Fever in focus: Symptoms, diagnoses and treatment of febrile children in Ghana-A longitudinal hospital study.

BACKGROUND: Healthcare resources are often limited in areas of sub-Saharan Africa. This makes accurate and timely diagnoses challenging and delays treatment of childhood febrile illness. We explored longitudinal characteristics related to symptoms, diagnosis and treatment of hospitalised febrile children in a rural area of Ghana highly endemic for malaria. METHODS: Febrile children under 15 years, admitted to the study hospital paediatric ward, were recruited to the study and clinical data were collected throughout hospitalisation. Descriptive statistics were reported for all cases; for longitudinal analyses, a subset of visits with limited missing data was used. RESULTS: There were 801 hospitalised children included in longitudinal analyses. Malaria (n = 581, 73%) and sepsis (n = 373, 47%) were the most prevalent suspected diagnoses on admission. One-third of malaria suspected diagnoses (n = 192, 33%) were changed on the discharge diagnosis, compared to 84% (n = 315) of sepsis suspected diagnoses. Among malaria-only discharge diagnoses, 98% (n/N = 202/207) received an antimalarial and 33% (n/N = 69/207) an antibiotic; among discharge diagnoses without malaria, 28% (n/N = 108/389) received an antimalarial and 83% (n/N = 324/389) an antibiotic. CONCLUSIONS: Suspected diagnoses were largely based on clinical presentation and were frequently changed; changed diagnoses were associated with lingering symptoms, underscoring the need for faster and more accurate diagnostics. Medications were over-prescribed regardless of diagnosis stability, possibly because of a lack of confidence in suspected diagnoses. Thus, better diagnostic tools are needed for childhood febrile illnesses to enhance the accuracy of and confidence in diagnoses, and to cut down unjustified medication use, reducing the risk of antimicrobial and malaria resistance.

Spatiotemporal variation in risk of Shigella infection in childhood: a global risk mapping and prediction model using individual participant data.

BACKGROUND: Diarrhoeal disease is a leading cause of childhood illness and death globally, and Shigella is a major aetiological contributor for which a vaccine might soon be available. The primary objective of this study was to model the spatiotemporal variation in paediatric Shigella infection and map its predicted prevalence across low-income and middle-income countries (LMICs). METHODS: Individual participant data for Shigella positivity in stool samples were sourced from multiple LMIC-based studies of children aged 59 months or younger. Covariates included household-level and participant-level factors ascertained by study investigators and environmental and hydrometeorological variables extracted from various data products at georeferenced child locations. Multivariate models were fitted and prevalence predictions obtained by syndrome and age stratum. FINDINGS: 20 studies from 23 countries (including locations in Central America and South America, sub-Saharan Africa, and south and southeast Asia) contributed 66 563 sample results. Age, symptom status, and study design contributed most to model performance followed by temperature, wind speed, relative humidity, and soil moisture. Probability of Shigella infection exceeded 20% when both precipitation and soil moisture were above average and had a 43% peak in uncomplicated diarrhoea cases at 33°C temperatures, above which it decreased. Compared with unimproved sanitation, improved sanitation decreased the odds of Shigella infection by 19% (odds ratio [OR]=0·81 [95% CI 0·76-0·86]) and open defecation decreased them by 18% (OR=0·82 [0·76-0·88]). INTERPRETATION: The distribution of Shigella is more sensitive to climatological factors, such as temperature, than previously recognised. Conditions in much of sub-Saharan Africa are particularly propitious for Shigella transmission, although hotspots also occur in South America and Central America, the Ganges-Brahmaputra Delta, and the island of New Guinea. These findings can inform prioritisation of populations for future vaccine trials and campaigns. FUNDING: NASA, National Institutes of Health-The National Institute of Allergy and Infectious Diseases, and Bill & Melinda Gates Foundation.

Prevalence, Characterization, and Antimicrobial Resistance of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli from Domestic Free-Range Poultry in Agogo, Ghana.

Poultry has been suggested as an important source for extended-spectrum beta-lactamase (ESBL)-producing bacteria that can lead to difficult-to treat infections in humans. Therefore, this study aims to determine the frequency, the genetics, and antimicrobial resistance profiles of ESBL-producing Escherichia coli in domestic free-range poultry in Agogo, Ghana. The study was set up and piloted from January 2019 until June 2019. Between June and December 2019, fecal samples (N = 144) were collected from free-roaming chickens from domestic farms in the regions of Sukuumu, Bontodiase, and Freetown and cultured on ESBL screening agar. Strain identification and antibiotic susceptibility were performed using the VITEK 2 compact system. ESBL-producing E. coli were confirmed using the double disk synergy test. Molecular characterization of ESBL-associated genes (blaTEM, blaSHV, and blaCTX-M) were performed using conventional polymerase chain reaction (PCR) and further sequencing of obtained PCR amplicons. The result showed that 56.2% (n/N = 81/144) of collected fecal samples were positive for ESBL-producing E. coli. Majority of the isolates showed resistance to tetracycline (93.8%, n/N = 76/81) and trimethoprim-sulfamethoxazole (66.7, n/N = 54/81), whereas resistance to carbapenems was not found. The majority of ESBL-producing E. coli carried the blaCTX-M genes, with blaCTX-M-15 being the dominant (95.1%, n/N = 77/81) genotype. In this study, we report high frequencies of ESBL-producing E. coli in smallholder free-range poultry representing a potential source of infection, highlighting the need for control of antibiotic use and animal hygiene/sanitation measures, both important from a One Health perspective.

Pathogens associated with hospitalization due to acute lower respiratory tract infections in children in rural Ghana: a case-control study.

Respiratory infections are one of the most common causes of death among children under the age of five years. Data on prevalence and relevance of specific organisms in African children are still lacking. This case-control-study investigated prevalence and relevance of specific organisms in Ghanaian children admitted to hospital with symptoms of lower respiratory tract infection (LRTI). Pharyngeal swabs were taken and tested by PCR for 19 respiratory isolates. Adjusted odds ratios (aORs) were calculated to estimate associations between isolates and admission with LRTI. Population attributable fractions (PAFs) were calculated to assess the proportion of LRTI cases due to a particular pathogen. The study included 327 cases and 562 controls. We found associations between detection and admission for LRTI for influenza (aOR 98.6; 95% confidence interval (CI) 20.0-1789.6), respiratory syncytial virus (aOR 40.2; 95% CI 7.2-758.6), H. influenzae (aOR 4.1; 95% CI 2.2-7.9) and S. pneumoniae (aOR 2.4; 95% CI 1.7-3.4). PAFs ≥ 10% were observed for S. pneumoniae (30%; 95% CI 26-42), H. influenzae (10%; 95% CI 2-19) and influenza (10%; 95% CI 2-18). This study highlights the need for heightened surveillance and development of effective vaccines for respiratory pathogens other than SARS-CoV-2 in the future.

The person-to-person transmission landscape of the gut and oral microbiomes.

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

Impact of antibiotic intake on the incidence of extended-spectrum ß-lactamase-producing Enterobacterales in sub-Saharan Africa: results from a community-based longitudinal study.

OBJECTIVES: The global prevalence of intestinal extended-spectrum ß-lactamase-producing Enterobacterales (ESBL-PE) is approximately 17% in communities, with significant variations among regions. This longitudinal study aimed to assess the impact of antibiotic intake on the incidence of intestinal ESBL-PE in Ghanaian pharmacy customers outside of hospitals. METHODS: Screening for ESBL-PE was performed in four independent pharmacies in Kumasi, Ghana, using rectal swabs and an ESBL-PE-selective medium. Pharmacy customers purchasing antibiotics were recruited, and those buying non-antibiotic drugs served as controls. Participants who were negative for ESBL-PE provided follow-up swabs for up to 28 days. RESULTS: At baseline, 302 (75%) of 404 participants were colonized with ESBL-PE. Sixty-three participants who were negative for ESBL-PE at baseline received per-protocol follow-up, including 28 individuals who took antibiotics and 35 controls. The cumulative proportions of ESBL-PE in the antibiotics and control groups were 71% (20/28) and 54% (19/35) at the first follow-up (p 0.258), 86% (24/28) and 80% (28/35) at the second follow-up (p 0.741) and 86% (24/28) and 94% (33/35) at the third follow-up (p 0.393), respectively. DISCUSSION: The rate of intestinal ESBL-PE carriage among pharmacy customers outside of hospitals was higher than expected at baseline and further increased during the 28 days of follow-up, irrespective of antibiotic intake. This alarming finding needs to be considered in the antibiotic treatment of outpatients and emphasizes the urgent need for improved prevention strategies, development of new antibiotic drugs and potential future elimination strategies. Further longitudinal studies on ESBL-PE in African communities, also outside of pharmacy settings, are required.

Laboratory-based surveillance of antimicrobial resistance in regions of Kenya: An assessment of capacities, practices, and barriers by means of multi-facility survey.

Background: Adequate laboratory capacity is critical in the implementation of coherent surveillance for antimicrobial resistance (AMR). We describe capacities and deficiencies in laboratory infrastructure and AMR surveillance practices among health facilities in Kenya to support progress toward broader sustainable laboratory-based AMR surveillance. Methods: A convenience sample of health facilities from both public and private sectors across the country were selected. Information was obtained cross-sectionally between 5th October and 8th December 2020 through online surveys of laboratory managers. The assessment covered quality assurance, management and dissemination of AMR data, material and equipment, staffing, microbiology competency, biosafety and certification. A scoring scheme was developed for the evaluation and interpreted as (80% and above) facility is adequate (60-79%) requires some strengthening and (<60%) needing significant strengthening. Average scores were compared across facilities in public and private sectors, rural and urban settings, as well as national, county, and community levels. Results: Among the participating facilities (n = 219), the majority (n = 135, 61.6%) did not offer bacterial culture testing, 47 (21.5%) offered culture services only and 37 (16.9%) performed antimicrobial susceptibility testing (AST). The major gaps identified among AST facilities were poor access to laboratory information management technology (LIMT) (score: 45.9%) and low uptake of external quality assessment (EQA) programs for cultures (score 67.7%). Access to laboratory technology was more than two-fold higher in facilities in urban (58.6%) relative to rural (25.0%) areas. Whilst laboratories that lacked culture services were found to have significant infrastructural gaps (average score 59.4%), facilities that performed cultures only (average score: 83.6%) and AST (average score: 82.9%) recorded significantly high scores that were very similar across areas assessed. Lack of equipment was identified as the leading challenge to the implementation of susceptibility testing among 46.8% of laboratories. Conclusions: We identified key gaps in laboratory information management technology, external quality assurance and material and equipment among the surveyed health facilities in Kenya. Our findings suggest that by investing in equipment, facilities performing cultures can be successfully upgraded to provide additional antimicrobial susceptibility testing, presenting a chance for a major leap toward improved AMR diagnostics and surveillance in the country.

High seroprevalence of SARS-CoV-2 in Burkina-Faso, Ghana and Madagascar in 2021: a population-based study.

BACKGROUND: The current COVID-19 pandemic affects the entire world population and has serious health, economic and social consequences. Assessing the prevalence of COVID-19 through population-based serological surveys is essential to monitor the progression of the epidemic, especially in African countries where the extent of SARS-CoV-2 spread remains unclear. METHODS: A two-stage cluster population-based SARS-CoV-2 seroprevalence survey was conducted in Bobo-Dioulasso and in Ouagadougou, Burkina Faso, Fianarantsoa, Madagascar and Kumasi, Ghana between February and June 2021. IgG seropositivity was determined in 2,163 households with a specificity improved SARS-CoV-2 Enzyme-linked Immunosorbent Assay. Population seroprevalence was evaluated using a Bayesian logistic regression model that accounted for test performance and age, sex and neighbourhood of the participants. RESULTS: Seroprevalence adjusted for test performance and population characteristics were 55.7% [95% Credible Interval (CrI) 49·0; 62·8] in Bobo-Dioulasso, 37·4% [95% CrI 31·3; 43·5] in Ouagadougou, 41·5% [95% CrI 36·5; 47·2] in Fianarantsoa, and 41·2% [95% CrI 34·5; 49·0] in Kumasi. Within the study population, less than 6% of participants performed a test for acute SARS-CoV-2 infection since the onset of the pandemic. CONCLUSIONS: High exposure to SARS-CoV-2 was found in the surveyed regions albeit below the herd immunity threshold and with a low rate of previous testing for acute infections. Despite the high seroprevalence in our study population, the duration of protection from naturally acquired immunity remains unclear and new virus variants continue to emerge. This highlights the importance of vaccine deployment and continued preventive measures to protect the population at risk.

Clustering of Cryptosporidium species infections among sheep and cattle but not children in remote highland communities of Madagascar.

BACKGROUND: The aim of this study was to identify local transmission patterns of Cryptosporidium spp. infections among livestock and humans in four extremely rural and remote highland communities in Madagascar. METHODS: In this cross-sectional study, households were randomly sampled throughout a 1-year study period, with one feces sample collected from each child (≤ 5 years old), sheep and cattle. Cryptosporidium spp. were identified using a nested PCR assay targeting the 18S ribosomal RNA gene. All samples positive for Cryptosporidium hominis were further subtyped by sequencing the 60-kDa glycoprotein gene (gp60). Spatial clustering methods were applied to analyze potential transmission patterns. RESULTS: In total, 252 households participated in the study, and samples from 197 children, 862 cattle and 334 sheep were collected and included in the study. Of the samples collected, 11 (5.6%) from children, 30 (3.5%) from cattle and 42 (12.6%) from sheep tested positive for Cryptosporidium spp. Very little overlap in the species distribution between human and animal infections was found. Global (overall) and local (spatially defined) clustering was observed for Cryptosporidium spp. infections in sheep and for Cryptosporidium xiaoi/bovis infections among sheep and cattle. DISCUSSION: The results of this analysis do not support the occurrence of defined disease outbreaks, rather they point to a continuous series of transmission events that are spatially aggregated. Despite the close coexistence between humans, sheep and cattle in the study area, mutual transmission was not observed. Hence, the study underlines the importance of sustained sanitation and hygiene measures to prevent cryptosporidiosis transmission among infants, since asymptomatic children serve as an infection reservoir. Similarly, the study highlights the importance of improving hygiene to reduce the transmission of Cryptosporidium spp. in livestock, an infection with serious consequences, especially in newborn calves.

Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon.

During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.

Fighting Antimicrobial Resistance: Development and Implementation of the Ghanaian National Action Plan (2017-2021).

In recent years, Ghana has been recognised as a leading player in addressing antimicrobial resistance (AMR) in Africa. However, based on our literature review, we could not ascertain whether the core elements of the national action plan (NAP) were implemented in practice. In this paper, we present a qualitative analysis of the development of AMR-related policies in Ghana, including the NAP. We conducted 13 semi-structured expert interviews to obtain at a more thorough understanding of the implementation process for the AMR NAP and to highlight its accomplishments and shortcomings. The results show that AMR policies, as embodied in the NAP, have led to an extended network of cooperation between stakeholders in many political fields. Broadly, limited allocation of financial resources from the government and from international cooperation have been deplored. Furthermore, the opportunity for using the NAP in mainstreaming the response to the threat of AMR has not been seized. To the general public, this remained hidden behind a number of other relevant health topics such as infection prevention, veterinary services and pharmaceutical regulation. As a One Health (OH) challenge, developing countries could integrate AMR NAPs into other health and environmental programmes to improve its implementation in practice.

Global Population Genomics of Two Subspecies of Cryptosporidium hominis during 500 Years of Evolution.

Cryptosporidiosis is a major global health problem and a primary cause of diarrhea, particularly in young children in low- and middle-income countries (LMICs). The zoonotic Cryptosporidium parvum and anthroponotic Cryptosporidium hominis cause most human infections. Here, we present a comprehensive whole-genome study of C. hominis, comprising 114 isolates from 16 countries within five continents. We detect two lineages with distinct biology and demography, which diverged circa 500 years ago. We consider these lineages two subspecies and propose the names C. hominis hominis and C. hominis aquapotentis (gp60 subtype IbA10G2). In our study, C. h. hominis is almost exclusively represented by isolates from LMICs in Africa and Asia and appears to have undergone recent population contraction. In contrast, C. h. aquapotentis was found in high-income countries, mainly in Europe, North America, and Oceania, and appears to be expanding. Notably, C. h. aquapotentis is associated with high rates of direct human-to-human transmission, which may explain its success in countries with well-developed environmental sanitation infrastructure. Intriguingly, we detected genomic regions of introgression following secondary contact between the subspecies. This resulted in high diversity and divergence in genomic islands of putative virulence genes, including muc5 (CHUDEA2_430) and a hypothetical protein (CHUDEA6_5270). This diversity is maintained by balancing selection, suggesting a co-evolutionary arms race with the host. Finally, we find that recent gene flow from C. h. aquapotentis to C. h. hominis, likely associated with increased human migration, maybe driving the evolution of more virulent C. hominis variants.

Associations Between Eight Earth Observation-Derived Climate Variables and Enteropathogen Infection: An Independent Participant Data Meta-Analysis of Surveillance Studies With Broad Spectrum Nucleic Acid Diagnostics.

Diarrheal disease, still a major cause of childhood illness, is caused by numerous, diverse infectious microorganisms, which are differentially sensitive to environmental conditions. Enteropathogen-specific impacts of climate remain underexplored. Results from 15 studies that diagnosed enteropathogens in 64,788 stool samples from 20,760 children in 19 countries were combined. Infection status for 10 common enteropathogens-adenovirus, astrovirus, norovirus, rotavirus, sapovirus, Campylobacter, ETEC, Shigella, Cryptosporidium and Giardia-was matched by date with hydrometeorological variables from a global Earth observation dataset-precipitation and runoff volume, humidity, soil moisture, solar radiation, air pressure, temperature, and wind speed. Models were fitted for each pathogen, accounting for lags, nonlinearity, confounders, and threshold effects. Different variables showed complex, non-linear associations with infection risk varying in magnitude and direction depending on pathogen species. Rotavirus infection decreased markedly following increasing 7-day average temperatures-a relative risk of 0.76 (95% confidence interval: 0.69-0.85) above 28°C-while ETEC risk increased by almost half, 1.43 (1.36-1.50), in the 20-35°C range. Risk for all pathogens was highest following soil moistures in the upper range. Humidity was associated with increases in bacterial infections and decreases in most viral infections. Several virus species' risk increased following lower-than-average rainfall, while rotavirus and ETEC increased with heavier runoff. Temperature, soil moisture, and humidity are particularly influential parameters across all enteropathogens, likely impacting pathogen survival outside the host. Precipitation and runoff have divergent associations with different enteric viruses. These effects may engender shifts in the relative burden of diarrhea-causing agents as the global climate changes.

Seroprevalence of SARS-CoV-2 in urban settings in three sub-Saharan African countries (SeroCoV): a study protocol for a household-based cross-sectional prevalence study using two-stage cluster sampling.

INTRODUCTION: The current COVID-19 pandemic has impacted the entire world with increasing morbidity and mortality and has resulted in serious economic and social consequences. Assessing the burden of COVID-19 is essential for developing efficient pandemic preparedness and response strategies and for determining the impact of implemented control measures. Population-based seroprevalence surveys are critical to estimate infection rates, monitor the progression of the epidemic and to allow for the identification of persons exposed to the infection who may either have been asymptomatic or were never tested. This is especially important for countries where effective testing and tracking systems could not be established and where non-severe cases or under-reported deaths might have blurred the true burden of COVID-19. Most seroprevalence surveys performed in sub-Saharan Africa have targeted specific high risk or more easily accessible populations such as healthcare workers or blood donors, and household-based estimates are rarely available. Here, we present the study protocol for a SARS-CoV-2 seroprevalence estimation in the general population of Burkina Faso, Ghana and Madagascar in 2021. METHODS AND ANALYSIS: The SeroCoV study is a household-based cross-sectional prevalence investigation in persons aged 10 years and older living in urban areas in six cities using a two-stage geographical cluster sampling method stratified by age and sex. The presence of anti-SARS-CoV-2 IgG antibodies will be determined using a sensitive and specific SARS-CoV-2 IgG ELISA. In addition, questionnaires will cover sociodemographic information, episodes of diseases and history of testing and treatment for COVID-like symptoms, travel history and safety measures. We will estimate the seroprevalence of SARS-CoV-2, taking into account test performance and adjusting for the age and sex of the respective populations. ETHICS AND DISSEMINATION: Ethical approval was received for all participating countries. Results will be disseminated through reports and presentations at the country level as well as peer-reviewed publications and international scientific conferences presentations.

Molecular surveillance and genetic divergence of rotavirus A antigenic epitopes in Gabonese children with acute gastroenteritis.

BACKGROUND: Rotavirus A (RVA) causes acute gastroenteritis in children <5 years of age in sub-Saharan Africa. In this study, we described the epidemiology and genetic diversity of RVA infecting Gabonese children and examined the antigenic variability of circulating strains in relation to available vaccine strains to maximize the public health benefits of introducing rotavirus vaccine through the Expanded Programme on Immunization (EPI) in Gabon. METHODS: Stool samples were collected consecutively between April 2018 and November 2019 from all hospitalized children <5 years with gastroenteritis and community controls without gastroenteritis. Children were tested for rotavirus A by quantitative RT-PCR and subsequently sequenced to identify circulating rotavirus A genotypes in the most vulnerable population. The VP7 and VP4 (VP8*) antigenic epitopes were mapped to homologs of vaccine strains to assess structural variability and potential impact on antigenicity. FINDINGS: Infections were mostly acquired during the dry season. Rotavirus A was detected in 98/177 (55%) hospitalized children with gastroenteritis and 14/67 (21%) of the control children. The most common RVA genotypes were G1 (18%), G3 (12%), G8 (18%), G9 (2%), G12 (25%), with G8 and G9 reported for the first time in Gabon. All were associated either with P[6] (31%) or P[8] (38%) genotypes. Several non-synonymous substitutions were observed in the antigenic epitopes of VP7 (positions 94 and 147) and VP8* (positions 89, 116, 146 and 150), which may modulate the elicited immune responses. INTERPRETATION: This study contributes to the epidemiological surveillance of rotavirus A required before the introduction of rotavirus vaccination in the EPI for Gabonese children.

Prevalence of Pathogens in Young Children Presenting to Hospital with Diarrhea from Lambaréné, Gabon.

Diarrheal disease is the second most frequent cause of mortality in children younger than 5 years worldwide, causing more than half a million deaths each year. Our knowledge of the epidemiology of potentially pathogenic agents found in children suffering from diarrhea in sub-Saharan African countries is still patchy, and thereby hinders implementation of effective preventative interventions. The lack of cheap, easy-to-use diagnostic tools leads to mostly symptomatic and empirical case management. An observational study with a total of 241 participants was conducted from February 2017 to August 2018 among children younger than 5 years with diarrhea in Lambaréné, Gabon. Clinical and demographic data were recorded, and a stool sample was collected. The samples were examined using a commercial rapid immunoassay to detect Rotavirus/adenovirus, conventional bacterial culture for Salmonella spp., and multiplex real-time PCR for Cryptosporidium spp., Giardia lamblia, Cyclospora cayetanensis, enterotoxigenic Escherichia coli (ETEC), and enteroinvasive Escherichia coli (EIEC)/Shigella. At least one infectious agent was present in 121 of 241 (50%) samples. The most frequently isolated pathogens were EIEC/Shigella and ETEC (54/179; 30.2% and 44/179; 24.6%, respectively), followed by G. lamblia (33/241; 13.7%), Cryptosporidium spp. (31/241; 12.9%), and Rotavirus (23/241; 9.5%). Coinfection with multiple pathogens was observed in 33% (40/121) of the positive cases with EIEC/Shigella, ETEC, and Cryptosporidium spp. most frequently identified. Our results provide new insight into the possible causes of diarrheal disease in the Moyen-Ogooué region of Gabon and motivate further research on possible modes of infection and targeted preventive measures.

Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon.

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

Molecular and epidemiologic characterization of the diphtheria outbreak in Venezuela.

In 2016, Venezuela faced a large diphtheria outbreak that extended until 2019. Nasopharyngeal or oropharyngeal samples were prospectively collected from 51 suspected cases and retrospective data from 348 clinical records was retrieved from 14 hospitals between November 2017 and November 2018. Confirmed pathogenic Corynebactrium isolates were biotyped. Multilocus Sequence Typing (MLST) was performed followed by next-generation-based core genome-MLST and minimum spanning trees were generated. Subjects between 10 and 19 years of age were mostly affected (n = 95; 27.3%). Case fatality rates (CFR) were higher in males (19.4%), as compared to females (15.8%). The highest CFR (31.1%) was observed among those under 5, followed by the 40 to 49 age-group (25.0%). Nine samples corresponded to C. diphtheriae and 1 to C. ulcerans. Two Sequencing Types (ST), ST174 and ST697 (the latter not previously described) were identified among the eight C. diphtheriae isolates from Carabobo state. Cg-MLST revealed only one cluster also from Carabobo. The Whole Genome Sequencing analysis revealed that the outbreak seemed to be caused by different strains with C. diphtheriae and C. ulcerans coexisting. The reemergence and length of this outbreak suggest vaccination coverage problems and an inadequate control strategy.

Molecular epidemiology of respiratory syncytial virus in children in sub-Saharan Africa.

OBJECTIVES: This study investigated the molecular epidemiology of respiratory syncytial virus (RSV) among febrile children with acute respiratory tract infection in Ghana, Gabon, Tanzania and Burkina Faso between 2014 and 2017 as well as the evolution and diversification of RSV strains from other sub-Saharan countries. METHODS: Pharyngeal swabs were collected at four study sites (Agogo, Ghana: n = 490; Lambaréné, Gabon: n = 182; Mbeya, Tanzania: n = 293; Nouna, Burkina Faso: n = 115) and analysed for RSV and other respiratory viruses using rtPCR. For RSV-positive samples, sequence analysis of the second hypervariable region of the G gene was performed. A dataset of RSV strains from sub-Saharan Africa (2011-2017) currently available in GenBank was compiled. Phylogenetic analysis was conducted to identify the diversity of circulating RSV genotypes. RESULTS: In total, 46 samples were tested RSV positive (Ghana n = 31 (6.3%), Gabon n = 4 (2.2%), Tanzania n = 9 (3.1%) and Burkina Faso n = 2 (1.7%)). The most common RSV co-infection was with rhinovirus. All RSV A strains clustered with genotype ON1 strains with a 72-nucleotide duplication and all RSV B strains belonged to genotype BAIX. Phylogenetic analysis of amino acid sequences from sub-Saharan Africa revealed the diversification into 11 different ON1 and 22 different BAIX lineages and differentiation of ON1 and BAIX strains into potential new sub-genotypes, provisionally named ON1-NGR, BAIX-KEN1, BAIX-KEN2 and BAIX-KEN3. CONCLUSION: The study contributes to an improved understanding of the molecular epidemiology of RSV infection in sub-Saharan Africa. It provides the first phylogenetic data for RSV from Tanzania, Gabon and Burkina Faso and combines it with RSV strains from all other sub-Saharan countries currently available in GenBank.

Limited specificity of commercially available SARS-CoV-2 IgG ELISAs in serum samples of African origin.

OBJECTIVES: Specific serological tests are mandatory for reliable SARS-CoV-2 diagnostics and seroprevalence studies. Here, we assess the specificities of four commercially available SARS-CoV-2 IgG ELISAs in serum/plasma panels originating from Africa, South America, and Europe. METHODS: 882 serum/plasma samples collected from symptom-free donors before the COVID-19 pandemic in three African countries (Ghana, Madagascar, Nigeria), Colombia, and Germany were analysed with three nucleocapsid-based ELISAs (Euroimmun Anti-SARS-CoV-2-NCP IgG, EDI™ Novel Coronavirus COVID-19 IgG, Mikrogen recomWell SARS-CoV-2 IgG), one spike/S1-based ELISA (Euroimmun Anti-SARS-CoV-2 IgG), and in-house common cold CoV ELISAs. RESULTS: High specificity was confirmed for all SARS-CoV-2 IgG ELISAs for Madagascan (93.4-99.4%), Colombian (97.8-100.0%), and German (95.9-100.0%) samples. In contrast, specificity was much lower for the Ghanaian and Nigerian serum panels (Ghana: NCP-based assays 77.7-89.7%, spike/S1-based assay 94.3%; Nigeria: NCP-based assays 39.3-82.7%, spike/S1-based assay 90.7%). 15 of 600 African sera were concordantly classified as positive in both the NCP-based and the spike/S1-based Euroimmun ELISA, but did not inhibit spike/ACE2 binding in a surrogate virus neutralisation test. IgG antibodies elicited by previous infections with common cold CoVs were found in all sample panels, including those from Madagascar, Colombia, and Germany and thus do not inevitably hamper assay specificity. Nevertheless, high levels of IgG antibodies interacting with OC43 NCP were found in all 15 SARS-CoV-2 NCP/spike/S1 ELISA positive sera. CONCLUSIONS: Depending on the chosen antigen and assay protocol, SARS-CoV-2 IgG ELISA specificity may be significantly reduced in certain populations probably due to interference of immune responses to endemic pathogens like other viruses or parasites.