John A. Crump

Investigating Bacillus anthracis genomic diversity and trait-specific lineages in an endemic area in northern Tanzania through a combination of traditional and culture-free sequencing approaches

This study investigates genomic diversity of Bacillus anthracis in northern Tanzania using traditional and culture-free sequencing, finding high strain diversity and limited host-specific clustering.

Mass spectrometry-based quantification of proteins and post-translational modifications in dried blood: longitudinal sampling of patients with sepsis in Tanzania

The paper quantifies proteins and post-translational modifications in dried blood from sepsis patients in Tanzania, revealing proteome signatures of inflammation and correlations with clinical markers.

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

The TyphiNET data visualisation dashboard: Unlocking Salmonella Typhi genomics data to support public health

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

Prospective cohort study reveals unexpected aetiologies of livestock abortion in northern Tanzania

The paper investigates causes of livestock abortion in Tanzania using a cohort study and serosurveillance, identifying several infectious agents associated with abortions.

Classification and characterisation of livestock production systems in northern Tanzania

The paper classifies livestock production systems in northern Tanzania using quantitative methods and finds three distinct clusters corresponding to traditional pastoral, agro-pastoral, and smallholder systems, with notable shifts toward crop agriculture.

The genomic epidemiology of multi-drug resistant nontyphoidal Salmonella causing invasive disease in sub-Saharan Africa

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