Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms

Abstract

Traditional and molecular typing schemes for the characterization of pathogenic microorganisms are poorly portable because they index variation that is difficult to compare among laboratories. To overcome these problems, we propose multilocus sequence typing (MLST), which exploits the unambiguous nature and electronic portability of nucleotide sequence data for the characterization of microorganisms. To evaluate MLST, we determined the sequences of approximately 470-bp fragments from 11 housekeeping genes in a reference set of 107 isolates of Neisseria meningitidis from invasive disease and healthy carriers. For each locus, alleles were assigned arbitrary numbers and dendrograms were constructed from the pairwise differences in multilocus allelic profiles by cluster analysis. The strain associations obtained were consistent with clonal groupings previously determined by multilocus enzyme electrophoresis. A subset of six gene fragments was chosen that retained the resolution and congruence achieved by using all 11 loci. Most isolates from hyper-virulent lineages of serogroups A, B, and C meningococci were identical for all loci or differed from the majority type at only a single locus. MLST using six loci therefore reliably identified the major meningococcal lineages associated with invasive disease. MLST can be applied to almost all bacterial species and other haploid organisms, including those that are difficult to cultivate. The overwhelming advantage of MLST over other molecular typing methods is that sequence data are truly portable between laboratories, permitting one expanding global database per species to be placed on a World-Wide Web site, thus enabling exchange of molecular typing data for global epidemiology via the Internet.

Figure 1

Chromosomal locations of gene fragments. The locations are drawn on the physical map of strain Z2491 (12), a subgroup IV-1 strain. The six loci chosen for MLST are shown in boldfaced, underlined text. aroE and mtg are located next to each other (14) on BglII fragment B14 (41 kb). pip and opaJ are also next to each other (13) (data not shown) and are located on BglII fragment B16 (32 kb). serC and opaB are located within a few kilobases of each other (13) as are abcZ and opc (unpublished data). pgm and adk hybridized to the same set of fragments, including B7 and P3, which overlap by ≈50 kb. gdh mapped on SpeI fragment S17 (35 kb).

Figure 2

Dendrogram of genetic relationships among 107 strains based on 6 gene fragments. Linkage distance is indicated by a scale at the top, and the MLEE or ST assignments of lineages are indicated by shaded rectangles. The asterisk indicates ST-21 (serogroup A strain B534).