Recombination events drives the emergence of Colombian Helicobacter pylori subpopulations with self-identity ancestry

ABSTRACT

Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America, H. pylori has evolved into several subpopulations. We analysed the genome of 154 Colombian strains along with 1,091 strains from worldwide populations to discern the ancestry and adaption to Colombian people. Population structure and ancestry was inferred with FineStructure and ChromoPainter. Phylogenetic relationship and the relative effect of recombination were analysing the core SNPs. Also, a Fst index was calculated to identify the gene variants with the strongest fixation in the Colombian subpopulations compared to their parent population hspSWEurope. FineStructure allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia, that included three subgroups following their geographic origin. Colombian subpopulations represent an admixture of European, African and Indigenous ancestry; although some genomes showed a high proportion of self identity, suggesting an advanced adaption to these mestizo Colombian groups. We found that recombination is more important that punctual mutations in H. pylori genome diversity, 13.9 more important in hspSWEurope, 12.5 in hspSWEColombia and 10.5 in hspColombia, reflecting the divergence of these subpopulations. Fst analysis identified 82 SNPs fixed in 26 genes of the hspColombia subpopulation that encode for outer membrane and central metabolism proteins. Strongest fixation indexes were identified in genes encoding HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations with a self identity ancestry, reflected in allele changes on genes encoding for outer membrane proteins.

KEYWORDS:

• Helicobacter pylori
• Colombia
• population structure
• ancestry
• evolution
• recombination

Acknowledgments

To the researchers who participated in this study, L’oréal-UNESCO for Women In Science Community program; Unidad de Investigación en Enfermedades Infecciosas of Instituto Mexicano del Seguro Social in Mexico City, Mexico; Grupo de Investigación en Citogenética, Filogenia y Evolución de Poblaciones of Universidad del Tolima, Tolima, Colombia; Laboratorio de Inmunología of Instituto Nacional de Cancerología, Bogotá, Colombia; and the Genome Center, Department of Biochemistry and Molecular Medicine, School of Medicine-University of California, Davis, California, USA.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The H. pylori genomes that support the findings of this study are publicly available

at Enterobase (https://doi.org/10.1080/21505594.2022.2095737), Genbank (https://doi.org/10.1080/21505594.2022.2095737), and BIGSdb (https://doi.org/10.1080/21505594.2022.2095737).

Data deposition

The information into this paper was deposited in Biorxiv and is available at: https://biorxiv.org/cgi/content/short/2021.12.14.472690v1.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/21505594.2022.2095737.

Additional information

Funding

This work was supported by the Universidad del Tolima under Grant [number 30113, 350113, 160114, 10110, 40218] and contracts [398-2017 and 851-2020]; MinCiencias under Grant [number 110565843382 and 874-2020] contracts [204-2015]; Unidad de Investigación en Enfermedades Infecciosas, UMAE Pediatria of Instituto Mexicano del Seguro Social; National Cancer Institute under Grant [R01CA223978 and P30CA093373]; US National Institutes of Health and The Auburn Community Cancer Endowed Chair in Basic Science; and Programa para la Formación de Capital Humano de Alto Nivel of Tolima Department, MinCiencias and Tolima governorate under Grant [755 -2016].The content of this article is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.