Manuel Jara

The paper uses chain graphs to identify risk factors for fluoroquinolone- and macrolide-resistance in Campylobacter coli from swine farms, finding genotype and host exposures explain significant variance in MICs.

This study compares short-read and long-read sequencing technologies for detecting antimicrobial resistance genes in ESKAPE pathogens, highlighting the strengths and limitations of each approach and advocating for hybrid assembly for comprehensive analysis.

This study quantifies the genomic determinants of fitness in E. coli ST131 using phylodynamic models, finding that fluoroquinolone resistance mutations provide a major fitness advantage.