1
|
Gutiérrez-Escobar AJ, Velapatiño B, Borda V, Rabkin CS, Tarazona-Santos E, Cabrera L, Cok J, Hooper CC, Jahuira-Arias H, Herrera P, Noureen M, Wang D, Romero-Gallo J, Tran B, Peek RM, Berg DE, Gilman RH, Camargo MC. Identification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru. Front Microbiol 2020; 11:601839. [PMID: 33381095 PMCID: PMC7767971 DOI: 10.3389/fmicb.2020.601839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/16/2020] [Indexed: 01/01/2023] Open
Abstract
Region-specific Helicobacter pylori subpopulations have been identified. It is proposed that the hspAmerind subpopulation is being displaced from the Americans by an hpEurope population following the conquest. Our study aimed to describe the genomes and methylomes of H. pylori isolates from distinct Peruvian communities: 23 strains collected from three groups of Native Americans (Asháninkas [ASHA, n = 9], Shimaas [SHIM, n = 5] from Amazonas, and Punos from the Andean highlands [PUNO, n = 9]) and 9 modern mestizos from Lima (LIM). Closed genomes and DNA modification calls were obtained using SMRT/PacBio sequencing. We performed evolutionary analyses and evaluated genomic/epigenomic differences among strain groups. We also evaluated human genome-wide data from 74 individuals from the selected Native communities (including the 23 H. pylori strains donors) to compare host and bacterial backgrounds. There were varying degrees of hspAmerind ancestry in all strains, ranging from 7% in LIM to 99% in SHIM. We identified three H. pylori subpopulations corresponding to each of the Native groups and a novel hspEuropePeru which evolved in the modern mestizos. The divergence of the indigenous H. pylori strains recapitulated the genetic structure of Native Americans. Phylogenetic profiling showed that Orthogroups in the indigenous strains seem to have evolved differentially toward epigenomic regulation and chromosome maintenance, whereas OGs in the modern mestizo (LIM) seem to have evolved toward virulence and adherence. The prevalence of cagA+/vacA s1i1m1 genotype was similar across populations (p = 0.32): 89% in ASHA, 67% in PUNO, 56% in LIM and 40% in SHIM. Both cagA and vacA sequences showed that LIM strains were genetically differentiated (p < 0.001) as compared to indigenous strains. We identified 642 R-M systems with 39% of the associated genes located in the core genome. We found 692 methylation motifs, including 254 population-specific sequences not previously described. In Peru, hspAmerind is not extinct, with traces found even in a heavily admixed mestizo population. Notably, our study identified three new hspAmerind subpopulations, one per Native group; and a new subpopulation among mestizos that we named hspEuropePeru. This subpopulation seems to have more virulence-related elements than hspAmerind. Purifying selection driven by variable host immune response may have shaped the evolution of Peruvian subpopulations, potentially impacting disease outcomes.
Collapse
Affiliation(s)
| | - Billie Velapatiño
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Victor Borda
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC/MCTIC), Petrópolis, Brazil
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Eduardo Tarazona-Santos
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Jaime Cok
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | - Mehwish Noureen
- National Institute of Genetics, Mishima, Japan.,Department of Genetics, Graduate School of Life Sciences, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Judith Romero-Gallo
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bao Tran
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Richard M Peek
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Douglas E Berg
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Robert H Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| |
Collapse
|
2
|
van Vliet AHM. Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori. FEMS Microbiol Lett 2016; 364:fnw296. [PMID: 28011701 DOI: 10.1093/femsle/fnw296] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/08/2016] [Accepted: 12/22/2016] [Indexed: 12/23/2022] Open
Abstract
The human bacterial pathogen Helicobacter pylori has a highly variable genome, with significant allelic and sequence diversity between isolates and even within well-characterised strains, hampering comparative genomics of H. pylori In this study, pan-genome analysis has been used to identify lineage-specific genes of H. pylori A total of 346 H. pylori genomes spanning the hpAfrica1, hpAfrica2, hpAsia2, hpEurope, hspAmerind and hspEAsia multilocus sequence typing (MLST) lineages were searched for genes specifically overrepresented or underrepresented in MLST lineages or associated with the cag pathogenicity island. The only genes overrepresented in cag-positive genomes were the cag pathogenicity island genes themselves. In contrast, a total of 125 genes were either overrepresented or underrepresented in one or more MLST lineages. Of these 125 genes, alcohol/aldehyde-reducing enzymes linked with acid resistance and production of toxic aldehydes were found to be overrepresented in African lineages. Conversely, the FecA2 ferric citrate receptor was missing from hspAmerind genomes, but present in all other lineages. This work shows the applicability of pan-genome analysis for identification of lineage-specific genes of H. pylori, facilitating further investigation to allow linkage of differential distribution of genes with disease outcome or virulence of H. pylori.
Collapse
Affiliation(s)
- Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7AD, UK
| |
Collapse
|
3
|
Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility. J Clin Microbiol 2015; 53:2877-88. [PMID: 26135867 PMCID: PMC4540916 DOI: 10.1128/jcm.01357-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/19/2015] [Indexed: 12/18/2022] Open
Abstract
Whole-genome sequencing is becoming a leading technology in the typing and epidemiology of microbial pathogens, but the increase in genomic information necessitates significant investment in bioinformatic resources and expertise, and currently used methodologies struggle with genetically heterogeneous bacteria such as the human gastric pathogen Helicobacter pylori. Here we demonstrate that the alignment-free analysis method feature frequency profiling (FFP) can be used to rapidly construct phylogenetic trees of draft bacterial genome sequences on a standard desktop computer and that coupling with in silico genotyping methods gives useful information for comparative and clinical genomic and molecular epidemiology applications. FFP-based phylogenetic trees of seven gastric Helicobacter species matched those obtained by analysis of 16S rRNA genes and ribosomal proteins, and FFP- and core genome single nucleotide polymorphism-based analysis of 63 H. pylori genomes again showed comparable phylogenetic clustering, consistent with genomotypes assigned by using multilocus sequence typing (MLST). Analysis of 377 H. pylori genomes highlighted the conservation of genomotypes and linkage with phylogeographic characteristics and predicted the presence of an incomplete or nonfunctional cag pathogenicity island in 18/276 genomes. In silico analysis of antibiotic susceptibility markers suggests that most H. pylori hspAmerind and hspEAsia isolates are predicted to carry the T2812C mutation potentially conferring low-level clarithromycin resistance, while levels of metronidazole resistance were similar in all multilocus sequence types. In conclusion, the use of FFP phylogenetic clustering and in silico genotyping allows determination of genome evolution and phylogeographic clustering and can contribute to clinical microbiology by genomotyping for outbreak management and the prediction of pathogenic potential and antibiotic susceptibility.
Collapse
|
4
|
Maldonado-Contreras A, Mane SP, Zhang XS, Pericchi L, Alarcón T, Contreras M, Linz B, Blaser MJ, Domínguez-Bello MG. Erratum to: Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance. BMC Microbiol 2014. [PMCID: PMC4041143 DOI: 10.1186/1471-2180-14-122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|