Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of Helicobacter pylori Clinical Isolates from the Democratic Republic of Congo.

Autor:	Tshibangu-Kabamba E; Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan.; Department of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, Congo., Ngoma-Kisoko PJ; Department of Internal Medicine, Gastroenterology and Hepatology Section, Faculty of Medicine, University of Kinshasa, Kinshasa, Congo.; Department of Gastroenterology and Hepatology, Cinquantenaire's Hospital, Kinshasa, Congo.; Department of Internal Medicine, Gastroenterology and Hepatology Section, General Referential Hospital of Bukavu, Congo., Tuan VP; Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan.; Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 70000, Vietnam., Matsumoto T; Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan., Akada J; Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan., Kido Y; Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan.; Department of Parasitology, Osaka City University, Osaka 545-8585, Japan., Tshimpi-Wola A; Department of Internal Medicine, Gastroenterology and Hepatology Section, Faculty of Medicine, University of Kinshasa, Kinshasa, Congo.; Department of Internal Medicine, Gastroenterology and Hepatology Section, Marie-Yvettes Clinics, Kinshasa, Congo., Tshiamala-Kashala P; Department of Internal Medicine, Gastroenterology and Hepatology Section, Astryd Clinics, Kinshasa, Congo., Ahuka-Mundeke S; Department of Virology, National Institute of Biomedical Research, Kinshasa, Congo., Ngoy DM; Department of Parasitology, National Institute of Biomedical Research, Kinshasa, Congo.; Department of Tropical Medicine, School of Medicine, University of Kinshasa, Kinshasa, Congo., Disashi-Tumba G; Department of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, Congo., Yamaoka Y; Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan.; Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA.
Jazyk:	angličtina
Zdroj:	Microorganisms [Microorganisms] 2020 Jun 11; Vol. 8 (6). Date of Electronic Publication: 2020 Jun 11.
DOI:	10.3390/microorganisms8060887
Abstrakt:	Antimicrobial susceptibility testing (AST) is increasingly needed to guide the Helicobacter pylori ( H. pylori ) treatment but remains laborious and unavailable in most African countries. To assess the clinical relevance of bacterial whole genome sequencing (WGS)-based methods for predicting drug susceptibility in African H. pylori , 102 strains isolated from the Democratic Republic of Congo were subjected to the phenotypic AST and next-generation sequencing (NGS). WGS was used to screen for the occurrence of genotypes encoding antimicrobial resistance (AMR). We noted the broad-spectrum AMR of H. pylori (rates from 23.5 to 90.0%). A WGS-based method validated for variant discovery in AMR-related genes (discovery rates of 100%) helped in identifying mutations of key genes statistically related to the phenotypic AMR. These included mutations often reported in Western and Asian populations and, interestingly, several putative AMR-related new genotypes in the pbp1A (e.g., T558S, F366L), gyrA (e.g., A92T, A129T), gyrB (e.g., R579C), and rdxA (e.g., R131_K166del) genes. WGS showed high performance for predicting AST phenotypes, especially for amoxicillin, clarithromycin, and levofloxacin (Youden's index and Cohen's Kappa > 0.80). Therefore, WGS is an accurate alternative to the phenotypic AST that provides substantial decision-making information for public health policy makers and clinicians in Africa, while providing insight into AMR mechanisms for researchers. Competing Interests: The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.
Databáze:	MEDLINE
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