Comparative phenotypic and genotypic antimicrobial susceptibility surveillance in Achromobacter spp. through whole genome sequencing.

Abstract

Treatment of Achromobacter infections remains challenging due to intrinsic and acquired resistance to commonly used antimicrobial agents and no established clinical breakpoints. We attempted accurate species-level identification and compared the presence of genotypic resistance markers to phenotypic susceptibility patterns in retrospectively collected clinical isolates of Achromobacter spp. Our study concludes that Achromobacter xylosoxidans is the most prevalent species. Commercial matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) systems cannot accurately identify all Achromobacter species due to the limited inclusion of spectra in the databases. Phenotypic antimicrobial susceptibility testing (AST) confirms resistance to the majority of antibiotics tested. Newer agents like delafloxacin, plazomicin, and omadacycline showed little or no activity, while minimum inhibitory concentrations were low for eravacycline. In general, the species other than A. xylosoxidans showed lower MIC₅₀ and MIC₉₀, especially to carbapenems and β-lactamase inhibitor combinations like piperacillin-tazobactam, meropenem-vaborbactam, and imipenem-relebactam. Genotypic analysis confirmed that A. xylosoxidans carries a high number of resistance genes, including multidrug efflux pump AxyXY-OprZ, several class D (OXA-type), and the Class A ß-lactamase bla_AXC, while Achromobacter mucicolens has the lowest number of resistance genes and no efflux pumps. This study concludes that there is significant genotypic and phenotypic diversity within the different species of Achromobacter, which are important for the identification of the species and for appropriate antimicrobial therapy.IMPORTANCEIdentification and susceptibility testing of Gram-negative non-fermenting bacteria belonging to the genus Achromobacter is difficult due to the lack of robust databases in commercial identification systems such as matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and clinical breakpoints for antimicrobial agents. Most clinical laboratories interpret minimum inhibitory concentration data using the "non-Enterobacterales" breakpoints included in the Clinical and Laboratory Standards Institute (CLSI) M100. These are breakpoints used for a group of organisms for which data is insufficient to provide species-specific interpretation. Our study provides phenotypic data regarding identification and susceptibility testing and correlates this with the genotypic characterization of 109 clinical isolates belonging to Achromobacter spp. This comprehensive study sheds light on the phenotypic and genotypic character of this bacteria, that is of increasing clinical relevance in hospital-acquired infections.