Achromobacter xylosoxidans isolates exhibit genome diversity, variable virulence, high levels of antibiotic resistance and potential intrahost evolution

Abstract Achromobacter xylosoxidans is an emerging pathogen characterized by high levels of antibiotic resistance and increasing infection rates worldwide. This motile, opportunistic pathogen is widely distributed in the environment and can cause various infections, including pneumonia, bacteremia, endocarditis, meningitis, and others. In this study, we analyzed the population structure, antibiotic resistance profiles, and virulence factors of over 200 publicly available genomes. Core genome analysis revealed that A. xylosoxidans is highly adaptable, possessing a relatively small core genome. Antibiotic susceptibility testing of isolates from the United States revealed high resistance to multiple antibiotics including ceftolozane/tazobactam, aztreonam, cefepime, and ciprofloxacin. Our data show that imipenem/relebactam (IMR) is not more effective against A. xylosoxidans than imipenem (IMI) alone, indicating that relebactam does not inhibit β-lactamase activity in Achromobacter. The species features multiple secretion systems, including the Type III secretion system (T3SS) of the YscN family, which is similar to those found in Bordetella pertussis and Pseudomonas aeruginosa . Isolates collected from the same patients showed dynamic changes in cytotoxicity, flagella motility, biofilm and antibiotic resistance suggesting its dynamic adaptation to host environment. Intra-host evolved isolates, NIH-010 and NIH-016, demonstrated the loss of flagella motility and variable cytotoxicity while exhibiting increased antibiotic resistance and enhanced biofilm formation. Sequence analysis suggests that NIH-016-3 has tyrosine to histidine mutation at position 330 (Y330H) near the FlhF Guanosine triphosphate (GTP)-binding domain that may affect flagellar assembly. Interestingly, virulence assays showed significant variation in the ability of different A. xylosoxidans isolates to induce cell death in in vitro models, suggesting its dynamic adaptation to host environment. These findings highlight the complexity of this pathogen group and underscore the urgent need for further research into its mechanisms of antibiotic resistance and virulence. Impact statement This study provides a comprehensive examination of Achromobacter xylosoxidans , an emerging pathogen of global concern due to its high antibiotic resistance and increasing clinical relevance. By analyzing over 200 genomes, we offer critical insights into the population structure, resistance mechanisms, and virulence factors of this species. The identification of a relatively small core genome underscores the adaptability of A. xylosoxidans and its potential for genomic plasticity. The existence of multiple secretion systems (T1SS to T6SS) highlights the great capacity of A. xylosoxidans as a pathogen. Variations in virulence among A. xylosoxidans isolates indicate the complexity of this pathogen and underscore the need for further studies on its virulence mechanisms. The dynamic within-host evolution including the loss of motility-associated systems and the acquisition of enhanced antibiotic resistance and biofilm formation, adds new dimensions to our understanding of its pathogenesis. Flagella, an important virulence mechanism, exhibit variable motility in different isolates, suggesting the bacteria use flagella as an adaptive mechanism. This work also showed that A. xylosoxidans are resistant to relebactam, which are effective in other bacteria. These findings emphasize the urgent need for targeted therapeutic strategies to combat this opportunistic pathogen.