Global multi-host genomic epidemiology of a superbug reveals transmission at One Health interfaces

Antibiotic resistance is a significant global health issue, and Acinetobacter baumannii is one of the most important antibiotic-resistant bacterial pathogens. Due to this, much genomic information has been generated mostly for human clinical isolates. Recently, some studies have focused on A. baumannii from non-human sources. Yet, these studies analyse one or a few sources, and most are limited in terms of the sampling. Clearly, an extensive view of non-human A. baumannii is lacking, as no single study has tried to integrate all the information for both human and non-human A. baumannii populations. Here, gathering a data set of > 23,000 genomes from multiple sources and hosts, we provide a comprehensive view of non-human populations of A. baumannii .Importantly, we conduct a genomic intra-species unit delimitation to properly handle this vast amount of information. We noted that A. baumannii was present in 97 different sources. Our results show that non-human populations of this pathogen are as diverse as the human ones in terms of genetic diversity and have an open pangenome. Remarkably, we found that frequent transmission occurs between humans and non-human sources. Even more, some non-human sources (dogs, horses and wastewater) carry significant antibiotic resistance genes (ARGs) and non-human populations are an open source of ARGs. Thus, non-human A. baumannii is vastly diverse and may pose a public health concern. This study highlights the need for more research on the non-human sources of A. baumannii employing an explicit One Health surveillance approach. We anticipate that similar multi-host genomic epidemiology approximations will be implemented with other important human pathogens.