Stephen G. Baker

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

This study shows that colistin resistance in K. pneumoniae modifies LPS, leading to different inflammatory responses in host cells.

This study assesses cross-neutralisation of sarbecoviruses by COVID-19 vaccines in older adults, finding reduced neutralisation of Omicron variants and some animal sarbecoviruses but enhanced neutralisation of specific bat and pangolin coronaviruses.

This paper introduces modular RNA:DNA nanostructures for direct, amplification-free rRNA profiling, enabling detection of rRNA variants and processing states.

This paper develops a dual-target glycoconjugate vaccine against Shigella sonnei using a carrier protein and O-antigen, showing it elicits IgG responses to both components.

The paper isolates antibodies from a Shigella outbreak in non-human primates, showing some target O-antigen and T3SS proteins, with some antibodies enhancing virulence.

The paper identifies megaplasmids in Enterobacteriaceae species, showing they are self-transmissible, encode drug resistance, and may enhance bacterial competitiveness.

The paper provides 15 genomically characterized Shigella sonnei isolates representing diverse sub-clades, with complete genome sequences and public availability for research.

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

This paper introduces RGStraP, a tool to infer genetic population structure from RNAseq data and shows it can control for population structure in gene expression analyses.

This study investigates the genomic structure and evolution of Salmonella ST34 in Southeast Asia, showing that multidrug resistance plasmids drive its clonal expansion and international spread.

The paper reports the persistent circulation of third-generation cephalosporin-resistant Salmonella Typhi in Mumbai, India, linked to an IncX3 plasmid carrying resistance genes.

The paper introduces Pathogenwatch, a tool for genomic surveillance of Salmonella Typhi, enabling AMR prediction and population-level risk assessment through global data sharing.

The paper identifies azithromycin-resistant Salmonella Typhi in Northern India, showing independent emergence of resistance and highlighting the need for typhoid conjugate vaccines.

This study investigates the genomic epidemiology of multi-drug resistant nontyphoidal Salmonella in sub-Saharan Africa, identifying key serotypes and transmission patterns.

The paper characterizes nine novel multidrug-resistant hypervirulent Klebsiella pneumoniae isolates in India, which harbor mosaic plasmids containing both antimicrobial resistance and virulence genes.

The paper describes the development of a validated SARS-CoV-2 diagnostic workflow in an academic laboratory to support local screening during the pandemic.

The paper identifies a host gene signature using machine learning to distinguish enteric fever from other febrile diseases with high accuracy.

The paper introduces mSWEEP, a method for high-resolution bacterial lineage quantification from plate sweeps, showing improved accuracy in detecting and estimating abundances of bacterial lineages.

This study uses whole genome sequencing to analyze Salmonella Typhi isolates from Thailand before and after a national immunization program, showing that post-vaccine isolates were imported from neighboring countries rather than persisting locally.