Biology subjects

Mwakibete, L.

Publications and source records attributed to Mwakibete, L..

4 recordsLinked to original sources

bioRxiv2024

Birds affected by a 2021 avian mortality event are strongly associated with supplemental feeding and ground foraging behaviors

In 2021, news outlets and state natural resources agencies reported a large number of avian deaths across several states in the eastern and midwestern USA. This event fomented a rapid and robust response from animal health experts from across the country. Given the clustered pattern of disease and death, an infectious etiology was rigorously investigated. No single causative pathogen was identified, leaving the cause and thus epidemiology of the mortality event unex-plained. In this study, we attempted to hone in on potential causes or contributors to this event by constructing a dataset on affected birds life history, phylogeny, and ecology. After a preliminary analysis of these features, we developed a statistical pipeline to test two hypotheses regarding features of birds associated with the mortality event: (1) that a significant proportion of affected birds in the total sample are members of the Cornell Feederwatch list (i.e., birds that consume supplemental feed, and their predators), and that (2) ground-feeding species would be significantly represented in the sample. While logistic regression models support the plausibility of the two hypotheses, they are statistically indistinguishable. We discuss the implications of these findings, propose future work, and highlight the importance of ecological and behavioral expertise in understanding epidemiological phenomena.

ecology↗

bioRxiv2024

DNA damage drives antigen diversification through mosaic VSG formation in Trypanosoma brucei

Antigenic variation, using large genomic repertoires of antigen-encoding genes, allows pathogens to evade host antibody. Many pathogens, including the African trypanosome Trypanosoma brucei, extend their antigenic repertoire through genomic diversification. While evidence suggests that T. brucei depends on the generation of new variant surface glycoprotein (VSG) genes to maintain a chronic infection, a lack of experimentally tractable tools for studying this process has obscured its underlying mechanisms. Here, we present a highly sensitive targeted sequencing approach for measuring VSG diversification. Using this method, we demonstrate that a Cas9-induced DNA double-strand break within the VSG coding sequence can induce VSG recombination with patterns identical to those observed during infection. These newly generated VSGs are antigenically distinct from parental clones and thus capable of facilitating immune evasion. Together, these results provide insight into the mechanisms of VSG diversification and an experimental framework for studying the evolution of antigen repertoires in pathogenic microbes.

microbiology↗

bioRxiv2024

CZ ID: a cloud-based, no-code platform enabling advanced long read metagenomic analysis

Metagenomics has enabled the rapid, unbiased detection of microbes across diverse sample types, leading to exciting discoveries in infectious disease, microbiome, and viral research. However, the analysis of metagenomic data is often complex and computationally resource-intensive. CZ ID is a free, cloud-based genomic analysis platform that enables researchers to detect microbes using metagenomic data, identify antimicrobial resistance genes, and generate viral consensus genomes. With CZ ID, researchers can upload raw sequencing data, find matches in NCBI databases, get per-sample taxon metrics, and perform a variety of analyses and data visualizations. The intuitive interface and interactive visualizations make exploring and interpreting results simple. Here, we describe the expansion of CZ ID with a new long read mNGS pipeline that accepts Oxford Nanopore generated data (czid.org). We report benchmarking of a standard mock microbial community dataset against Kraken2, a widely used tool for metagenomic analysis. We evaluated the ability of this new pipeline to detect divergent viruses using simulated datasets. We also assessed the detection limit of a spiked-in virus to a cell line as a proxy for clinical samples. Lastly, we detected known and novel viruses in previously characterized disease vector (mosquitoes) samples.

bioinformatics↗

bioRxiv2023

Metagenomics for pathogen detection during a wildlife mortality event in songbirds

Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria comprising the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds, and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events. Article Summary LineThe causative agent of a mass mortality event in passerines remains inconclusive after metagenomic high-throughput sequencing with results prompting further investigation into non-pathogenic causes.

genomics↗