Publicly available Neisseria gonorrhoeae genomes predominantly represent in vitro-derived nonpiliated variants

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This repository contains raw data used in the Manuscript "Publicly available Neisseria gonorrhoeae genomes predominantly represent in vitro-derived nonpiliated variants".

Abstract

Background. The Neisseria gonorrhoeae pilE gene encodes the PilE protein, the major subunit of the Type IV pilus and a primary colonization and virulence factor. The pilE gene undergoes high-frequency diversification mainly through gene conversion from one of many pilS copies. Pilin antigenic variation (AV) can result in piliated, underpiliated, or nonpiliated cells, and other mechanisms also produce nonpiliated variants. These unique molecular processes contribute to gonococcal population diversity, facilitating immune evasion. While the process of pilin variation is understood, the diversity of pilE and pilS genes from clinical isolates is understudied.

Methods. We analyzed 15,186 N. gonorrhoeae genomes, including finished (n = 65) and draft ( n =15,121) genomes, in the PubMLST database to characterize pilE and pilS gene diversity. We developed an in-silico PCR assay and used multiple alignments, protein structural analysis, and bioinformatics pipelines to characterize the pilin loci.

Results. The finished genomes had one to nine pilS loci at conserved chromosomal locations. Only 52.13% of genomic sequences contained a pilE gene, despite all genomes having other Type IV pilus genes. When the pilE gene was present, most of the defined conserved sequences were preserved. However, most predicted PilE protein sequences contained premature stop codons, which were found in several silent copies.

Conclusion. This analysis revealed that all N. gonorrhoeae strains possess genes content necessary for pilin AV; however, most of the genomic sequences were derived from nonpiliated variants that emerged during in vitro culture through reversible pilus phase variation and irreversible deletion of the pilE gene.

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