Last modified: 2014-04-11
Abstract
In the microbiological study of Nesseria gonorrhoeae carried out by the Center for Skin and Venereal Diseases and Cosmetology (Moscow, Russia), 612 isolates collected in Russia in 2006-2012 were genotyped using NG-MAST scheme and their minimum inhibitory concentrations (MICs) of six antibiotics were measured. The question in mind was to determine the genetic markers of antibiotic resistance. Because of low number of samples per genotype and slight inaccuracy in genotyping, phylogenetic-distance-based clustering was needed to estimate the hot-spots of antibiotic resistance.
N.gonorrhoeae multi-antigen sequence typing (NG-MAST) is based on fragments of two hypervariable genes por and tbpB. A significant part of the genes’ variability is due to indel mutations. This renders the standard approaches to calculation of phylogenetic distance ineffective because they disregard indel information. Also, alignment of the genetic sequences becomes problematic.
In the talk, presented will be the results of analysis of correlation between various types of genetic clustering and MIC level of each of six antibiotics. Alignment will be produces using PRANK algorithm with some manual corrections. Phylogenetic distances will be calculated both using full NG-MAST genes (with and without indels) and using scan-window approach to determine local markers of resistance. Potential hot-spots of antibiotic resistance will be highlighted.