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Background  Clinical characteristics (taxonomy, virulence genes and antimicrobial resistance ) of  Aeromonas  in isolated from extra-intestinal and intestinal infections were investigated to describe epidemiology, associated virulence factors and optimal therapy options.    Methods  Clinical samples ( n  = 115) of  Aeromonas  were collected from a general hospital in Beijing between the period 2015 and 2017. Taxonomy was investigate by Multilocus phylogenetic analysis (MLPA), 10 putative virulence factors by use of polymerase chain reaction (PCR) and antimicrobial resistance to 15 antibiotics by use of the microbroth dilution method.    Results  The most common species of  Aeromonas  detected in samples of intestinal tract included;  A. caviae  (43.9%),  A. veronii  (35.7%), and  A. dhakensis  (12.2%). Prevalent species of  Aeromonas  collected from extra-intestinal infections included;  A. hydrophila  (29.4%),  A. caviae  (29.4%), and  A. dhakensis  (23.5%).  A. hydrophila  were detected in 1% of stool samples and 29.4% (5/17) of extra-intestinal infections.  A. hydrophila  strains in extra-intestinal infections were related to malignancy. The most common medical conditions among patients with  Aeromonas  infections included malignancy and liver-transplant related cholecystitis. Multiple drug resistance (MDR) was prevalent in extra-intestinal isolates (82.3%, 14/17) and was greater than the prevalence in intestinal isolates (30.6%, 30/98) ( P  < 0.05). Resistant rates of extra-intestinal isolates were 70.6, 35.3, 23.5 and 5.9% for ceftriaxone, ciprofloxacin, gentamicin and imipenem, respectively, and were higher than found in previous studies. Despite differences in the number and type of virulence genes among samples of  Aeromonas , no significant correlation was found between invasion and virulent genes in intestinal or extra-intestinal infections.    Conclusions  Overall results of this study support a role for  Aeromonas spp.  as a potential causative infectious agent of gastroenteritis, and malignancy, liver cirrhosis, post liver transplantation in immunocompromised patients.  A. hydrophila  was more prevalent in samples of extra-intestinal infections when compared to samples of intestinal infections, and was especially prominent in samples of patients presenting with malignancy.  Aeromonas  isolates from extra-intestinal samples had high rates of drug resistance but 3rd generation cephalosporins, fluoroquinolones and aminoglycosides remain as options to treat severe diarrhea. However, increasing MDR of extra-intestinal infection samples warrants monitoring.    Electronic supplementary material  The online version of this article (10.1186/s12879-019-3766-0) contains supplementary material, which is available to authorized users.

Taxonomy, virulence genes and antimicrobial resistance of Aeromonas isolated from extra-intestinal and intestinal infections