Many microbial functions happen within communities of interacting species. Explaining how species with disparate growth rates can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Here, we ask how microbes interacting through their chemical environment can achieve coexistence in a continuous growth setup (similar to an industrial bioreactor or gut microbiota) where external resources are being supplied. We formulate and experimentally constrain a model in which mediators of interactions (e.g. metabolites or waste-products) are explicitly incorporated. Our model highlights facilitation and self-restraint as interactions that contribute to coexistence, consistent with our intuition. When interactions are strong, we observe that coexistence is determined primarily by the topology of facilitation and inhibition influences not their strengths. Importantly, we show that consumption or degradation of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest.

While globally, there has been great success in increasing child survival, the decline in under-five mortality over the last three decades has not been uniform among ages. In 2020, nearly half (47%) of all under-five deaths occurred during the neonatal period (first 27 days of life), up from just 40% in 1990 [1]. In addition, […]

Background: Residual blood specimens offer a cost- and time-efficient alternative for conducting serological surveys. However, their use is often criticized due to potential issues with the representativeness of the target population and/or limited availability of associated metadata. We conducted a scoping review to examine where, when, how, and why residual blood specimens have been used in serological surveys for vaccine-preventable diseases (VPDs) and how potential selection biases are addressed. Methods: The review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines and identified relevant papers published in 1990–2022. Results: A total of 601 articles met the inclusion criteria after title, abstract screening, and full-text review. The most studied VPDs using residual blood specimens were COVID-19 (27%), hepatitis E (16%), hepatitis B (10%), influenza (9%), HPV (7%), and measles (7%). Residual blood specimens were primarily sourced from diagnostic specimens (61%) or blood and plasma donations (37%). Almost all articles used specimens linked to basic demographic data (e.g., age and sex), with 47% having access to extended demographic data (e.g., geographic location). Common strategies to address potential biases included comparing results with published estimates (78%) and performing stratified analyses (71%). Conclusions: Residual blood specimens are widely used in seroprevalence studies, particularly during emerging disease outbreaks when rapid estimates are critical. However, this review highlighted inconsistencies in how researchers analyze and report the use of residual specimens. We propose a set of recommendations to improve the analysis, reporting, and ethical considerations of serological surveys using residual specimens.

Background Since the emergence of the COVID-19 pandemic, substantial concern has surrounded its impact among the Rohingya refugees living in the Kutupalong-Balukhali refugee camps in Bangladesh. Early modeling work projected a massive outbreak was likely after an introduction of the SARS-CoV-2 virus into the camps. Despite this, only 317 laboratory-confirmed cases and 10 deaths were reported through October 2020. While these official numbers portray a situation where the virus has been largely controlled, other sources contradict this, suggesting the low reported numbers to be a result of limited care seeking and testing, highlighting a population not willing to seek care or be tested. SARS-CoV-2 seroprevalence estimates from similar a timeframe in India (57%) and Bangladesh (74%) further sow doubt that transmission had been controlled. Here we explore multiple data sources to understand the plausibility of a much larger SARS-CoV-2 outbreak among the Rohingya refugees. Methods We used a mixed approach to analyze SARS-CoV-2 transmission using multiple available datasets. Using data from reported testing, cases, and deaths from the World Health Organization (WHO) and from WHO’s Emergency Warning, Alert, and Response System, we characterized the probabilities of care seeking, testing, and being positive if tested. Unofficial death data, including reported pre-death symptoms, come from a community-based mortality survey conducted by the International Organization for Migration (IOM),) in addition to community health worker reported deaths. We developed a probabilistic inference framework, drawing on these data sources, to explore three scenarios of what might have happened among the Rohingya refugees. Results Among the 144 survey-identified deaths, 48 were consistent with suspected COVID-19. These deaths were consistent with viral exposures during Ramadan, a period of increased social contacts, and coincided with a spike in reported cases and testing positivity in June 2020. The age profile of suspected COVID-19 deaths mirrored that expected. Through the probability framework, we find that under each scenario, a substantial outbreak likely occurred, though the cumulative size and timing vary considerably. In conjunction with the reported and suspected deaths, the data suggest a large outbreak could have occurred early during spring 2020. Furthermore, while many mild and asymptomatic infections likely occurred, death data analyzed suggest there may have been significant unreported mortality. Conclusions With the high population density, inability to home isolate adequately, and limited personal protective equipment, infection prevention and control in the Rohingya population is extremely challenging. Despite the low reported numbers of cases and deaths, our results suggest an early large-scale outbreak is consistent with multiple sources of data, particularly when accounting for limited care seeking behavior and low infection severity among this young population. While the currently available data do not allow us to estimate the precise incidence, these results indicate substantial unrecognized SARS-CoV-2 transmission may have occurred in these camps. However, until serological testing provides more conclusive evidence, we are only able to speculate about the extent of transmission among the Rohingya.

Global health agencies and regional and national stakeholders collaborated to develop the Immunization Agenda 2030 Scorecard, a digital data visualization platform displaying global, regional, and country-level immunization progress. The scorecard serves to focus attention and enable strategic actions around the measures visualized. To assess the scorecard’s usability, appropriateness, and context for use, we interviewed 15 immunization officers working across five global regions. To further understand the implementation context, we also reviewed the characteristics of 15 public platforms visualizing population health data. We integrated thematic findings across both methods. Many platforms highlight service gaps and enable comparisons between geographies to foster political pressure for service improvements. We observed heterogeneity regarding the platforms’ focus areas and participants’ leading concerns, which were management capacity and resourcing. Furthermore, one-third of platforms were out of date. Results yielded recommendations for the scorecard, which participants felt was well suited to focus the attention of decision makers on key immunization data. A simpler design coupled with implementation strategies that more actively engage policymakers would better align the scorecard with other public platforms engaging intended users. For population health platforms to serve as effective accountability mechanisms, studying implementation determinants, including usability testing, is vital to meet stakeholder needs.

Background: Despite the existence of evidence-based interventions, substantial progress in reducing neonatal mortality is lagging, indicating that small and sick newborns (SSNs) are likely not receiving the care they require to survive and thrive. The “three delays model” provides a framework for understanding the challenges in accessing care for SSNs. However, the extent to which each of the delays impacts access to care for SSNs is not well-understood. To fill this evidence gap, we explored the impact of each of the three delays on access to care for SSNs in Malawi, Mozambique, and Tanzania. Methods: Secondary analyses of data from three different surveys served as the foundation of this study. To understand the impact of delays in the decision to seek care (delay 1) and the ability to reach an appropriate point of care (delay 2), we investigated time trends in place of birth disaggregated by facility type and explored care-seeking behaviors for newborns who died. To understand the impact of delays accessing high-quality care after reaching a facility (delay 3), we measured facility readiness to manage care for SSNs and used this measure to adjust institutional delivery coverage for SSN care readiness. Findings: Coverage of institutional deliveries was substantially lower after adjusting for facility readiness to manage SSN care, with decreases of 30 percentage points (pp) in Malawi, 14pp in Mozambique, and 24pp in Tanzania. While trends suggest more SSNs are born in facilities, substantial gaps remain in facilities’ capacities to provide lifesaving interventions. In addition, exploration of care-seeking pathways revealed that a substantial proportion of newborn deaths occurred outside of health facilities, indicating barriers in the decision to seek care or ability to reach an appropriate source of care may also prevent SSNs from receiving these interventions. Conclusions: Investments are needed to overcome delays in accessing high quality care for the most vulnerable newborns – those who are born small or sick. As more mothers and newborns access health services in low- and middle-income countries, ensuring that life-saving interventions for SSNs are available at the locations where newborns are born and seek care after birth is critical.