Baobab Index

The Between April 2022 and March 2023, samples from neonates, mothers, healthcare workers and hospital environments were analysed. ECC isolates underwent European Committee on Antimicrobial Susceptibility Testing-guided antimicrobial susceptibility testing and whole-genome sequencing to determine sequence types (STs), resistance determinants, plasmids and phylogenetic relationships. A total of 132 ESBL-producing ECC isolates were recovered, with the majority originating from environmental sources (65.9%, These findings demonstrate substantial MDR ECC colonization in neonatal wards, suggesting hospital environments as reservoirs for resistant ECC. Temporally clustered isolates across environmental and patient samples underscore the need for strengthened infection prevention and genomic surveillance.

Anthrax, caused by Bacillus anthracis (BA), is a prominent neglected zoonosis with major impacts on human, livestock, and wildlife health. Despite this, limited genomic investigation at the One Health interface constrains current understanding of BA transmission and of the ecological and host factors shaping its diversity and population structure. This includes the possibility of host-specific BA lineages, given that anthrax outbreaks often disproportionally affect individual species. This study characterises the genomic diversity of BA in an endemic area, the Ngorongoro Conservation Area (NCA), in northern Tanzania. We analysed 213 BA genomes from livestock, wildlife and humans from cultured isolates combined with a culture-free targeted capture (TC) approach. NCA sequences formed a distinct genetic cluster compared with those from surrounding areas, and we observed surprisingly high levels of strain diversity within apparent epidemiological clusters, as well as within single animals, though strain diversity was lowest at the within host scale. We found limited evidence for seasonal clustering of cases as well as for BA lineages clustering by host species. This indicates that disproportional impacts on certain species during outbreaks are more likely driven by host ecology factors or, hypothetically, by accessory parts of the bacterial genome not represented in our data. TC-derived data significantly expanded the range of host species and geographic locations for genomic analysis, demonstrating the value of this approach. Although TC data may contain artefactual variation, shared SNP profiles between isolate- and TC-derived genomes gave confidence in its use for genotyping. Our analysis demonstrates unexpectedly high BA strain diversity and limited population structure in this endemic area across a range of spatial scales, including within-host. It further highlights the need for high density sampling and adaptable sequencing strategies to generate adequate BA genomic datasets that can enable informative molecular epidemiological studies of anthrax at the One Health interface.

Interpreting postmortem microbiological data is challenging, especially when enteric organisms are isolated. We evaluated whether virulence gene profiles could distinguish hospitalized decedents in whom Escherichia coli was adjudicated to be in the causal pathway to death from those in whom it was not. We conducted a prospective autopsy study from 2016 through 2019 at 2 hospitals in northern Tanzania. Postmortem cultures were collected from multiple specimen types. The role of E coli in the causal pathway to death was adjudicated using clinical, microbiological, and histopathologic data. Separate from adjudication, whole-genome sequencing was performed on E coli isolates for classification as extraintestinal pathogenic E coli (ExPEC) vs non-ExPEC based on their virulence genes. Logistic regression assessed the odds of isolating ExPEC when E coli was adjudicated as being in the causal pathway to death. We identified 74 E coli isolates from 57 (26.4%) of the 216 decedents enrolled in our study. Among decedents with E coli growth in culture, median (IQR) age was 38 (24-61) years, 14 (24.6%) were female, and E coli was adjudicated as being in the causal pathway to death in 17 (29.8%). Of these 17 decedents, 13 (76.5%) had at least 1 isolate designated as ExPEC compared with 24 (60.0%) of 40 decedents for whom E coli was not deemed causative of death. The odds of isolating ExPEC when E coli was in the causal pathway to death was 2.78 (95% CI, 0.62-12.3; P = .18). No single genomic marker, including ExPEC status, was sufficient to establish the causal role of E coli in death.

Healthcare systems in low- and middle-income countries are under pressure to adapt services for ageing populations, and frailty screening has gained interest as a means of identifying older adults at risk of adverse outcomes. The aim of this study was to examine two frailty instruments for the prediction of mortality in older adults admitted to hospital in Tanzania. This study followed 308 people, aged ≥ 60 years, admitted to four hospitals in the Kilimanjaro Region between March and August 2022. Baseline frailty was assessed using the Clinical Frailty Scale (CFS) and the Brief Frailty Instrument for Tanzania (B-FIT). The primary outcome was all-cause mortality, with secondary outcomes of length of stay and change in functional status. Cox regression estimated hazard ratios (HRs) for mortality, with Harrell's C statistic and receiver operator characteristics used to compare instrument performance. Follow-up data were available for 194 participants (63%). After a mean of 10.8 months of follow-up, adjusted models demonstrated frailty was associated with higher mortality (CFS HR 2.26, 95% CI 1.34-3.83; B-FIT HR 2.63, 95% CI 1.45-4.77, Frailty screening, using either the CFS or B-FIT, offered a feasible method for identifying older adults at the greatest risk of adverse outcomes. Such tools should be investigated as a means of targeting limited resources towards the most vulnerable older adults in an African setting.

Cholera remains a persistent public health challenge in Tanzania, with recurrent outbreaks across multiple regions overwhelming the health systems. Despite the ongoing surveillance to control the transmission, limited genomic characterization of circulating

The Kingdom of Eswatini is a Party to the Convention on Biological Diversity and to the Cartagena Protocol on Biosafety. As Party, Eswatini has domesticated these agreements by passing the Biosafety Act, of 2012 to provide for the safe handling, transfer, and use of living modified organisms (LMOs) in the country. The Act regulates living modified organisms to be used for confined field trials, commercial release, import, export, and transit, and for food, feed, and processing. Guidance is provided for prospective applicants before any application is made to the Competent Authority. This framework also provides for the regulation of emerging technologies such as synthetic biology and genome editing. The regulatory framework for living modified organisms aims to provide an enabling environment for the precautionary use of modern biotechnology and its products in the country in order to safeguard biological diversity and human health.

Accurate knowledge of species distributions is foundational for effective conservation efforts. Bats are a diverse group of mammals, with important roles in ecosystem functioning. However, our understanding of bats and their ecological importance is hindered by poorly defined ranges, mostly as a result of under-recording. This issue is exacerbated in Africa by the ongoing rapid discovery of new species, both de novo and splits of existing species, and by inaccessibility to museum specimens that are mostly hosted outside of the continent. Here we present the African bat database - a curated set of 17,285 unique locality records of all 266 species of bats from sub-Saharan Africa, vouched for by specimens and/or genetic sequencing, and aligned with current taxonomy. Based on these records, we also present Maxent-based distribution models and calculate the IUCN Red List metrics for Extent of Occurrence and Area of Occupancy. This database and online visualization tool provide an important open-source resource and is expected to significantly advance studies in ecology, and aid in bat conservation.

Interactions between microbial communities and the host can modulate mosquito biology, including vector competence. Therefore, future vector biocontrol measures will utilize these interactions and require extensive monitoring of the mosquito microbiome. Metabarcoding strategies will be useful for conducting vector monitoring on a large scale. We used 16S and 18S rRNA gene metabarcoding through iSeq100 sequencing to characterize the microbiome and eukaryome of Aedes albopictus (Skuse 1894) and Culex pipiens (Linnaeus 1758), two globally important vectors present in South Korea. Mosquitoes were collected from an urban and a semi-urban location in South Korea. Bacterial alpha and beta diversities varied by population. Pseudomonadota dominated the microbiomes of both species. The microbiome composition varied by population and was dominated by different taxa. At the genus level, Wolbachia sp. was the most enriched genus in Cx. pipiens, followed by Aeromonas sp. In Ae. Albopictus, the most abundant group was Enterococcus sp. The gregarine parasite Ascogregarina taiwanensis was highly prevalent in Ae. Albopictus and its absence was marked by the presence of seven bacterial taxa. To our knowledge, this is the first characterization of the microbiome of Ae. albopictus and Cx. pipiens in these regions of South Korea and contributes to the current information on the microbiome of mosquito species, which can be used in further studies to assess pathogen-microbiome and microbiome-microbiome interactions.