Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of Congo
Antimicrobial susceptibility testing (AST) is increasingly needed to guide the <i>Helicobacter pylori</i> (<i>H. pylori</i>) treatment but remains laborious and unavailable in most African countries. To assess the clinical relevance of bacterial whole genome sequencing (WGS)-...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-06-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/8/6/887 |
| _version_ | 1797565580639731712 |
|---|---|
| author | Evariste Tshibangu-Kabamba Patrick de Jesus Ngoma-Kisoko Vo Phuoc Tuan Takashi Matsumoto Junko Akada Yasutoshi Kido Antoine Tshimpi-Wola Pascal Tshiamala-Kashala Steve Ahuka-Mundeke Dieudonné Mumba Ngoy Ghislain Disashi-Tumba Yoshio Yamaoka |
| author_facet | Evariste Tshibangu-Kabamba Patrick de Jesus Ngoma-Kisoko Vo Phuoc Tuan Takashi Matsumoto Junko Akada Yasutoshi Kido Antoine Tshimpi-Wola Pascal Tshiamala-Kashala Steve Ahuka-Mundeke Dieudonné Mumba Ngoy Ghislain Disashi-Tumba Yoshio Yamaoka |
| author_sort | Evariste Tshibangu-Kabamba |
| collection | DOAJ |
| description | Antimicrobial susceptibility testing (AST) is increasingly needed to guide the <i>Helicobacter pylori</i> (<i>H. pylori</i>) 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 <i>H. pylori</i>, 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 <i>H. pylori</i> (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 <i>pbp1A</i> (e.g., T558S, F366L), <i>gyrA</i> (e.g., A92T, A129T), <i>gyrB</i> (e.g., R579C), and <i>rdxA</i> (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. |
| first_indexed | 2024-03-10T19:14:10Z |
| format | Article |
| id | doaj.art-90b862e3f59c4daaac53441f9c9d58e3 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T19:14:10Z |
| publishDate | 2020-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-90b862e3f59c4daaac53441f9c9d58e32023-11-20T03:31:59ZengMDPI AGMicroorganisms2076-26072020-06-018688710.3390/microorganisms8060887Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of CongoEvariste Tshibangu-Kabamba0Patrick de Jesus Ngoma-Kisoko1Vo Phuoc Tuan2Takashi Matsumoto3Junko Akada4Yasutoshi Kido5Antoine Tshimpi-Wola6Pascal Tshiamala-Kashala7Steve Ahuka-Mundeke8Dieudonné Mumba Ngoy9Ghislain Disashi-Tumba10Yoshio Yamaoka11Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, JapanDepartment of Internal Medicine, Gastroenterology and Hepatology Section, Faculty of Medicine, University of Kinshasa, Kinshasa, DR CongoDepartment of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, JapanDepartment of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, JapanDepartment of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, JapanDepartment of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, JapanDepartment of Internal Medicine, Gastroenterology and Hepatology Section, Faculty of Medicine, University of Kinshasa, Kinshasa, DR CongoDepartment of Internal Medicine, Gastroenterology and Hepatology Section, Astryd Clinics, Kinshasa, DR CongoDepartment of Virology, National Institute of Biomedical Research, Kinshasa, DR CongoDepartment of Parasitology, National Institute of Biomedical Research, Kinshasa, DR CongoDepartment of Internal Medicine, Faculty of Medicine, University of Mbujimayi, Mbujimayi, DR CongoDepartment of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, JapanAntimicrobial susceptibility testing (AST) is increasingly needed to guide the <i>Helicobacter pylori</i> (<i>H. pylori</i>) 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 <i>H. pylori</i>, 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 <i>H. pylori</i> (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 <i>pbp1A</i> (e.g., T558S, F366L), <i>gyrA</i> (e.g., A92T, A129T), <i>gyrB</i> (e.g., R579C), and <i>rdxA</i> (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.https://www.mdpi.com/2076-2607/8/6/887<i>Helicobacter pylori</i>whole genome sequencingdrug resistanceantimicrobial susceptibility testingnext-generation sequencingDemocratic Republic of Congo |
| spellingShingle | Evariste Tshibangu-Kabamba Patrick de Jesus Ngoma-Kisoko Vo Phuoc Tuan Takashi Matsumoto Junko Akada Yasutoshi Kido Antoine Tshimpi-Wola Pascal Tshiamala-Kashala Steve Ahuka-Mundeke Dieudonné Mumba Ngoy Ghislain Disashi-Tumba Yoshio Yamaoka Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of Congo Microorganisms <i>Helicobacter pylori</i> whole genome sequencing drug resistance antimicrobial susceptibility testing next-generation sequencing Democratic Republic of Congo |
| title | Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of Congo |
| title_full | Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of Congo |
| title_fullStr | Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of Congo |
| title_full_unstemmed | Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of Congo |
| title_short | Next-Generation Sequencing of the Whole Bacterial Genome for Tracking Molecular Insight into the Broad-Spectrum Antimicrobial Resistance of <i>Helicobacter pylori</i> Clinical Isolates from the Democratic Republic of Congo |
| title_sort | next generation sequencing of the whole bacterial genome for tracking molecular insight into the broad spectrum antimicrobial resistance of i helicobacter pylori i clinical isolates from the democratic republic of congo |
| topic | <i>Helicobacter pylori</i> whole genome sequencing drug resistance antimicrobial susceptibility testing next-generation sequencing Democratic Republic of Congo |
| url | https://www.mdpi.com/2076-2607/8/6/887 |
| work_keys_str_mv | AT evaristetshibangukabamba nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT patrickdejesusngomakisoko nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT vophuoctuan nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT takashimatsumoto nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT junkoakada nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT yasutoshikido nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT antoinetshimpiwola nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT pascaltshiamalakashala nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT steveahukamundeke nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT dieudonnemumbangoy nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT ghislaindisashitumba nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo AT yoshioyamaoka nextgenerationsequencingofthewholebacterialgenomefortrackingmolecularinsightintothebroadspectrumantimicrobialresistanceofihelicobacterpyloriiclinicalisolatesfromthedemocraticrepublicofcongo |