Evolution, persistence, and host adaption of a gonococcal AMR plasmid that emerged in the pre-antibiotic era

Abstract

Plasmids are diverse extrachromosomal elements significantly contributing to interspecies dissemination of antimicrobial resistance (AMR) genes. However, within clinically important bacteria, plasmids can exhibit unexpected narrow host ranges, a phenomenon that has scarcely been examined. Here we show that pConj is largely restricted to the human-specific pathogen, Neisseria gonorrhoeae. pConj can confer tetracycline resistance and is central to the dissemination of other AMR plasmids. We tracked pConj evolution from the pre-antibiotic era 80 years ago to the modern day and demonstrate that, aside from limited gene acquisition and loss events, pConj is remarkably conserved. Notably, pConj has remained prevalent in gonococcal populations despite cessation of tetracycline use, thereby demonstrating pConj adaptation to its host. Equally, pConj imposes no measurable fitness costs and is stably inherited by the gonococcus. Its maintenance depends on the co-operative activity of plasmid-encoded Toxin:Antitoxin (TA) and partitioning systems rather than host factors. An orphan VapD toxin encoded on pConj forms a split TA with antitoxins expressed from an ancestral co-resident plasmid or a horizontally-acquired chromosomal island, potentially explaining pConj’s limited distribution. Finally, ciprofloxacin can induce loss of this highly stable plasmid, reflecting epidemiological evidence of transient local falls in pConj prevalence when fluoroquinolones were introduced to treat gonorrhoea.

Evolution and exchange of plasmids in pathogenic Neisseria

“…We found that pConj is the commonest gonococcal plasmid in N. meningitidis , with 104 of 19,951 (0.52%) meningococcal isolates carrying this plasmid. Although pConj is associated with pCryp in N. gonorrhoeae ( 26 ), none of the meningococcal isolates harboring pConj had pCryp. Meningococcal isolates carrying pConj were significantly more likely to be obtained from carriage rather than IMD compared with the other N. meningitidis isolates in the database ( P < 0.0001, odds ratio 3.708, 95% CI: 2.338 to 5.848, Fig.…”

“…A maximum likelihood tree was constructed of meningococcal pConj from strains with a known year of isolation and with the plasmid sequence on a single contig ( n = 89 out of 104 plasmids), together with a selection of gonococcal pConj ( n = 126) including examples of all seven pConj variants ( 26 ) ( Table S3 ); the tetM + Tn 916 transposon was excluded as HGT can distort evolutionary relationships ( 30 ). The resulting tree was run through ClonalFrameML to further adjust for recombination which is frequent in Neisseria spp ( 31 ).…”

“…There are only a few instances of this plasmid in commensals given the relative lack of WGS data. pConj in N. meningitidis is much more genetically diverse than the plasmid in the gonococcus; much of the variation occurs as insertions and deletions in the 9- to 13-kb genetic load (GL) region which harbors genes involved in plasmid maintenance +/- tetM ( 9 , 26 ); however, even after we eliminated the GL region from analysis (as large-scale recombination distorts phylogenetic relationships), the backbone of N. meningitidis pConj is highly diverse compared with the gonococcal plasmid, indicating that pConj has a much longer evolutionary history with the meningococcus than the gonococcus. The identification of virtually identical plasmids in different clonal complexes (cc) of N. meningitidis indicates that the plasmid continues to disseminate within the meningococcal population.…”

Unraveling the evolutionary dynamics of toxin-antitoxin systems in diverse genetic lineages of Escherichia coli including the high-risk clonal complexes

“…S7). There have been multiple lines of evidences entailing orphan antitoxins/toxins in literature ( 36 – 38 ). Neisseria gonorrhoeae , the causative agent of gonorrhea, carries a split TA system composed of an orphan toxin VapD encoded on pConj and antitoxin VapX encoded by other mobile genetic elements.…”

“…Neisseria gonorrhoeae , the causative agent of gonorrhea, carries a split TA system composed of an orphan toxin VapD encoded on pConj and antitoxin VapX encoded by other mobile genetic elements. pConj conserved across N. gonorrhoeae strains harbors genes encoding resistance against beta-lactams and tetracyclines, and it is possible to use interventions targeting the functioning of this split TA system to overcome the harm posed by this plasmid in gonococcus ( 37 ). Orphan toxins, such as OrtT in E. coli , have been implicated in their ability to alleviate the stress associated with amino acid and DNA synthesis.…”