Northwestern Medicine investigators have identified issues with most genomic sequence data for the Neisseria gonorrhoeae bacterium, findings that could complicate future epidemiological and pathogenesis studies, according to a recent study published in the Journal of Infectious Diseases.  

Hank Seifert, PhD, the John Edward Porter Professor of Biomedical Research, was the senior author of the study.   

N. gonorrhoeae is the strain of bacteria that causes gonorrhea, one of the most common sexually transmitted infections. If not treated promptly with antibiotics, the disease can cause infertility, sepsis, and pregnancy complications.  

The N. gonorrhoeae pilE gene encodes the PilE protein, which is a subunit of the Type IV pilus — a hairlike structure found on the bacteria’s surface — which helps the bacteria infect the host cell and spread. 

“Clinical isolates are almost always piliated upon isolation but become nonpiliated during in vitro growth,” Seifert said.  

The pilE gene also undergoes high-frequency diversification through gene conversion. Pilin antigenic variation — a mechanism used by bacteria to evade the immune system by changing their Type IV proteins — can result in piliated, underpiliated, or nonpiliated cells, which affects how well the bacteria can evade the immune system.  

“This diversity generation system can change the protein that makes up this fiber on the cell surface or can change its level of expression to lower or to none at all, and we think that’s part of this complex program. What we also know is that in the laboratory, when you lose expression of the pilus, the bacteria grow faster,” said Seifert, who is also a professor of Microbiology-Immunology.  

In the current study, investigators analyzed more than 15,000 N. gonorrhoeae genomic sequences in an open-access whole-genome database to characterize pilE and pilS gene diversity. The scientists then developed an in-silico PCR assay and used other bioinformatics techniques to characterize pilin loci.   

From this analysis, the scientists found that approximately half of the genomic sequences contained a pilE gene, despite all genomes having other Type IV pilus genes. 

“The most surprising finding was that half of the genomes had actually deleted the pilE gene, and that is an irreversible modification. For the other half, most of them wouldn’t produce a pilus but would be able to revert back to normal, and those are more predictable of what you would find,” Seifert said.  

The findings demonstrate that all N. gonorrhoeae strains contain the genes necessary for pilus expression; however, because most isolates are piliated when isolated, the authors suggest that these samples were in vitro-derived variants based on the amount of irreversible, non-piliated pilE deletions.  

The findings also underscore the variability of pilin loci and raise questions about how this genomic data should be interpreted in future studies, Seifert said.  

“The clinical labs that isolate the bacteria and the laboratories that then determine the genomic sequence should, in this case, pay attention to whether they retain piliation or not,” Seifert said.  

Iryna Boiko, MD, PhD, a postdoctoral fellow in the Department of Microbiology-Immunology, and Selma Metaane, PharmD, PhD, a postdoctoral fellow in the Department of Microbiology-Immunology, were co-lead authors of the study.  

This work was supported by National Institutes of Health grants R37AI033493 and R01AI146073.