A. S. Walker

Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine learning approaches.

This paper predicts pyrazinamide resistance in Mycobacterium tuberculosis using machine learning models trained on pncA mutations and structural features, achieving 80.2% sensitivity and 76.9% specificity.

A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing

The paper validates a workflow for detecting antibiotic residues and measuring water chemistry in hospital sink samples, and confirms boric acid preserves microbial and resistome composition for metagenomic sequencing.

Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning

This study uses machine learning to predict fungal secondary metabolite bioactivity from biosynthetic gene clusters, finding higher accuracy when combining bacterial and fungal data.

M. tuberculosis microvariation is common and is associated with transmission: analysis of three years prospective universal sequencing in England

This study identifies microvariation in M. tuberculosis strains using sequencing data from England, finding that mixed infections are associated with increased tuberculosis transmission.

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

The paper identifies amino acid substitutions in penicillin binding proteins (PBPs) PBP1 and PBP3 as a mechanism of cephalosporin resistance in C. difficile, which co-occurs with fluoroquinolone resistance in epidemic lineages.

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

This study evaluates four AMR gene typing methods using simulated and real E. coli data, revealing significant discrepancies and highlighting issues with current bioinformatic approaches.

BashTheBug: a crowd of volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates.

BashTheBug uses crowdsourced volunteers to accurately measure MICs of 13 antitubercular drugs from microdilution plates, showing median/mode of classifications is sufficient.

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

The paper analyzes the pangenome dynamics of Enterobacteriaceae from environmental sources, finding that plasmids carry more AMR genes and are influenced by niche and geography rather than phylogeny.

The unintended consequences of a surge in antibiotic resistance when removing wastewater drain biofilm

This study shows that replacing contaminated sink drains with new plumbing increases antimicrobial resistance genes and Enterobacterales abundance due to disrupted biofilms.

Multi-omic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

The paper shows hospital sink drains are colonized by diverse E. coli and Klebsiella strains, including resistant ones, and may contribute to patient infections.

DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform

This paper develops a thermo-protection buffer to enable direct whole genome sequencing of Mycobacteria from clinical samples using Nanopore technology, achieving high coverage at low bacterial concentrations.

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

This study shows that amoxicillin-clavulanate resistance in E. coli is quantitative, not binary, and that WGS-based predictions outperform traditional phenotyping methods.

Hash-based core genome multi-locus sequencing typing for Clostridium difficile

This paper introduces hash-cgMLST, a method for rapid genome comparison in Clostridium difficile, showing it matches standard cgMLST performance but with faster processing.

Metagenomic Nanopore sequencing of influenza virus direct from clinical respiratory samples

This study uses metagenomic Nanopore sequencing to detect influenza virus in clinical respiratory samples, achieving high sensitivity and complete genome sequencing.

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

This study evaluates how sequencing depth affects taxonomic composition and AMR gene detection in metagenomic samples, finding that higher depth is needed for AMR gene richness.

Modelling microbiome recovery after antibiotics using a stability landscape framework

The paper develops a quantitative stability landscape model to analyze microbiome recovery after antibiotics and finds support for long-term state transitions in gut and salivary microbiomes after ciprofloxacin and clindamycin.

Selective culture enrichment and sequencing of faeces to enhance detection of antimicrobial resistance genes

This study develops a hybrid protocol combining culture enrichment and plasmid extraction to improve detection of antimicrobial resistance genes in faecal samples.

Nanopore metagenomic sequencing of full length human metapneumovirus (HMPV) within a unique sub-lineage

This study uses Nanopore metagenomic sequencing to directly sequence the full-length HMPV genome from a UK patient, identifying a unique genetic group and demonstrating the utility of Nanopore for clinical diagnosis.

MinION Nanopore Sequencing of Multiple Displacement Amplified Mycobacteria DNA Direct from Sputum

This study evaluates the effectiveness of multiple displacement amplification followed by MinION sequencing for detecting Mycobacteria DNA in sputum samples.

Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

The paper tracks K. quasipneumoniae's acquisition of carbapenemase plasmids and environmental persistence in a hospital setting over multiple years.

Identifying mixed Mycobacterium tuberculosis infection and laboratory cross-contamination during Mycobacterial sequencing programs

The paper develops metrics to detect mixed Mycobacterium tuberculosis infections and cross-contamination in sequencing data from tuberculosis diagnostic labs.

A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

The paper investigates the evolutionary history of Clostridium difficile RT078, finding that tetracycline resistance genes, particularly tetM, were acquired independently in multiple clonal expansions, contributing to its increased prevalence.

Control of artefactual variation in reported inter-sample relatedness during clinical use of a Mycobacterium tuberculosis sequencing pipeline

The paper identifies genomic regions in Mycobacterium tuberculosis that contribute to artefactual variation in bacterial similarity searches and proposes a method to reduce such variation.

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

This paper develops a low-cost WGS method for TB diagnosis and surveillance using direct respiratory samples, achieving rapid results with high concordance with reference labs.