Modeling scenarios for mitigating outbreaks in congregate settings.

The explosive outbreaks of COVID-19 seen in congregate settings such as prisons and nursing homes, has highlighted a critical need for effective outbreak prevention and mitigation strategies for these settings. Here we consider how different types of control interventions impact the expected number of symptomatic infections due to outbreaks. Introduction of disease into the resident population from the community is modeled as a stochastic point process coupled to a branching process, while spread between residents is modeled via a deterministic compartmental model that accounts for depletion of susceptible individuals. Control is modeled as a proportional decrease in the number of susceptible residents, the reproduction number, and/or the proportion of symptomatic infections. This permits a range of assumptions about the density dependence of transmission and modes of protection by vaccination, depopulation and other types of control. We find that vaccination or depopulation can have a greater than linear effect on the expected number of cases. For example, assuming a reproduction number of 3.0 with density-dependent transmission, we find that preemptively reducing the size of the susceptible population by 20% reduced overall disease burden by 47%. In some circumstances, it may be possible to reduce the risk and burden of disease outbreaks by optimizing the way a group of residents are apportioned into distinct residential units. The optimal apportionment may be different depending on whether the goal is to reduce the probability of an outbreak occurring, or the expected number of cases from outbreak dynamics. In other circumstances there may be an opportunity to implement reactive disease control measures in which the number of susceptible individuals is rapidly reduced once an outbreak has been detected to occur. Reactive control is most effective when the reproduction number is not too high, and there is minimal delay in implementing control. We highlight the California state prison system as an example for how these findings provide a quantitative framework for understanding disease transmission in congregate settings. Our approach and accompanying interactive website (https://phoebelu.shinyapps.io/DepopulationModels/) provides a quantitative framework to evaluate the potential impact of policy decisions governing infection control in outbreak settings.

COVID-19 outbreak in a state prison: a case study on the implementation of key public health recommendations for containment and prevention.

BACKGROUND: People incarcerated in US prisons have been disproportionately harmed by the COVID-19 pandemic. That prisons are such efficient superspreading environments can be attributed to several known factors: small, communal facilities where people are confined for prolonged periods of time; poor ventilation; a lack of non-punitive areas for quarantine/medical isolation; and staggeringly high numbers of people experiencing incarceration, among others. While health organizations have issued guidance on preventing and mitigating COVID-19 infection in carceral settings, little is known about if, when, and how recommendations have been implemented. We examined factors contributing to containment of one of the first California prison COVID-19 outbreaks and remaining vulnerabilities using an adapted multi-level determinants framework to systematically assess infectious disease risk in carceral settings. METHODS: Case study employing administrative data; observation; and informal discussions with: people incarcerated at the prison, staff, and county public health officials. RESULTS: Outbreak mitigation efforts were characterized by pre-planning (e.g., designation of ventilated, single-occupancy quarantine) and a quickly mobilized inter-institutional response that facilitated systematic, voluntary rapid testing. However, several systemic- and institutional-level vulnerabilities were unaddressed hindering efforts and posing significant risk for future outbreaks, including insufficient decarceration, continued inter-facility transfers, incomplete staff cohorting, and incompatibility between built environment features (e.g., dense living conditions) and public health recommendations. CONCLUSIONS: Our adapted framework facilitates systematically assessing prison-based infectious disease outbreaks and multi-level interventions. We find implementing some recommended public health strategies may have contributed to outbreak containment. However, even with a rapidly mobilized, inter-institutional response, failure to decarcerate created an overreliance on chance conditions. This left the facility vulnerable to future catastrophic outbreaks and may render standard public health strategies - including the introduction of effective vaccines - insufficient to prevent or contain those outbreaks.

Stress and Anxiety Among Correctional Health Care Professionals in a U.S. State Prison System During COVID-19.

Since prisons were an epicenter of the coronavirus disease 2019 (COVID-19) pandemic, the experience of correctional health care professionals (HCPs) may differ from HCPs in other settings. This cross-sectional descriptive study assessed stress, anxiety, and burnout levels in home and work environments among HCPs employed by one U.S. state prison system during the period of initial COVID-19 vaccine rollout. Participants (N = 444) were invited to voluntarily participate in an anonymous questionnaire distributed by prison administration from March 1 through May 17, 2021. Measures were adapted from a prior study of noncorrectional HCPs during the COVID-19 pandemic. Descriptive statistics (mean; standard deviation; 25th, 50th, and 75th percentiles), ranking measures that could alleviate anxiety and stress related to the pandemic, and qualitative responses were analyzed. Responses from 43% of HCPs (192) revealed that correctional HCPs experienced high levels of stress and anxiety at work and at home during the pandemic, with particularly high levels among females and registered nurses. Understanding and addressing these stressors will be of critical importance as prison systems work to avoid turnover of experienced HCPs in such specialized settings and also help inform human resource planning at state prison systems for future public health responses.

Strength and durability of indirect protection against SARS-CoV-2 infection through vaccine and infection-acquired immunity.

Early investigation revealed that COVID-19 vaccines confer indirect protection to fully susceptible and unvaccinated persons, defined as a reduced risk of SARS-CoV-2 infection among social contacts of vaccinated individuals. However, indirect protection from infection-acquired immunity and its comparative strength and durability to vaccine-derived indirect protection in the current epidemiologic context of high levels of vaccination, prior infection, and novel variants are not well characterized. Here, we show that both infection-acquired and vaccine-derived immunity independently yield indirect protection to close social contacts with key differences in their strength and waning. Analyzing anonymized data from a system-wide SARS-CoV-2 surveillance program of 177,319 residents across 35 California state prisons from December 2021 to December 2022 in a case-control design, we find that vaccine-derived indirect protection against Omicron SARS-CoV-2 infection is strongest within three months post-vaccination [30% (95% confidence interval: 20-38%)] with subsequent modest protection, whereas infection-acquired immunity provides 38% (24-50%) indirect protection to roommates for 6 months after SARS-CoV-2 infection, with moderate indirect protection persisting for over one year. Variant-targeted vaccines (bivalent formulation including Omicron subvariants BA.4/BA.5) confer strong indirect protection for at least three months [40% (3-63%)]. These results have important implications for understanding the long-term transmission dynamics of SARS-CoV-2 and can guide vaccine policy and public health measures, especially in high-risk environments such as prisons.

Infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) breakthrough infections in vaccinated individuals and reinfections in previously infected individuals have become increasingly common. Such infections highlight a broader need to understand the contribution of vaccination, including booster doses, and natural immunity to the infectiousness of individuals with SARS-CoV-2 infections, especially in high-risk populations with intense transmission, such as in prisons. Here we show that both vaccine-derived and naturally acquired immunity independently reduce the infectiousness of persons with Omicron variant SARS-CoV-2 infections in a prison setting. Analyzing SARS-CoV-2 surveillance data from December 2021 to May 2022 across 35 California state prisons with a predominately male population, we estimate that unvaccinated Omicron cases had a 36% (95% confidence interval (CI): 31-42%) risk of transmitting infection to close contacts, as compared to a 28% (25-31%) risk among vaccinated cases. In adjusted analyses, we estimated that any vaccination, prior infection alone and both vaccination and prior infection reduced an index case's risk of transmitting infection by 22% (6-36%), 23% (3-39%) and 40% (20-55%), respectively. Receipt of booster doses and more recent vaccination further reduced infectiousness among vaccinated cases. These findings suggest that, although vaccinated and/or previously infected individuals remain highly infectious upon SARS-CoV-2 infection in this prison setting, their infectiousness is reduced compared to individuals without any history of vaccination or infection. This study underscores benefit of vaccination to reduce, but not eliminate, transmission.

Infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave.

SARS-CoV-2 breakthrough infections in vaccinated individuals and reinfections among previously infected individuals have become increasingly common. Such infections highlight a broader need to understand the contribution of vaccination, including booster doses, and natural immunity to the infectiousness of persons with SARS-CoV-2 infections, especially in high-risk populations with intense transmission such as prisons. Here, we show that both vaccine-derived and naturally acquired immunity independently reduce the infectiousness of persons with Omicron variant SARS-CoV-2 infections in a prison setting. Analyzing SARS-CoV-2 surveillance data from December 2021 to May 2022 across 35 California state prisons with a predominately male population, we estimate that unvaccinated Omicron cases had a 36% (95% confidence interval (CI): 31-42%) risk of transmitting infection to close contacts, as compared to 28% (25-31%) risk among vaccinated cases. In adjusted analyses, we estimated that any vaccination, prior infection alone, and both vaccination and prior infection reduced an index case's risk of transmitting infection by 22% (6-36%), 23% (3-39%) and 40% (20-55%), respectively. Receipt of booster doses and more recent vaccination further reduced infectiousness among vaccinated cases. These findings suggest that although vaccinated and/or previously infected individuals remain highly infectious upon SARS-CoV-2 infection in this prison setting, their infectiousness is reduced compared to individuals without any history of vaccination or infection, underscoring some benefit of vaccination to reduce but not eliminate transmission.

Tuberculosis diagnosis and management in the public versus private sector: a standardised patients study in Mumbai, India.

BACKGROUND: There are few rigorous studies comparing quality of tuberculosis (TB) care in public versus private sectors. METHODS: We used standardised patients (SPs) to measure technical quality and patient experience in a sample of private and public facilities in Mumbai. RESULTS: SPs presented a 'classic, suspected TB' scenario and a 'recurrence or drug-resistance' scenario. In the private sector, SPs completed 643 interactions. In the public sector, 164 interactions. Outcomes included indicators of correct management, medication use and client experience. Public providers used microbiological testing (typically, microscopy) more frequently, in 123 of 164 (75%; 95% CI 68% to 81%) vs 223 of 644 interactions (35%; 95% CI 31% to 38%) in the private sector. Private providers were more likely to order chest X-rays, in 556 of 639 interactions (86%; 95% CI 84% to 89%). According to national TB guidelines, we found higher proportions of correct management in the public sector (75% vs 35%; (adjusted) difference 35 percentage points (pp); 95% CI 25 to 46). If X-rays were considered acceptable for the first case but drug-susceptibility testing was required for the second case, the private sector correctly managed a slightly higher proportion of interactions (67% vs 51%; adjusted difference 16 pp; 95% CI 7 to 25). Broad-spectrum antibiotics were used in 76% (95% CI 66% to 84%) of the interactions in public hospitals, and 61% (95% CI 58% to 65%) in private facilities. Costs in the private clinics averaged rupees INR 512 (95% CI 485 to 539); public facilities charged INR 10. Private providers spent more time with patients (4.4 min vs 2.4 min; adjusted difference 2.0 min; 95% CI 1.2 to 2.9) and asked a greater share of relevant questions (29% vs 43%; adjusted difference 13.7 pp; 95% CI 8.2 to 19.3). CONCLUSIONS: While the public providers did a better job of adhering to national TB guidelines (especially microbiological testing) and offered less expensive care, private sector providers did better on client experience.

Mitigating outbreaks in congregate settings by decreasing the size of the susceptible population.

While many transmission models have been developed for community spread of respiratory pathogens, less attention has been given to modeling the interdependence of disease introduction and spread seen in congregate settings, such as prisons or nursing homes. As demonstrated by the explosive outbreaks of COVID-19 seen in congregate settings, the need for effective outbreak prevention and mitigation strategies for these settings is critical. Here we consider how interventions that decrease the size of the susceptible populations, such as vaccination or depopulation, impact the expected number of infections due to outbreaks. Introduction of disease into the resident population from the community is modeled as a branching process, while spread between residents is modeled via a compartmental model. Control is modeled as a proportional decrease in both the number of susceptible residents and the reproduction number. We find that vaccination or depopulation can have a greater than linear effect on anticipated infections. For example, assuming a reproduction number of 3.0 for density-dependent COVID-19 transmission, we find that reducing the size of the susceptible population by 20% reduced overall disease burden by 47%. We highlight the California state prison system as an example for how these findings provide a quantitative framework for implementing infection control in congregate settings. Additional applications of our modeling framework include optimizing the distribution of residents into independent residential units, and comparison of preemptive versus reactive vaccination strategies.

Quality of care for tuberculosis and HIV in the private health sector: a cross-sectional, standardised patient study in South Africa.

BACKGROUND: South Africa has high burdens of tuberculosis (TB) and TB-HIV, yet the quality of patient care in the private sector is unknown. We describe quality of TB and TB-HIV care among private general practitioners (GPs) in two South African cities using standardised patients (SPs). METHODS: Sixteen SPs presented one of three cases during unannounced visits to private GPs in selected high-TB burden communities in Durban and Cape Town: case 1, typical TB symptoms, HIV-positive; case 2, TB-specified laboratory report, HIV-negative and case 3, history of incomplete TB treatment, HIV-positive. Clinical practices were recorded in standardised exit interviews. Ideal management was defined as relevant testing or public sector referral for any reason. The difference between knowledge and practice (know-do gap) was assessed through case 1 vignettes among 25% of GPs. Factors associated with ideal management were assessed using bivariate logistic regression. RESULTS: 511 SP visits were completed with 212 GPs. Respectively, TB and HIV were ideally managed in 43% (95% CI 36% to 50%) and 41% (95% CI 34% to 48%) of case 1, 85% (95% CI 78% to 90%) and 61% (95% CI 73% to 86%) of case 2 and 69% (95% CI 61% to 76%) and 80% (95% CI 52% to 68%) of case 3 presentations. HIV status was queried in 35% (95% CI 31% to 39%) of visits, least with case 1 (24%, 95% CI 18% to 30%). The difference between knowledge and practice was 80% versus 43% for TB and 55% versus 37% for HIV, resulting in know-do gaps of 37% (95% CI 19% to 55%) and 18% (95% CI -1% to 38%), respectively. Ideal TB management was associated with longer visit time (OR=1.1, 95% CI 1.1 to 1.2), female GPs (3.2, 95% CI 2.0 to 5.1), basic symptom inquiry (2.0, 95% CI 1.7 to 2.3), HIV-status inquiry (OR=11.2, 95% CI 6.4 to 19.6), fewer medications dispensed (OR=0.6, 95% CI 0.5 to 0.7) and Cape Town (OR=2.2, 95% CI 1.5 to 3.1). Similar associations were observed for HIV. CONCLUSIONS: Private providers ideally managed TB more often when a diagnosis or history of TB was implied or provided. Management of HIV in the context of TB was less than optimal.

Tissue fractionation by hydrostatic pressure cycling technology: the unified sample preparation technique for systems biology studies.

Major bottlenecks in systems biology studies arise from limitations of current sample preparation techniques. Multiple mutually exclusive sample preparation methods, which are often required to extract distinct classes of molecules from cells and tissues, are incompatible with studies of precious or very limited samples. Moreover, the strong detergents and chaotropic agents commonly required to solubilize sample constituents often interfere with subsequent separation and analysis. Here we describe a rapid, detergent-free sample preparation technique that allows efficient concurrent isolation and fractionation of protein, DNA, RNA, and lipids from biological samples, eliminating the need for multiple replicates. The method relies on a synergistic combination of physical disruption of the cellular material by hydrostatic pressure (pressure cycling technology) and novel extraction conditions to dissolve and partition distinct classes of molecules into separate fractions. We demonstrate parallel recovery of proteins, lipids, and intact DNA and RNA, from animal cells and tissues, for proteomic, lipidomic, and genomic analyses. The protein extracts require minimal cleanup and are compatible with 1D and 2D PAGE, liquid chromatography coupled with tandem mass spectrometry, and Western blotting. The lipid fractions have been profiled by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without further processing. The isolated DNA and RNA were shown to be intact by agarose gel visualization, and the presence of intact mRNA was confirmed by real time reverse transcription polymerase chain reaction. Analysis and comparison of samples extracted using this method and a more traditional extraction technique revealed several protein species preferentially extracted by the new method.