A Generalizable Decision-Making Framework for Selecting Onsite versus Send-out Clinical Laboratory Testing.

BACKGROUND: Laboratory networks provide services through onsite testing or through specimen transport to higher-tier laboratories. This decision is based on the interplay of testing characteristics, treatment characteristics, and epidemiological characteristics. OBJECTIVES: Our objective was to develop a generalizable model using the threshold approach to medical decision making to inform test placement decisions. METHODS: We developed a decision model to compare the incremental utility of onsite versus send-out testing for clinical purposes. We then performed Monte Carlo simulations to identify the settings under which each strategy would be preferred. Tuberculosis was modeled as an exemplar. RESULTS: The most important determinants of the decision to test onsite versus send-out were the clinical utility lost due to send-out testing delays and the accuracy decrement with onsite testing. When the sensitivity decrements of onsite testing were minimal, onsite testing tended to be preferred when send-out delays reduced clinical utility by >20%. By contrast, when onsite testing incurred large reductions in sensitivity, onsite testing tended to be preferred when utility lost due to delays was >50%. The relative cost of onsite versus send-out testing affected these thresholds, particularly when testing costs were >10% of treatment costs. CONCLUSIONS: Decision makers can select onsite versus send-out testing in an evidence-based fashion using estimates of the percentage of clinical utility lost due to send-out delays and the relative accuracy of onsite versus send-out testing. This model is designed to be generalizable to a wide variety of use cases. HIGHLIGHTS: The design of laboratory networks, including the decision to place diagnostic instruments at the point-of-care or at higher tiers as accessed through specimen transport, can be informed using the threshold approach to medical decision making.The most important determinants of the decision to test onsite versus send-out were the clinical utility lost due to send-out testing delays and the accuracy decrement with onsite testing.The threshold approach to medical decision making can be used to compare point-of-care testing accuracy decrements with the lost utility of treatment due to send-out testing delays.The relative cost of onsite versus send-out testing affected these thresholds, particularly when testing costs were >10% of treatment costs.

Spatially-targeted tuberculosis screening has limited impact beyond household contact tracing in Lima, Peru: A model-based analysis.

Mathematical models have suggested that spatially-targeted screening interventions for tuberculosis may efficiently accelerate disease control, but empirical data supporting these findings are limited. Previous models demonstrating substantial impacts of these interventions have typically simulated large-scale screening efforts and have not attempted to capture the spatial distribution of tuberculosis in households and communities at a high resolution. Here, we calibrate an individual-based model to the locations of case notifications in one district of Lima, Peru. We estimate the incremental efficiency and impact of a spatially-targeted interventions used in combination with household contact tracing (HHCT). Our analysis reveals that HHCT is relatively efficient with a median of 40 (Interquartile Range: 31.7 to 49.9) household contacts required to be screened to detect a single case of active tuberculosis. However, HHCT has limited population impact, producing a median incidence reduction of only 3.7% (Interquartile Range: 5.8% to 1.9%) over 5 years. In comparison, spatially targeted screening (which we modeled as active case finding within high tuberculosis prevalence areas 100 m2 grid cell) is far less efficient, requiring evaluation of ≈12 times the number of individuals as HHCT to find a single individual with active tuberculosis. Furthermore, the addition of the spatially targeted screening effort produced only modest additional reductions in tuberculosis incidence over the 5 year period (≈1.3%) in tuberculosis incidence. In summary, we found that HHCT is an efficient approach for tuberculosis case finding, but has limited population impact. Other screening approaches which target areas of high tuberculosis prevalence are less efficient, and may have limited impact unless very large numbers of individuals can be screened.

Network Types and Functional Health in Old Age: It is Not Just the Size of the Network That Matters.

OBJECTIVES: Findings on the effect of network size and support on functional health are mixed. We examine whether network types, that simultaneously incorporate multiple network characteristics, are associated with functional health in late life. METHODS: Data are from the National Social Life, Health, and Aging Project (N = 3005). We estimated the longitudinal effect of membership in five multidimensional network types on disability in six activities of daily living using negative binomial regression, and on mobility (assessed using a timed walk test) using a generalized linear mixed model. RESULTS: Compared to those in the large without strain network, older adults in the small, restricted, high contact network had fewer disabilities but worse mobility, while those in the large network with strain also had worse mobility. DISCUSSION: Care plans focusing on function and mobility should consider multiple aspects of older adults' social networks including network size, diversity, and relationship strain.

Methods for measuring short-term geographical mobility used in infectious disease research: a scoping review protocol.

INTRODUCTION: Geographical mobility, the movement of individuals or populations, may increase an individual's risk of acquiring or transmitting infectious diseases, including HIV, tuberculosis, malaria and COVID-19. Many studies have collected information on short-term mobility through self-reported travel histories or using GPS trackers, but there has been no consistent conceptualisation and operationalisation of such geographical mobility in global health research. This protocol aims to describe and synthesise different approaches to measuring short-term mobility. METHODS AND ANALYSIS: We will search three databases (PubMed, Embase and Global Health) for peer-reviewed articles. After removing duplicates, two reviewers will first screen the titles and abstracts and then proceed to full-text screening. We will include studies that measure mobility at the individual level in the context of infectious diseases, including clinical trials, epidemiological studies and analyses of register data. Additional articles for inclusion may be identified through review of references in selected papers. We will summarise the method of data collection (GPS trackers, cellphones, retrospective self-report, travel journal, etc) and the specific measures used (overnight travel, having a secondary residence, travel outside of district, etc). ETHICS AND DISSEMINATION: This study consists of reviewing and abstracting existing data from publicly available materials, and therefore does not require ethical approval. The results of this study will be submitted for peer reviewed publication and may be presented at a relevant global health conference.

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.

Invited Commentary: To Make Long-Term Gains Against Infection Inequity, Infectious Disease Epidemiology Needs to Develop a More Sociological Imagination.

In a recent article in the Journal, Noppert et al. (Am J Epidemiol. 2023;192(3):475-482) articulated in detail the mechanisms connecting high-level "fundamental social causes" of health inequity to inequitable infectious disease outcomes, including infection, severe disease, and death. In this commentary, we argue that while intensive focus on intervening mechanisms is welcome and necessary, it cannot occur in isolation from examination of the way that fundamental social causes-including racism, socioeconomic inequity, and social stigma-sustain infection inequities even when intervening mechanisms are addressed. We build on the taxonomy of intervening mechanisms laid out by Noppert et al. to create a road map for strengthening the connection between fundamental cause theory and infectious disease epidemiology and discuss its implications for future research and intervention.

Burkitt lymphoma risk shows geographic and temporal associations with Plasmodium falciparum infections in Uganda, Tanzania, and Kenya.

Endemic Burkitt lymphoma (eBL) is a pediatric cancer coendemic with malaria in sub-Saharan Africa, suggesting an etiological link between them. However, previous cross-sectional studies of limited geographic areas have not found a convincing association. We used spatially detailed data from the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) study to assess this relationship. EMBLEM is a case-control study of eBL from 2010 through 2016 in six regions of Kenya, Uganda, and Tanzania. To measure the intensity of exposure to the malaria parasite, Plasmodium falciparum, among children in these regions, we used high-resolution spatial data from the Malaria Atlas Project to estimate the annual number of P. falciparum infections from 2000 through 2016 for each of 49 districts within the study region. Cumulative P. falciparum exposure, calculated as the sum of annual infections by birth cohort, varied widely, with a median of 47 estimated infections per child by age 10, ranging from 4 to 315 infections. eBL incidence increased 39% for each 100 additional lifetime P. falciparum infections (95% CI: 6.10 to 81.04%) with the risk peaking among children aged 5 to 11 and declining thereafter. Alternative models using estimated annual P. falciparum infections 0 to 10 y before eBL onset were inconclusive, suggesting that eBL risk is a function of cumulative rather than recent cross-sectional exposure. Our findings provide population-level evidence that eBL is a phenotype related to heavy lifetime exposure to P. falciparum malaria and support emphasizing the link between malaria and eBL.

Did the public attribute the Flint Water Crisis to racism as it was happening? Text analysis of Twitter data to examine causal attributions to racism during a public health crisis.

The Flint Water Crisis (FWC) was an avoidable public health disaster that has profoundly affected the city's residents, a majority of whom are Black. Although many scholars and journalists have called attention to the role of racism in the water crisis, little is known about the extent to which the public attributed the FWC to racism as it was unfolding. In this study, we used natural language processing to analyze nearly six million Flint-related tweets posted between April 1, 2014, and June 1, 2016. We found that key developments in the FWC corresponded to increases in the number and percentage of tweets that mentioned terms related to race and racism. Similar patterns were found for other topics hypothesized to be related to the water crisis, including water and politics. Using sentiment analysis, we found that tweets with a negative polarity score were more common in the subset of tweets that mentioned terms related to race and racism when compared to the full set of tweets. Next, we found that word pairs that included terms related to race and racism first appeared after the January 2016 state and federal emergency declarations and a corresponding increase in media coverage of the FWC. We conclude that many Twitter users connected the events of the water crisis to race and racism in real-time. Given growing evidence of negative health effects of second-hand exposure to racism, this may have implications for understanding minority health and health disparities in the US.

Optimizing laboratory-based surveillance networks for monitoring multi-genotype or multi-serotype infections.

With the aid of laboratory typing techniques, infectious disease surveillance networks have the opportunity to obtain powerful information on the emergence, circulation, and evolution of multiple genotypes, serotypes or other subtypes of pathogens, informing understanding of transmission dynamics and strategies for prevention and control. The volume of typing performed on clinical isolates is typically limited by its ability to inform clinical care, cost and logistical constraints, especially in comparison with the capacity to monitor clinical reports of disease occurrence, which remains the most widespread form of public health surveillance. Viewing clinical disease reports as arising from a latent mixture of pathogen subtypes, laboratory typing of a subset of clinical cases can provide inference on the proportion of clinical cases attributable to each subtype (i.e., the mixture components). Optimizing protocols for the selection of isolates for typing by weighting specific subpopulations, locations, time periods, or case characteristics (e.g., disease severity), may improve inference of the frequency and distribution of pathogen subtypes within and between populations. Here, we apply the Disease Surveillance Informatics Optimization and Simulation (DIOS) framework to simulate and optimize hand foot and mouth disease (HFMD) surveillance in a high-burden region of western China. We identify laboratory surveillance designs that significantly outperform the existing network: the optimal network reduced mean absolute error in estimated serotype-specific incidence rates by 14.1%; similarly, the optimal network for monitoring severe cases reduced mean absolute error in serotype-specific incidence rates by 13.3%. In both cases, the optimal network designs achieved improved inference without increasing subtyping effort. We demonstrate how the DIOS framework can be used to optimize surveillance networks by augmenting clinical diagnostic data with limited laboratory typing resources, while adapting to specific, local surveillance objectives and constraints.

COVID-19 vaccination and mask wearing behaviors in the United States, August 2020 - June 2021.

BACKGROUND: During the rollout of COVID-19 vaccination, many states relaxed mask wearing guidance for those vaccinated. The aim of this study was to examine the association between vaccination status and mask wearing behaviors. METHODS: Seven waves of surveys (n = 6721) were conducted between August 2020 and June 2021. Participants were asked about initiation of COVID-19 vaccination and mask wearing behavior at work/school or a grocery store. Odds ratios (ORs) and 95% confidence intervals (CIs) from logistic regression were used to estimate associations between vaccination status and mask wearing at work/school and at the grocery store. RESULTS: Between April and June 2021, mask wearing at work or school declined among both those vaccinated (74% to 49%) and unvaccinated (46% to 35%). There was a similar decline for mask wearing at grocery stores. The odds of wearing a mask were 2.35 times higher at work/school (95% CI: 1.82, 3.04) and 1.65 times at a grocery store (95% CI: 1.29, 2.11) among the vaccinated compared to unvaccinated. CONCLUSION: Mask wearing decreased after mask guidelines were relaxed, with consistently lower mask wearing among the unvaccinated, indicating a reluctance among the unvaccinated to adopt COVID-19 risk reduction behaviors.

A guide to backward paper writing for the data sciences.

In this perspective, we outline a set of best practices for the planning, writing, and revision of scientific papers and other forms of professional communication in the data sciences. We propose a backward approach that begins with clearly identifying the scientific and professional goals motivating the work, followed by a purposeful mapping from those goals to each section of a paper. This approach is motivated by the conviction that manuscript writing can be more effective, efficient, creative, and even enjoyable-particularly for early-career researchers-when the overarching goals of the paper and its individual components are clearly mapped out.

Rapid response modeling of SARS-CoV-2 transmission.

What can modelers learn from recent history to help prepare for the next pandemic?

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.

There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk.

Mathematical models have come to play a key role in global pandemic preparedness and outbreak response: helping to plan for disease burden, hospital capacity, and inform nonpharmaceutical interventions. Such models have played a pivotal role in the COVID-19 pandemic, with transmission models-and, by consequence, modelers-guiding global, national, and local responses to SARS-CoV-2. However, these models have largely not accounted for the social and structural factors, which lead to socioeconomic, racial, and geographic health disparities. In this piece, we raise and attempt to clarify several questions relating to this important gap in the research and practice of infectious disease modeling: Why do epidemiologic models of emerging infections typically ignore known structural drivers of disparate health outcomes? What have been the consequences of a framework focused primarily on aggregate outcomes on infection equity? What should be done to develop a more holistic approach to modeling-based decision-making during pandemics? In this review, we evaluate potential historical and political explanations for the exclusion of drivers of disparity in infectious disease models for emerging infections, which have often been characterized as "equal opportunity infectors" despite ample evidence to the contrary. We look to examples from other disease systems (HIV, STIs) and successes in including social inequity in models of acute infection transmission as a blueprint for how social connections, environmental, and structural factors can be integrated into a coherent, rigorous, and interpretable modeling framework. We conclude by outlining principles to guide modeling of emerging infections in ways that represent the causes of inequity in infection as central rather than peripheral mechanisms.

Multidimensional Social Network Types and Their Correlates in Older Americans.

BACKGROUND AND OBJECTIVES: Social support networks of older adults have been linked to their health and well-being; however, findings regarding the effects of specific network characteristics have been mixed. Additionally, due to demographic shifts increasing numbers of older adults live outside of traditional family structures. Previous studies have not systematically examined the resulting complexity and heterogeneity of older adults' social networks. Our objectives were to examine this complexity and heterogeneity by developing a multidimensional typology of social networks that simultaneously considers multiple structural and functional network characteristics, and to examine differences in network type membership by sociodemographic characteristics, health characteristics, and birth cohort. RESEARCH DESIGN AND METHODS: Participants included 5,192 adults aged 57-85 years in the National Social Life, Health, and Aging Project at rounds 1 (2005-2006) and 3 (2015-2016). Data were collected on social relationships including network size, diversity, frequency of contact, and perceived support and strain in relationships. We used latent class analysis to derive the network typology and multinomial logistic regression to examine differences in network type membership by sociodemographic characteristics, health characteristics, and birth cohort. RESULTS: Older adults were classified into 5 distinct social network types: (i) large, with strain; (ii) large, without strain; (iii) small, diverse, low contact; (iv) small, restricted, high contact; and (v) medium size and support. Membership in these network types varied by age, gender, marital status, race/ethnicity, education, mental health, and birth cohort. DISCUSSION AND IMPLICATIONS: Network typologies can elucidate the varied interpersonal environments of older adults and identify individuals who lack social connectedness on multiple network dimensions and are therefore at a higher risk of social isolation.

Accounting for uncertainty during a pandemic.

We discuss several issues of statistical design, data collection, analysis, communication, and decision-making that have arisen in recent and ongoing coronavirus studies, focusing on tools for assessment and propagation of uncertainty. This paper does not purport to be a comprehensive survey of the research literature; rather, we use examples to illustrate statistical points that we think are important.

Evaluating Michigan's Administrative Rule Change on Nonmedical Vaccine Exemptions.

OBJECTIVES: Vaccine hesitancy is a growing threat to health in the United States. Facing the fourth highest vaccine exemption rate in the United States in 2014, Michigan changed its state Administrative Rules, effective January 1, 2015, requiring parents to attend an in-person vaccine education session at their local health department before obtaining a nonmedical exemption (NME). In this article, we evaluate the longer-term impact of this policy change on the rate, spatial distribution, and sociodemographic predictors of NMEs in Michigan. METHODS: Using school-level kindergarten vaccination data from Michigan from 2011 to 2018, we evaluated sociodemographic predictors of NMEs before and after this Administrative Rule change using Bayesian binomial regression. We measured the persistence and location of school district-level geographic clustering using local indicators of spatial association. RESULTS: Immediately after the rule change, rates of NMEs fell by 32%. However, NME rates rebounded in subsequent years, increasing by 26% by 2018, although income disparities in NME rates decreased after the rule change. Philosophical, religious, and medical vaccine exemptions exhibited distinct geographic patterns across the state, which largely persisted after 2015, illustrating that NME clusters remain a concern despite this rule change. CONCLUSIONS: Although Michigan's Administrative Rule change caused a short-term decline in NME rates, NME rates have risen dramatically in the following 4 years since the policy was implemented. Michigan's administrative effort to require parental education at the local health department before receiving an exemption did not cause a sustained reduction in the rate or spatial distribution of NMEs.

Has the relationship between wealth and HIV risk in Sub-Saharan Africa changed over time? A temporal, gendered and hierarchical analysis.

This study examines the relationship between wealth and HIV infection in Sub-Saharan Africa to determine whether and how this relationship has varied over time, within and across countries, by gender, and urban environment. The analysis draws on DHS and AIS data from 27 Sub-Saharan African countries, which spanned the 14 years between 2003 and 2016. We first use logistic regression analyses to assess the relationship between individual wealth, HIV infection and gender by country and year stratified on urban environment. We then use meta-regression analyses to assess the relationship between country level measures of wealth and the odds of HIV infection by gender and individual level wealth, stratified on urban environment. We find that there is a persistent and positive relationship between wealth and the odds of HIV infection across countries, but that the strength of this association has weakened over time. The rate of attenuation does not appear to differ between urban/rural strata. Likewise, we also find that these associations were most pronounced for women and that this relationship was persistent over the study period and across urban and rural strata. Overall, our findings suggest that the relationship between wealth and HIV infection is beginning to reverse and that in the coming years, the relationship between wealth and HIV infection in Sub-Saharan Africa may more clearly mirror the predominant global picture.

Coccidioidomycosis and COVID-19 Co-Infection, United States, 2020.

We review the interaction between coronavirus disease (COVID-19) and coccidioidomycosis, a respiratory infection caused by inhalation of Coccidioides fungal spores in dust. We examine risk for co-infection among construction and agricultural workers, incarcerated persons, Black and Latino populations, and persons living in high dust areas. We further identify common risk factors for co-infection, including older age, diabetes, immunosuppression, racial or ethnic minority status, and smoking. Because these diseases cause similar symptoms, the COVID-19 pandemic might exacerbate delays in coccidioidomycosis diagnosis, potentially interfering with prompt administration of antifungal therapies. Finally, we examine the clinical implications of co-infection, including severe COVID-19 and reactivation of latent coccidioidomycosis. Physicians should consider coccidioidomycosis as a possible diagnosis when treating patients with respiratory symptoms. Preventive measures such as wearing face masks might mitigate exposure to dust and severe acute respiratory syndrome coronavirus 2, thereby protecting against both infections.