Prevalence and Clinical Profile of Severe Acute Respiratory Syndrome Coronavirus 2 Infection among Farmworkers, California, USA, June-November 2020.

During the ongoing coronavirus disease (COVID-19) pandemic, farmworkers in the United States are considered essential personnel and continue in-person work. We conducted prospective surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and antibody prevalence among farmworkers in Salinas Valley, California, during June 15-November 30, 2020. We observed 22.1% (1,514/6,864) positivity for SARS-CoV-2 infection among farmworkers compared with 17.2% (1,255/7,305) among other adults from the same communities (risk ratio 1.29, 95% CI 1.20-1.37). In a nested study enrolling 1,115 farmworkers, prevalence of current infection was 27.7% among farmworkers reporting >1 COVID-19 symptom and 7.2% among farmworkers without symptoms (adjusted odds ratio 4.16, 95% CI 2.85-6.06). Prevalence of SARS-CoV-2 antibodies increased from 10.5% (95% CI 6.0%-18.4%) during July 16-August 31 to 21.2% (95% CI 16.6%-27.4%) during November 1-30. High SARS-CoV-2 infection prevalence among farmworkers underscores the need for vaccination and other preventive interventions

Assessment of public health interventions to mitigate SARS-CoV-2 transmission and risk factors for infection in California

Vaccination and non-pharmaceutical interventions (NPIs) have been of central importance to mitigate the ongoing COVID-19 pandemic. In collaboration with California Department of Public Health, I designed and managed a test-negative design case-control study to assess risk factors for SARS-CoV-2 infection and the effectiveness of various mitigation strategies including vaccination and the use of face masks. Throughout the study period, a team of trained interviewers placed over 40,000 telephone calls and enrolled over 4,000 total cases and controls, testing positive and negative for SARS-CoV-2, respectively. In Chapter 1, I present COVID-19 vaccine effectiveness estimates using data collected between February ¬– April 2021 when Epsilon (B.1.427 and B.1.429) and Alpha (B.1.1.7) were the dominant SARS-CoV-2 variants of concern circulating in California. I demonstrate mRNA-based vaccines (BNT-162b2 [Pfizer] and mRNA-1273 [Moderna]) conferred substantial protection against documented SARS-CoV-2 infection. However, nearly one-third of participants expressed reluctance to initiate the COVID-19 vaccination series, primarily due to concerns about vaccine side effects or safety. In Chapter 2, I evaluate predictors of SARS-CoV-2 infection amongst a subset of participants who reported history of social contact with a person confirmed or suspected to have been infected with SARS-CoV-2 within 14 days of testing. Among the unvaccinated, participants had a significantly higher odds of testing SARS-CoV-2 positive when social contact was long-lasting (>3 hours), involved a household member, or occurred indoors. Additionally, in the context of these high-risk exposures, I demonstrate mask wearing was most protective among the unvaccinated or partially unvaccinated. Last, in Chapter 3, I estimate the real-world effectiveness of face masks in reducing the risk of acquiring a SARS-CoV-2 infection in public indoors settings. Participants self-reported their frequency of mask use and the type of mask typically worn in public indoor settings. I found that any mask use in public indoor settings reduced the odds the wearer acquired a SARS-CoV-2 infection and mask use exhibited additional protection with increasing frequency of use. Upgrading face masks to masks with higher filtration capacity (N95/KN95s) conferred additional protection. This work has demonstrated the value of case-control studies to rapidly collect real-time data to address and monitor emerging issues in the COVID-19 pandemic and advance public health policy

Model-based assessment of SARS-CoV-2 Delta variant transmission dynamics within partially vaccinated K-12 school populations.

BackgroundWe examined school reopening policies amidst ongoing transmission of the highly transmissible Delta variant, accounting for vaccination among individuals ≥12 years.MethodsWe collected data on social contacts among school-aged children in the California Bay Area and developed an individual-based transmission model to simulate transmission of the Delta variant of SARS-CoV-2 in schools. We evaluated the additional infections in students and teachers/staff resulting over a 128-day semester from in-school instruction compared to remote instruction when various NPIs (mask use, cohorts, and weekly testing of students/teachers) were implemented, across various community-wide vaccination coverages (50%, 60%, 70%), and student (≥12 years) and teacher/staff vaccination coverages (50% - 95%).FindingsAt 70% vaccination coverage, universal masking reduced infections by >57% among students. Masking plus 70% vaccination coverage enabled achievement of <50 excess cases per 1,000 students/teachers, but stricter risk tolerances, such as <25 excess infections per 1,000 students/teachers, required a cohort approach in elementary and middle school populations. In the absence of NPIs, increasing the vaccination coverage of community members from 50% to 70% or elementary teachers from 70% to 95% reduced the excess rate of infection among elementary school students attributable to school transmission by 24% and 37%, respectively.InterpretationsAmidst Delta variant circulation, we found that schools are not inherently low risk, yet can be made so with high community vaccination coverages and masking. Vaccination of adults protects unvaccinated children.FundingNational Science Foundation grant no. 2032210; National Institutes of Health grant nos. R01AI125842 and R01AI148336; MIDAS Coordination Center (MIDASSUP2020-4)

Antimicrobial resistance in paediatric Streptococcus pneumoniae isolates amid global implementation of pneumococcal conjugate vaccines: a systematic review and meta-regression analysis

Background: Pneumococcal diseases are a leading cause of morbidity and mortality among children globally, and the burden of these diseases might be worsened by antimicrobial resistance. To understand the effect of pneumococcal conjugate vaccine (PCV) deployment on antimicrobial resistance in pneumococci, we assessed the susceptibility of paediatric pneumococcal isolates to various antimicrobial drugs before and after PCV implementation. Methods: We did a systematic review of studies reporting antimicrobial susceptibility profiles of paediatric pneumococcal isolates between 2000 and 2020 using PubMed and the Antimicrobial Testing Leadership and Surveillance database (ATLAS; Pfizer). Population-based studies of invasive pneumococcal disease or nasopharyngeal colonisation were eligible for inclusion. As primary outcome measures, we extracted the proportions of isolates that were non-susceptible or resistant to penicillin, macrolides, sulfamethoxazole–trimethoprim, third-generation cephalosporins, and tetracycline from each study. Where available, we also extracted data on pneumococcal serotypes. We estimated changes in the proportion of isolates with reduced susceptibility or resistance to each antibiotic class using random-effects meta-regression models, adjusting for study-level and region-level heterogeneity, as well as secular trends, invasive or colonising isolate source, and countries' per-capita gross domestic product. Findings: From 4910 studies screened for inclusion, we extracted data from 559 studies on 312 783 paediatric isolates. Susceptibility of isolates varied substantially across regions both before and after implementation of any PCV product. On average across all regions, we estimated significant absolute reductions in the proportions of pneumococci showing non-susceptibility to penicillin (11·5%, 95% CI 8·6–14·4), sulfamethoxazole–trimethoprim (9·7%, 4·3–15·2), and third-generation cephalosporins (7·5%, 3·1–11·9), over the 10 years after implementation of any PCV product, and absolute reductions in the proportions of pneumococci resistant to penicillin (7·3%, 5·3–9·4), sulfamethoxazole–trimethoprim (16·0%, 11·0–21·2), third-generation cephalosporins (4·5%, 0·3–8·7), macrolides (3·6%, 0·7–6·6) and tetracycline (2·0%, 0·3–3·7). We did not find evidence of changes in the proportion of isolates non-susceptible to macrolides or tetracycline after PCV implementation. Observed changes in penicillin non-susceptibility were driven, in part, by replacement of vaccine-targeted serotypes with non-vaccine serotypes that were less likely to be non-susceptible. Interpretation: Implementation of PCVs has reduced the proportion of circulating pneumococci resistant to first-line antibiotic treatments for pneumonia. This effect merits consideration in assessments of vaccine impact and investments in coverage improvements. Funding: Bill & Melinda Gates Foundation.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Anticipated Effects of Higher-valency Pneumococcal Conjugate Vaccines on Colonization and Acute Otitis Media

BACKGROUND: Bacterial etiologies of acute otitis media (AOM) have shifted from the introduction of pneumococcal conjugate vaccines (PCVs), antibiotic selection and competition among species. We characterized Streptococcus pneumoniae ( Spn ), Haemophilus influenzae ( Hflu ) and Moraxella catarrhalis ( Mcat ) in the nasopharynx during well-child healthy visits and at the onset of AOM, and in middle ear fluid (MEF) of children with AOM to assess anticipated effects of higher-valency PCVs (PCV15 and PCV20). METHODS: From September 2021 to September 2023, we conducted a prospective longitudinal cohort study of PCV13 immunized children 6-36 months old. MEF was collected via tympanocentesis. Serotyping and antibiotic susceptibility testing were performed on Spn , Hflu and Mcat isolates. RESULTS: We obtained 825 nasopharyngeal and 216 MEF samples from 301 children. The order of frequency of nasopharyngeal colonization was Mcat , Spn and Hflu ; Hflu was the predominant otopathogen in MEF. Among Spn isolates, non-PCV15, non-PCV20 serotypes predominated in the nasopharynx and in MEF; the most frequent serotype was 35B. Among MEF samples, 30% of Spn isolates were amoxicillin nonsusceptible; 23% of Hflu isolates and 100% of Mcat isolates were β-lactamase-producing. CONCLUSION: The majority of Spn isolates among young children were non-PCV15, non-PCV20 serotypes, especially serotype 35B; therefore, the impact of higher-valency PCVs in reducing pneumococcal colonization or AOM is expected to be limited. Hflu continues to be the most frequent AOM pathogen. Antibiotic susceptibility data suggest a high dose of amoxicillin/clavulanate or alternative drugs that are effective against contemporary mix of otopathogens could be considered for optimal empiric selection to provide the best efficacy