Long-term evolution of antigen repertoires among carried meningococci

Abstract

Most studies of bacterial pathogen populations have been based on isolates collected from individuals with disease, or their contacts, over short time periods. For commensal organisms that occasionally cause disease, such as Neisseria meningitidis, however, the analysis of isolates from long-term asymptomatic carriage is necessary to elucidate their evolution and population structure. Here, we use mathematical models to analyse the structuring and dynamics of three vaccine-candidate antigens among carried meningococcal isolates collected over nearly 30 years in the Czech Republic. The data indicate that stable combinations of antigenic alleles were maintained over this time period despite evidence for high rates of recombination, consistent with theoretical models in which strong immune selection can maintain non-overlapping combinations of antigenic determinants in the presence of recombination. We contrast this antigenic structure with the overlapping but relatively stable combinations of the housekeeping genes observed among the same isolates, and use a novel network approach to visualize these relationships.

Figure 1.

The association between different pairs of loci over 26 years in the Czech Republic. D* values for each pair of loci was calculated. The boxplots show the median (red line), lower and upper quartiles (blue box) and the extent of the range (whiskers) for those loci that involved more than one comparison; for example, the calculation of D* for each housekeeping gene compared with every other housekeeping gene led to a total of 21 D* scores. For the PorA VR associations, only a single metric was computed between VR1 and VR2 (hence the single line shown on the plot). For the FetA∶PorA VR comparisons, two calculations were made: FetA versus PorA VR1 and FetA versus PorA VR2 (shown by the blue box). ‘VR’ refers to the variable regions of PorA, ‘hk’ refers to housekeeping genes, and ‘FetA’ represents the variable region of FetA. The concatenation of these indicates the comparison made. The PorA VR and housekeeping gene associations were significantly higher than the other two-locus comparisons (F = 108.15, p = 10⁻¹¹), and the PorA VR associations were significantly different from the housekeeping gene associations, but only marginally (F = 6.32, p = 0.0189).

Figure 2.

The distribution of f* scores from the data split into the 1970s (1971–1983) and the 1990s (1992–1997). The number of calculations for each type of two-locus comparison was the same as for the D* scores. The housekeeping gene comparisons represent all three types of comparison: housekeeping gene versus housekeeping gene or PorA VRs or FetA scores (these three groups are not significantly different from each other, as expected).

Figure 3.

The longevity and prevalence of PorA VR2∶FetA VR variant combinations in the dataset. Each bar represents a particular combination of variants that are seen at least twice within the dataset and their order is determined by their frequencies in successive time periods.

Figure 4.

(a) Network visualization of the relationships between isolates for the three antigenic determinants, PorA VR1, PorA VR2 and FetA, showing the time period of combinations: the 1970s (blue), the 1990s (red) and both time periods (purple). (b) Three housekeeping genes, in this case gdh, pdhC and pgm, coloured in the same way as (a). (c) The antigen network, coloured according to two different clonal complexes—ST-41/44 (green) and ST-11 (yellow)—showing the different types of association between the antigens and housekeeping genes in the data.