Genomic Characterization of a Fluoroquinolone Intermediate Resistance Herbaspirillum sp. Strain HhutSZ1 Rarely...

This study aims to conduct a whole-genome analysis of the isolated strain HhutSZ1, providing more reliable clinical experience for the treatment of patients infected with such bacteria.

A patient with IgA nephropathy failed to respond to treatment with ciprofloxacin for an infection. A rare strain of Herbaspirillum was isolated from the patient's blood. The VITEK MS Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) System and VITEK 2 Automated Microbial Identification System were used to conduct a preliminary identification and antibiotic susceptibility tests. Then we performed whole-genome sequencing of this strain along with comparative genomic analysis.

VITEK 2 System identified HhutSZ1 as Burkholderia cepacia, while the VITEK MS System identified it as Herbaspirillum huttiense with a high confidence coefficient. The phylogenetic tree based on the 16S rRNA gene showed that HhutSZ1 belonged to the genus Herbaspirillum. Average Nucleotide Identity (ANI) analysis showed that the scores of this strain compared with other Herbaspirillum huttiense strains were all lower than 95, confirming that this strain did not belong to Herbaspirillum huttiense. The patient's infection failed to resolve despite ciprofloxacin treatment. Subsequent antimicrobial susceptibility testing revealed that HhutSZ1 exhibited intermediate resistance to ciprofloxacin, which is consistent with the clinical treatment failure. Six genes were detected in the Comprehensive Antibiotic Resistance Database (CARD). And among them, five RND family efflux pump genes resistant to fluoroquinolone were all located on chromosomes.

For the genus Herbaspirillum, mass spectrometry identification cannot accurately identify the species. The analysis based on 16s rRNA combined with ANI can be more accurate. Some Herbaspirillum spp may have inherent resistance to fluoroquinolone antibiotics. In conclusion, our findings suggest that the low detection rate and low drug resistance of this strain cannot be overlooked, and the study provides valuable clinical insight for managing infections in immunocompromised patients.