Genome analysis of manure and soil-dwelling Acinetobacter strains indicates potential health risks associated with antibiotic resistance and virulence factors

The genus Acinetobacter includes opportunistic pathogenic species of increasing clinical importance due to their ability to resist multiple antibiotics and to face multiple environmental stresses. Here, comprehensive whole-genome analysis was used to reveal the presence of genes potentially related to pathogenicity in 11 tetracycline-resistant Acinetobacter isolates from manure of dairy cows under tetracycline and amoxicillin prophylaxis and from soils affected by this manure. The isolates were identified as Acinetobacter pseudolwoffii, A. gerneri, A. gandensis, and A. amyesii and screened their genomes for the presence of genes related to host colonization, infection, or environmental persistence. We detected 164 genes of antimicrobial resistance, virulence factors, mobile genetic elements, or biofilm formation. All isolates were predicted to be human pathogens with high probability (0.7–0.8) and the manure isolates identified as A. pseudolwoffii carried a top-risk human-associated aminoglycoside resistance gene. The phenotypic characterization of the isolates showed that they could all grow at 37 °C, some up to 41 °C, and that they showed differential susceptibility to several antibiotics, with one isolate identified as A. gandensis being multi-resistant. Our analyses suggest that environmental Acinetobacter strains from fresh manure and manured soils possess risky antibiotic-resistance genes and phenotypic traits of clinical relevance indicating potential pathogenicity.