T. E. Peto

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.

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.

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.

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.

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.

Validating a 14-drug microtitre plate containing bedaquiline and delamanid for large-scale research susceptibility testing of Mycobacterium tuberculosis

The paper validates a 14-drug microtitre plate for measuring MICs of anti-TB compounds in M. tuberculosis isolates, finding optimal reading with the Vizion system after 14 days incubation.

Automated detection of bacterial growth on 96-well plates for high-throughput drug susceptibility testing of Mycobacterium tuberculosis

This paper introduces AMyGDA, a software tool for automated detection of M. tuberculosis growth on 96-well plates to determine drug susceptibility.

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.