Biology subjects

Lembo, T.

Publications and source records attributed to Lembo, T..

5 recordsLinked to original sources

bioRxiv2026

Home is where the host is: Evolutionary history of geographic spread, host switching, and adaptive genomic signatures in two generalist Group B Streptococcus clonal groups

Group B Streptococcus (GBS) is a pathogen of global relevance in neonatal and maternal disease as well as bovine mastitis. Two closely related clonal groups, denoted 103 and 314 (CG103/314) have been detected in humans and cattle on multiple continents in recent decades but are poorly characterised compared to other host-generalist clades. We examined their potential origins, host-switching events and presence of a suite of genetic markers for antimicrobial resistance, virulence and host association using a newly assembled dataset of 248 CG103/314 genomes from humans, cattle, and food originating from five continents. We detected multiple host switches between humans and cattle, and significant regional differences in AMR gene distribution, possibly reflecting local differences in antimicrobial use across countries and hosts and indicating a capacity for regional adaptation to selective pressures. Across the evolutionary history of CG103/314 from both host species, the prevalence of the Lac.2 operon, a genetic marker associated with bovine host adaptation, was high, whereas the prevalence of the scpB-lmb gene pair, a genetic marker of human host adaptation in other GBS clonal groups, was very low. All isolates with scpB-lmb were associated with human disease rather than carriage. Our dataset displayed biases typical of research into multi-host pathogens, when sampling is often focused on a specific host species or setting. Consistent, balanced, contemporaneous and sympatric sampling efforts across host species and sources are needed for a full understanding of the distribution and emergence of CG103/314 and similar multi-host pathogens impacting food safety and public health. Impact statementThis study provides a comprehensive, global genomic overview of generalist clonal groups 103/314 of the human and animal pathogen Group B Streptococcus (GBS). By analysing host switching, antimicrobial resistance and virulence-associated markers, we show that these clonal groups display adaptation patterns shaped by region- and host-specific selective pressures. Our findings include potential expansion of the host range from humans and cattle into porcupines and pigs, and provides detailed discussion around anthropocentric sampling bias, highlighting the importance of balanced, multi-host sampling of generalist GBS lineages and One Health pathogens in general. This work reinforces the need for coordinated One Health surveillance to monitor emerging sub-lineages with relevance for food safety, human and animal health.

evolutionary biology↗

bioRxiv2025

Investigating Bacillus anthracis genomic diversity and trait-specific lineages in an endemic area in northern Tanzania through a combination of traditional and culture-free sequencing approaches

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. Author SummaryAnthrax continues to threaten the health of people, livestock, and wildlife in many parts of the world, yet we still know surprisingly little about how this disease spreads in nature. One major gap is understanding why some species are affected more strongly during outbreaks, despite assumed equal susceptibility. To investigate this, we studied the genomic diversity of the anthrax-causing bacterium Bacillus anthracis in a large conservation area in northern Tanzania. We combined two ways of generating genetic data: traditional laboratory culture and a culture-free method that allowed us to recover bacterial DNA from a wider range of samples. By analysing a uniquely large and species-diverse dataset of over 200 bacterial genomes from people, livestock and wildlife, we found that bacteria from the study area formed a clearly defined group compared to those from surrounding regions. We also discovered unexpectedly high diversity of strains, not only across the landscape but even within single animals. Despite this diversity, we saw little evidence that certain bacterial lineages are tied to specific host species. Our results suggest that the behaviour and ecology of different animals, rather than host-adapted lineages of the bacterium, likely explain why some species are more affected than others.

genomics↗

bioRxiv2023

Continent-wide genomic analysis of the African buffalo (Syncerus caffer).

The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights into the evolutionary history of the species, and the key selective pressures shaping populations, including assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, scaffold N50 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from across the species distribution. Principal component and admixture analyses provided surprisingly little support for the currently described four subspecies, but indicated three main lineages, in Western/Central, Eastern and Southern Africa, respectively. Estimating Effective Migration Surfaces analysis suggested that geographical barriers have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes indicated a substantial drop occurring in all populations 5-10,000 years ago, coinciding with the increase in human populations. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure upon the African buffalo. These findings have important implications for understanding bovid evolution, buffalo conservation and population management.

genomics↗

bioRxiv2021

Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity

Genomic sequencing has revolutionized our understanding of bacterial disease epidemiology, but remains underutilized for zoonotic pathogens in remote endemic settings. Anthrax, caused by the spore-forming bacterium Bacillus anthracis, remains a threat to human and animal health and rural livelihoods in low- and middle-income countries. While the global genomic diversity of B. anthracis has been well-characterized, there is limited information on how its populations are genetically structured at the scale at which transmission occurs, critical for understanding the pathogens evolution and transmission dynamics. Using a uniquely rich dataset, we quantified genome-wide single nucleotide polymorphisms (SNPs) among 73 B. anthracis isolates derived from 33 livestock carcasses sampled over one year throughout the Ngorongoro Conservation Area, Tanzania, an area hyperendemic for anthrax. Genome-wide SNPs distinguished 22 unique B. anthracis genotypes within the study area. However, phylogeographic structure was lacking, as identical SNP profiles were found throughout the study area, likely the result of the long and variable periods of spore dormancy and long-distance livestock movements. Significantly, divergent genotypes were obtained from spatio-temporally linked cases and even individual carcasses. The high number of SNPs distinguishing isolates from the same host is unlikely to have arisen during infection, as supported by our simulation models. This points to an unexpectedly wide transmission bottleneck for B. anthracis, with an inoculum comprising multiple variants being the norm. Our work highlights that inferring transmission patterns of B. anthracis from genomic data will require analytical approaches that account for extended and variable environmental persistence as well as co-infection. ImportancePathogens transmitted between animals and people affect the health and livelihoods of farmers, particularly in developing countries dependent on livestock. Understanding over what distances these pathogens are transmitted and how they evolve is important to inform control strategies towards reducing disease impacts. Information on the circulation of Bacillus anthracis, which causes the often-lethal disease anthrax, is lacking for settings where the disease is commonplace. Consequently, we examined its genetic variability in an area in Tanzania where anthrax is widespread. We found no clear link between how closely cases were sampled and their genetic similarity. We suspect this lack of congruence is primarily driven by large-scale livestock movements, which control efforts should take into consideration. Another significant finding was the co-occurrence of multiple B. anthracis types within individual hosts, suggesting animals are commonly infected with a mixture of variants. This needs to be accounted for when investigating possible connections between cases.

genomics↗

bioRxiv2020

Practical and effective diagnosis of animal anthrax in endemic low-resource settings

BackgroundAnthrax threatens human and animal health, and peoples livelihoods in many rural communities in Africa and Asia. In these areas, anthrax surveillance is challenged by a lack of tools for on-site detection. Furthermore, cultural practices and infrastructure may affect sample availability and quality. Practical yet accurate diagnostic solutions are greatly needed to quantify anthrax impacts. We validated microscopic and molecular methods for the detection of Bacillus anthracis in field-collected blood smears and identified alternative samples suitable for anthrax confirmation in the absence of blood smears. Methodology/Principal FindingsWe investigated livestock mortalities suspected to be caused by anthrax in northern Tanzania. Field-prepared blood smears (n = 152) were tested by microscopy using four staining techniques as well as polymerase chain reaction (PCR) followed by Bayesian latent class analysis. Median sensitivity (91%, CI 95% [84-96%]) and specificity (99%, CI 95% [96-100%]) of microscopy using azure B were comparable to those of the recommended standard, polychrome methylene blue, PMB (92%, CI 95% [84-97%] and 98%, CI 95% [95-100%], respectively), but azure B is more available and convenient. Other commonly-used stains performed poorly. Blood smears could be obtained for <50% of suspected anthrax cases due to local customs and conditions. However, PCR on DNA extracts from dried skin, which was almost always available, had high sensitivity and specificity (95%, CI 95% [90-98%] and 95%, CI 95% [87-99%], respectively), even after extended storage at ambient temperature. Conclusions/SignificanceAzure B microscopy represents an accurate diagnostic test for animal anthrax that can be performed with basic laboratory infrastructure and in the field. When blood smears are unavailable, PCR using skin tissues provides a valuable alternative for confirmation. Our findings lead to a practical diagnostic approach for anthrax in low-resource settings that can support surveillance and control efforts for anthrax-endemic countries globally. Author summaryAnthrax, an ancient disease largely controlled in the developed world, is still widespread in remote and rural communities of low- and middle-income countries where it affects human and animal health, and livelihoods. To control anthrax effectively, detection and accurate confirmation are important, but solutions need to be feasible for the most-affected areas where resources and infrastructure are typically limited. To achieve this, we assessed a newly proposed stain, azure B, for microscopic confirmation on animal blood smears, as this method can be implemented in low-resource laboratories and in the field. Microscopy using azure B was highly accurate compared to other recommended stains and has the added advantage of being more readily available and convenient. However, blood smear samples were unavailable for more than half of suspected cases. We therefore evaluated a molecular test (PCR) on other sample types - whole blood, blood swabs, skin, and flies - stored at ambient temperature. We show high performance of PCR with skin tissues which were available for 90% of carcasses. Thus, under field conditions, smear samples (when available) and tissue samples are most suitable for diagnostic testing of animal anthrax, whereby microscopy can be conducted in affected areas and PCR in in-country reference laboratories.

microbiology↗