrated genomic, community exposure, and statewide hospital discharge data to infer MRSA origin. RESULTS: Among 1020 individuals with available WGS, most were USA300 wound infections (580 CO, 143 HO, 297 HACO). USA300 HO, CO, and HACO infections were intermixed on the USA300 phylogeny, consistent with common strains circulating across community and healthcare settings. Community exposures (eg, substance abuse, incarceration, homelessness) were associated with HACO and HO infections, and genetically linked individuals from both groups had little overlap in healthcare facilities, supporting community origins. Most repeat infections-over months to years-occurred in individuals persistently carrying their own strains. These individuals were more likely to have genetic linkages, suggesting a role of persistent colonization in transmission. CONCLUSIONS: Efforts to reduce presumed nosocomial USA300 spread may require understanding and controlling community sources and transmission networks, particularly for repeat infections.

Genomic Update of Phenotypic Prediction Rule for Methicillin-Resistant Staphylococcus aureus (MRSA) USA300 Discloses Jail Transmission Networks with Increased Resistance.

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.

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

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.

MRSA Transmission in Intensive Care Units: Genomic Analysis of Patients, Their Environments, and Healthcare Workers.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA)-and now USA300 MRSA-is a significant intensive care unit (ICU) pathogen; healthcare worker (HCW) contamination may lead to patient cross-transmission. METHODS: From September 2015 to February 2016, to study the spread of MRSA, we enrolled HCWs in 4 adult ICUs caring for patients on MRSA contact precautions. Samples were collected from patient body sites and high-touch surfaces in patient rooms. HCW hands, gloves, and personal protective equipment were sampled pre/post-patient encounter. Whole genome sequencing (WGS) was used to compare isolates from patients, HCWs, and environment. RESULTS: There were 413 MRSA isolates sequenced (38% USA300, 52% USA100) from 66 patient encounters. Six of 66 HCWs were contaminated with MRSA prior to room entry. Isolates from a single patient encounter were typically either USA100 or USA300; in 8 (12%) encounters both USA300 and USA100 were isolated. WGS demonstrated that isolates from patients, HCWs, and environment often were genetically similar, although there was substantial between-encounter diversity. Strikingly, there were 5 USA100 and 1 USA300 clusters that contained similar strains (<22 single-nucleotide variants [SNVs], with most <10 SNVs) within the cluster despite coming from different encounters, suggesting intra- and inter-ICU spread of strains, that is, 4 of these genomic clusters were from encounters in the same ICU; 5 of 6 clusters occurred within 1 week. CONCLUSIONS: We demonstrated frequent spread of MRSA USA300 and USA100 strains among patients, environment, and HCWs. WGS identified possible spread within and even between ICUs. Future analysis with detailed contact tracing in conjunction with genomic data may further elucidate pathways of MRSA spread and points for intervention.

Frequent Methicillin-Resistant Staphylococcus aureus Introductions Into an Inner-city Jail: Indications of Community Transmission Networks.

BACKGROUND: Jails 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. METHODS: Males 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. RESULTS: There 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). CONCLUSIONS: A 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.