Abstract
ESKAPE pathogens are the leading cause of nosocomial infections. The Global Priority List of WHO has categorized ESKAPE as priority 1 and 2 pathogens. Even though several mechanisms contribute to antimicrobial resistance, OXA β-lactamase has emerged as a new threat in combating nosocomial infections. In the present study we have investigated the presence of OXA and their variants, copy number, distribution on chromosomes/plasmids, subfamilies, phylogenetic relationships, amino acid identities and variabilities in ESKAPE pathogens. Our results revealed that a total of 929 OXA were present in 2258 completely assembled genomes, which could be further subdivided into 16 sub-families. Among all the ESKAPE pathogens, OXA were highly prevalent in A. baumannii, followed by P. aeruginosa and K. pneumoniae but completely absent in E. faecium and S. aureus while, only a few copies were found in Enterobacter spp. Most of the OXA variants belonged to the OXA-51-like subfamily (200 proteins), followed by OXA-50-like subfamily (189 proteins), OXA-23-like subfamily (156 proteins) and OXA-1-like subfamily (154 proteins). OXA-51-like, OXA-213-like, OXA-134-like, OXA-58-like, OXA-24-like and OXA-20-like subfamilies were present exclusively in A. baumannii. Phylogenetic tree of the subfamilies revealed that OXA-1-like and OXA-33-like, OXA-51-like and OXA-213-like and, OXA-5-like and OXA-10-like belonged to the same branches with amino acid identities as 100%, 97.10% and 80.90% respectively. This indicates that the members of these subfamily-pairs might have evolved from the same ancestor or have recently diverged. Thus, a judicious use of carbapenems is warranted to curtail the rise of new OXA enzymes and preserve them. This is the first detailed report about the OXA of ESKAPE pathogens.
Highlights
Indiscriminate use, misuse and overuse of antibiotics has escalated into antimicrobial resistance (AMR) and multidrug resistance (MDR) which are regarded as the greatest scourges of the 21st century [1,2]
Of the 2256, 12,397, 10,383, 5057, 5711 and 2680 entries enlisted in the NCBI genome database corresponding to E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa and Enterobacter spp. only; 187, 590, 732, 233, 291 and 225 entries corresponded to the complete genomes of E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa and Enterobacter spp., respectively (Table 1)
12 entries corresponded to only chromosomes and 175 corresponded to both chromosomes and plasmids of E. faecium
Summary
Indiscriminate use, misuse and overuse of antibiotics has escalated into antimicrobial resistance (AMR) and multidrug resistance (MDR) which are regarded as the greatest scourges of the 21st century [1,2]. ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are of global concern due to their involvement in several hospital-acquired infections (nosocomial infections). WHO has included them in the ‘Global Priority List of Antibioticresistant Bacteria to Guide Research, Discovery and Development of New Antibiotics’ [5]. Four members of this group viz. K_pneumoniae, A. baumannii, P. aeruginosa and Enterobacter spp. are included in priority 1 category (critical) while two members E. faecium and S. aureus come in priority 2 (high) category.
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