Non- Species: Occurrence in Infections in Hospitalized Patients, Identification, and Antibiotic Resistance.

BACKGROUND

species other than are becoming increasingly more important as opportunistic pathogens for humans. The primary aim of this study was to assess the prevalence, species distribution, antimicrobial resistance patterns, and carbapenemase gene content of clinical non- () isolates that were collected as part of a sentinel surveillance program of bacterial infections in hospitalized patients. The secondary aim was to evaluate the performance of MALDI-TOF MS systems for the species-level identification of isolates.

METHODS

Clinical bacterial isolates were collected from multiple sites across Russia and Kazakhstan in 2016-2022. Species identification was performed by means of MALDI-TOF MS, with the Autobio and Bruker systems used in parallel. The PCR detection of the species-specific gene was used as a means of differentiating from species, and the partial sequencing of the gene was used as a reference method for species identification. The susceptibility of isolates to antibiotics (amikacin, cefepime, ciprofloxacin, colistin, gentamicin, imipenem, meropenem, sulbactam, tigecycline, tobramycin, and trimethoprim-sulfamethoxazole) was determined using the broth microdilution method. The presence of the most common in -acquired carbapenemase genes (, , , , , and ) was assessed using real-time PCR.

RESULTS

In total, 234 isolates were identified as belonging to 14 species. These comprised 6.2% of spp. and 0.7% of all bacterial isolates from the observations. Among the species, the most abundant were (42.7%), (13.7%), the group (9.0%), (7.7%), and (6.0%). Notably, two environmental species, and , were found for the first time in the clinical samples of patients with urinary tract infections. The prevalence of resistance to different antibiotics in species varied from <4% (meropenem and colistin) to 11.2% (gentamicin). Most isolates were susceptible to all antibiotics; however, sporadic isolates of , , , , , and were resistant to carbapenems. was more frequently resistant to sulbactam, aminoglycosides, trimethoprim-sulfamethoxazole, and tigecycline than the other species. Four (1.7%) isolates of , , were found to carry carbapenemase genes ( and , either alone or in combination). The overall accuracy rates of the species-level identification of isolates with the Autobio and Bruker systems were 80.8% and 88.5%, with misidentifications occurring in 5 and 3 species, respectively.

CONCLUSIONS

This study provides important new insights into the methods of identification, occurrence, species distribution, and antibiotic resistance traits of clinical isolates.