The impact of antimicrobials on gonococcal evolution

Abstract

The sexually transmitted pathogen Neisseria gonorrhoeae is regarded as being on the way to becoming an untreatable superbug. Despite its clinical importance, little is known about its emergence and evolution, and how this corresponds with the introduction of antimicrobials. We present a genome-based phylogeographical analysis of 419 gonococcal isolates from across the globe. Results indicate that modern gonococci originated in Europe or Africa, possibly as late as the sixteenth century and subsequently disseminated globally. We provide evidence that the modern gonococcal population has been shaped by antimicrobial treatment of sexually transmitted infections as well as other infections, leading to the emergence of two major lineages with different evolutionary strategies. The well-described multidrug-resistant lineage is associated with high rates of homologous recombination and infection in high-risk sexual networks. A second, multisusceptible lineage is more associated with heterosexual networks, with potential implications for infection control.

Figure 1. Geographic and phylogenetic distribution of Neisseria gonorrhoeae isolates.

The map shows the countries of isolation of the strains in the collection coloured by continent. The phylogeny shows the relationship among the strains (n=419). Coloured strips show (from inside out) the continent of isolation (CONT), year and further typing information (BAPS clusters, NG-MAST, MLST and penA types; colours represent different types or alleles). Mosaic penA types are marked in the outermost black strip.

Figure 2. Global phylogeographic analysis.

The dated maximum likelihood phylogenetic tree shows the posterior probabilities for each continent in every node (pie charts). Continents of isolation (prior) are shown as metadata next to the tips (n=419). The top left legend contains information on the proportion of strains from different continents before (n=121) and after (n=298) the introduction to Asia.

Figure 3. Evolution of antimicrobial resistance genetic determinants in Neisseria gonorrhoeae.

Antimicrobial resistance determinants (chromosomal mutations and presence/absence of the tetM and bla_TEM genes on plasmids (p)) detected in the new 413 strains included in this study using ARIBA and mapped on the maximum likelihood dated tree. Purple represents presence of the determinant and orange its absence. Grey indicates isolates possessing porB1a rather than porB1b. The two main lineages are marked as A (n=294) and B (n=119). The left graph shows the proportion of strains with each resistance determinant for both lineages. Statistical significance from a two-sided test for equality of proportions is also shown in the graph with asterisks. ****p-value<0.0001, ***p-value<0.001, **p-value<0.01, *p-value<0.05.

Figure 4. Characterization of the lineages of Neisseria gonorrhoeae.

Distribution of the proportions of homoplasic sites in all terminal (a) and short terminal branches (<=100 SNPs) (b) in lineages A (n=298), B (n=121) and all strains (n=419) represented as boxplots. Each point represents the proportion of homoplasies in one branch drawn from the total variation found in that branch. Horizontal box lines represent the first quartile, the median and the third quartile. Whiskers extend from the first quartile – 1.5x the interquartile range and the third quartile + 1.5x the interquartile range. Statistical significance between lineages A and B was assessed using a two-sided Wilcoxon test and shown as asterisks. (c) Distribution of the total number of antimicrobial resistance genetic determinants in the strains of each lineage as detected using ARIBA (lineage A n=294; lineage B n=119). (d) Proportion of strains isolated from female (F, n=114) and male (M, n=566) patients in each lineage obtained from combining the global dataset with 376 isolates from two North-American genomic studies, (total n=639; lineage A n=503; lineage B n=136). Asterisks show the significance level from a two-sided test for equality of proportions with continuity correction (c-d). ****p-value<0.0001, ***p-value<0.001, **p-value<0.01.