Mycoplasma pneumoniae is a common bacterial cause of respiratory infection and a leading cause of childhood community-acquired pneumonia (CAP). Increases in M. pneumoniae infection occur every 3-5 years. In the United States, M. pneumoniae prevalence decreased during and immediately after the COVID-19 pandemic. Information from 42 U.S. children's hospitals that provided information to the Pediatric Health Information System, a database of clinical and resource use information, was used to identify discharge diagnostic codes for 2018-2024 indicating M. pneumoniae infection. M. pneumoniae-associated CAP incidence among children aged ≤18 years was significantly higher in 2024 (12.5 per 1,000 hospitalizations) than during 2018-2023 (2.1). During the study period, an M. pneumoniae diagnostic code was listed in 11.5% of pediatric CAP hospitalizations, peaking at 53.8% in July 2024. Among pediatric M. pneumoniae CAP cases, the highest percentage occurred among children aged 6-12 years (42.6%), followed by children aged 2-5 years (25.7%) and 13-18 years (21.1%). The lowest occurred among those aged 12-23 months (6.4%) and 0-11 months (4.2%). M. pneumoniae infections in 2024 were not more severe than 2018-2023 infections, as assessed by length of hospitalization and percentage of patients admitted to an intensive care unit. The increase in M. pneumoniae infections in the United States in 2024 might be higher than previous periodic increases because the susceptible population was larger after sustained low incidence during and immediately after the COVID-19 pandemic. Health care providers should be aware of the periodicity of M. pneumoniae CAP and consider testing for this pathogen as a cause of respiratory illness among children of all ages.

Trachoma is targeted for global elimination as a public health problem by 2030. Measurement of IgG antibodies in children is being considered for surveillance and programmatic decision-making. There are currently no programmatic guidelines based on serology, which represents a generalizable problem in seroepidemiology and disease elimination. Here, we collate Chlamydia trachomatis Pgp3 and CT694 IgG measurements from 48 serosurveys across Africa, Latin America, and the Pacific Islands (41,168 children ages 1-5 years) and propose a novel approach to estimate the probability that population C. trachomatis transmission is below or above levels requiring ongoing programmatic action. We determine that trachoma programs could halt control measures with >90% certainty when seroconversion rates (SCRs) are ≤2.2 per 100 person-years. Conversely, SCRs ≥4.5 per 100 person-years correspond with >90% certainty that further control interventions are needed. More extreme SCR thresholds correspond with higher levels of confidence of elimination (lower SCR) or ongoing action needed (higher SCR). This study demonstrates a robust approach for using trachoma serosurveys to guide elimination program decisions.

OBJECTIVE: Longer-acting pre-exposure prophylaxis (LA-PrEP) products have potential to increase PrEP uptake and continuation. This study sought to elicit preferences for LA-PrEP product and delivery program characteristics among populations disproportionately impacted by HIV to identify factors important to adoption and anticipate potential use challenges. DESIGN: Cross-sectional, online discrete choice experiment. METHODS: We recruited 940 men who have sex with men (MSM), people who inject drugs (PWID), and Black heterosexual men and women (BHMW) with PrEP indications. In a series of 10 tasks, participants chose between two hypothetical LA-PrEP options composed of 5 attributes (product type, side effects, clinic type, appointment duration, cost), or neither (their current HIV prevention method). Analysis used random-parameters logit models. RESULTS: Respondents chose an LA-PrEP method over their current HIV prevention option in 96.8% of tasks. Cost was the most important determinant of LA-PrEP choice for all populations (relative importance [RI] of 10]. Side effects and product type were 1/3 to 1/2 as important as cost (RI 3.5-5.1). MSM and PWID most preferred the 12-month implant followed by semiannual dual injections and least preferred the monthly oral pill and 2-month single injection. BHMW most preferred the monthly pill and semiannual injections and least preferred the 12-month implant and 2-month injection. Clinic type and appointment duration had minimal influence (RI 0.1-2.1). CONCLUSIONS: Results suggest high demand for LA-PrEP among populations with disproportionately high HIV incidence. To facilitate use, programs should offer a range of LA-PrEP products, minimize out-of-pocket costs, and counsel on side effects.

The Next-Generation Sequencing (NGS) Quality Initiative addresses laboratory challenges faced when performing NGS by developing tools and resources to build a robust quality management system. Here, we illustrate how those products support laboratories in navigating complex regulatory environments and quality-related challenges while implementing NGS effectively in an evolving landscape.

Antiretroviral therapy (ART) has been adopted as a form of HIV treatment and prevention. This study assesses rapid ART initiation using clinical outcomes such as viral load (VL) and CD4+ T lymphocytes count. Over the course of one year, the progress of newly diagnosed people living with HIV who started ART early in a hospital in Panama City was followed. The evaluation of early initiation of ART in achieving viral suppression (VL <200 copies/ml) was analyzed using descriptive statistics. Additionally, the cost difference between early (first 7 days) and late initiation of ART was evaluated from the perspective of the service provider. In total, 209 people were followed up during the study; 85% were male, 70% started ART on same day from hospital arrival, 80% had suppressed viral load at 6 months, and the median count of CD4 increased from 285 (IQR: 166-429) to 509 (IQR: 373-696) over 12 months. Starting ART early led to a 42% increase for the provider in terms of staffing costs; however, the clients had the opportunity to decrease absenteeism in daily activities. The results reveal that early initiation of ART generates clinical and economic benefits for the person in treatment.

Access to hand hygiene (HH) resources in clinical settings is important to prevent healthcare-associated infections, including COVID-19. However, many countries, including Belize, have limited national data on the availability of HH resources and healthcare worker (HCW) hand hygiene adherence (HHA) in healthcare facilities (HCFs). We conducted a study in the 11 largest public HCFs across Belize to evaluate access to HH resources and HHA before and after an intervention (provision of alcohol-based hand rub (ABHR) wall mounts and HH training). Descriptive statistics and multilevel logistic regressions were used to assess changes in HH resources and HHA from baseline to follow-up and explore factors associated with HHA. There was a 19 percent increase in rooms with functional wall-mounted ABHR dispensers (44% to 63%) post-intervention. HHA did not improve from baseline (52%) to follow-up (50%). Combining baseline and follow-up data, HHA was higher when ABHR and soap and water were present (aOR = 4.19, 95% CI = 2.11, 8.32) and when only ABHR was present (aOR = 3.85, 95% CI = 1.92, 7.72) compared with when soap and water were present alone. The decreased perceived risk of COVID-19 at follow-up may explain the null HHA findings. However, our assessment of HH resources and practices provides a useful foundation for future HH programs in HCFs.

BACKGROUND: Marburg virus disease (MVD) is a severe viral infection caused by the Marburg marburgvirus species. In February 2023, Equatorial Guinea declared its first outbreak. This case series describes the natural history of MVD in five laboratory confirmed patients. METHODS: Patients with confirmed MVD admitted to the national treatment center in Bata, Equatorial Guinea, were monitored for vital signs and symptoms. Comprehensive clinical data was collected to understand the progression and outcome of the disease. RESULTS: Five patients were confirmed to have MVD. Three male healthcare workers were diagnosed early in their disease and subsequently survived. The other two patients, both females, were admitted later in their disease progression and died within 24 hours of admission. Four patients received remdesivir under a protocol for the Monitored Emergency Use of Unregistered and Experimental Interventions. The early symptoms were non-specific, with rapid progression to more severe conditions in the later stages of the disease. Early treatment with remdesivir showed the drug to be well tolerated. CONCLUSIONS: Contrary to some reports and the recommended case definition for MVD, our patients presented with a rash but did not exhibit vomiting or diarrhea. Hemorrhagic signs were solely observed in the terminal stage, preceding demise. Despite the limited sample size, these findings emphasize the importance of tailoring the case definition to the specific outbreak. Further evidence on the efficacy and safety of therapeutics for MVD, including remdesivir, should be gathered through well-designed trials during future epidemic responses.

INTRODUCTION: E-cigarette unit sales have been estimated using the number of items typically available in a package to standardize unit sales of each product type. However, recent market changes, such as increases in e-liquid volume and nicotine concentration, challenge the validity of assessing sales according to item count without accounting for product attributes. This study measured nicotine content (mg) in e-cigarettes sold as a function of e-liquid volume (mL) and nicotine concentration (mg/mL), compared with e-cigarette unit sales standardized by item count. METHODS: U.S. e-cigarette retail sales data from Circana (February 2019 to June 2024) were analyzed. Trends in mg nicotine sold were compared with standardized unit sales. Additionally, sales-weighted average e-liquid volume, nicotine concentration, and price per milligram of nicotine were measured by product type. Trends were assessed using Joinpoint regression. Analyses were conducted in 2024. RESULTS: From February 2020 to June 2024, monthly milligrams of nicotine content sold increased by 249.2% (p<0.001)-an increase 7.2 times greater than the 34.7% increase in standardized unit sales. Disposable e-cigarettes experienced the greatest increase in mg nicotine sold, which was largely driven by the rise in e-liquid volume. By June 2024, a disposable device contained 9.0 times more e-liquid than a prefilled cartridge. However, the price per milligram of nicotine in prefilled cartridges was 3.7 times greater than that of disposable devices. CONCLUSIONS: Nicotine is an addictive drug added to most e-cigarettes. Measuring e-cigarette sales in milligrams of nicotine content sold could better account for rapid changes in product attributes and inform policy strategies.

OBJECTIVE: To establish baseline seroprevalence of soil-borne, waterborne, and foodborne diseases and to monitor diseases that are eliminated or on the path to elimination in the Paraguayan Chaco. METHODS: A total of 1 100 school-age children (6-15 years) were tested in urban and rural schools selected for a cross-cutting population-based survey using a two-stage probabilistic sample design in the three departments of the Paraguayan Chaco. Blood samples were taken on filter paper to measure IgG antibodies using a multiplex bead assay. Data collection was carried out through interviews with parents and caregivers. Access to basic sanitation and improved water was assessed. Differences in pathogen seropositivity and seroprotection were estimated by urban and rural areas. RESULTS: Seroprotection against measles was 62.9% and against rubella was 78.2%. Minimal diphtheria and tetanus seroprotection (≥0.01 IU/ml) was 92.9% and 98.3%, respectively. Seroprotective levels against these four vaccine-preventable diseases significantly decreased with increasing age (p < 0.05). The following pathogens and respective antigens showed significantly higher seroprevalence (p < 0.05) in rural areas compared with urban areas: Cryptosporidium parvum Cp17: 80.4% vs 64.6%, and Cp23: 60.6% vs 44.8%; Giardia lamblia VSP3: 26.9% vs 16.6%; Strongyloides stercoralis NIE: 11.5% vs 4.1%; and Taenia solium T24H: 7.1% vs 1.6%. Seroprevalence for these pathogens was also higher in Indigenous population when compared to non-Indigenous. Basic sanitation conditions showed significant differences (p < 0.05) between rural and urban areas: adobe and soil dwelling floor (65.3% vs 30.2%), use of pit latrine (90.3% vs 44.2%), availability of drainage or septic tank (8.7% vs 55.2%), access to safe water (19.7% vs 44.9%), and water treatment (6.8% vs 32.3%). CONCLUSIONS: We identified high exposure to soil-borne, waterborne, and foodborne diseases in rural areas and Indigenous population in the Paraguayan Chaco. Low seroprotection against measles and rubella alerts about the risk of immunity gaps to maintain elimination targets.

Water quality assessments are critical for ensuring timely responses to water-related concerns, particularly in low-resource areas with limited water, sanitation, and hygiene (WASH) infrastructure. In collaboration with the Belize Ministry of Health and Wellness and the Ministry of Education, Culture, Science and Technology, we conducted a survey on WASH infrastructure and resources among 221 schools. We identified 65 schools across all six districts of Belize for water quality testing. Among these 65 schools, 83% had at least one water sample that did not meet the WHO's recommended free chlorine residual level for drinking water. Additionally, coliforms and Escherichia coli were detected in at least one drinking or handwashing water sample from 43 (66%) and 14 (22%) schools, respectively. These findings underscore the importance of routine water quality testing in schools to inform timely public health responses.

In February 2023, the government of Equatorial Guinea declared an outbreak of Marburg virus disease. We describe the response structure and epidemiologic characteristics, including case-patient demographics, clinical manifestations, risk factors, and the serial interval and timing of symptom onset, treatment seeking, and recovery or death. We identified 16 laboratory-confirmed and 23 probable cases of Marburg virus disease in 5 districts and noted several unlinked chains of transmission and a case-fatality ratio of 90% (35/39 cases). Transmission was concentrated in family clusters and healthcare settings. The median serial interval was 18.5 days; most transmission occurred during late-stage disease. Rapid isolation of symptomatic case-patients is critical in preventing transmission and improving patient outcomes; community engagement and surveillance strengthening should be prioritized in emerging outbreaks. Further analysis of this outbreak and a One Health surveillance approach can help prevent and prepare for future potential spillover events.

We compared the number of Aedes aegypti females per trap and the number of detections of this mosquito species per week during 8 wk in 3 types of autocidal gravid traps, the Centers for Disease Control and Prevention (CDC) Autocidal Gravid Ovitrap (AGO), Biogents Gravid Aedes Trap (GAT), and Singapore Gravitrap (SGT), in central Puerto Rico. These traps use the same principles for attracting gravid Ae. aegypti females as traditional ovitraps, such as dark colors, standing water, and decomposing plant materials. The traps differ in size, AGO being the biggest and SGT the smallest. Average captures of female Ae. aegypti per trap per week were 11.1, 7.2, and 1.7 in AGO, GAT, and SGT traps, respectively, a pattern consistent with the sizes of the traps. These results indicated that GAT traps and SGT traps captured 35.5% and 84.7% fewer females of Ae. aegypti, respectively, than AGO traps. Although Ae. aegypti was present in all 20 sites during the 8 wk of observations, AGO, GAT, and SGT traps did not catch specimens in 1, 9, and 58 out of 160 observations per trap type (trap-wk), respectively. Trap failures were 1, 6, and 1 for the AGO, GAT, and SGT traps, respectively. Despite the absence of females of Ae. aegypti at some sites and weeks in each of the traps, all 3 traps were able to detect the presence of this mosquito at each of the 20 sites during the 8 wk of observations and could be used for Ae. aegypti surveillance.

Background/Purpose: The burden and epidemiology of Mycoplasma pneumoniae (Mp) community-acquired pneumonia (CAP) among hospitalized U. S. adults (≥ 18 years) are poorly understood. Methods: In the Etiology of Pneumonia in the Community (EPIC) study, we prospectively enrolled 2272 adults hospitalized with radiographically-confirmed pneumonia between January 2010-June 2012 and tested nasopharyngeal/oropharyngeal swabs for Mp by real-time polymerase chain reaction (PCR). Clinical and epidemiological features of Mp-PCR-positive and -negative adults were compared using logistic regression. Macrolide susceptibility was assessed by genotyping isolates. Results: Among 2272 adults, 43 (1.8%) were Mp-PCR-positive (median age: 45 years); 52% were male, and 56% were non-Hispanic white. Only one patient had Mp macrolide resistance. Four (9%) were admitted to the intensive care unit (ICU). No in-hospital deaths were reported. Of the 9 (21%) who received an outpatient antibiotic ≤5 days pre-admission, 2 (22%) received an antibiotic with Mp activity. Variables significantly associated with higher odds of Mp detection included age {18-29 years [(adjusted odds ratio (aOR): 11.7 (95% confidence interval (CI): 5.1- 26.6) versus ≥50 years]} and radiographic lymphadenopathy [aOR: 3.5 (95% CI: 1.2- 9.3)]. Conclusions: M. pneumoniae, commonly known to cause "walking pneumonia", was detected among hospitalized adults, with the highest prevalence among young adults. Although associated with clinically non-specific symptoms, approximately one out of every ten patients were admitted to the ICU. Increasing access to M. pneumoniae point-of-care testing could facilitate targeted treatment and avoid hospitalization.

CONTEXT: Laboratory-based hepatitis C virus (HCV) clearance cascades are an important tool for health departments to track progress toward HCV elimination, but a laboratory-based definition of HCV clearance has not yet been validated. OBJECTIVE: To compare agreement between a laboratory-based HCV clearance definition with a clinical cure definition. DESIGN: Observational. SETTING: New York City Department of Health and Mental Hygiene HCV surveillance system data and New York City hepatitis C linkage-to-care program data. PARTICIPANTS: Linkage-to-care program participants who were diagnosed with hepatitis C and enrolled in the linkage-to-care program from July 1, 2016, through June 30, 2020. MAIN OUTCOME MEASURE: Percent agreement between a laboratory-based HCV clearance definition (surveillance system) and a clinical cure definition (program data). RESULTS: Among 591 program participants with known treatment outcome, the laboratory-based HCV clearance definition and clinical cure definition were concordant in 573 cases (97%). CONCLUSIONS: A laboratory-based HCV clearance definition based on public health surveillance data can be a reliable source for monitoring HCV elimination.

Multiplex-based serological surveillance is a valuable but underutilized tool to understand gaps in population-level exposure, susceptibility, and immunity to infectious diseases. Assays for which blood samples can be tested for antibodies against several pathogens simultaneously, such as multiplex bead immunoassays, can more efficiently integrate public health surveillance in low- and middle-income countries. On March 7-8, 2023 a group of experts representing research institutions, multilateral organizations, private industry, and country partners met to discuss experiences, identify challenges and solutions, and create a community of practice for integrated, multi-pathogen serosurveillance using multiplex bead assay technologies. Participants were divided into six working groups: 1) supply chain; 2) laboratory assays; 3) seroepidemiology; 4) data analytics; 5) sustainable implementation; and 6) use case scenarios. These working groups discussed experiences, challenges, solutions, and research needs to facilitate integrated, multi-pathogen serosurveillance for public health. Several solutions were proposed to address challenges that cut across working groups.

OBJECTIVE: To estimate the national and regional population attributable fraction (PAF) and potential number of preventable anemia cases for three nutritional risk factors (iron, red blood cell folate [RBCF], and vitamin B12 deficiencies) among women of childbearing age in Belize. METHODS: A national probability-based household and micronutrient survey capturing sociodemographic and health information was conducted among 937 nonpregnant Belizean women aged 15-49 years. Blood samples were collected to determine hemoglobin, ferritin, alpha-1-glycoprotein (AGP), RBCF, and vitamin B12 status. All analyses used sample weights and design variables to reflect a complex sample survey. Logistic regression was used to determine adjusted prevalence risk (aPR) ratios, which were then used to estimate national and regional PAF for anemia. RESULTS: The overall prevalence of anemia (hemoglobin <12 g/dL) was 21.2% (95% CI [18.7, 25.3]). The prevalence of anemia was significantly greater among women with iron deficiency (59.5%, 95% CI [48.7, 69.5]) compared to women without iron deficiency (15.2%, 95% CI [12.2, 18.3]; aPR 3.9, 95% CI [2.9, 5.1]). The three nutritional deficiencies examined contributed to 34.6% (95% CI [22.1, 47.1]) of the anemia cases. If all these nutritional deficiencies could be eliminated, then an estimated 5 953 (95% CI [3 807, 8 114]) anemia cases could be prevented. CONCLUSIONS: This study suggests that among women of child-bearing age in Belize, anemia cases might be reduced by a third if three modifiable nutritional risk factors (iron, RBCF, and vitamin B12 deficiencies) could be eliminated. Fortification is one potential strategy to improve nutritional status and reduce the burden of anemia in this population.

BACKGROUND: Dengue is a leading cause of febrile illness among international travellers. We aimed to describe the epidemiology and clinical characteristics of imported dengue in returning travellers evaluated at GeoSentinel sites from 2007-2022. METHODS: We retrieved GeoSentinel records of dengue among travellers residing in non-endemic countries. We considered dengue confirmed when diagnosed by a positive DENV-specific RT-PCR, positive NS-1 antigen, and/or anti-DENV IgG seroconversion, and probable when diagnosed by single anti-DENV IgM or high titre anti-DENV IgG detection. Severe dengue was defined as evidence of clinically significant plasma leakage or bleeding, organ failure, or shock, according to the 2009 WHO guidance. Complicated dengue was defined as either severe dengue or dengue with presence of any warning sign. Analyses were descriptive. RESULTS: This analysis included 5958 travellers with confirmed (n = 4859; 81.6%) or probable (n = 1099; 18.4%) dengue. The median age was 33 years (range: < 1-91); 3007 (50.5%) travellers were female. The median travel duration was 21 days (interquartile range [IQR]: 15-32). The median time between illness onset and GeoSentinel site visit was 7 days (IQR: 4-15). The most frequent reasons for travel were tourism (67.3%), visiting friends or relatives (12.2%), and business (11.0%). The most frequent regions of acquisition were Southeast Asia (50.4%), South-Central Asia (14.9%), the Caribbean (10.9%), and South America (9.2%). Ninety-five (1.6%) travellers had complicated dengue, of whom 27 (0.5%) had severe dengue, and one died. Of 2710 travellers with data available, 724 (26.7%) were hospitalized. The largest number of cases (n = 835) was reported in 2019. CONCLUSIONS: A broad range of international travellers should be aware of the risk of acquiring dengue and receive appropriate pretravel counselling regarding preventive measures. Prospective cohort studies are needed to further elucidate dengue risk by destination and over time, as well as severe outcomes and prolonged morbidity (long-dengue) due to travel-related dengue.

Anopheles stephensi, an Asian malaria vector, continues to expand across Africa. The vector is now firmly established in urban settings in the Horn of Africa. Its presence in areas where malaria resurged suggested a possible role in causing malaria outbreaks. Here, using a prospective case-control design, we investigated the role of An. stephensi in transmission following a malaria outbreak in Dire Dawa, Ethiopia in April-July 2022. Screening contacts of patients with malaria and febrile controls revealed spatial clustering of Plasmodium falciparum infections around patients with malaria in strong association with the presence of An. stephensi in the household vicinity. Plasmodium sporozoites were detected in these mosquitoes. This outbreak involved clonal propagation of parasites with molecular signatures of artemisinin and diagnostic resistance. To our knowledge, this study provides the strongest evidence so far for a role of An. stephensi in driving an urban malaria outbreak in Africa, highlighting the major public health threat posed by this fast-spreading mosquito.

Fecal-orally transmitted gastroenteritis viruses, particularly human noroviruses (HuNoVs), are a public health concern. Viral transmission risk through contaminated water results underexplored as they have remained largely unculturable until recently and the robust measuring of gastroenteritis viruses infectivity in a single cell line is challenging. This study primarily aimed to test the feasibility of the human intestinal enteroids (HIE) model to demonstrate the infectivity of multiple gastroenteritis viruses in wastewater. Initially, key factors affecting viral replication in HIE model were assessed, and results demonstrated that the reagent-assisted disruption of 3D HIE represents an efficient alternative to syringe pass-through, and the filtering of HuNoV stool suspensions could be avoided. Moreover, comparable replication yields of clinical strains of HuNoV genogroup I (GI), HuNoV GII, rotavirus (RV), astrovirus (HAstV), and adenoviruses (HAdV) were obtained in single and multiple co-infections. Then, the optimized HIE model was used to demonstrate the infectivity of multiple naturally occurring gastroenteritis viruses from wastewater. Thus, a total of 28 wastewater samples were subjected to (RT)-qPCR for each virus, with subsequent testing on HIE. Among these, 16 samples (57 %) showed replication of HuNoVs (n = 3), RV (n = 5), HAstV (n = 8), and/or HAdV (n = 5). Three samples showed HuNoV replication, and sequences assigned to HuNoV GI.3[P13] and HuNoV GII.4[P16] genotypes. Concurrent replication of multiple gastroenteritis viruses occurred in 4 wastewater samples. By comparing wastewater concentrate and HIE supernatant sequences, diverse HAstV and HAdV genotypes were identified in 4 samples. In summary, we successfully employed HIE to demonstrate the presence of multiple infectious human gastroenteritis viruses, including HuNoV, in naturally contaminated wastewater samples.

BACKGROUND: Bacillus cereus is a ubiquitous gram-positive rod-shaped bacterium that can cause sepsis and neuroinvasive disease in patients with acute leukemia or neutropenia. METHODS: A single-center retrospective review was conducted to evaluate patients with acute leukemia, positive blood or cerebrospinal fluid test results for B cereus, and abnormal neuroradiographic findings between January 2018 and October 2022. Infection control practices were observed, environmental samples obtained, a dietary case-control study completed, and whole genome sequencing performed on environmental and clinical Bacillus isolates. RESULTS: Five patients with B cereus neuroinvasive disease were identified. All patients had acute myeloid leukemia (AML), were receiving induction chemotherapy, and were neutropenic. Neurologic involvement included subarachnoid or intraparenchymal hemorrhage or brain abscess. All patients were treated with ciprofloxacin and survived with limited or no neurologic sequelae. B cereus was identified in 7 of 61 environmental samples and 1 of 19 dietary protein samples-these were unrelated to clinical isolates via sequencing. No point source was identified. Ciprofloxacin was added to the empiric antimicrobial regimen for patients with AML and prolonged or recurrent neutropenic fevers; no new cases were identified in the ensuing year. CONCLUSIONS: B cereus is ubiquitous in the hospital environment, at times leading to clusters with unrelated isolates. Fastidious infection control practices addressing a range of possible exposures are warranted, but their efficacy is unknown and they may not be sufficient to prevent all infections. Thus, including B cereus coverage in empiric regimens for patients with AML and persistent neutropenic fever may limit the morbidity of this pathogen.

PURPOSE: Population-based prevalence surveys are essential for decision-making on interventions to achieve trachoma elimination as a public health problem. This paper outlines the methodologies of Tropical Data, which supports work to undertake those surveys. METHODS: Tropical Data is a consortium of partners that supports health ministries worldwide to conduct globally standardised prevalence surveys that conform to World Health Organization recommendations. Founding principles are health ministry ownership, partnership and collaboration, and quality assurance and quality control at every step of the survey process. Support covers survey planning, survey design, training, electronic data collection and fieldwork, and data management, analysis and dissemination. Methods are adapted to meet local context and needs. Customisations, operational research and integration of other diseases into routine trachoma surveys have also been supported. RESULTS: Between 29(th) February 2016 and 24(th) April 2023, 3373 trachoma surveys across 50 countries have been supported, resulting in 10,818,502 people being examined for trachoma. CONCLUSION: This health ministry-led, standardised approach, with support from the start to the end of the survey process, has helped all trachoma elimination stakeholders to know where interventions are needed, where interventions can be stopped, and when elimination as a public health problem has been achieved. Flexibility to meet specific country contexts, adaptation to changes in global guidance and adjustments in response to user feedback have facilitated innovation in evidence-based methodologies, and supported health ministries to strive for global disease control targets.

BACKGROUND: One of the three main targets of the World Health Organization (WHO) End TB Strategy (2015-2035) is that no tuberculosis (TB) patients or their households face catastrophic costs (defined as exceeding 20% of the annual household income) because of the disease. Our study seeks to determine, as a baseline, the magnitude and main drivers of the costs associated with TB disease for patients and their households and to monitor the proportion of households experiencing catastrophic costs in Brazil. METHODS: A national cross-sectional cluster-based survey was conducted in Brazil in 2019-2021 following WHO methodology. TB patients of all ages and types of TB were eligible for the survey. Adult TB patients and guardians of minors (<18 years old) were interviewed once about costs, time loss, coping measures, income, household expenses, and asset ownership. Total costs, including indirect costs measured as reported household income change, were expressed as a percentage of annual household income. We used descriptive statistics to analyze the cost drivers and multivariate logistic regression to determine factors associated with catastrophic costs. RESULTS: We interviewed 603 patients, including 538 (89%) with drug-sensitive (DS) and 65 (11%) with drug-resistant (DR) TB. Of 603 affected households, 48.1% (95%CI: 43-53.2) experienced costs above 20% of their annual household income during their TB episode. The proportion was 44.4% and 78.5% among patients with DS- and DR-TB, respectively. On average, patients incurred costs of US$1573 (95%CI: 1361.8-1785.0) per TB episode, including pre-diagnosis and post-diagnosis expenses. Key cost drivers were post-diagnosis nutritional supplements (US$317.6, 95%CI: 232.7-402.6) followed by medical costs (US$85.5, 95%CI: 54.3-116.5) and costs of travel for clinic visits during treatment (US$79.2, 95%CI: 61.9-96.5). In multivariate analysis, predictors of catastrophic costs included positive HIV status (aOR = 3.0, 95%CI:1.1-8.6) and self-employment (aOR = 2.7, 95%CI:1.1-6.5); high education was a protective factor (aOR = 0.1, 95%CI:0.0-0.9). CONCLUSIONS: Although the services offered to patients with TB are free of charge in the Brazilian public health sector, the availability of free diagnosis and treatment services does not alleviate patients' financial burden related to accessing TB care. The study allowed us to identify the costs incurred by patients and suggest actions to mitigate their suffering. In addition, this study established a baseline for monitoring catastrophic costs and fostering a national policy to reduce the costs to patients for TB care in Brazil.

The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.

The term "dark citations," which has been previously used to refer to citations of information products outside of traditional peer-reviewed journal articles, is adapted here to refer to those that are not linked to a known indexed identifier and are effectively invisible to traditional bibliometric analysis. We investigate an unexplored source of citations in the biomedical and public health literature by surveying the extent of dark citations across the U.S. government. We systematically focus on public health, quantify their occurrences across the government, and provide a comprehensive dataset for all dark citations within PubMed.

BACKGROUND: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. FUNDING: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]). | Salmonella Typhi (Typhi) is a type of bacteria that causes typhoid fever. More than 110,000 people die from this disease each year, predominantly in areas of sub-Saharan Africa and South Asia with limited access to safe water and sanitation. Clinicians use antibiotics to treat typhoid fever, but scientists worry that the spread of antimicrobial-resistant Typhi could render the drugs ineffective, leading to increased typhoid fever mortality. The World Health Organization has prequalified two vaccines that are highly effective in preventing typhoid fever and may also help limit the emergence and spread of resistant Typhi. In low resource settings, public health officials must make difficult trade-off decisions about which new vaccines to introduce into already crowded immunization schedules. Understanding the local burden of antimicrobial-resistant Typhi and how it is spreading could help inform their actions. The Global Typhoid Genomics Consortium analyzed 13,000 Typhi genomes from 110 countries to provide a global overview of genetic diversity and antimicrobial-resistant patterns. The analysis showed great genetic diversity of the different strains between countries and regions. For example, the H58 Typhi variant, which is often drug-resistant, has spread rapidly through Asia and Eastern and Southern Africa, but is less common in other regions. However, distinct strains of other drug-resistant Typhi have emerged in other parts of the world. Resistance to the antibiotic ciprofloxacin was widespread and accounted for over 85% of cases in South Africa. Around 70% of Typhi from Pakistan were extensively drug-resistant in 2020, but these hard-to-treat variants have not yet become established elsewhere. Variants that are resistant to both ciprofloxacin and ceftriaxone have been identified, and azithromycin resistance has also appeared in several different variants across South Asia. The Consortium’s analyses provide valuable insights into the global distribution and transmission patterns of drug-resistant Typhi. Limited genetic data were available fromseveral regions, but data from travel-associated cases helped fill some regional gaps. These findings may help serve as a starting point for collective sharing and analyses of genetic data to inform local public health action. Funders need to provide ongoing supportto help fill global surveillance data gaps. | eng

Four Chlamydia psittaci isolates were recovered from clinical specimens from ill workers during a multistate outbreak at two chicken processing plants. Whole genome sequencing analyses revealed high similarity to C. psittaci genotype D. The isolates differed from each other by only two single nucleotide polymorphisms, indicating a common source.

Balancing the control of SARS-CoV-2 transmission with the resumption of travel is a global priority. Current recommendations include mitigation measures before, during, and after travel. Pre- and post-travel strategies including symptom monitoring, testing, and quarantine can be combined in multiple ways considering different trade-offs in feasibility, adherence, effectiveness, cost and adverse consequences. Here we use a mathematical model to analyze the expected effectiveness of symptom monitoring, testing, and quarantine under different estimates of the infectious period, test-positivity relative to time of infection, and test sensitivity to reduce the risk of transmission from infected travelers during and after travel. If infection occurs 0-7 days prior to travel, immediate isolation following symptom onset prior to or during travel reduces risk of transmission while traveling by 26-30%. Pre-departure testing can further reduce risk if testing is close to the time of departure. For example, testing on the day of departure can reduce risk while traveling by 37-61%. For transmission risk after travel with infection time up to 7 days prior to arrival at the destination, isolation based on symptom monitoring reduced introduction risk at the destination by 42-56%. A 14-day quarantine after arrival, without symptom monitoring or testing, can reduce risk by 97-100% on its own. However, a shorter quarantine of 7 days combined with symptom monitoring and a test on day 3-4 after arrival is also effective (95-99%) at reducing introduction risk and is less burdensome, which may improve adherence. To reduce the risk of introduction without quarantine, optimal test timing after arrival is close to the time of arrival; with effective quarantine after arrival, testing a few days later optimizes sensitivity to detect those infected immediately before or while traveling. These measures can complement recommendations such as social distancing, using masks, and hand hygiene, to further reduce risk during and after travel.Competing Interest StatementThe authors have declared no competing interest.Funding StatementNo external funding supported this research.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:Centers for Disease Control and PreventionAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesOnly publicly available data informed this research.

The term "dark citations", which has been previously used to refer to citations of information products outside of traditional peer-reviewed journal articles, is adapted here to refer to those that are not linked to a known indexed identifier and are effectively invisible to traditional bibliometric analysis. We investigate an unexplored source of citations in the biomedical and public health literature by surveying the extent of dark citations across the U.S. government. We systematically focus on public health, quantify their occurrences across the government, and provide a comprehensive dataset for all dark citations within PubMed. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.