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Acinetobacter cumulans sp. nov., isolated from hospital sewage and capable of acquisition of multiple antibiotic resistance genes

Qin, Jiayuan, Maixnerová, Martina, Nemec, Matěj, Feng, Yu, Zhang, Xinzhuo, Nemec, Alexandr, Zong, Zhiyong
Systematic and applied microbiology 2019 v.42 no.3 pp. 319-325
Acinetobacter, aminoglycosides, antibiotic resistance genes, carbapenems, cluster analysis, hospitals, matrix-assisted laser desorption-ionization mass spectrometry, multiple drug resistance, nucleic acid hybridization, phylogeny, sequence analysis, sewage, China
We studied the taxonomic position of six phenetically related strains of the genus Acinetobacter, which were recovered from hospital sewage in China and showed different patterns of resistance to clinically important antibiotics. Whole-genome sequencing of these strains and genus-wide phylogeny reconstruction based on a set of 107 Acinetobacter core genes indicated that they formed a separate and internally cohesive clade within the genus. The average nucleotide identity based on BLAST and digital DNA–DNA hybridization values between the six new genomes were 97.25–98.67% and 79.2–89.3%, respectively, whereas those between them and the genomes of the known species were ≤78.57% and ≤28.5%, respectively. The distinctness of the strains at the species level was also supported by the results of the cluster analysis of the whole-cell protein fingerprints generated by MALDI-TOF MS. Moreover, the strains displayed a catabolically unique profile and could be differentiated from the phylogenetically closest species at least by their inability to grow on d,l-lactate. A total of 18 different genes were found in the six genome sequences which encode resistance to seven classes of antimicrobial agents, including clinically important carbapenems, oxyimino-cephalosporins, or aminoglycosides. These genes occurred in five different combinations, with three to 10 different genes per strain. We conclude that the six strains represent a novel Acinetobacter species, for which we propose the name Acinetobacter cumulans sp. nov. to reflect its ability to acquire and cumulate diverse resistance determinants. The type strain is WCHAc060092T (ANC 5797T=CCTCC AB 2018119T=GDMCC 1.1380T=KCTC 62576T).