Biology subjects

Moyo, S.

Publications and source records attributed to Moyo, S..

6 recordsLinked to original sources

bioRxiv2026

Learning and forecasting shared evolutionary pathways to multi-drug resistance across global pathogens

Infections with bacteria which have evolved multi-drug resistance (MDR) cause millions of deaths worldwide. Large-scale efforts are gathering genotypic and phenotypic data on MDR bacteria, but methods for learning the structure, diversity, and predictors of evolutionary pathways to MDR have yet to take full advantage of these data. Here, we use evolutionary accumulation modelling (EvAM), an emerging class of machine learning methods with roots in cancer progression, to infer these evolutionary pathways across ESKAPEE pathogens (seven bacterial species that dominate health burdens), using a database of over 635k genotyped phenotypic observations from around the world. We identify global patterns in MDR evolutionary pathways, remarkably shared across multiple ESKAPEE species. Species-specific deviations from these stereotypical pathways are connected with geographical and demographic covariates, facilitating predictions of future MDR evolution. We verify these predictions with several hundred new phenotypes from ESKAPEE samples spanning decades of clinical infections in sub-Saharan Africa, demonstrating the capacity to forecast future MDR evolution from these inferred shared pathways.

evolutionary biology↗

bioRxiv2026

Antimicrobial activity of polymyxin A, and characterisation of the cognate biosynthetic gene cluster within the genome of the producing Paenibacillus polymyxa.

We report the isolation and identification of a Paenibacillus polymyxa strain from the citizen science project; Swab and Send. Through whole genome sequencing we are able to describe the biosynthetic gene cluster of polymyxin A produced by P. polymyxa 1G (NCBI accession no. JBVPZV000000000), compare the pmxA, pmxB and pmxE genes to five other polymyxin genes encoding known polymyxin variants, and provide mass spectrometry data that supports the production of polymyxin A1 (1157 m/z) and A2 (1143 m/z). Polymyxins are ranked in the highest priority critically important antimicrobials classification by the WHO and are of particular importance for treating gram-negative multidrug resistant pathogens. Due to the discovery of polymyxins occurring in the 1940s, there is little genetic research around polymyxins, and the literature focusses primarily on clinically used polymyxin E (colistin) and polymyxin B. Previous literature suggests that polymyxin A1 has similar/lower toxicity to clinically used polymyxins E and B. To test if polymyxin A was able to overcome current resistance mechanisms to clinically used polymyxins, the cell free supernatant from P. polymyxa 1G was tested against a panel of clinical isolates with various resistance genes. We found that resistance genes mcr-1 and mcr-4 confer resistance to polymyxin A produced by our isolate meaning that, while polymyxin A has good antimicrobial activity, clinical resistance mechanisms already confer resistance to this variant of polymyxin.

microbiology↗

bioRxiv2026

A citywide metagenomic analysis reveals surface-specific microbiome and resistome patterns in outdoor urban environments across Liverpool, UK.

Urbanisation is rapidly increasing worldwide, with increasing attention focused on its consequences for human populations and the environment. Despite the importance of outdoor urban environments for biodiversity and human wellbeing, their microbial ecology remains poorly characterised, particularly in relation to emerging microbial threats including antimicrobial resistance (AMR). Here, we present a citywide metagenomic study of outdoor public surfaces across Liverpool, United Kingdom, examining microbial community composition, diversity, and antimicrobial resistance gene (ARG) distribution across five distinct surface types. We show that patterns of human activity and surface use strongly influence both microbial community structure and AMR signatures in outdoor urban environments. Touchpoints were enriched for human-associated taxa and exhibited the highest overall resistome burdens, whereas Pathway and Waterside niches showed no strong taxonomic enrichment and exhibited low ARG prevalence. Refuse surfaces showed mixed patterns, characterised by sporadic but occasionally high-abundance ARG detections. Soil harboured the most distinct microbial communities but showed minimal ARG prevalence, which may partly reflect the limited representation of environmental taxa in current ARG databases. This study provides a baseline for understanding how urban infrastructure and behaviour shape microbial and resistance landscapes, and highlights the value of outdoor metagenomic surveillance for future environmental and public health research.

microbiology↗

bioRxiv2026

Whole-genome sequencing reveals inter-household networks of gut-colonising ESBL-producing Escherichia coli in two rural Malawian districts

Infection with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) is a global health concern that disproportionately affects sub-Saharan Africa (SSA). Gut mucosal colonisation is thought to precede invasive infection. Understanding ESBL-Ec colonisation and transmission across communities is therefore essential. We investigated the genomic epidemiology and spatial structure of 159 gut-colonising ESBL-Ec isolates from the faeces of 211 people in two rural Malawian villages using longitudinal sampling (2023-24), whole-genome sequencing and household mapping. Colonisation prevalence rose from 34.1% (95% CI: 27.8-41.0) to 54.2% (95% CI: 46.0-62.3) over one year. Isolates belonged to 33 sequence types (STs), most commonly ST38 and ST131, harbouring 46 distinct antimicrobial resistance gene types. Fifteen strains were identified in [≥]3 households that were typically separated by short geographic distances (<400 m). Of 190 pairwise comparisons between same-strain isolates from different households sampled concurrently within villages, 88.9% differed by [≤]10 single nucleotide polymorphisms, consistent with multi-household involvement in community transmission networks. Lineage-specific ST38 and ST131 network analyses linked rural isolates to urban Malawian isolates collected within the last decade. Our findings provide a transferable framework for inferring ESBL-Ec flow in community settings and highlight the need for One Health surveillance and improved sanitation infrastructure to limit transmission.

microbiology↗

bioRxiv2025

Fresh Paraformaldehyde Preserves Thrombus Biochemistry - An ATR-FTIR and PCA Investigation of Pulmonary Artery Thrombi

BackgroundBiochemical analyses of pulmonary embolism derived thrombi depend critically on fixative quality. ObjectiveTo quantify the impact of paraformaldehyde (PFA) shelf life on thrombus molecular integrity using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and time-of-flight secondary ion mass spectroscopy (SIMS) combined with principal component analysis. MethodsTen pulmonary artery thrombi were fixed in either aged PFA (6 months; n = 6) or freshly prepared 4% PFA (n = 4); an in-vitro plasma clot control received the same fresh PFA. Triplicate ATR-FTIR spectra (400-4000 cm-1) were collected and vector-normalized to the Amide I band. ToF-SIMS measurements were performed using a 30 keV Bi primary ion beam Fixative chemistry was assessed by the carbonyl absorbance at 1700 cm-1. ResultsFreshly fixed thrombi displayed narrow Amide I (~1650 cm-1) and Amide II (~1540 cm-1) bands with a higher signal-to-noise ratio (SNR; median 41.8) than aged-PFA samples (18.2; P < .01). Carbonyl absorbance at 1700 cm-1 was markedly higher in fresh PFA. Aged PFA introduces chemical variances of biological samples in low-mass molecule fragments. PCA showed clear separation of fresh versus aged specimens and alignment of fresh thrombi with plasma controls across spectral windows. ConclusionsPFA solutions older than three months markedly deteriorate thrombus biochemical fidelity. ATR-FTIR and ToF-SIMS offer a rapid quality-control assay prior to molecular analyses. Key pointsO_LIPFA stored [≥]3 months loses >70% of reactive aldehydes, yielding broad Amide envelopes, attenuated lipid bands and a two fold SNR drop. C_LIO_LIAged PFA introduces chemical variances of biological samples in low-mass molecule fragments. C_LIO_LIPCA of fingerprint, protein or lipid windows cleanly separates aged from fresh fixations (PC1 up to 80% variance). C_LIO_LIA rapid QC workflow (carbonyl absorbance [≥]0.25 a.u. plus PCA verification) safeguards molecular integrity irrespective of patient age, DVT history or clinical severity. C_LIO_LIAdopting this workflow will harmonise multi centre clot biorepositories and enhance the reproducibility of proteomic, lipidomic and imaging studies. C_LI

biophysics↗

bioRxiv2024

OPTIMIZATION OF DRIED BLOOD SPOT ASSAYS FOR HEPATITIS B VIRUS SURFACE ANTIBODY QUANTIFICATION

Dried blood spot (DBS) cards can be used as an alternative sample collection method to plasma, however, there is no optimized elution protocol for DBS cards specifically for hepatitis B surface antibody (anti-HBs) testing. The study aimed to develop a DBS elution protocol for anti-HBs quantification. Our study sought to determine the ideal phosphate-buffered saline (PBS) buffer volume to use by comparing three PBS volumes (300uL, 450uL, and 500uL), and the optimal time to agitate DBS discs on a plate shaker (1hr, 2hrs, 3hrs, and 4hrs) to yield DBS anti-HBs concentrations that are comparable to corresponding plasma anti-HBs concentrations. The optimal DBS storage temperature (25{degrees}C, -20{degrees}C, and -80{degrees}C) was investigated to determine the ideal longterm storage temperature of the cards. Residual samples were used for optimization (2019-2021). A total of 50 DBS-plasma pairs was used throughout the study, with plasma anti-HBs concentrations being used as the golden standard to compare. The analysis of results was carried out by determining the p-values of the Wilcoxon sign rank. A two-way analysis of variance (ANOVA) was also performed to determine the impact of PBS elution volumes, elution time, and storage temperature on the anti-HBs concentration of DBS samples on STATA Version 15.0. No statistically significant difference between the DBS-plasma anti-HBs pairs was observed when using 450 or 500uL of PBS buffer and when samples were agitated for 3 hours (p=0.594, p=0.499 respectively). The optimal storage temperature for DBS cards was 25{degrees}C because the results showed no statistically significant difference between DBS-plasma anti-HBs titers (p=0.594). The two-way ANOVA analysis showed that elution volumes and time had no statistically significant impact on the DBS anti-HBs concentrations, p=0.948 and p=0.381 respectively. Storage temperature had a statistically significant impact on the DBS anti-HBs concentrations, p=0.002. The optimized DBS elution protocol for anti-HBs quantification will help monitor vaccine efficacy in infants due to the low sample volumes required compared to plasma and also can be used for anti-HBs testing in resource-limited areas around the country.

microbiology↗