INTRODUCTION: We sought to characterize social and structural drivers of HIV vulnerability for transgender women (TGW) in Zimbabwe, where TGW are not legally recognized, and explore differences in vulnerability by feminine presentation. METHODS: A secondary analysis was conducted with a sub-sample of participants recruited from a 2019 respondent-driven sampling survey that comprised men who have sex with men, TGW and genderqueer individuals assigned male sex at birth, from two cities in Zimbabwe. Survey questionnaires captured information related to socio-demographics, sexual and substance use behaviours, and social and structural barriers to HIV services. Secondary analyses were restricted to participants who identified as female, transfemale or transwomen (236/1538) and were unweighted. Descriptive statistics were used to calculate sample estimates and chi-square and Fisher's exact tests were used to assess differences in vulnerability by feminine presentation. RESULTS: Among 236 TGW, almost half (45.3%) presented as feminine in the 6 months preceding the survey and 8.5% had ever used hormones to affirm their gender identities. Median age among TGW was 23 years (interquartile range: 20-26). Feminine presenting TGW in our sample had higher prevalence of arrest (15.9% vs. 3.9%), rejection by family/friends (38.3% vs. 14.0%), employment termination (11.2% vs. 3.9%), employment refusal (14.0% vs. 3.9%), denial of healthcare (16.8% vs. 2.3%), physical, sexual or verbal harassment or abuse (59.8% vs. 34.1%), alcohol dependence (32.7% vs. 12.4%), recent transactional sex with a male or TGW partner (30.8% vs. 13.3%) and recent non-injection drug use (38.3% vs. 20.2%) than non-feminine presenting TGW (all p-value <0.05). CONCLUSIONS: Findings suggest that TGW, particularly feminine presenting TGW, experience social and structural inequities which may contribute to HIV vulnerability. Interventions aimed at addressing inequities, including trans competency training for providers and gender-affirming, psychosocial and legal support services for TGW, might mitigate risk.

OBJECTIVES: To measure HIV and Hepatitis B virus (HBV) prevalence and associated risk behaviors among men who have sex with men (MSM) and transgender women/genderqueer individuals (TGW/GQ) in Zimbabwe. METHODS: We conducted a biobehavioral survey using respondent-driven sampling (RDS) among adult MSM and TGW/GQ in Harare and Bulawayo, Zimbabwe in 2019. Participants completed a questionnaire and underwent testing for HIV and HBV. RESULTS: Overall, 1,510 (Harare: 694, Bulawayo 816) participants were enrolled and consented to testing; 3.8 % (58) tested positive for HBV, 22.5 % (339) tested positive for HIV, and 2.2 % (33) tested positive for both HIV and HBV. HBV prevalence was higher among participants with HIV compared to HIV-negative participants (9.7 % vs. 2.1 %, p < 0.0001). Overall, HBV prevalence was not statistically different between MSM and TGW/GQ (3.7 % vs 4.5 %, p = 0.49) nor between Harare and Bulawayo (3.3 % vs 4.3 %, p = 0.33). CONCLUSIONS: Our survey demonstrates the prevalence of HBV among MSM and TGW/GQ is lower than other estimates of HBV among MSM in Africa but remains high among our survey population living with HIV highlighting the need to expand HBV testing and treatment services, especially among people with HIV in Zimbabwe.

To better understand male and female sexual partnerships among men who have sex with men (MSM), we used data from a 2019 biobehavioral survey among MSM in Harare and Bulawayo, Zimbabwe to conduct bivariate analyses and multivariable logistic regression to determine whether sociodemographic characteristics and HIV-related factors were associated with having both male and female sexual partnerships within the last 6 months. Of included MSM (N = 1143), 31% reported both male and female partnerships in the last 6 months. Being married/cohabiting (adjusted odds ratio (aOR) = 8.58, 95% confidence interval (CI) = 4.92-14.95) or separated/divorced/widowed (aOR = 1.96, 95% CI = 1.24-3.08) vs. being single, and hazardous alcohol consumption (aOR = 1.58, 95% CI 1.19-2.09) were associated with higher odds of having both male and female recent partnerships. Being aged 35 + vs. 18-24 (aOR = 0.50, 95% CI = 0.31-0.81), condomless receptive anal intercourse at last sex with the main male partner (aOR = 0.43, 95% CI = 0.26-0.74), and positive HIV status (aOR = 0.46, 95% CI = 0.31-0.67) were associated with lower odds of recent male and female partnerships. MSM in Harare who reported harassment/abuse (aOR = 3.16, 95% CI = 1.72-5.79) had higher odds of both male and female partnerships than MSM in Bulawayo reporting harassment/abuse. The prevalence of both male and female recent partnerships (31%) was lower among MSM in this survey than in other biobehavioral surveys of MSM in sub-Saharan Africa. Findings suggest that MSM with recent male and female partnerships compared to MSM with only male recent partners have lower odds of positive HIV status and participate in behaviors that lower HIV risk; however, the direction of these relationships cannot be determined due to the cross-sectional nature of the data. The findings also suggest a possible connection between experiences of stigma of MSM behavior and not having both male and female partnerships that warrants further exploration. Accessible, stigma-free HIV testing and education programming that considers the potential overlap between the MSM and general populations via both male and female partnerships and the associated behaviors could be a key component of HIV elimination in Zimbabwe.

Micronutrient deficiency is a common global health problem, and accurately assessing micronutrient biomarkers is crucial for planning and managing effective intervention programs. However, analyzing micronutrient data and applying appropriate cutoffs to define deficiencies can be challenging, particularly when considering the confounding effects of inflammation on certain micronutrient biomarkers. To address this challenge, we developed the Statistical Apparatus of Micronutrient Biomarker Analysis (SAMBA) R package, a new tool that increases ease and accessibility of population-based micronutrient biomarker analysis. The SAMBA package can analyze various micronutrient biomarkers to assess status of iron, vitamin A, zinc, and B vitamins, adjust for inflammation, account for complex survey design when appropriate, and produce reports of summary statistics and prevalence estimates of micronutrient deficiencies using recommended age- and sex-specific cutoffs. We have provided a step-by-step procedure for how to use the SAMBA R package, including how to customize it for broader use, and made both the package and user manual publicly available on GitHub. SAMBA was validated by comparing results from analyzing 24 datasets on non-pregnant women of reproductive age from 23 countries and 30 datasets on preschool-age children from 26 countries with those obtained by an independent analyst. SAMBA generated identical means, percentiles, and prevalence of micronutrient deficiencies to those calculated by the independent analyst. In conclusion, SAMBA simplifies and standardizes the process for deriving survey-weighted and inflammation-adjusted (when appropriate) estimates of the prevalence of micronutrient deficiencies, reducing the time from data cleaning to result generation. SAMBA is a valuable tool that facilitates the accurate and rapid analysis of population-based micronutrient biomarker data, which can inform public health research, programs, and policy across contexts.

BACKGROUND: Pneumonia is the leading cause of death among children younger than 5 years. In this study, we estimated causes of pneumonia in young African and Asian children, using novel analytical methods applied to clinical and microbiological findings. METHODS: We did a multi-site, international case-control study in nine study sites in seven countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. All sites enrolled in the study for 24 months. Cases were children aged 1-59 months admitted to hospital with severe pneumonia. Controls were age-group-matched children randomly selected from communities surrounding study sites. Nasopharyngeal and oropharyngeal (NP-OP), urine, blood, induced sputum, lung aspirate, pleural fluid, and gastric aspirates were tested with cultures, multiplex PCR, or both. Primary analyses were restricted to cases without HIV infection and with abnormal chest x-rays and to controls without HIV infection. We applied a Bayesian, partial latent class analysis to estimate probabilities of aetiological agents at the individual and population level, incorporating case and control data. FINDINGS: Between Aug 15, 2011, and Jan 30, 2014, we enrolled 4232 cases and 5119 community controls. The primary analysis group was comprised of 1769 (41·8% of 4232) cases without HIV infection and with positive chest x-rays and 5102 (99·7% of 5119) community controls without HIV infection. Wheezing was present in 555 (31·7%) of 1752 cases (range by site 10·6-97·3%). 30-day case-fatality ratio was 6·4% (114 of 1769 cases). Blood cultures were positive in 56 (3·2%) of 1749 cases, and Streptococcus pneumoniae was the most common bacteria isolated (19 [33·9%] of 56). Almost all cases (98·9%) and controls (98·0%) had at least one pathogen detected by PCR in the NP-OP specimen. The detection of respiratory syncytial virus (RSV), parainfluenza virus, human metapneumovirus, influenza virus, S pneumoniae, Haemophilus influenzae type b (Hib), H influenzae non-type b, and Pneumocystis jirovecii in NP-OP specimens was associated with case status. The aetiology analysis estimated that viruses accounted for 61·4% (95% credible interval [CrI] 57·3-65·6) of causes, whereas bacteria accounted for 27·3% (23·3-31·6) and Mycobacterium tuberculosis for 5·9% (3·9-8·3). Viruses were less common (54·5%, 95% CrI 47·4-61·5 vs 68·0%, 62·7-72·7) and bacteria more common (33·7%, 27·2-40·8 vs 22·8%, 18·3-27·6) in very severe pneumonia cases than in severe cases. RSV had the greatest aetiological fraction (31·1%, 95% CrI 28·4-34·2) of all pathogens. Human rhinovirus, human metapneumovirus A or B, human parainfluenza virus, S pneumoniae, M tuberculosis, and H influenzae each accounted for 5% or more of the aetiological distribution. We observed differences in aetiological fraction by age for Bordetella pertussis, parainfluenza types 1 and 3, parechovirus-enterovirus, P jirovecii, RSV, rhinovirus, Staphylococcus aureus, and S pneumoniae, and differences by severity for RSV, S aureus, S pneumoniae, and parainfluenza type 3. The leading ten pathogens of each site accounted for 79% or more of the site's aetiological fraction. INTERPRETATION: In our study, a small set of pathogens accounted for most cases of pneumonia requiring hospital admission. Preventing and treating a subset of pathogens could substantially affect childhood pneumonia outcomes. FUNDING: Bill & Melinda Gates Foundation.

Since the Global Polio Eradication Initiative (GPEI) began in 1988, the number of wild poliovirus (WPV) cases has declined by >99.99%. Five of the six World Health Organization (WHO) regions have been certified free of indigenous WPV, and WPV serotypes 2 and 3 have been declared eradicated globally (1). WPV type 1 (WPV1) remains endemic only in Afghanistan and Pakistan (2,3). Before the outbreak described in this report, WPV1 had not been detected in southeastern Africa since the 1990s, and on August 25, 2020, the WHO African Region was certified free of indigenous WPV (4). On February 16, 2022, WPV1 infection was confirmed in one child living in Malawi, with onset of paralysis on November 19, 2021. Genomic sequence analysis of the isolated poliovirus indicated that it originated in Pakistan (5). Cases were subsequently identified in Mozambique. This report summarizes progress in the outbreak response since the initial report (5). During November 2021-December 2022, nine children and adolescents with paralytic polio caused by WPV1 were identified in southeastern Africa: one in Malawi and eight in Mozambique. Malawi, Mozambique, and three neighboring countries at high risk for WPV1 importation (Tanzania, Zambia, and Zimbabwe) responded by increasing surveillance and organizing up to six rounds of national and subnational polio supplementary immunization activities (SIAs).* Although no cases of paralytic WPV1 infection have been reported in Malawi since November 2021 or in Mozambique since August 2022, undetected transmission might be ongoing because of poliovirus surveillance gaps and testing delays. Efforts to further enhance poliovirus surveillance sensitivity, improve SIA quality, and strengthen routine immunization are needed to ensure that WPV1 transmission has been interrupted within 12 months of the first case, thereby preserving the WHO African Region's WPV-free status.

In Africa, rapid testing for recent HIV infection (RTRI) is being scaled up; however, use of the recent infection testing algorithm (RITA), which uses viral load (VL) to confirm RTRI-recent infections, is not a widespread practice. We present results of recently acquired HIV infections among men who have sex with men (MSM), transgender women, and genderqueer individuals (TGW/GQ) with newly diagnosed HIV infection in Zimbabwe per the national approach (RTRI) and applying a RITA. In 2019, 1538 MSM and TGW/GQ in Harare and Bulawayo, Zimbabwe were recruited to participate in a biobehavioral survey using respondent-driven sampling. Consenting participants received HIV testing and all HIV-positive specimens were tested with the RTRI Asanté HIV-1 Rapid Recency Assay, and for VL and CD4 count. RTRI-recent participants with unsuppressed VL (≥1,000 copies/mL) were classified as RITA-recent. Descriptive statistics were used to summarize results among RTRI-recent and RITA-recent participants. Among those tested for HIV (1511/1538), 22.5% (340/1511) tested positive and of those, 55.0% (187/340) self-reported an HIV-negative or unknown status. Among these, 8.6% (16/187) were classified as RTRI-recent and 91.4% (171/187) were classified as RTRI-long term. After accounting for VL, RITA-recency was 1.1% (2/187). Two of sixteen (12.5%) RTRI-recent infections were RITA-recent. VL among RITA-recent cases were 9,052 copies/mL and 40,694 copies/mL and both had CD4 counts <500. Data highlight misclassification of recent infections among MSM and TGW/GQ with newly diagnosed HIV infection using RTRI. With the incorporation of VL, >85% of RTRI-recent cases were reclassified as RITA-long term. True characterization of recent infections may not be possible without VL testing, which remains challenging in resource-limited settings.

Sierra Leone is highly endemic for hepatitis B virus (HBV) infection and thus recommends three doses of hepatitis B vaccine (HepB3) from 6weeks of age but does not recommend a birth dose (HepB-BD) to prevent mother-to-child transmission (MTCT). We evaluated impact of the existing HepB3 schedule and risk for MTCT of HBV. We conducted a community-based serosurvey among 4-30-month-olds, their mothers, and 5-9-year-olds in three districts in Sierra Leone. Participants had an HBV surface antigen (HBsAg) rapid test; all HBsAg-positive and one HBsAg-negative mother per cluster were tested for HBV markers. We collected children's HepB3 vaccination history. Among 1889 children aged 4-30months, HepB3 coverage was 85% and 20 (13% [95% CI 08-20]) were HBsAg-positive, of whom 70% had received HepB3. Among 2025 children aged 5-9years, HepB3 coverage was 77% and 32 (16% [11-23]) were HBsAg-positive, of whom 56% had received HepB3. Of 1776 mothers, 169 (98% [81-117]) were HBsAg-positive. HBsAg prevalence was 59% among children of HBsAg-positive mothers compared to 07% among children of HBsAg-negative mothers (adjusted OR=106 [28-408]). HBsAg positivity in children was associated with maternal HBsAg (p=0026), HBV e antigen (p<0001), and HBV DNA levels200 000IU/mL (p<0001). HBsAg prevalence was lower among children than mothers, for whom HepB was not available, suggesting routine infant HepB vaccination has lowered HBV burden. Since HBsAg positivity in children was strongly associated with maternal HBV infection and most of the HBsAg-positive children in the survey received HepB3, HepB-BD may prevent MTCT and chronic HBV infection.

Though stigma is a recognized contributor to the disproportionate HIV burden among sexual and gender minorities (SGM) in sub-Saharan Africa, data describing this association among Zimbabwean SGM are limited. We examined relationships between SGM stigma and HIV and the potential for social cohesion to moderate the association among Zimbabwean men who have sex with men, transgender women, and genderqueer individuals. Consenting participants (n = 1511) recruited through respondent-driven sampling for a biobehavioral survey in Harare and Bulawayo completed structured interviews and received HIV testing. Reported SGM stigma was common (68.9% in Harare and 65.3% in Bulawayo) and associated with HIV infection in Harare (adjusted prevalence ratio [aPR] = 1.82, 95% confidence interval [CI] = 1.27-2.62) and Bulawayo (aPR = 1.51, 95% CI = 1.15-2.00) in relative risk regression. Social cohesion did not moderate these relationships. Findings demonstrate stigma's association with HIV vulnerability among Zimbabwean SGM, highlighting the need for stigma-mitigation to reduce HIV transmission in this population.

BACKGROUND: Globally, men who have sex with men (MSM), transgender women, and genderqueer individuals are at greater risk for HIV than the general population although little data are available from these groups in Zimbabwe, a country with a national adult HIV prevalence of 12·9%. We aimed to examine progress towards the UNAIDS 90-90-90 treatment targets and factors associated with meeting the targets among a sample of MSM, transgender women, and genderqueer individuals in Zimbabwe. METHODS: In this cross-sectional survey in 2019, we used respondent-driven sampling to identify MSM, transgender women, and genderqueer individuals aged at least 18 years to participate in a biobehavioural survey in Harare and Bulawayo, Zimbabwe. Participants were eligible to participate if they were assigned male at birth; had engaged in anal or oral sex with a man in the past 12 months; resided in Harare or Bulawayo for at least 1 month; spoke English, Shona, or Ndebele; provided written informed consent; and were in possession of a valid recruitment coupon if applicable. Enrolled participants completed a questionnaire and underwent HIV testing, and off-site viral load testing was done on all HIV-positive samples. Unweighted bivariate analyses and multivariable logistic regression models were used to evaluate the association of sociodemographic, behavioural, and other factors with HIV-positive status awareness among MSM, transgender women, and genderqueer individuals, and with viral load suppression among MSM. Analyses were done firstly using self-reported information and then by classifying those with a viral load of less than 200 copies per mL as being aware of their status and on treatment (viral load recategorisation). FINDINGS: Among MSM, 248 (21%; 95% CI 19-24) of 1176 tested positive for HIV. Of those who tested positive, based on self-report, 119 (48%; 95% CI 42-54) reported knowing their HIV status, of whom 112 (94%; 88-98) reported using antiretroviral therapy (ART), of whom 89 (79%; 71-87) had viral load suppression. Based on viral load recategorisation, 180 (73%; 67-78) of 248 MSM testing HIV positive reported knowing their HIV status, of whom 174 (97%; 93-99) reported using ART, of whom 151 (87%; 81-91) had viral load suppression. 92 (28%; 23-33) of 335 transgender women and genderqueer individuals tested positive for HIV. Based on self-reports from these individuals 34 (37%; 27-48) of 92 participants reported knowing their HIV status, of whom 31 (91%; 76-98) reported using ART, of whom 27 (87%; 70-96%) had viral load suppression. Based on viral load recategorisation of data from transgender women and genderqueer participants, 53 (58%; 47-58) of 92 reported awareness of their HIV status, of whom 50 (94%; 84-99) reported using ART, of whom 46 (92%; 81-98) had viral load suppression. HIV-positive MSM aged 18-24 years had lower odds of being aware of their status than those aged at least 35 years (adjusted odds ratio [aOR] 0·34; 95% CI 0·13-0·92), as did HIV-positive MSM aged 25-34 years (aOR 0·26; 0·12-0·56). HIV-positive MSM aged 18-24 years also had a lower odds of having viral load suppression than those aged 35 years and older (aOR 0·35; 0·16-0·78), as did those aged 25-34 years (aOR 0·36; 0·19-0·67). No factors were significantly associated with awareness among transgender women and genderqueer individuals in multivariable models. INTERPRETATION: Our survey showed that HIV prevalence was high and the largest difference between our results and the 90-90-90 treatment targets was in HIV status awareness, indicating the need for improvements in engaging MSM (especially young MSM), transgender women, and genderqueer individuals in HIV testing services. FUNDING: US President's Emergency Plan for AIDS Relief through the US Centers for Disease Control and Prevention.

INTRODUCTION: Zimbabwe is scaling up pre-exposure prophylaxis (PrEP) for key populations, including men who have sex with men (MSM) and transgender women (TGW). To assess implementation and inform HIV programming, we evaluated gaps in PrEP awareness, uptake and use, and correlates of awareness and uptake among a sample of MSM, TGW and genderqueer individuals (GQ) in Harare and Bulawayo, Zimbabwe. METHODS: Respondent-driven sampling was used to recruit 1194 MSM and 344 TGW/GQ aged ≥18 to participate in a cross-sectional survey assessing HIV-related outcomes in 2019. Consenting participants completed a questionnaire on socio-demographic information, sexual risk practices and engagement in HIV services and underwent HIV testing. Descriptive statistics were used to assess the PrEP cascade. Multiple logistic regression models were used to identify factors associated with PrEP awareness and uptake among HIV-negative participants. Data were unweighted as the sample did not reach convergence on key estimates. RESULTS: Among the 1167 HIV-negative participants, most (79.2%) were MSM compared to TGW/GQ (20.8%). Median age was 24 years. Overall, 45.8% were aware of PrEP and of those, 31.3% had ever taken PrEP. Most (71.1%) reporting never taking PrEP were willing to start PrEP; the main reasons for never starting PrEP included not knowing where to access it (24.8%) and fearing side effects (20.4%). Among those who had ever taken PrEP, 74.9% had taken PrEP in the last 6 months; of these, 42.4% had taken PrEP the day of or day preceding the survey. Side effects represented the most common (59.5%) reason for discontinuing PrEP. MSM (adjusted odds ratio [aOR]: 2.5, 95% confidence interval [CI]: 1.8-3.6) and TGW/GQ in Harare (aOR: 3.1, 95% CI: 2.1-4.7), and TGW/GQ in Bulawayo (aOR: 2.4, 95% CI: 1.1-5.3) had higher awareness of PrEP than MSM in Bulawayo. Overall, TGW/GQ were more likely to have ever taken PrEP compared to MSM (aOR: 1.6, 95% CI: 1.01-2.4). CONCLUSIONS: Findings emphasize the need for tailored interventions to promote PrEP among key populations. As HIV programs in Zimbabwe continue to expand PrEP services, these data, including barriers to starting and continuing PrEP, can inform strategies to address gaps along the PrEP cascade.

BACKGROUND: Syphilis increases human immunodeficiency virus (HIV) acquisition risk and impacts the immunologic and virologic response among people living with HIV (PLHIV). We assessed the prevalence of active or current syphilis and HIV/syphilis and their correlates among men who have sex with men (MSM), transwomen, and genderqueer (TGW/GQ) individuals in Zimbabwe. METHODS: Among a respondent-driven sample of MSM and TGW/GQ who were tested for HIV and syphilis in Harare and Bulawayo, Zimbabwe in 2019 (n = 1511), multiple logistic regression was used to assess correlates of active syphilis. Unadjusted logistic regression was used among PLHIV (n = 340) due to small sample size. All analyses were unweighted as data did not reach convergence for HIV. RESULTS: Prevalence of active syphilis overall and among PLHIV was 5.5% and 10.1%, respectively, in Harare, and 5.6% and 11.0%, respectively, in Bulawayo. Participants were more likely to have active syphilis if they were PLHIV (adjusted odds ratio [aOR], 2.2; 95% confidence interval [CI], 1.4-3.6), aged 25-34 years (aOR, 2.2 years; 95% CI, 1.3-3.8 years; reference, 18-24 years), or self-report sexually transmitted infection symptoms (aOR, 1.8; 95% CI, 1.1-3.0). Compared with Bulawayo TGW/GQ, MSM in Harare (aOR, 0.2; 95% CI, 0.1-0.5) and Bulawayo (aOR, 0.2; 95% CI, 0.1-0.4), and TGW/GQ in Harare (aOR, 0.2; 95% CI, 0.1-0.6) were less likely to have active syphilis. Among PLHIV, coinfection was 13.0% among TGW/GQ and 9.7% among MSM. Odds of coinfection were higher for those aged 25 to 34 years (OR, 3.7 years; 95% CI, 1.2-11.1 years) and lower among Harare MSM (OR, 0.2; 95% CI, 0.1-0.7), Bulawayo MSM (OR, 0.1; 95% CI, 0.0-0.4), and Harare TGW/GQ (OR, 0.1; 95% CI, 0.0-0.4) compared with Bulawayo TGW/GQ. CONCLUSIONS: Findings highlight a high burden of syphilis among MSM and TGW/GQ and underscore the importance of HIV/syphilis detection and improved service delivery for these groups.

BACKGROUND: Point-of-care (POC) nucleic acid tests (NAT) have potential to diagnose acute HIV infection and monitor persons taking pre-exposure prophylaxis (PrEP) or antiretroviral treatment (ART). POC NATs have not yet been evaluated in the US. METHODS: From June 2018-March 2019, we conducted a cross-sectional evaluation of the SAMBA II POC NAT. PWH and persons testing for HIV were tested with the SAMBA II qualitative (Qual) whole blood (WB) test. From April-September 2019, the Qual test was used on persons who were ART-naïve, and SAMBA II semi-quantitative (Semi-Q) WB was used with ART-experienced PWH. Both were performed on unprocessed venipuncture (VP) and, when indicated by protocol, fingerstick (FS) WB and plasma. SAMBA results were compared to Abbott RealTime HIV-1 PCR results on plasma. We calculated sensitivity, specificity, and concordance between tests. RESULTS: SAMBA was used in 330 visits among 280 participants: 202 (61.2%) visits from PWH, and 128 (38.8%) from HIV-negative persons. Qual test sensitivity with ART-naïve participants was 91.4% (32/35, 95% CI: 77.6-97.0%) using VP WB and 100% (27/27, 95% CI: 87.5-100%) using FS WB. Specificity was 100% using both specimen types. Concordance between the gold standard and Semi-Q at 1000 copies/mL among PWH on ART was 97.7% (86/88, 95% CI: 92.1-99.4%) and 100% (30/30, 95% CI: 88.7-100%) using VP and FS WB, respectively. Conclusion: The SAMBA II POC NATs showed high sensitivity, specificity, and concordance with the gold-standard assay, indicating its potential use in diagnostics and monitoring. Future work will evaluate POC NAT implementation in the US.

BACKGROUND: World Health Organization African region is wild poliovirus-free; however, outbreaks of vaccine-derived poliovirus type 2 (VDPV2) continue to expand across the continent including in Chad. We conducted a serological survey of polio antibodies in polio high-risk areas of Chad to assess population immunity against poliovirus and estimate the risk of future outbreaks. METHODS: This was a community-based, cross-sectional survey carried out in September 2019. Children between 12 and 59 months were randomly selected using GIS enumeration of structures. Informed consent, demographic and anthropometric data, vaccination history, and blood spots were collected. Seropositivity against all 3 poliovirus serotypes was assessed using a microneutralization assay at Centers for Disease Control and Prevention, Atlanta, GA, USA. RESULTS: Analyzable data were obtained from 236 out of 285 (82.8%) enrolled children. Seroprevalence of polio antibodies for serotypes 1, 2, and 3 was 214/236 (90.7%); 145/236 (61.4%); and 196/236 (86.2%), respectively. For serotype 2, the seroprevalence significantly increased with age (P = .004); chronic malnutrition was a significant risk factor for being type 2-seronegative. INTERPRETATION: Poliovirus type 2 seroprevalence in young children was considered insufficient to protect against the spread of paralytic diseases caused by VDPV2. Indeed, VDPV2 outbreaks were reported from Chad in 2019 and 2020. High-quality immunization response to these outbreaks is needed to prevent further spread.

The geographic information system (GIS) mapping was used to improve the efficiency of vaccination teams. This paper documents the process in the deployment of geographical information system in response to polio eradication in Chad. It started with a careful review of government official documents as well as review of literature and online resources on Chad, which confirmed that official boundaries existed at two levels, namely Regions and Districts. All settlement locations in the target Districts were identified by manual feature extraction of high-resolution, recent satellite imagery, and map layers created for the following categories: hamlets, hamlet areas, small settlements, and built-up areas (BUAs). This clearly improved microplanning and provided valuable feedback in identifying missed settlements, leading to increased coverage and fewer missed children.

In 2015, the Sierra Leone Ministry of Health and Sanitation (MoHS) and the Centers for Disease Control and Prevention (CDC) agreed to consolidate data recorded by MoHS and international partners during the Ebola epidemic and create the Sierra Leone Ebola Database (SLED). The primary objectives were helping families to identify the location of graves of their loved ones who died from any cause at the time of the Ebola epidemic and creating a data source for epidemiological research. The Family Reunification Program fulfils the first SLED objective. The purpose of this paper is to describe the Family Reunification Program (Program) development, functioning and results. The MoHS, CDC, SLED Team, and Concern Worldwide developed, tested, and implemented methodology and tools to conduct the Program. Family liaisons were trained in protection of the personally identifiable information. The SLED Family Reunification Program allows families in Sierra Leone, who did not know the final resting place of their loved ones, to be reunited with their graves and to bring them relief and closure. Continuing family requests in search of the burial place of loved ones five years after the end of the epidemic shows that the emotional burden of losing a family member and not knowing the place of burial does not diminish with time. As of February 2021, the Program continues and is described to allow its replication for other emergency events including COVID-19 and new Ebola outbreaks.

BACKGROUND: During the 2014-2016 Ebola outbreak in West Africa, the Sierra Leone Ministry of Health and Sanitation (MoHS), the US Centers for Disease Control and Prevention, and responding partners under the coordination of the National Ebola Response Center (NERC) and the MoHS's Emergency Operation Center (EOC) systematically recorded information from the 117 Call Center system and district alert phone lines, case investigations, laboratory sample testing, clinical management, and safe and dignified burial records. Since 2017, CDC assisted MoHS in building and managing the Sierra Leone Ebola Database (SLED) to consolidate these major data sources. The primary objectives of the project were helping families to identify the location of graves of their loved ones who died at the time of the Ebola epidemic through the SLED Family Reunification Program and creating a data source for epidemiological research. The objective of this paper is to describe the process of consolidating epidemic records into a useful and accessible data collection and to summarize data characteristics, strength, and limitations of this unique information source for public health research. METHODS: Because of the unprecedented conditions during the epidemic, most of the records collected from responding organizations required extensive processing before they could be used as a data source for research or the humanitarian purpose of locating burial sites. This process required understanding how the data were collected and used during the outbreak. To manage the complexity of processing the data obtained from various sources, the Sierra Leone Ebola Database (SLED) Team used an organizational strategy that allowed tracking of the data provenance and lifecycle. RESULTS: The SLED project brought raw data into one consolidated data collection. It provides researchers with secure and ethical access to the SLED data and serves as a basis for the research capacity building in Sierra Leone. The SLED Family Reunification Program allowed Sierra Leonean families to identify location of the graves of loved ones who died during the Ebola epidemic. DISCUSSION: The SLED project consolidated and utilized epidemic data recorded during the Sierra Leone Ebola Virus Disease outbreak that were collected and contributed to SLED by national and international organizations. This project has provided a foundation for developing a method of ethical and secure SLED data access while preserving the host nation's data ownership. SLED serves as a data source for the SLED Family Reunification Program and for epidemiological research. It presents an opportunity for building research capacity in Sierra Leone and provides a foundation for developing a relational database. Large outbreak data systems such as SLED provide a unique opportunity for researchers to improve responses to epidemics and indicate the need to include data management preparedness in the plans for emergency response.

BACKGROUND: Severity of viral respiratory illnesses can be increased with bacterial coinfection and can vary by sex, but influence of coinfection and sex on human endemic coronavirus (CoV) species, which generally cause mild to moderate respiratory illness, is unknown. We evaluated CoV and pneumococcal co-detection by sex in childhood pneumonia. METHODS: In the 2011-2014 Pneumonia Etiology Research for Child Health study, nasopharyngeal and oropharyngeal (NP/OP) swabs and other samples were collected from 3981 children <5 years hospitalized with severe or very severe pneumonia in 7 countries. Severity by NP/OP detection status of CoV (NL63, 229E, OC43 or HKU1) and high-density (≥6.9 log10 copies/mL) pneumococcus (HDSpn) by real-time polymerase chain reaction was assessed by sex using logistic regression adjusted for age and site. RESULTS: There were 43 (1.1%) CoV+/HDSpn+, 247 CoV+/HDSpn-, 449 CoV-/HDSpn+ and 3149 CoV-/HDSpn- cases with no significant difference in co-detection frequency by sex (range 51.2%-64.0% male, P = 0.06). More CoV+/HDSpn+ pneumonia was very severe compared with other groups for both males (13/22, 59.1% versus range 29.1%-34.7%, P = 0.04) and females (10/21, 47.6% versus 32.5%-43.5%, P = 0.009), but only male CoV+/HDSpn+ required supplemental oxygen more frequently (45.0% versus 20.6%-28.6%, P < 0.001) and had higher mortality (35.0% versus 5.3%-7.1%, P = 0.004) than other groups. For females with CoV+/HDSpn+, supplemental oxygen was 25.0% versus 24.8%-33.3% (P = 0.58) and mortality was 10.0% versus 9.2%-12.9% (P = 0.69). CONCLUSIONS: Co-detection of endemic CoV and HDSpn was rare in children hospitalized with pneumonia, but associated with higher severity and mortality in males. Findings may warrant investigation of differences in severity by sex with co-detection of HDSpn and SARS-CoV-2.

BACKGROUND: The Global Enteric Multicenter Study (GEMS) determined the etiologic agents of moderate-to-severe diarrhea (MSD) in children under 5 years old in Africa and Asia. Here, we describe the prevalence and antimicrobial susceptibility of non-typhoidal Salmonella (NTS) serovars in GEMS and examine the phylogenetics of Salmonella Typhimurium ST313 isolates. METHODS: Salmonella isolated from children with MSD or diarrhea-free controls were identified by classical clinical microbiology and serotyped using antisera and/or whole genome sequence data. We evaluated antimicrobial susceptibility using the Kirby-Bauer disk diffusion method. Salmonella Typhimurium sequence types were determined using multi-locus sequence typing and whole genome sequencing was performed to assess the phylogeny of ST313. RESULTS: Out of 370 Salmonella-positive individuals, 190 (51.4%) were MSD cases and 180 (48.6%) were diarrhea-free controls. The most frequent Salmonella serovars identified were Salmonella Typhimurium, serogroup O:8 (C2-C3), serogroup O:6,7 (C1), Salmonella Paratyphi B Java and serogroup O:4 (B). The prevalence of NTS was low but similar across sites, regardless of age, and was similar amongst both cases and controls except in Kenya, where Salmonella Typhimurium was more commonly associated with cases than controls. Phylogenetic analysis showed that these Salmonella Typhimurium isolates, all ST313, were highly genetically related to isolates from controls. Generally, Salmonella isolates from Asia were resistant to ciprofloxacin and ceftriaxone but African isolates were susceptible to these antibiotics. CONCLUSION: Our data confirms that NTS is prevalent, albeit at low levels, in Africa and South Asia. Our findings provide further evidence that multi-drug resistant Salmonella Typhimurium ST313 can be carried asymptomatically by humans in sub-Saharan Africa.

In 2016, Mali reported a bacterial meningitis outbreak consisting of 39 suspected cases between epidemiologic weeks 9 and 17 with 15% case fatality ratio in the health district of Ouelessebougou, 80 kilometers from the capital Bamako. Cerebrospinal fluid specimens from 29 cases were tested by culture and real-time polymerase chain reaction; 22 (76%) were positive for bacterial meningitis pathogens, 16 (73%) of which were Neisseria meningitidis (Nm). Of the Nm-positive specimens, 14 (88%) were N meningitidis serogroup C (NmC), 1 was NmW, and 1 was nongroupable. Eight NmC isolates recovered by culture from the outbreak were characterized using whole genome sequencing. Genomics analysis revealed that all 8 isolates belonged to a new sequence type (ST) 12446 of clonal complex 10217 that formed a distinct clade genetically similar to ST-10217, a NmC strain that recently caused large epidemics of meningitis in Niger and Nigeria. The emergence of a new ST of NmC associated with an outbreak in the African meningitis belt further highlights the need for continued molecular surveillance in the region.

Background: Verbal autopsies (VAs) can provide important epidemiological information about the causes of child deaths. Though studies have been conducted to assess the validity of various types of VAs, the programmatic experience of engaging local communities in collecting and using VA has received little attention in the published literature. Concern Worldwide, an international non-governmental organization (NGO), in collaboration with the Ministry of Health and Sanitation (MOHS), has implemented a VA protocol in five urban slums of Freetown, Sierra Leone. This paper provides VA results and describes lessons learned from the VA process. Methods: Under-five child deaths were registered by Community Health Workers (CHWs) in five urban slums between 2014 and 2017, and a specially trained local clinician used a VA protocol to interview caretakers. Symptoms were analysed using InterVA-4 computerized algorithm, a probabilistic expert-driven model to determine the most likely cause of death. Themes in care-seeking were extracted from multiple-choice and open-ended questions. VAs were implemented in collaboration with the community and the results were shared with community stakeholders in participatory review meetings. Results: Main challenges included limitations in death notification and capacity to conduct VA for all notified deaths. A total of 215 VA were available for analysis. Among 79 neonatal deaths aged 0-27 days, the most common cause of death was neonatal pneumonia (55%); among 136 children deaths aged 1-4 years, the most common causes were malaria (56%) and pneumonia (41%). Key themes in care-seeking identified included use of traditional medicine (14% of deaths), absence of care-seeking (23% of deaths), and difficultly reaching the health facility (8% of deaths that occurred at home) during fatal illness. Conclusions: Conducting VAs as a collaborative process with communities is challenging but can provide valuable data that can be used for local-level decision-making. The findings have practical implications for engaging the community and CHWs in reducing the number of these preventable deaths through expanded efforts at prevention, early and appropriate treatment, and reduction of barriers to care-seeking. A functional end-to-end VA system can enhance meaningful routine vital events monitoring by community, national, and international stakeholders.

BACKGROUND: Enterotoxigenic Escherichia coli (ETEC) encoding heat-stable enterotoxin (ST) alone or with heat-labile enterotoxin (LT) cause moderate-to-severe diarrhea (MSD) in developing country children. The Global Enteric Multicenter Study (GEMS) identified ETEC encoding ST among the top four enteropathogens. Since the GEMS objective was to provide evidence to guide development and implementation of enteric vaccines and other interventions to diminish diarrheal disease morbidity and mortality, we examined colonization factor (CF) prevalence among ETEC isolates from children age <5 years with MSD and from matched controls in four African and three Asian sites. We also assessed strength of association of specific CFs with MSD. METHODOLOGY/PRINCIPAL FINDINGS: MSD cases enrolled at healthcare facilities over three years and matched controls were tested in a standardized manner for many enteropathogens. To identify ETEC, three E. coli colonies per child were tested by polymerase chain reaction (PCR) to detect genes encoding LT, ST; confirmed ETEC were examined by PCR for major CFs (Colonization Factor Antigen I [CFA/I] or Coli Surface [CS] antigens CS1-CS6) and minor CFs (CS7, CS12, CS13, CS14, CS17, CS18, CS19, CS20, CS21, CS30). ETEC from 806 cases had a single toxin/CF profile in three tested strains per child. Major CFs, components of multiple ETEC vaccine candidates, were detected in 66.0% of LT/ST and ST-only cases and were associated with MSD versus matched controls by conditional logistic regression (p</=0.006); major CFs detected in only 25.0% of LT-only cases weren't associated with MSD. ETEC encoding exclusively CS14, identified among 19.9% of 291 ST-only and 1.5% of 259 LT/ST strains, were associated with MSD (p = 0.0011). No other minor CF exhibited prevalence >/=5% and significant association with MSD. CONCLUSIONS/SIGNIFICANCE: Major CF-based efficacious ETEC vaccines could potentially prevent up to 66% of pediatric MSD cases due to ST-encoding ETEC in developing countries; adding CS14 extends coverage to ~77%.

BACKGROUND: Access to point-of-care HIV testing shortens turn-around times, time to diagnosis and reduces loss to follow-up hence minimizing barriers to early linkage to care and treatment among HIV infected infants. Currently samples for early infant HIV diagnosis are sent to centralized testing facilities which are few and located only at specific regions in Kenya. However, there are Point of Care (POC) early infant diagnosis [EID] technologies elsewhere such as SAMBA and ALERE-Q that are yet to be evaluated in Kenya despite the urgent need for data to inform policy formulation regarding EID. The Cepheid GeneXpert HIV-1 Qual (GeneXpert) technology for POC EID offers a great opportunity to minimize HIV associated morbidity, mortality and loss to follow-up through decentralization of early infant HIV testing to the clinics. This technology also allows for same-day results thus facilitating prompt linkage to care. METHODS: We evaluated the GeneXpert HIV Qual EID POC in Homabay County against the standard of care platform, Roche CAP/CTM HIV-1 qualitative PCR, using dried blood spots (DBS). Between February-July 2016, DBS samples were collected from HIV exposed children <18 months of age enrolled in a cross-sectional study. Samples were collected by qualified nurse counselors, and were tested by trained technicians using field based GeneXpert and conventional laboratory based Roche CAP/CTM HIV-1 qualitative PCR. Sensitivity and specificity were determined. RESULTS: Overall, 3,814 mother/infant pairs were included in the study, out of which 921 infants were HIV exposed as per the mothers' HIV status and based on the infant's HIV rapid test. A total of 969 PCR tests were performed, out of which 30 (3.3%) infants were concordantly positive using both platforms. GeneXpert HIV-1 Qual yielded a sensitivity of 94.1% and specificity of 99.8% with an overall error rate of 0.7%. CONCLUSION: Our findings show that GeneXpert HIV-1 Qual performs well compared to CAP/CTM using DBS samples, suggesting that this technology may be adopted in decentralized laboratories as a near POC device. It may contribute to prompt diagnosis of HIV exposed infants hence enabling early linkage to care, thus advancing further gains in EID.

INTRODUCTION: Early diagnosis of HIV-1 infection and the prompt initiation of antiretroviral therapy are critical to achieving a reduction in the morbidity and mortality of infected infants. The SAMBA HIV-1 Qual Whole Blood Test was developed specifically for early infant diagnosis and prevention of mother-to-child transmission programs implemented at the point-of-care in resource-limited settings. METHODS: We have evaluated the performance of this test run on the SAMBA I semi-automated platform with fresh whole blood specimens collected from 202 adults and 745 infants in Kenya, Uganda, and Zimbabwe. Results were compared with those obtained with the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 assay as performed with fresh whole blood or dried blood spots of the same subjects, and discrepancies were resolved with alternative assays. RESULTS: The performance of the SAMBA and CAP/CTM assays evaluated at five laboratories in the three countries was similar for both adult and infant samples. The clinical sensitivity, specificity, and positive and negative predictive values for the SAMBA test were 100%, 99.2%, 98.7%, and 100%, respectively, with adult samples, and 98.5%, 99.8%, 99.7%, and 98.8%, respectively, with infant samples. DISCUSSION: Our data suggest that the SAMBA HIV-1 Qual Whole Blood Test would be effective for early diagnosis of HIV-1 infection in infants at point-of care settings in sub-Saharan Africa.

Background.: We investigated the performance of polymerase chain reaction (PCR) on blood in the diagnosis of pneumococcal pneumonia among children from 7 low- and middle-income countries. Methods.: We tested blood by PCR for the pneumococcal autolysin gene in children aged 1-59 months in the Pneumonia Etiology Research for Child Health (PERCH) study. Children had World Health Organization-defined severe or very severe pneumonia or were age-frequency-matched community controls. Additionally, we tested blood from general pediatric admissions in Kilifi, Kenya, a PERCH site. The proportion PCR-positive was compared among cases with microbiologically confirmed pneumococcal pneumonia (MCPP), cases without a confirmed bacterial infection (nonconfirmed), cases confirmed for nonpneumococcal bacteria, and controls. Results.: In PERCH, 7.3% (n = 291/3995) of cases and 5.5% (n = 273/4987) of controls were blood pneumococcal PCR-positive (P < .001), compared with 64.3% (n = 36/56) of MCPP cases and 6.3% (n = 243/3832) of nonconfirmed cases (P < .001). Blood pneumococcal PCR positivity was higher in children from the 5 African countries (5.5%-11.5% among cases and 5.3%-10.2% among controls) than from the 2 Asian countries (1.3% and 1.0% among cases and 0.8% and 0.8% among controls). Among Kilifi general pediatric admissions, 3.9% (n = 274/6968) were PCR-positive, including 61.7% (n = 37/60) of those with positive blood cultures for pneumococcus. Discussion.: The utility of pneumococcal PCR on blood for diagnosing childhood pneumococcal pneumonia in the 7 low- and middle-income countries studied is limited by poor specificity and by poor sensitivity among MCPP cases.

Background.: Detection of pneumococcus by lytA polymerase chain reaction (PCR) in blood had poor diagnostic accuracy for diagnosing pneumococcal pneumonia in children in 9 African and Asian sites. We assessed the value of blood lytA quantification in diagnosing pneumococcal pneumonia. Methods.: The Pneumonia Etiology Research for Child Health (PERCH) case-control study tested whole blood by PCR for pneumococcus in children aged 1-59 months hospitalized with signs of pneumonia and in age-frequency matched community controls. The distribution of load among PCR-positive participants was compared between microbiologically confirmed pneumococcal pneumonia (MCPP) cases, cases confirmed for nonpneumococcal pathogens, nonconfirmed cases, and controls. Receiver operating characteristic analyses determined the "optimal threshold" that distinguished MCPP cases from controls. Results.: Load was available for 290 of 291 cases with pneumococcal PCR detected in blood and 273 of 273 controls. Load was higher in MCPP cases than controls (median, 4.0 x 103 vs 0.19 x 103 copies/mL), but overlapped substantially (range, 0.16-989.9 x 103 copies/mL and 0.01-551.9 x 103 copies/mL, respectively). The proportion with high load (≥2.2 log10 copies/mL) was 62.5% among MCPP cases, 4.3% among nonconfirmed cases, 9.3% among cases confirmed for a nonpneumococcal pathogen, and 3.1% among controls. Pneumococcal load in blood was not associated with respiratory tract illness in controls (P = .32). High blood pneumococcal load was associated with alveolar consolidation on chest radiograph in nonconfirmed cases, and with high (>6.9 log10 copies/mL) nasopharyngeal/oropharyngeal load and C-reactive protein ≥40 mg/L (both P < .01) in nonconfirmed cases but not controls. Conclusions.: Quantitative pneumococcal PCR in blood has limited diagnostic utility for identifying pneumococcal pneumonia in individual children, but may be informative in epidemiological studies.

Background.: Previous studies suggested an association between upper airway pneumococcal colonization density and pneumococcal pneumonia, but data in children are limited. Using data from the Pneumonia Etiology Research for Child Health (PERCH) study, we assessed this potential association. Methods.: PERCH is a case-control study in 7 countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. Cases were children aged 1-59 months hospitalized with World Health Organization-defined severe or very severe pneumonia. Controls were randomly selected from the community. Microbiologically confirmed pneumococcal pneumonia (MCPP) was confirmed by detection of pneumococcus in a relevant normally sterile body fluid. Colonization density was calculated with quantitative polymerase chain reaction analysis of nasopharyngeal/oropharyngeal specimens. Results.: Median colonization density among 56 cases with MCPP (MCPP cases; 17.28 x 106 copies/mL) exceeded that of cases without MCPP (non-MCPP cases; 0.75 x 106) and controls (0.60 x 106) (each P < .001). The optimal density for discriminating MCPP cases from controls using the Youden index was >6.9 log10 copies/mL; overall, the sensitivity was 64% and the specificity 92%, with variable performance by site. The threshold was lower (≥4.4 log10 copies/mL) when MCPP cases were distinguished from controls who received antibiotics before specimen collection. Among the 4035 non-MCPP cases, 500 (12%) had pneumococcal colonization density >6.9 log10 copies/mL; above this cutoff was associated with alveolar consolidation at chest radiography, very severe pneumonia, oxygen saturation <92%, C-reactive protein ≥40 mg/L, and lack of antibiotic pretreatment (all P< .001). Conclusions.: Pneumococcal colonization density >6.9 log10 copies/mL was strongly associated with MCPP and could be used to improve estimates of pneumococcal pneumonia prevalence in childhood pneumonia studies. Our findings do not support its use for individual diagnosis in a clinical setting.

Although access to antiretroviral therapy for HIV infection is increasing in resource-poor countries, viral load testing for monitoring of treatment efficacy remains limited, expensive, and confined to centralized laboratories. The SAMBA HIV-1 Semi-Q Test is a nucleic acid-based amplification assay developed for viral load monitoring performed on either the semi-automated SAMBA I system for laboratory use or the fully automated SAMBA II system for point-of care use. We have assessed the performance characteristics of the SAMBA HIV-1 Semi-Q Test on SAMBA I and SAMBA II systems according to the Common Technical Specifications of the European Community's 98/79 In Vitro Diagnostic Medical Devices Directive. The sensitivity, specificity, reproducibility, and viral subtype coverage of the test were similar on the SAMBA I and SAMBA II platforms. The clinical performance on the SAMBA I system was compared with the Roche CAP/CTM assay and evaluated in-house with 130 patient specimens from London as well as in the field with 390 specimens in Kenya and Zimbabwe. The overall concordance between the SAMBA and CAP/CTM assays was 98.1%. The clinical performance of the test on the SAMBA II platform in comparison with the Abbott HIV-1 RealTime Assay was evaluated in-house with 150 specimens from Ukraine, yielding a concordance of 98.0%. The results thus show that the SAMBA HIV-1 Semi-Q Test performs equivalently on SAMBA I and SAMBA II, and they suggest that the test is suitable for implementation at the point-of-care in resource-poor regions where viral load testing is desperately needed but often unavailable.

BACKGROUND: Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS). METHODS: GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children. FINDINGS: We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni o C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1.5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89.3% (95% CI 83.2-96.0) at the population level, compared with 51.5% (48.0-55.0) in the original GEMS analysis. The top six pathogens accounted for 77.8% (74.6-80.9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42.5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38.9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections. INTERPRETATION: A quantitative molecular diagnostic approach improved population-level and case-level characterisation of the causes of diarrhoea and indicated a high burden of disease associated with six pathogens, for which targeted treatment should be prioritised. FUNDING: Bill & Melinda Gates Foundation.

An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa.