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Background  Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are  Klebsiella pneumoniae  and  Enterobacter cloacae . Despite this, most of our knowledge about the changing patterns of disease caused by these two pathogens is based on studies with limited timeframes that provide few insights into their population dynamics or the dynamics in AMR elements that they can carry.    Results  We investigate the population dynamics of two priority AMR pathogens over 7 years between 2007 and 2012 in a major UK hospital, spanning changes made to UK national antimicrobial prescribing policy in 2007. Between 2006 and 2012,  K. pneumoniae  showed epidemiological cycles of multi-drug-resistant (MDR) lineages being replaced approximately every 2 years. This contrasted  E. cloacae  where there was no temporally changing pattern, but a continuous presence of the mixed population.    Conclusions  The differing patterns of clonal replacement and acquisition of mobile elements shows that the flux in the  K. pneumoniae  population was linked to the introduction of globally recognized MDR clones carrying drug resistance markers on mobile elements. However,  E. cloacae  carries a chromosomally encoded  ampC  conferring resistance to front-line treatments and shows that MDR plasmid acquisition in  E. cloacae  was not indicative of success in the hospital. This led to markedly different dynamics in the AMR populations of these two pathogens and shows that the mechanism of the resistance and its location in the genome or mobile elements is crucial to predict population dynamics of opportunistic pathogens in clinical settings.    Electronic supplementary material  The online version of this article (10.1186/s13059-019-1785-1) contains supplementary material, which is available to authorized users.

genome biology

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center