Genome-wide identification and oxacillinase OXA distribution characteristics of spp. based on a global database.

OBJECTIVE

To use genomic analysis to identify spp. and to explore the distribution characteristics of ß-lactamase oxallicinases (OXA) among species globally.

METHODS

Genomes of global spp. were downloaded from GenBank using Aspera batch. After quality check using CheckM and QUAST software, the genomes were annotated using Prokka software to investigate the distribution of OXAs across spp.; a phylogenetic tree was constructed to explore the evolutionary relationship among the OXA genes in spp. Average-nucleotide identification (ANI) was performed to re-type the spp. BLASTN comparison analysis was implemented to determine the sequence type (ST) of strain.

RESULTS

A total of 7,853 genomes were downloaded, of which only 6,639 were left for further analysis after quality check. Among them, 282 OXA variants were identified from the genomes of 5,893 spp.; OXA-23 ( = 3,168, 53.8%) and OXA-66 (2,630, 44.6%) were the most frequent OXAs, accounting for 52.6% (3,489/6639), and the co-carriage of OXA-23 and OXA-66 was seen in 2223 (37.7%) strains. The 282 OXA variants were divided into 27 clusters according to the phylogenetic tree. The biggest clade was OXA-51-family carbapenem-hydrolyzing enzymes composed of 108 OXA variants. Overall, 4,923 . were identified out of the 6,639 spp. strains and 291 distinct STs were identified among the 4,904 OXA-carrying . . The most prevalent ST was ST2 ( = 3,023, 61.6%) followed by ST1 ( = 228, 4.6%).

CONCLUSION

OXA-like carbapenemases were the main OXA-type β-lactamase spread widely across spp. Both OXA-23 and OXA-66 were the predominant OXAs, among all . strains, with ST2 (belonging to CC2) being the main clone disseminated globally.