Identification of a novel Providencia species showing multi-drug-resistant in three patients with hospital-acquired infection

Abstract

Providencia species are important opportunistic pathogens for humans and are associated with several infectious diseases. In this study, we found three clinical strains belonging to a novel Providencia species, namely Providencia huashanensis, including strains CRE-3FA-0001T, CRE-138-0026, and CRE-138-0111. These strains were recovered from three patients, and all of them were associated with nosocomial infections, including surgical site, urinary tract, and intracranial infections. The three strains showed high-level resistance to many types of antimicrobials, including amikacin, aztreonam, ceftazidime, cefepime, ciprofloxacin, colistin, polymyxin B, imipenem, meropenem, ceftazidime-avibactam, imipenem-relebactam. Investigation of the resistance mechanism revealed that acquired resistance genes such as blaKPC, blaNDM, blaPER, blaOXA, aac, ant, qnrD, etc., played an important role in the multidrug-resistant phenotype for the three strains. The phylogenetic trees were reconstructed based on the 16S rRNA gene sequences, multi-locus sequence analysis, and core SNPs. The genome sequence of the strains had a range of 83.5-85.8% average nucleotide identity (ANI) and 21-25.5% in silico DNA-DNA hybridization (isDDH) score with other Providencia type strains. The ANI&isDDH values and the phylogenetic tree indicated that the strains CRE-3FA-0001T, CRE-138-0026, and CRE-138-0111 strains should be considered as a novel species of the genus Providencia, for which the name P. huashanensis sp. nov. is proposed. The type strain is CRE-3FA-0001T =CCTCC AB 2023186T=KCTC 8373T.