Phylogenomic and phenotypic analyses highlight the diversity of antibiotic resistance and virulence in both human and non-humanAcinetobacter baumannii

Abstract

AbstractAcinetobacter baumanniiis a Gram-negative opportunistic pathogen causing infections of the immunocompromised. With a high incidence of muti-drug resistance, carbapenem-resistantA. baumanniiis as a priority 1 pathogen designated by the WHO. The current literature has expertly characterized clinical isolates ofA. baumannii.As the challenge of these infections has recently been classified as a One Health issue, we set out to explore the diversity of isolates from human and non-clinical sources such as agricultural surface water, urban streams, various effluents from wastewater-treatment plants and tank milk; and, importantly, these isolates came from a wide geographic distribution. Phylogenomic analysis considering almost 200 isolates showed that our diverse set is well-differentiated from the main international clones ofA. baumannii. We discovered novel sequence types in both hospital and non-clinical settings, and five strains that overexpress the RND efflux pumpadeIJKwithout changes in susceptibility. Further, we detected ablaADC-79in a non-human isolate despite its sensitivity to all antibiotics. There was no significant differentiation between the virulence profiles of clinical and non-clinical isolates in theGalleria mellonellainsect model of virulence suggesting that virulence is neither dependent on geographic origin nor isolation source. Detection of antibiotic resistance and virulence genes in non-human strains suggests that these isolates may act as a genetic reservoir for clinical strains. This endorses the notion that in order to combat multi-drug resistant infection caused byA. baumannii,a One Health approach is required, and a deeper understanding of non-clinical strains must be achieved.ImportanceThe global crisis of antibiotic resistance is a silent one. More and more bacteria are becoming resistant to all antibiotics available for treatment, leaving no options remaining. This includesAcinetobacter baumannii.This Gram-negative opportunistic pathogen shows a high frequency of multi-drug resistance, and many strains are resistant to last-resort drugs carbapenem and colistin. Research has focused on strains of clinical origin, but there is a knowledge gap regarding virulence traits, particularly, howA. baumanniibecome the notorious pathogen of today. Antibiotic resistance and virulence genes have been detected in strains from animals, and environmental locations such as grass and soil. As such,A. baumanniiis a One Health concern which includes the health of humans, animals and the environment. Thus, in order to truly combat the antibiotic resistance crisis, we need to understand antibiotic resistance and virulence gene reservoirs of this pathogen under the One Health continuum.RepositoriesNCBI GenBank Accession numbers: Bioproject PRJNA819071, Biosamples SAMN26898552 - SAMN26898587.