Enterobacter pseudoroggenkampii sp. nov. carrying quinolone-resistant gene qnrE recovered from clinical samples in China.

Abstract

Two Enterobacter strains 155092T and 170,225 were isolated from clinical samples, pus and sputum, from two hospitalised patients separately, in China. Preliminary identification using Vitek II microbiology system assigned the strains to the Enterobacter cloacae complex. The two strains were subjected to genome sequencing and genome-based taxonomy analysis with type strains of all Enterobacter species and those within closely related genera Huaxiibacter, Leclercia, Lelliottia, and Pseudoenterobacter. The average nucleotide identity (ANI) and in silico DNA-DNA hybridisation (isDDH) values between the two strains were 98.35% and 89.4%, respectively, suggesting that they belong to one species. The two strains had the highest ANI (95.02% and 95.04%) with the type strain of Enterobacter quasiroggenkampii. Their highest isDDH values, also seen with the type strain of E. quasiroggenkampii, were 59.5% and 59.8%, well below the 70% cutoff to define species. The two strains were also characterised for morphological and biochemical features by a set of experiments and observations. The abilities of metabolising gelatin and L-rhamnose could differentiate the two strains from all currently known Enterobacter species. Collectively, the two strains represent a novel Enterobacter species, for which we propose Enterobacter pseudoroggenkampii sp. nov. as the species name. The type strain of this novel species is155092T (= GDMCC 1.3415T = JCM 35646T). The two strains also carried multiple virulence factors comprising aerobactin-encoding iucABCD-iutA and salmochelin-encoding iroN. The two strains also had chromosomally located qnrE, a gene associated with reduced susceptibility to quinolones, suggesting that this species is a potential reservoir of qnrE genes.