Use of surveillance data to elucidate household clustering of SARS-CoV-2 in Fulton County, Georgia a major metropolitan area.

BACKGROUND: Households are important for SARS-CoV-2 transmission due to high intensity exposure in enclosed spaces over prolonged durations. We quantified and characterized household clustering of COVID-19 cases in Fulton County, Georgia. METHODS: We used surveillance data to identify all confirmed COVID-19 cases in Fulton County. Household clustered cases were defined as cases with matching residential address. We described the proportion of COVID-19 cases that were clustered, stratified by age over time and explore trends in age of first diagnosed case within households and subsequent household cases. RESULTS: Between June 1, 2020 and October 31, 2021, 31,449(37%) of 106,233 cases were clustered in households. Children were the most likely to be in household clusters than any other age group. Initially, children were rarely (∼ 10%) the first cases diagnosed in the household but increased to almost 1 of 3 in later periods. DISCUSSION: One-third of COVID-19 cases in Fulton County were part of a household cluster. Increasingly children were the first diagnosed case, coinciding with temporal trends in vaccine roll-out among the elderly and the return to in-person schooling in Fall 2021. Limitations include restrictions to cases with a valid address and unit number and that the first diagnosed case may not be the infection source for the household.

The Role of Staff in Transmission of SARS-CoV-2 in Long-term Care Facilities.

BACKGROUND: US long-term care facilities (LTCFs) have experienced a disproportionate burden of COVID-19 morbidity and mortality. METHODS: We examined SARS-CoV-2 transmission among residents and staff in 60 LTCFs in Fulton County, Georgia, from March 2020 to September 2021. Using the Wallinga-Teunis method to estimate the time-varying reproduction number, R(t), and linear-mixed regression models, we examined associations between case characteristics and R(t). RESULTS: Case counts, outbreak size and duration, and R(t) declined rapidly and remained low after vaccines were first distributed to LTCFs in December 2020, despite increases in community incidence in summer 2021. Staff cases were more infectious than resident cases (average individual reproduction number, R i = 0.6 [95% confidence intervals [CI] = 0.4, 0.7] and 0.1 [95% CI = 0.1, 0.2], respectively). Unvaccinated resident cases were more infectious than vaccinated resident cases (R i = 0.5 [95% CI = 0.4, 0.6] and 0.2 [95% CI = 0.0, 0.8], respectively), but estimates were imprecise. CONCLUSIONS: COVID-19 vaccines slowed transmission and contributed to reduced caseload in LTCFs. However, due to data limitations, we were unable to determine whether breakthrough vaccinated cases were less infectious than unvaccinated cases. Staff cases were six times more infectious than resident cases, consistent with the hypothesis that staff were the primary drivers of SARS-CoV-2 transmission in LTCFs.

Characteristics and Risk Factors for Mortality by Coronavirus Disease 2019 Pandemic Waves in Fulton County, Georgia: A Cohort Study March 2020-February 2021.

Background: We examined differences in mortality among coronavirus disease 2019 (COVID-19) cases in the first, second, and third waves of the COVID-19 pandemic. Methods: A retrospective cohort study of COVID-19 cases in Fulton County, Georgia, USA, reported to a public health surveillance from March 2020 through February 2021. We estimated case-fatality rates (CFR) by wave and used Cox proportional hazards random-effects models in each wave, with random effects at individual and long-term-care-facility level, to determine risk factors associated with rates of mortality. Results: Of 75 289 confirmed cases, 4490 (6%) were diagnosed in wave 1 (CFR 31 deaths/100 000 person days [pd]), 24 293 (32%) in wave 2 (CFR 7 deaths/100 000 pd), and 46 506 (62%) in wave 3 (CFR 9 deaths/100 000 pd). Compared with females, males were more likely to die in each wave: wave 1 (adjusted hazard ratio [aHR], 1.5; 95% confidence interval [CI], 1.2-1.8), wave 2 (aHR 1.5, 95% CI, 1.2-1.8), and wave 3 (aHR 1.7, 95% CI, 1.5-2.0). Compared with non-Hispanic whites, non-Hispanic blacks were more likely to die in each wave: wave 1 (aHR, 1.4; 95% CI, 1.1-1.8), wave 2 (aHR, 1.5; 95% CI, 1.2-1.9), and wave 3 (aHR, 1.7; 95% CI, 1.4-2.0). Cases with any disability, chronic renal disease, and cardiovascular disease were more likely to die in each wave compared with those without these comorbidities. Conclusions: Our study found gender and racial/ethnic disparities in COVID-19 mortality and certain comorbidities associated with COVID-19 mortality. These factors have persisted throughout the COVID-19 pandemic waves, despite improvements in diagnosis and treatment.

Appraisal of groundwater recharge in Neelum watershed (Upper Indus Basin) using geospatial water balance technique.

Water availability is important for survival of millions of people living in the Himalayan region of Upper Indus Basin and adequate monitoring system is for better water resources management. In the present study, groundwater recharge appraisals in the Neelum watershed (Upper Indus Basin) were investigated by using water balance and geospatial modeling techniques on monthly time-scale climate data from 1989 to 2015. Results demonstrated that on an average out of total annual rainfall (i.e., 2028 mm), about 46% of the rainfall convert to surface runoff and 35% loss to atmosphere via evapo-transpiration (ET), while the remaining 18% contribute to infiltrate the groundwater recharge. Groundwater recharge enhanced during snow-melt from December to March and the rainfall infiltration increased during July and August months. Similarly, the infiltration ranges 106-177 mm from January to March and 45-51 mm from December to July. The groundwater discharge in the form of oozing from the spring occurred during the remaining six months, which ultimately contributed to the baseflow of the stream. Findings from the study revealed variations in groundwater recharge during the years and hence recommended more hydrological studies to predict future changes in climate and land use for sustainable development of freshwater resources in the Upper Indus Basin.

Retrospective cohort study of COVID-19 among children in Fulton County, Georgia, March 2020-June 2021.

OBJECTIVE: To describe case rates, testing rates and percent positivity of COVID-19 among children aged 0-18 years by school-age grouping. DESIGN: We abstracted data from Georgia's State Electronic Notifiable Disease Surveillance System on all 10 437 laboratory-confirmed COVID-19 cases among children aged 0-18 years during 30 March 2020 to 6 June 2021. We examined case rates, testing rates and percent positivity by school-aged groupings, namely: preschool (0-4 years), elementary school (5-10 years), middle school (11-13 years), and high school (14-18 years) and compared these data among school-aged children with those in the adult population (19 years and older). SETTING: Fulton County, Georgia. MAIN OUTCOME MEASURES: COVID-19 case rates, testing rates and percent positivity. RESULTS: Over time, the proportion of paediatric cases rose substantially from 1.1% (April 2020) to 21.6% (April 2021) of all cases in the county. Age-specific case rates and test rates were consistently highest among high-school aged children. Test positivity was similar across school-age groups, with periods of higher positivity among high-school aged children. CONCLUSIONS: Low COVID-19 testing rates among children, especially early in the pandemic, likely underestimated the true burden of disease in this age group. Despite children having lower measured incidence of COVID-19, we found when broader community incidence increased, incidence also increased among all paediatric age groups. As the COVID-19 pandemic continues to evolve, it remains critical to continue learning about the incidence and transmissibility of COVID-19 in children.

Estimating the Unknown: Greater Racial and Ethnic Disparities in COVID-19 Burden After Accounting for Missing Race and Ethnicity Data.

BACKGROUND: Black, Hispanic, and Indigenous persons in the United States have an increased risk of SARS-CoV-2 infection and death from COVID-19, due to persistent social inequities. However, the magnitude of the disparity is unclear because race/ethnicity information is often missing in surveillance data. METHODS: We quantified the burden of SARS-CoV-2 notification, hospitalization, and case fatality rates in an urban county by racial/ethnic group using combined race/ethnicity imputation and quantitative bias analysis for misclassification. RESULTS: The ratio of the absolute racial/ethnic disparity in notification rates after bias adjustment, compared with the complete case analysis, increased 1.3-fold for persons classified Black and 1.6-fold for those classified Hispanic, in reference to classified White persons. CONCLUSIONS: These results highlight that complete case analyses may underestimate absolute disparities in notification rates. Complete reporting of race/ethnicity information is necessary for health equity. When data are missing, quantitative bias analysis methods may improve estimates of racial/ethnic disparities in the COVID-19 burden.

Characteristics and Risk Factors for Hospitalization and Mortality among Persons with COVID-19 in Atlanta Metropolitan Area.

Background: We present data on risk factors for severe outcomes among patients with coronavirus disease 2019 (COVID-19) in the southeast United States (U.S.). Objective: To determine risk factors associated with hospitalization, intensive care unit (ICU) admission, and mortality among patients with confirmed COVID-19. Design: A retrospective cohort study. Setting: Fulton County in Atlanta Metropolitan Area, Georgia, U.S. Patients: Community-based individuals of all ages that tested positive for SARS-CoV-2. Measurements: Demographic characteristics, comorbid conditions, hospitalization, ICU admission, death (all-cause mortality), and severe COVID-19 disease, defined as a composite measure of hospitalization and death. Results: Between March 2 and May 31, 2020, we included 4322 individuals with various COVID-19 outcomes. In a multivariable logistic regression random-effects model, patients in age groups ≥45 years compared to those <25 years were associated with severe COVID-19. Males compared to females (adjusted odds ratio [aOR] 1.4, 95% confidence interval [CI]: 1.1-1.6), non-Hispanic blacks (aOR 1.9, 95%CI: 1.5-2.4) and Hispanics (aOR 1.7, 95%CI: 1.2-2.5) compared to non-Hispanic whites were associated with increased odds of severe COVID-19. Those with chronic renal disease (aOR 3.6, 95%CI: 2.2-5.8), neurologic disease (aOR 2.8, 95%CI: 1.8-4.3), diabetes (aOR 2.0, 95%CI: 1.5-2.7), chronic lung disease (aOR 1.7, 95%CI: 1.2-2.3), and "other chronic diseases" (aOR 1.8, 95%CI: 1.3-2.6) compared to those without these conditions were associated with increased odds of having severe COVID-19. Conclusions: Multiple risk factors for hospitalization, ICU admission, and death were observed in this cohort from an urban setting in the southeast U.S. Improved screening and early, intensive treatment for persons with identified risk factors is urgently needed to reduce COVID-19 related morbidity and mortality.

Measuring the missing: greater racial and ethnic disparities in COVID-19 burden after accounting for missing race/ethnicity data.

Black, Hispanic, and Indigenous persons in the United States have an increased risk of SARS-CoV-2 infection and death from COVID-19, due to persistent social inequities. The magnitude of the disparity is unclear, however, because race/ethnicity information is often missing in surveillance data. In this study, we quantified the burden of SARS-CoV-2 infection, hospitalization, and case fatality rates in an urban county by racial/ethnic group using combined race/ethnicity imputation and quantitative bias-adjustment for misclassification. After bias-adjustment, the magnitude of the absolute racial/ethnic disparity, measured as the difference in infection rates between classified Black and Hispanic persons compared to classified White persons, increased 1.3-fold and 1.6-fold respectively. These results highlight that complete case analyses may underestimate absolute disparities in infection rates. Collecting race/ethnicity information at time of testing is optimal. However, when data are missing, combined imputation and bias-adjustment improves estimates of the racial/ethnic disparities in the COVID-19 burden.

Preventing COVID-19 Outbreaks in Long-Term Care Facilities Through Preemptive Testing of Residents and Staff Members - Fulton County, Georgia, March-May 2020.

Long-term care facility (LTCF) residents are at particularly high risk for morbidity and mortality associated with infection with SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), given their age and high prevalence of chronic medical conditions, combined with functional impairment that often requires frequent, close contact with health care providers, who might inadvertently spread the virus to residents (1,2). During March-May 2020 in Fulton County, Georgia, >50% of COVID-19-associated deaths occurred among LTCF residents, although these persons represented <1% of the population (3,4). Mass testing for SARS-CoV-2 has been an effective strategy for identifying asymptomatic and presymptomatic infections in LTCFs (5). This analysis sought to evaluate the timing at which mass testing took place in relation to the known presence of a COVID-19 infection and the resulting number of infections that occurred. In 15 LTCFs that performed facility-wide testing in response to an identified case, high prevalences of additional cases in residents and staff members were found at initial testing (28.0% and 7.4%, respectively), suggesting spread of infection had already occurred by the time the first case was identified. Prevalence was also high during follow-up, with a total of 42.4% of residents and 11.8% of staff members infected overall in the response facilities. In comparison, 13 LTCFs conducted testing as a preventive strategy before a case was identified. Although the majority of these LTCFs identified at least one COVID-19 case, the prevalence was significantly lower at initial testing in both residents and staff members (0.5% and 1.0%, respectively) and overall after follow-up (1.5% and 1.7%, respectively). These findings indicate that early awareness of infections might help facilities prevent potential outbreaks by prioritizing and adhering more strictly to infection prevention and control (IPC) recommendations, resulting in fewer infections than would occur when relying on symptom-based screening (6,7).

Mass Screening for SARS-CoV-2 Infection among Residents and Staff in Twenty-eight Long-term Care Facilities in Fulton County, Georgia.

Mass screening for SARS-CoV-2 infection in long-term care facilities revealed significantly higher prevalence of infection in facilities that screened in response to a known infection compared to those that screened as a prevention measure. "Response" facilities had a SARS-CoV-2 prevalence of 28.9% while "preventive" facilities' prevalence was 1.6% (p <0.001).

Genetic characterization of the Makrani people of Pakistan from mitochondrial DNA control-region data.

To estimate genetic and forensic parameters, the entire mitochondrial DNA control region of 100 unrelated Makrani individuals (males, n=96; females, n=4) living in Pakistan (Turbat, Panjgur, Awaran, Kharan, Nasirabad, Gwadar, Buleda, Karachi and Burewala) was sequenced. We observed a total of 70 different haplotypes of which 54 were unique and 16 were shared by more than one individual. The Makrani population showed a high genetic diversity (0.9688) and, consequently, a high power of discrimination (0.9592). Our results revealed a strongly admixed mtDNA pool composed of African haplogroups (28%), West Eurasian haplogroups (26%), South Asian haplogroups (24%), and East Asian haplogroups (2%), while the origin of the remaining individuals (20%) could not be confidently assigned. The results of this study are a valuable contribution to build a database of mtDNA variation in Pakistan.

Mitochondrial DNA control region sequences study in Saraiki population from Pakistan.

The analysis of mitochondrial DNA (mtDNA) control region was carried in 85 unrelated Sariki individuals living in the different provinces of Pakistan. DNA was extracted from blood preserved in EDTA vacutainers. Hypervariable regions (HV1, HV2 & HV3) were PCR amplified and sequenced. Sequencing results were aligned and compared with revised Cambridge reference sequence (rCRS). The sequencing results showed presence of total 63 different haplotypes, 58 of them are unique and 05 are common haplotypes shared by more than one individual. The most common haplotype observed was (W6) with a frequency 12.9% of population sample. The Saraiki population was detected with genetic diversity (0.9570) and power of discrimination (0.9458). This study will be beneficial for forensic casework.

Building local human resources to implement SLMTA with limited donor funding: The Ghana experience.

BACKGROUND: In 2009, Ghana adopted the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme in order to improve laboratory quality. The programme was implemented successfully with limited donor funding and local human resources. OBJECTIVES: To demonstrate how Ghana, which received very limited PEPFAR funding, was able to achieve marked quality improvement using local human resources. METHOD: Local partners led the SLMTA implementation and local mentors were embedded in each laboratory. An in-country training-of-trainers workshop was conducted in order to increase the pool of local SLMTA implementers. Three laboratory cohorts were enrolled in SLMTA in 2011, 2012 and 2013. Participants from each cohort attended in a series of three workshops interspersed with improvement projects and mentorship. Supplemental training on internal audit was provided. Baseline, exit and follow-up audits were conducted using the Stepwise Laboratory Quality Improvement Process Towards Accreditation (SLIPTA) checklist. In November 2013, four laboratories underwent official SLIPTA audits by the African Society for Laboratory Medicine (ASLM). RESULTS: The local SLMTA team successfully implemented three cohorts of SLMTA in 15 laboratories. Seven out of the nine laboratories that underwent follow-up audits have reached at least one star. Three out of the four laboratories that underwent official ASLM audits were awarded four stars. Patient satisfaction increased from 25% to 70% and sample rejection rates decreased from 32% to 10%. On average, $40 000 was spent per laboratory to cover mentors' salaries, SLMTA training and improvement project support. CONCLUSION: Building in-country capacity through local partners is a sustainable model for improving service quality in resource-constrained countries such as Ghana. Such models promote country ownership, capacity building and the use of local human resources for the expansion of SLMTA.

Transmission risk factors and treatment of pediatric shigellosis during a large daycare center-associated outbreak of multidrug resistant Shigella sonnei: implications for the management of shigellosis outbreaks among children.

BACKGROUND: Shigellosis outbreaks in daycare centers result in substantial disease and economic burdens in the United States. The emergence of multidrug resistant Shigella strains raises questions regarding control of transmission within daycare centers and treatment for children. From May to October 2005, 639 Shigella sonnei cases were reported in northwest Missouri, mostly among persons exposed to daycare centers. METHODS: We conducted a case-control investigation among licensed daycare centers (LDCs) in northwest Missouri to determine transmission risk factors, tested isolates for antimicrobial resistance, and described treatment practices. Case LDCs had secondary attack rates of shigellosis>or=2% (range, 2%-25%) and control LDCsor=1 sink in every room (odds ratio [OR]: 0.1; 95% confidence interval [CI]: 0.02-0.5) or a diapering station in every room (OR: 0.1; 95% CI: 0.01-0.6) were less likely to be case-LDCs. Resistance to ampicillin and trimethoprim-sulfamethoxazole was found in 90% of the outbreak strains. Among 210 children treated with antimicrobial agents, azithromycin was used in 92 (44%) while a fluoroquinolone was used in 11 (5%) children. CONCLUSIONS: During a large daycare center-associated shigellosis outbreak, strains were highly resistant to ampicillin and trimethoprim-sulfamethoxazole. Children were frequently treated with azithromycin and occasionally fluoroquinolones. Appropriate handwashing and diapering infrastructure are necessary to minimize spread of shigellosis within daycare centers, and could reduce use of antimicrobial agents.

Occurrence of a USA300 vancomycin-intermediate Staphylococcus aureus.

A vancomycin-intermediate Staphylococcus aureus (VISA) isolated from the blood of a 46-year-old patient with endocarditis was determined to be pulsed-field type USA300, daptomycin nonsusceptible, and positive for the Panton-Valentine leukocidin genes. Development of the VISA phenotype does not appear limited to traditional health care strains of S. aureus.

Case-control study of vaccination history in relation to pertussis risk during an outbreak among school students.

BACKGROUND: Between September and December 2003, an outbreak of pertussis occurred in Cass County, MO, mostly among adolescent school children. METHODS: We conducted a 1:2 matched case-control study among school children and used conditional logistic regression to evaluate risk factors for pertussis, including the total number of vaccine doses received, age at administration of each dose of vaccine and the type of vaccine (whole cell or acellular). RESULTS: Of all 127 pertussis cases reported in this outbreak, the majority were adolescents (10-19 years of age, 50%) and adults (20 years or older, 22%); only 10% were infants and children less than 5 years of age. Because the focus of our investigation was on school-aged children, we enrolled 237 students (79 cases and 158 controls) in our study. Students missing at least one dose of the vaccine had higher risk for pertussis than those who received all 5 doses (odds ratio [OR], 2.36; 95% confidence interval [CI], 1.17-4.77). Early administration of the fifth dose of the vaccine at age 4 years was significantly associated with risk for pertussis compared with vaccination at age 5 years (adjusted OR, 2.45; 95% CI, 1.16-5.16). A short time interval (<36 months) between the fourth and fifth doses of the vaccine also tended to increase the risk for pertussis, although this association was not statistically significant. The type of vaccine was not a significant risk factor. CONCLUSION: Administering all 5 doses of pertussis vaccine and the fifth dose at age 5 years with at least 36 months between the fourth and fifth doses provided the best protection against pertussis among children and adolescents in this outbreak.