Computational protocol: Emerging azithromycin-resistance among the Neisseria gonorrhoeae strains isolated in Hungary

Similar protocols

Protocol publication

[…] Out of the 58 resistant and 42 intermediately resistant strains 29 and 21 were selected for N. gonorrhoeae multiantigen sequence typing (NG-MAST) according to a previously described method []. The sequences of porB and tbpB PCR products were determined after their preliminary purification by the Exosap IT purification kit (Affymetrix, USA). BigDye® Terminator v3.1 Cycle Sequencing Kit (Life Technologies, USA) was used and the same forward and reverse primers were applied as for porB and tbpB PCR methods. Last purification was carried out by NucleoSEQ Column PCR Purification Kit (Macherey–Nagel, Germany). Nucleotide sequences were determined by capillary electrophoresis, with a capillary length of 50 cm and POP-7 polymer on ABI 3130xl Genetic Analyzer (Applied Biosystems, Foster City, CA, USA).NG-MAST STs including the new alleles and STs were assigned on the NG-MAST website (www.ng-mast.net).Phylogenetic tree was constructed by MEGA6 (Molecular Evolutionary Genetics Analysis Version 6.0) Neighbour-Joining algorithm, using maximum composite likelihood model []. The degree of similarity was determined using the highly similar sequence (Megablast) BLASTN Program of the National Library of Medicine of the National Center for Biotechnology Information []. […]

Pipeline specifications

Software tools MEGA, BLASTN
Application Phylogenetics
Organisms Neisseria gonorrhoeae
Diseases Communicable Diseases
Chemicals Spectinomycin, Ceftriaxone, Ciprofloxacin, Tetracycline, Azithromycin, Cefixime