Structure variability and phylogeny of Klebsiella pneumoniae OXA-48 Class D carbapenemases

Abstract

Carbapenem antibiotics are considered last resort options in the treatment of infections caused by multidrug-resistant Enterobacteriaceae producing Extended Spectrum β-Lactamases (ESBLs). The emergence of Klebsiella pneumoniae OXA-48 in particular is steadily expanding and represents a major public health concern. The aim of the present study is to analyze the variability and phylogeny of K. pneumoniae OXA-48 amino acids structures from different geographic areas of the world .The data on K. pneumoniae OXA-48 amino acids structures were collected during the month of May 2019 from the Protein Data Bank (PDB). The alignment of protein sequences was carried using the Clustal Omega program available on the UniProt database. The phylogenetic analysis and dendrogram were realized using MEGA software version 6. Among 58 structures, 8 representative OXA-48 variants were selected for the study. The alignment demonstrated that the conserved motifs were in general well conserved except for the two mutations S70G and S70A remarked respectively in the two chains 5HAQ and 5HAP from the United States. However, the OXA-181 and OXA-245 variants displayed mutations far away from the active sites. In comparison with OXA-48, OXA-181 variant showed four substitutions at Thr104Ala, Asn110Asp, Glu168Gln, and Ser171Ala; while OXA-245 had a single amino acid substitution Glu125Tyr. The phylogenetic analysis revealed three distinct clusters; the first one consists of four OXA-48 structures (Canada, Norway, United States and Italy) and one OXA-245 (Norway), the second includes two OXA-48 structures from the United States, while the third cluster is formed by an individual OXA-181 from Norway. The results of this study confirm a similar evolutionary trend in the structure of K. pneumoniae OXA-48 variants worldwide. The current data on K. pneumoniae OXA-48 amino acids structures is limited to restricted geographic areas, and need broadening to provide the actual state of molecular changes and antimicrobial resistance evolution