Phenotypic and genotypic analysis of antimicrobial resistance and population structure of gastroenteritis-related Aeromonas isolates

Abstract

Background: The population structure and the correlation between antimicrobial resistance (AMR) phenotypes and genotypes in Aeromonas species isolated from patients with gastroenteritis are not well understood. The aims of the study were to: (1) investigate the antimicrobial susceptibility profiles of Aeromonas species isolated from patients with gastroenteritis; (2) explore the relationship between AMR genes and resistance phenotypes; and (3) describe the population structure of these isolates and provide evidence of transmission events among them.

Methods: This microbiological survey was performed at the Microbiology Laboratory of the Emek Medical Center in Afula, Israel. Cultivation of Aeromonas was attempted from stool samples that tested positive by PCR. Antimicrobial susceptibility testing (AST) was performed using the Sensititre GN3F microdilution panel. Whole genome sequencing (WGS) was done using the Illumina NextSeq500/550 system. Phylogenetic studies involved multi-locus sequence typing (MLST) and core genome (cg) MLST. Resistance mechanisms were identified using the Comprehensive Antibiotic Resistance Database and compared with the AST results.

Results: The study included 67 patient-unique isolates. The species that were identified included A. caviae (n = 58), A. dhakensis (n = 3), A. media (n = 2), A. veronii (n = 2) and A. hydrophila (n = 2). Isolates were almost uniformly susceptible to amikacin, gentamicin, aztreonam, cefepime, ceftazidime, ciprofloxacin and meropenem. All isolates with the exception of 1-2 isolates were resistant to ampicillin, cefazolin and ampicillin-sulbactam which was compatible with the presence of the bla_OXA genes. Variable resistance rates were observed to cefuroxime, cefoxitin, ceftriaxone, piperacillin-tazobactam that were not correlated with the presence of other β-lactamase genes. Resistance to tetracycline and trimethoprim-sulfamethoxazole correlated with the presence of tetA and sul1, respectively. The population structure of A. caviae was highly diverse with the minority of the isolates (16/57) clustering into six defined sequence types. A cgMLST-based distance of four genes was found in one pair of isolates, suggesting common source transmission.

Conclusions: A. caviae is the dominant species related to gastroenteritis and is characterized by a diverse population structure, with almost no evidence for common-source transmission. Resistance rates to most antimicrobial agents were low and partially matched with the presence of resistance genes.

Keywords: Aeromonas; Antimicrobial resistance; Gastroenteritis; Whole genome sequencing.

Fig. 1

The MIC distributions of 12 antimicrobials for 58 A. caviae isolates. The red, orange and green dots indicate the resistant, intermediate and susceptible breakpoints, respectively. Black dots were used if no breakpoints were available. MIC₅₀ and MIC₉₀ values are indicated by black dotted and black dashed lines, respectively. Dot/dash lines indicate identical MIC₅₀ and MIC₉₀ values

Fig. 2

Antimicrobial phenotypic-genotypic correlations of Aeromonas species. The correlation is presented in the context of a cgMLST-based neighbor-joining tree analysis. The phenotypic-genotypic correlations are presented from left to right for SXT, tetracycline and β-lactam antimicrobials, respectively

Fig. 3

CgMLST-based neighbor-joining tree comprising 58 A. caviae isolates. Sequence types (ST) are marked in different colors according to the nomenclature of the 6-loci MLST scheme hosted on PubMLST