[Antibiotic analysis and whole genome sequencing of two nocardia farcinica strains causing joint infection].

ABSTRACT

Objective: To analyze the molecular characteristics and antibiotic susceptibility of two strains of Nocardia farcinica isolated from patients with joint infection using whole genome sequencing. Methods: Two strains of Nocardia farcinica causing knee-joint infections in two elderly patients were collected in January 2020. Whole genome sequencing was used to determine the nocardia species. Drug sensitivity test was performed using the micro-broth dilution and E-test method according to CLSI M24 guideline. ABRicate was used to analyze drug resistance and virulence genes. Snippy and other bioinformatic tools were used for genomic comparison, and to construct SNP homologous tree. Results: The clinical isolates in this study were both Nocardia farcinica. Antimicrobial susceptibility test showed the isolates were resistant to ceftriaxone, cefepime, cefotaxime and trimethoprim/sulfamethoxazole (TMP/SMX). Imipenem, linezolid and amoxicillin-clavulanic acid showed good activity. Four antibiotic resistance genes including class A ß-lactamase gene far-1, RNA polymerase binding protein gene RbpA, multi-drug resistance efflux pump transcription activator gene MtrA and regulatory transcription factor gene vanR-O were identified in the Nocardia farcinica genomes, which conferred resistance to beta-lactams, rifampicin, macrolides and vancomycin respectively. No acquired TMP/SMX resistance genes were identified. There are multiple missense mutations in the dihydrofolate reductase family genes. Four virulence genes of icl, mbtH, phoP, and relA that are homologous to Mycobacterium tuberculosis were found. SNP homologous tree analysis showed the two Nocardia strains were closely related, and there were only ten SNP sites, six compound substitutions and one deletion mutation between them. Conclusions: Whole genome sequencing technology is helpful to explore the molecular characteristics and resistance mechanisms of Nocardia species. Nocardia farcinica has a trend of spreading in China. Resistance to TMP/SMX is worthy of attention. The mutation of genes involved in the metabolic pathway of dihydrofolate might be one of multiple TMP/SMX resistance mechanisms.