Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes

Abstract

Epidemiological studies and analysis of putative virulence genes have shown that Listeria monocytogenes has diverged into several phylogenetic divisions. We hypothesize that similar divergence has occurred for many genes that influence niche-specific fitness and virulence and that identifying these differences may offer new opportunities for the detection, treatment, and control of this important pathogen. To explore this issue further, we developed a microarray composed of fragmented DNA taken from 10 strains of L. monocytogenes. We then hybridized genomic DNA from 50 different strains to replicate arrays and analyzed the resulting hybridization patterns. A simple Euclidean distance metric permitted the reconstruction of previously described genetic relationships between serotypes, and only four microarray probes were needed to discriminate between the most important serotypes (1/2a, 1/2b, 1/2c, and 4). We calculated an index of linkage equilibrium from the microarray data and confirmed that L. monocytogenes has a strongly clonal population structure (I(A) = 3.85). Twenty-nine informative probes were retrieved from the library and sequenced. These included genes associated with repairing UV-damaged DNA, salt tolerance, biofilm formation, heavy metal transport, ferrous iron transport, and teichoic acid synthesis. Several membrane-bound lipoproteins and one internalin were identified, plus three phage sequences and six sequences with unknown function. Collectively, these data confirm that many genes have diverged between lineages of L. monocytogenes. Furthermore, these results demonstrate the value of mixed-genome microarrays as a tool for deriving biologically useful information and for identifying and screening genetic markers for clinically important microbes.

FIG. 1.

Euclidean distance between 55 microarray hybridization experiments. The dendrogram was constructed using the Ward's minimum variance algorithm. Division nomenclature follows that described by Piffaretti et al. (25).

FIG. 2.

Average signal intensity (error bar equals SEM) for the four probes used for serotype classification by DFA. Bars correspond to probe 1094 (open), probe 369 (black), probe 362 (grey), and probe 289 (lined).

FIG. 3.

Bootstrap distribution of I_A values for L. monocytogenes microarray data (bars). The point estimate for L. monocytogenes (d) is 3.85. Additional point estimates are provided for reference: (a) N. gonorrhoeae, (b) N. meningitidis, (c) Salmonella spp., and (e) Rhizobium spp. (21).