Co-Occurrence of the bla(KPC-2) and Mcr-3.3 Gene in Aeromonas caviae SCAc2001 Isolated from Patients with Diarrheal Disease

PURPOSE: To characterize the genetic feature of a multi-drug-resistant Aeromonas caviae strain isolated from the diarrhea sample of a 45-year-old male patient with acute diarrhea. MATERIALS AND METHODS: Whole-genome of the A. caviae strain SCAc2001 was sequenced via the Illumina system, followed by a series of bioinformatic analyses to describe the genetic feature. RESULTS: The genome sequence of A. caviae SCAc2001 was assembled into 340 scaffolds (305 of them were > 1000 bp in length and 4,487,370 bp in total) with an average G+C content of 61.09%. Phylogenetic analysis showed that the A. caviae SCAc2001 strain was highly similar to the A. caviae strain R25-2 and T25-39. Resistome analysis identified that A. caviae SCAc2001 carried 13 antimicrobial resistance genes, including β-lactams (bla(KPC), bla(CTX-M-14), bla(TEM-1), bla(OXA-10), bla(OXA-427), bla(VEB-3) and bla(MOX-6)), aminoglycosides (aadA1), fluoroquinolones (aac(6ʹ)-Ib-cr), phenicol resistance (catB3), sulfonamide (sul1), trimethoprim (dfrA5) and colistin resistance (mcr-3.3).And also, A. caviae ScAc2001 carried 54 putative virulence genes including the type IV pilus, fimbria, flagellarthe, and hemolysin A encoding genes, and 12 pathogen–host interactions (PHI) genes. There were also four genomic islands and eight prophages in the genome of A. caviae ScAc2001. In addition, A. caviae SCAc2001 also carried three secondary metabolism products coding clusters including nonribosomal peptide synthetases (nrps), hserlactone and bacteriocin. CONCLUSION: A. caviae ScAc2001 carries many resistance genes, a variety of virulence factors, PHI genes and four genomic islands and eight prophages, which poses a severe threat to infectious diseases control strategies, diagnosis methods and clinical treatment.