title: Analysis of multilocus sequence typing schemes for 35 different bacteria revealed that gene loci of 10 bacteria could be replaced to improve cost-effectiveness.
abstract: Although multilocus sequence typing (MLST) has been widely used for bacterial typing, the contribution of the gene loci to the discriminatory power of each MLST scheme is unknown. We analyzed the discriminatory powers of 36 MLST schemes using all combinations of the 7 loci and contributions of each locus to the schemes. In 10 schemes, sequencing 6 loci can achieve the discriminatory powers of 7 loci. For the other 26 schemes, the median marginal increase in discriminatory power when 7 instead of 6 loci were used is 0.0004. Sequencing the 7 loci of 50 strains each of Pseudomonas aeruginosa and Acinetobacter baumannii revealed that the discriminatory power for P. aeruginosa was 0.9861 when either 6 (without trp) or 7 loci were used and that for A. baumannii was 0.9363 when 5, 6, or 7 loci were used. Genes that have no additional or minimal contribution to the overall discriminatory powers should be replaced.
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong. pcywoo@hkucc.hku.hk
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
authors.forename: Alan K L
authors.initials: AK
authors.lastname: Tsang
authors.forename: Annette Y P
authors.initials: AY
authors.lastname: Wong
authors.forename: Hui
authors.initials: H
authors.lastname: Chen
authors.forename: Jocelyn
authors.initials: J
authors.lastname: Chu
authors.forename: Susanna K P
authors.initials: SK
authors.lastname: Lau
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D040981:Acinetobacter baumannii / Q000145:classification* / Q000235:genetics*; D003362:Cost-Benefit Analysis; D004269:DNA, Bacterial / Q000235:genetics; D056426:Genetic Loci; D006801:Humans; D058885:Multilocus Sequence Typing / Q000191:economics* / Q000379:methods*; D011550:Pseudomonas aeruginosa / Q000145:classification* / Q000235:genetics*; D012680:Sensitivity and Specificity
chemical_list: D004269:DNA, Bacterial