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.

Impact of measurement and feedback on chlorhexidine gluconate bathing among intensive care unit patients: A multicenter study

OBJECTIVE

To assess whether measurement and feedback of chlorhexidine gluconate (CHG) skin concentrations can improve CHG bathing practice across multiple intensive care units (ICUs).

DESIGN

A before-and-after quality improvement study measuring patient CHG skin concentrations during 6 point-prevalence surveys (3 surveys each during baseline and intervention periods).

SETTING

The study was conducted across 7 geographically diverse ICUs with routine CHG bathing.

PARTICIPANTS

Adult patients in the medical ICU.

METHODS

CHG skin concentrations were measured at the neck, axilla, and inguinal region using a semiquantitative colorimetric assay. Aggregate unit-level CHG skin concentration measurements from the baseline period and each intervention period survey were reported back to ICU leadership, which then used routine education and quality improvement activities to improve CHG bathing practice. We used multilevel linear models to assess the impact of intervention on CHG skin concentrations.

RESULTS

We enrolled 681 (93%) of 736 eligible patients; 92% received a CHG bath prior to survey. At baseline, CHG skin concentrations were lowest on the neck, compared to axillary or inguinal regions (P < .001). CHG was not detected on 33% of necks, 19% of axillae, and 18% of inguinal regions (P < .001 for differences in body sites). During the intervention period, ICUs that used CHG-impregnated cloths had a 3-fold increase in patient CHG skin concentrations as compared to baseline (P < .001).

CONCLUSIONS

Routine CHG bathing performance in the ICU varied across multiple hospitals. Measurement and feedback of CHG skin concentrations can be an important tool to improve CHG bathing practice.

COVID-19 symptom relationship to antibody response and ACE2 neutralization in recovered health systems employees before and after mRNA BNT162b2 COVID-19 vaccine

Background

The humoral response to SARS-CoV-2 can provide immunity and prevent reinfection. However, less is known about how the diversity, magnitude, and length of the antibody response after a primary infection is associated with symptoms, post-infection immunity, and post-vaccinated immunity.

Methods

Cook County Health employees provided blood samples and completed an online survey 8–10 weeks after a PCR-confirmed positive SARS-CoV-2 test (pre-vaccinated, N = 41) and again, 1–4 weeks after completion of a 2-dose series mRNA BNT162b2 COVID-19 vaccine (post-vaccinated, N = 27). Associations were evaluated between SARS-CoV-2 antibody titers, participant demographics, and clinical characteristics. Antibody titers and angiotensin-converting enzyme 2 (ACE2) neutralization were compared before and after the mRNA BNT162b2 COVID-19 vaccine.

Results

Antibody titers to the spike protein (ST4), receptor binding domain (RBD), and RBD mutant D614G were significantly associated with anosmia and ageusia, cough, and fever. Spike protein antibody titers and ACE2 neutralization were significantly higher in participants that presented with these symptoms. Antibody titers to the spike protein N-terminal domain (NTD), RBD, and ST4, and ACE2 IC50 were significantly higher in all post-vaccinated participant samples compared to pre-vaccinated participant sample, and not dependent on previously reported symptoms.

Conclusions

Spike protein antibody titers and ACE2 neutralization are associated with the presentation of anosmia and ageusia, cough, and fever after SARS-CoV-2 infection. Symptom response to previous SARS-CoV-2 infection did not influence the antibody response from subsequent vaccination. These results suggest a relationship between infection severity and the magnitude of the immune response and provide meaningful insights into COVID-19 immunity according to discrete symptom presentation.

Outbreak of COVID-19 and interventions in a large jail - Cook County, IL, United States, 2020

Background

Correctional and detention facilities are disproportionately affected by COVID-19 due to shared space, contact between staff and detained persons, and movement within facilities. On March 18, 2020, Cook County Jail, one of the United States’ largest, identified its first suspected case of COVID-19 in a detained person.

Methods

This analysis includes SARS-CoV-2 cases confirmed by molecular detection among detained persons and Cook County Sheriff's Office staff. We examined occurrence of symptomatic cases in each building and proportions of asymptomatic detained persons testing positive, and timing of interventions including social distancing, mask use, and expanded testing and show outbreak trajectory in the jail compared to case counts in Chicago.

Results

During March 1-April 30, 907 symptomatic and asymptomatic cases of SARS-CoV-2 infection were detected among detained persons (n = 628) and staff (n = 279). Among asymptomatic detained persons in quarantine, 23.6% tested positive. Programmatic activity and visitation stopped March 9, cells were converted into single occupancy beginning March 26, and universal masking was implemented for staff (April 2) and detained persons (April 13). Cases at the jail declined while cases in Chicago increased.

Discussion/Conclusions

Aggressive intervention strategies coupled with widespread diagnostic testing of detained and staff populations can limit introduction and mitigate transmission of SARS-CoV-2 infection in correctional and detention facilities.

Examining the impact of patient characteristics and symptomatology on knowledge, attitudes, and beliefs among foreign-born tuberculosis cases in the US and Canada

Foreign-born individuals represent the majority of TB cases in the US/Canada. Little is known about their TB knowledge, attitudes, and beliefs (KAB). Cross-sectional survey was conducted in 22 sites in the US/Canada among foreign-born adults with active TB. Multiple regression was used to examine KAB factors against covariates. Of 1,475 participants interviewed, most answered the six knowledge items correctly. Significant predictors of correct knowledge included region of origin, education, income, age, visa status, place of diagnosis, BCG vaccination, and TB symptoms. Significant predictors of higher perceived risk/stigma scores included region of origin, age, place of diagnosis, English fluency, time in the US/Canada, TB symptoms, and household rooms. This study examines associations between TB KAB and patient and disease characteristics in foreign-born individuals in the US/Canada. The findings call for improved health education, along with efforts to reduce stigma and enhance realistic risk assessments.

Clinical Outcomes of Carbapenem-Resistant Acinetobacter baumannii Bloodstream Infections: Study of a 2-State Monoclonal Outbreak

Objective.

To characterize the clinical outcomes of patients with bloodstream infection caused by carbapenem-resistant Acinetobacter baumannii during a 2-state monoclonal outbreak.

Design.

Multicenter observational study.

Setting.

Four tertiary care hospitals and 1 long-term acute care hospital.

Methods.

A retrospective medical chart review was conducted for all consecutive patients during the period January 1, 2005, through April 30, 2006, for whom 1 or more blood cultures yielded carbapenem-resistant A. baumannii.

Results.

We identified 86 patients from the 16-month study period. Their mortality rate was 41%; of the 35 patients who died, one-third (13) had positive blood culture results for carbapenem-resistant A. baumannii at the time of death. Risk factors associated with mortality were intensive care unit stay, malignancy, and presence of fever and/or hypotension at the time blood sample for culture was obtained. Only 5 patients received adequate empirical antibiotic treatment, but the choice of treatment did not affect mortality.

Fifty-seven patients (66.2%) had a single positive blood culture result for carbapenem-resistant A. baumannii; the only factor associated with a single positive blood culture result was the presence of decubitus ulcers. Interestingly, during the study period, a transition from single to multiple positive blood culture results was observed. Four patients, 3 of whom were in a burn intensive care unit, were bacteremic for more than 30 days (range, 36–86 days).

Conclusions.

To our knowledge, this is the first time a study has described 2 patterns of bloodstream infection with A. baumannii: single versus multiple positive blood culture results, as well as a subset of patients with prolonged bacteremia.

Costs of Management of Occupational Exposures to Blood and Body Fluids

Objective.

To determine the cost of management of occupational exposures to blood and body fluids.

Design.

A convenience sample of 4 healthcare facilities provided information on the cost of management of occupational exposures that varied in type, severity, and exposure source infection status. Detailed information was collected on time spent reporting, managing, and following up the exposures; salaries (including benefits) for representative staff who sustained and who managed exposures; and costs (not charges) for laboratory testing of exposure sources and exposed healthcare personnel, as well as any postexposure prophylaxis taken by the exposed personnel. Resources used were stratified by the phase of exposure management: exposure reporting, initial management, and follow-up. Data for 31 exposure scenarios were analyzed. Costs were given in 2003 US dollars.

Setting.

The 4 facilities providing data were a 600-bed public hospital, a 244-bed Veterans Affairs medical center, a 437-bed rural tertiary care hospital, and a 3,500-bed healthcare system.

Results.

The overall range of costs to manage reported exposures was $71-$4,838. Mean total costs varied greatly by the infection status of the source patient. The overall mean cost for exposures to human immunodeficiency virus (HIV)-infected source patients (n = 19, including those coinfected with hepatitis B or C virus) was $2,456 (range, $907-$4,838), whereas the overall mean cost for exposures to source patients with unknown or negative infection status (n = 8) was $376 (range, $71-$860). Lastly, the overall mean cost of management of reported exposures for source patients infected with hepatitis C virus (n = 4) was $650 (range, $186-$856).

Conclusions.

Management of occupational exposures to blood and body fluids is costly, the best way to avoid these costs is by prevention of exposures.

[Community self-help houses as a form of community social support]

Two forms of community-based social support were introduced by the Polish Mental Health Act--community specialist social help services and community self-help houses--for seriously mentally ill and severely mentally retarded persons. According to the art. 8 community social support should be organized by social help agencies in consultation with psychiatric facilities. Data obtained from the Ministry of Labour and Social Policy indicated that from 21th of January 1995 (when the Mental Health Act was put in force) until 30th of June 1997 social help agencies and non-governmental organizations sponsored by social help agencies have set up 134 community self-help houses with 4103 places. In the middle of last year nearly 3500 persons were using these houses. Most of the houses were located in the following districts: Gdańsk (20), Gorzów (16), Płock (12), Warszawa (8 for 164 persons). Vast majority of them served as day rehabilitation houses, while only a few provided sheltered housing as well. Tentative evaluation of functioning of these houses shows that: operational definition of community self-help house given in the target network of nursing homes and community self-help houses should be modified to include statutory purposes of community social support provided in art.8, selection of the persons using community self-help houses should follow the legal requirement of the Mental Health Act (art. 8), separated rehabilitation programs for mentally ill (psychotic) and mentally retarded persons need to be provided, participation of psychiatric facilities in the organization of the community self-help houses should be increased, functioning of the community self-help houses ought to be supervised by specialists, staff of the community self-help houses need to be systematically trained.

Infectious diseases and death among nursing home residents: results of surveillance in 13 nursing homes

An increasing proportion of the U.S. population resides in nursing homes (NHs). No surveillance system exists for infections in these facilities. To determine the incidence and types of infections in NH residents, and to identify predictors of death among residents with infections, we initiated a surveillance system at 13 NHs in California during a 6-month period from October 1989 through March 1990. The study included 1754 residents, among whom 835 infections were identified during the study period. The most common infections were urinary tract infections (UTIs; 286, 34.2%), respiratory tract infections (RTIs; 259, 31%), and skin infections (150, 17.9%). Of the 259 residents with respiratory tract infections, 69 (27%) had pneumonia. Antimicrobials were prescribed for 646 (77%) of the infectious episodes. Residents with pneumonia were more likely to die than residents with other infections (4 of 69 versus 12 of 766; P = 0.04). Symptoms of altered body temperature (fever, hypothermia, chills) and change in mental status also were associated with an increased risk of a fatal outcome (10 of 260 versus 6 of 575; P = 0.01) and (7 of 127 versus 9 of 708; P = 0.004). This study suggests that the most common infections among NH residents are UTIs, RTIs, and skin infections. Pneumonia, symptoms of fever, and mental status changes all were associated with increased mortality. The frequency of infections among NH residents and their impact on resident outcome highlights the need for infectious disease surveillance in this population.

Mycobacterium abscessus pseudoinfection traced to an automated endoscope washer: utility of epidemiologic and laboratory investigation

After 15 patients had positive cultures for Mycobacterium abscessus without evidence of infection (i.e., pseudoinfection) following endoscopy, retrospective cohort studies of patients undergoing endoscopy and microbiologic sampling of the environment were done to examine potential nosocomial transmission and to identify the source and risk factors for M. abscessus pseudoinfection. In the epidemic period, M. abscessus-positive cultures were significantly more likely to be obtained during bronchoscopy than gastroendoscopy (16/149 vs. 1/860, P < .001) and during procedures using bronchoscopes disinfected in an automated washer rather than by other methods (16/54 vs. 0/95, P < .001). M. abscessus was recovered from the automated washer, the inlet water feeding the washer, and a flexible bronchoscope. Environmental and case-patient isolates had identical large restriction fragment (LRF) patterns of genomic DNA separated by pulsed-field gel electrophoresis. Molecular typing using LRF analysis supported the epidemiologic results and demonstrate the utility of combined epidemiologic and laboratory investigations in nosocomial outbreaks of nontuberculous mycobacteria.