Uncovering Genetic Determinants of Antibiotic Resistance in Helicobacter pylori through Next-Generation Sequencing and Genome-Wide Association Study Phuc Bui Hoang1,*, Thanh Tran True2, Yamaoka Yoshio3,4,5 1Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, Vietnam 2Department of Biotechnology, Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT), VNU-HCM, Ho Chi Minh City, Vietnam 3Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan 4Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu, Oita, Japan 5Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA *Corresponding Author: phuc.bui@vlu.edu.vn
Online Published on 12 December, 2023. Keywords Helicobacter pylori, Antibiotic resistance, Next-generation sequencing (NGS), Bacterial genome-wide association study (GWAS), Genetic variants. Top |
The objective of this research was to uncover the genetic factors contributing to antibiotic resistance in Helicobacter pylori (H pylori), a bacterium linked to longterm gastroduodenal diseases (Tshibangu-Kabamba and Yamaoka 2021). Given the rising prevalence of antibiotic resistance, the study underscores the importance of swift detection techniques for effective treatment (Tuan et al. 2019). Despite significant strides in understanding the molecular underpinnings of drug resistance, knowledge gaps persist, particularly concerning amoxicillin (AMX) resistance mechanisms (Kuo et al. 2017). |
Leveraging the affordability of next-generation sequencing (NGS) for routine clinical isolate analysis, and in conjunction with the Genome-Wide Association Study (GWAS), this study identified genetic variants associated with specific phenotypes (Tuan et al. 2021). A linear-mixed model was employed to interpret the relationship between these variants and antibiotic resistance in H. pylori, taking into account covariates such as population structure (Lees et al. 2020). |
The research analysed 255 H. pylori strains from Vietnam, Cambodia, and the US using whole-genome sequencing. The susceptibility of each strain to five antimicrobial drugs was determined. The complete genome of the Vietnamese strain CHC97 was obtained through hybridassembly of long-reads (Pacific Biosciences) and short-reads (Illumina). |
A total of 672,042 variants were detected, with 318,757 variants tested for association with AMX resistance. To address the diversity in bacterial genomes, a graph-based unique kmers, called unitigs, were constructed from a total of 255 strains. A comprehensive analysis identified 3,928,855 unitigs, with 1,581,996 filtered-unitigs selected for further investigation into their association with antibiotic resistance. |
For AMX resistance, 152 kmers linked to 45 genes were identified, with the mrcA gene showing the strongest association. For levofloxacin (LEV) resistance, the gyrA gene had the top P-value. For clarithromycin (CLR) resistance, 8 kmers were identified, all mapping to 23S rRNA. However, no association was found between unitigs/SNP and metronidazole (MTZ) resistance, and all strains were found to be susceptible to tetracycline. The study concludes that antibiotic resistance in H. pylori is primarily due to specific mutations in candidate genes. |
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