Abstract
Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.
Highlights
Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR)
In addition to its concerning disease burden, shigellae are increasingly resistant to antimicrobials8,9 and ciprofloxacin-resistant Shigella, a phenotype conferred by mutations in the Quinolone Resistance Determining Regions (QRDR) of the chromosome, is recognised by the World Health Organisation as a priority AMR pathogen10
The national archive contains all S. flexneri and ~ 70% of S. sonnei isolated in hospital, private and regional laboratories, and basic epidemiological data were extracted from sample submission forms, i.e., region, gender, patient age and travel history where noted
Summary
Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). Horizontally acquired resistance genes encoding azithromycin resistance were present multiphyletically, and were strongly associated with MSMA sublineages (OR 58, 95% CI 20–231, p < 0.0001, Fig. 1, Supplementary Data 1).
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