Comprehensive Bioinformatic Assessments of the Variability of Neisseria gonorrhoeae Vaccine Candidates

Abstract

A protective vaccine is the only viable way to stop the spread of gonorrhea in the face of rising antibiotic resistance. However, the notorious phase and antigenic variation of Neisseria gonorrhoeae surface proteins remains one of the challenges in vaccine development. To facilitate vaccine advancement efforts, we carried out comprehensive bioinformatic analyses of sequence variation by comparing 34 gonorrhea antigen candidates among >5,000 clinical N. gonorrhoeae isolates deposited in the Neisseria PubMLST database. Eight protein antigens showed exceptional conservation by having a single allele variant distributed in >80% of isolates. An additional 18 vaccine candidates were represented by ≤3 alleles in >50% of N. gonorrhoeae isolates globally. Phylogenetic analyses highlighted closely related antigen variants and additionally showed that AniA and FetB were the closest between N. gonorrhoeae and N. meningitidis. Up to 44% of N. meningitidis alleles for both antigens have premature stop codons, suggesting differential expression. Mapping polymorphisms to the available three-dimensional structures of 12 antigens revealed low-frequency surface polymorphisms. PorB and TbpB possessed numerous high-prevalence polymorphic sites. While TbpA was also highly variable, conserved loops were nonetheless identified. A high degree of sequence conservation, the distribution of a single antigen variant among N. gonorrhoeae strains globally, or low-frequency sequence polymorphisms in surface loops make ACP, AniA, BamA, BamE, MtrE, NspA, NGO0778, NGO1251, NGO1985, OpcA, PldA, Slam2, and ZnuD promising candidates for a gonorrhea vaccine. Finally, the commonly used N. gonorrhoeae FA1090 strain emerges as a vaccine prototype, as it carries antigen sequence types identical to the most broadly distributed antigen variants. IMPORTANCE Neisseria gonorrhoeae, the Gram-negative bacterium responsible for the sexually transmitted infection gonorrhea, is categorized as a high-priority pathogen for research and development efforts. N. gonorrhoeae’s “superbug” status, its high morbidity, and the serious health impact associated with gonorrhea highlight the importance of vaccine development. One of the longstanding barriers to developing an effective vaccine against N. gonorrhoeae is the remarkable variability of surface-exposed antigens. In this report, we addressed this roadblock by applying extensive bioinformatic analyses to 34 gonorrhea antigen candidates among >5,000 clinical N. gonorrhoeae isolates. Our studies are important, as they reveal promising, conserved gonorrhea vaccine candidates and aid structural vaccinology. Moreover, these approaches are broadly applicable to other infectious diseases where surface antigen variability impedes successful vaccine design.

OpcA and PorB are novel bactericidal antigens of the 4CMenB vaccine in mice and humans

“…MafA and PilE were excluded from the in silico analysis as these are known to be very heterogenic antigens in Neisseria spp. due to frequent intrachromosomal recombination 43,44 . The mean and the range of amino acid identity of the 28 proteins with respect to NZ98/254 are indicated in Table 2.…”

Bacterium of one thousand and one variants: genetic diversity of Neisseria gonorrhoeae pathogenicity.

“…one can find the gonococcal genetic island in N. meningitidis , capsule biosynthesis ( cps ) loci in some commensal Neisseria ; similarly, iron transport systems like FetB or TbpB or adhesion structures such as type IV pili are present in both pathogenic Neisseria and commensals [56–59].…”

“…For example, several studies have shown that many virulence determinants are shared between both pathogenic Neisseria species and commensals; e.g. one can find the gonococcal genetic island in N. meningitidis, capsule biosynthesis (cps) loci in some commensal Neisseria; similarly, iron transport systems like FetB or TbpB or adhesion structures such as type IV pili are present in both pathogenic Neisseria and commensals [56][57][58][59].…”

Canary in the Coal Mine: How Resistance Surveillance in Commensals Could Help Curb the Spread of AMR in Pathogenic Neisseria

“…In closing, we highly encourage the Neisseria research community to support and focus on increasing the collection of commensal Neisseria by both clinical and academic laboratory groups, and sequence these isolates to broaden the database of genomic data for commensal Neisseria species. Not only will these isolates and corresponding sequence data sets aid in the fight against resistance by characterizing Neisseria alleles available for intragenus transfer, they may also aid the Neisseria research community by providing a pool of data to study other common/divergent genomic features and Neisseria biology at large, such as the presence and importance of prophages ( 160 ), the diversity of anti-phage defense systems ( 161 ), the identification of toxin/antitoxin systems ( 146 ), patterns of killing through DNA methylation ( 83 ), and identifying immunogenic antigens as candidate vaccines ( 162 ).…”