Benjamin Carter

PhD thesis: Genomic epidemiology, international travel and local persistence: Understanding antimicrobial resistance threats in emerging Shiga toxin-producing Escherichia coli (STEC)

Whole genome sequencing is revolutionising pathogen surveillance for the detection of antimicrobial resistance determinants (ARDs). Selection, exchange, and carriage of ARDs in the gut microbiota facilitate a severe public health crisis through the global dissemination of antimicrobial resistance (AMR). Shiga toxin-producing Escherichia coli (STEC) is an internationally prevalent zoonotic pathogen capable of life-threatening gastrointestinal disease, with significant variation in the proportion of isolates harbouring ARDs between emerging clonal complexes. Through retrospective analyses of over 10,000 STEC genomes, my research combines phylodynamic modelling with contextual epidemiological data to evaluate ARD accumulation and exchange dynamics in STEC clonal complexes, investigating the distribution and drivers of ARD variation. These investigations consider factors such as antimicrobial usage, contact patterns, and ARDs acquired from lineages associated with travel to countries with high rates of AMR. Through my research, I intend to optimise public health advice for effective targeted surveillance and intervention strategies for infection control.

Who or what inspired you to pursue your research interests?

During high school, I was captivated by Jim O’Neill’s global review on antimicrobial resistance. I was fascinated by mechanisms that drive AMR and surprised by its association with forecasts of 10 million annual deaths by 2050. My passion for public health grew when my father was admitted to intensive care during the COVID-19 pandemic. This inspired my biomedical scientist career at the UK Health Security Agency, where I was invigorated by my master’s thesis surrounding multidrug resistance in STEC O117:H7. This culminated in my current passion for genomic epidemiology, especially around applied public health research regarding AMR and STEC.