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Tuan VP, Yahara K, Dung HDQ, Binh TT, Tung PH, Tri TD, Thuan NPM, Khien VV, Trang TTH, Phuc BH, Tshibangu-Kabamba E, Matsumoto T, Akada J, Suzuki R, Okimoto T, Kodama M, Murakami K, Yano H, Fukuyo M, Takahashi N, Kato M, Nishiumi S, Azuma T, Ogura Y, Hayashi T, Toyoda A, Kobayashi I, Yamaoka Y. Corrigendum: 'Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates'. Microb Genom 2023; 9. [PMID: 37410636 PMCID: PMC10438799 DOI: 10.1099/mgen.0.001062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023] Open
Affiliation(s)
- Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Vu Van Khien
- Department of GI Endoscopy, 108 Central Hospital, Hanoi, Vietnam
| | | | - Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Microbiology, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Tadayoshi Okimoto
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Masaaki Kodama
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Chiba University, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Noriko Takahashi
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Mototsugu Kato
- Division of Endoscopy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Gastroenterology, National Hospital Organization Hakodate Hospital, Hakodate, Hokkaido, Japan
| | - Shin Nishiumi
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
- Department of Omics Medicine, Hyogo College of Medicine, Hyogo, Japan
| | - Takashi Azuma
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Ichizo Kobayashi
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Medicine, Gastroenterology Section, Baylor College of Medicine, Houston, TX, USA
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Phuc BH, Tuan VP, Binh TT, Tung PH, Tri TD, Dung HDQ, Thuan NPM, Fauzia KA, Tshibangu-Kabamba E, Alfaray RI, Saruuljavkhlan B, Matsumoto T, Akada J, Yamaoka Y. Comparative genomics of two Vietnamese Helicobacter pylori strains, CHC155 from a non-cardia gastric cancer patient and VN1291 from a duodenal ulcer patient. Sci Rep 2023; 13:8869. [PMID: 37258611 DOI: 10.1038/s41598-023-35527-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Helicobacter pylori is involved in the etiology and severity of several gastroduodenal diseases; however, plasticity of the H. pylori genome makes complete genome assembly difficult. We report here the full genomes of H. pylori strains CHC155 and VN1291 isolated from a non-cardia gastric cancer patient and a duodenal ulcer patient, respectively, and their virulence demonstrated by in vitro infection. Whole-genome sequences were obtained by combining long- and short-reads with a hybrid-assembly approach. Both CHC155 and VN1291 genome possessed four kinds of genomic island: a cag pathogenicity island (cagPAI), two type 4 secretion system islands within an integrative and conjugative element (tfs ICE), and prophage. CHC155 and VN1291 carried East Asian-type cagA and vacA s1m1, and outer membrane protein genes, including two copies of oipA. Corresponded to genetic determinants of antibiotic resistance, chromosomal mutations were identified in CHC155 (rdxA, gyrA, and 23S rRNA) and VN1291 (rdxA, 23S rRNA, and pbp1A). In vitro infection of AGS cells by both strains induced the cell scattering phenotype, tyrosine phosphorylation of CagA, and promoted high levels of IL8 secretion, indicating fully intact phenotypes of the cagPAI. Virulence genes in CHC155 and VN1291 genomes are crucial for H. pylori pathogenesis and are risk factors in the development of gastric cancer and duodenal ulcer. Our in vitro studies indicate that the strains CHC155 and VN1291 carry the pathogenic potential.
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Grants
- 21K08010 Ministry of Education, Culture, Sports, Science and Technology, Japan
- 21K07898 Ministry of Education, Culture, Sports, Science and Technology, Japan
- 221S0002 Ministry of Education, Culture, Sports, Science and Technology, Japan
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Affiliation(s)
- Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Faculty of Applied Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Ho Dang Quy Dung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | | | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan.
- Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu, Oita, Japan.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
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Tran BA, Dao TTP, Dung HDQ, Van NB, Ha CC, Pham NH, Nguyen TCHTNC, Nguyen TC, Pham MK, Tran MK, Tran TM, Tran MT. Support of deep learning to classify vocal fold images in flexible laryngoscopy. Am J Otolaryngol 2023; 44:103800. [PMID: 36905912 DOI: 10.1016/j.amjoto.2023.103800] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/19/2023] [Indexed: 02/26/2023]
Abstract
PURPOSE To collect a dataset with adequate laryngoscopy images and identify the appearance of vocal folds and their lesions in flexible laryngoscopy images by objective deep learning models. METHODS We adopted a number of novel deep learning models to train and classify 4549 flexible laryngoscopy images as no vocal fold, normal vocal folds, and abnormal vocal folds. This could help these models recognize vocal folds and their lesions within these images. Ultimately, we made a comparison between the results of the state-of-the-art deep learning models, and another comparison of the results between the computer-aided classification system and ENT doctors. RESULTS This study exhibited the performance of the deep learning models by evaluating laryngoscopy images collected from 876 patients. The efficiency of the Xception model was higher and steadier than almost the rest of the models. The accuracy of no vocal fold, normal vocal folds, and vocal fold abnormalities on this model were 98.90 %, 97.36 %, and 96.26 %, respectively. Compared to our ENT doctors, the Xception model produced better results than a junior doctor and was near an expert. CONCLUSION Our results show that current deep learning models can classify vocal fold images well and effectively assist physicians in vocal fold identification and classification of normal or abnormal vocal folds.
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Affiliation(s)
- Bich Anh Tran
- Otorhinolaryngology Department, Cho Ray Hospital, Ho Chi Minh City, Viet Nam.
| | - Thao Thi Phuong Dao
- University of Science, VNUHCM, Ho Chi Minh City, Viet Nam; John von Neumann Institute, VNUHCM, Ho Chi Minh City, Viet Nam; Vietnam National University, Ho Chi Minh City, Viet Nam; Department of Otolaryngology, Thong Nhat Hospital, Ho Chi Minh City, Viet Nam.
| | - Ho Dang Quy Dung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Viet Nam.
| | - Ngoc Boi Van
- Department of Otolaryngology, Vinmec Central Park International Hospital, Ho Chi Minh City, Viet Nam.
| | - Chanh Cong Ha
- Department of Otolaryngology, 7A Military Hospital, Ho Chi Minh City, Viet Nam.
| | - Nam Hoang Pham
- Otorhinolaryngology Department, Cho Ray Hospital, Ho Chi Minh City, Viet Nam.
| | | | - Tan-Cong Nguyen
- University of Science, VNUHCM, Ho Chi Minh City, Viet Nam; University of Social Sciences and Humanities, VNUHCM, Ho Chi Minh City, Vietnam; Vietnam National University, Ho Chi Minh City, Viet Nam.
| | - Minh-Khoi Pham
- University of Science, VNUHCM, Ho Chi Minh City, Viet Nam; Vietnam National University, Ho Chi Minh City, Viet Nam.
| | - Mai-Khiem Tran
- University of Science, VNUHCM, Ho Chi Minh City, Viet Nam; John von Neumann Institute, VNUHCM, Ho Chi Minh City, Viet Nam; Vietnam National University, Ho Chi Minh City, Viet Nam.
| | - Truong Minh Tran
- Otorhinolaryngology Department, Cho Ray Hospital, Ho Chi Minh City, Viet Nam.
| | - Minh-Triet Tran
- University of Science, VNUHCM, Ho Chi Minh City, Viet Nam; John von Neumann Institute, VNUHCM, Ho Chi Minh City, Viet Nam; Vietnam National University, Ho Chi Minh City, Viet Nam.
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4
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Tuan VP, Yahara K, Dung HDQ, Binh TT, Huu Tung P, Tri TD, Thuan NPM, Khien VV, Trang TTH, Phuc BH, Tshibangu-Kabamba E, Matsumoto T, Akada J, Suzuki R, Okimoto T, Kodama M, Murakami K, Yano H, Fukuyo M, Takahashi N, Kato M, Nishiumi S, Azuma T, Ogura Y, Hayashi T, Toyoda A, Kobayashi I, Yamaoka Y. Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates. Microb Genom 2021; 7. [PMID: 34846284 PMCID: PMC8743543 DOI: 10.1099/mgen.0.000680] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as Helicobacter pylori, which causes gastric cancer. We conducted a small-sample GWAS (125 gastric cancer cases and 115 controls) followed by prediction of gastric cancer and control (duodenal ulcer) H. pylori strains. We identified 11 single nucleotide polymorphisms (eight amino acid changes) and three DNA motifs that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into gastric cancer pathogenesis and a basis for identifying a set of biomarkers for distinguishing these H. pylori-related diseases.
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Affiliation(s)
- Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Koji Yahara
- Antimicrobial Resistance ResearchCenter, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Koji Yahara,
| | | | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Vu Van Khien
- Department of GI Endoscopy, 108 Central Hospital, Hanoi, Vietnam
| | | | - Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Microbiology, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Tadayoshi Okimoto
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Masaaki Kodama
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hirokazu Yano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masaki Fukuyo
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Molecular Oncology, Chiba University, Chiba, Japan
| | - Noriko Takahashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
| | - Mototsugu Kato
- Division of Endoscopy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Gastroenterology, National Hospital Organization Hakodate Hospital, Hakodate, Hokkaido, Japan
| | - Shin Nishiumi
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
- Department of Omics Medicine, Hyogo College of Medicine, Hyogo, Japan
| | - Takashi Azuma
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Advanced GenomicsCenter, National Institute of Genetics, Shizuoka, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
- *Correspondence: Ichizo Kobayashi, ;
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Medicine, gastroenterology section, Baylor College of Medicine, Houston TX, USA
- *Correspondence: Yoshio Yamaoka,
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5
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Akada J, Tshibangu-Kabamba E, Tuan VP, Kurogi S, Matsuo Y, Ansari S, Doohan D, Phuc BH, Subsomwong P, Waskito LA, Binh TT, Nguyen LT, Khien VV, Dung HDQ, Miftahussurur M, Syam AF, Tshering L, Vilaichone RK, Mahachai V, Ratanachu-Ek T, Shrestha PK, Yee TT, Htet K, Aftab H, Matsuhisa T, Uchida T, Okimoto T, Mizukami K, Kodama M, Murakami K, Takahashi N, Yamaoka Y. Serum Helicobacter pylori antibody reactivity in seven Asian countries using an automated latex aggregation turbidity assay. J Gastroenterol Hepatol 2021; 36:2198-2209. [PMID: 33609333 DOI: 10.1111/jgh.15467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 01/28/2021] [Accepted: 02/14/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIM To determine the application range of diagnostic kits utilizing anti-Helicobacter pylori antibody, we tested a newly developed latex aggregation turbidity assay (latex) and a conventional enzyme-linked immunosorbent assay (E-plate), both containing Japanese H. pylori protein lysates as antigens, using sera from seven Asian countries. METHODS Serum samples (1797) were obtained, and standard H. pylori infection status and atrophy status were determined by culture and histology (immunohistochemistry) using gastric biopsy samples from the same individuals. The two tests (enzyme-linked immunosorbent assay and latex) were applied, and receiver operating characteristics analysis was performed. RESULTS Area under the curve (AUC) from the receiver operating characteristic of E-plate and latex curves were almost the same and the highest in Vietnam. The latex AUC was slightly lower than the E-plate AUC in other countries, and the difference became statistically significant in Myanmar and then Bangladesh as the lowest. To consider past infection cases, atrophy was additionally evaluated. Most of the AUCs decreased using this atrophy-evaluated status; however, the difference between the two kits was not significant in each country, but the latex AUC was better using all samples. Practical cut-off values were 3.0 U/mL in the E-test and 3.5 U/mL in the latex test, to avoid missing gastric cancer patients to the greatest extent possible. CONCLUSIONS The kits were applicable in all countries, but new kits using regional H. pylori strains are recommended for Myanmar and Bangladesh. Use of a cut-off value lower than the best cut-off value is essential for screening gastric cancer patients.
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Affiliation(s)
- Junko Akada
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan
| | | | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan.,Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Shusaku Kurogi
- Clinical Laboratory Center, Oita University Hospital, Yufu, Japan.,Department of Molecular Pathology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Yuichi Matsuo
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan
| | - Shamshul Ansari
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan
| | - Dalla Doohan
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan.,Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan
| | - Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan
| | - Langgeng Agung Waskito
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan.,Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Lam Tung Nguyen
- Department of Hepatogastroenterology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Vu Van Khien
- Department of Hepatogastroenterology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Ho Dang Quy Dung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Muhammad Miftahussurur
- Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia.,Gastroentero-Hepatology Division, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Airlangga University, Surabaya, Indonesia
| | - Ari Fahrial Syam
- Division of Gastroenterology, Department of Intestinal Medicine, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Lotay Tshering
- Department of Surgery, Jigme Dorji Wangchuck National Referral Hospital, Thimphu, Bhutan
| | - Ratha-Korn Vilaichone
- Gastroenterology Unit, Digestive Diseases Research Center, Thammasat University Hospital, Khlong Luang, Thailand.,Department of Medicine, Chulabhorn International College of Medicine, Thammasat University Hospital, Khlong Luang, Thailand
| | | | | | - Pradeep Krishna Shrestha
- Department of Gastroenterology, Maharajgunj Medical Campus, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Than Than Yee
- Department of GI and HBP Surgery, No (2) Defense Service General Hospital, Nay Pyi Taw, Myanmar
| | - Kyaw Htet
- Department of GI and HBP Surgery, No (1) Defense Service General Hospital, Mingaladon, Myanmar
| | - Hafeza Aftab
- Department of Gastroenterology, Dhaka Medical Collage and Hospital, Dhaka, Bangladesh
| | - Takeshi Matsuhisa
- Department of Gastroenterology, Tama-Nagayama University Hospital, Nippon Medical School, Tama, Japan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Tadayoshi Okimoto
- Department of Gastroenterology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Kazuhiro Mizukami
- Department of Gastroenterology, Faculty of Medicine, Oita University, Yufu, Japan
| | - Masaaki Kodama
- Department of Gastroenterology, Faculty of Medicine, Oita University, Yufu, Japan.,Faculty of Welfare and Health Science, Oita University, Yufu, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Faculty of Medicine, Oita University, Yufu, Japan
| | | | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Yufu, Japan.,Global Oita Medical Advanced Research Center for Health, Oita University, Yufu, Japan.,Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, USA
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6
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Khien VV, Thang DM, Hai TM, Duat NQ, Khanh PH, Ha DT, Binh TT, Dung HDQ, Trang TTH, Yamaoka Y. Management of Antibiotic-Resistant Helicobacter pylori Infection: Perspectives from Vietnam. Gut Liver 2020; 13:483-497. [PMID: 31009957 PMCID: PMC6743798 DOI: 10.5009/gnl18137] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 11/13/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022] Open
Abstract
Antibiotic resistance is the most important factor leading to the failure of eradication regimens. This review focuses on the prevalence of Helicobacter pylori primary and secondary resistance to clarithromycin, metronidazole, amoxicillin, levofloxacin, tetracycline, and multidrug in Vietnam. We searched the PubMed, EMBASE, Vietnamese National Knowledge Infrastructure, and Vietnamese Biomedical databases from January 2000 to December 2016. The search terms included the following: H. pylori infection, antibiotic (including clarithromycin, metronidazole, amoxicillin, levofloxacin, tetracycline, and multidrug) resistance in Vietnam. The data were summarized in an extraction table and analyzed manually. Finally, Excel 2007 software was used to create charts. Ten studies (three studies in English and seven in Vietnamese) were included in this review. A total of 308, 412, 523, 408, 399, and 268 H. pylori strains were included in this review to evaluate the prevalence of H. pylori primary resistance to amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and multidrug resistance, respectively. Overall, the primary resistance rates of amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and multidrug resistance were 15.0%, 34.1%, 69.4%, 27.9%, 17.9% and 48.8%, respectively. Secondary resistance rates of amoxicillin, clarithromycin, metronidazole, levofloxacin, tetracycline, and multidrug resistance were 9.5%, 74.9%, 61.5%, 45.7%, 23.5% and 62.3%, respectively. In Vietnam, primary and secondary resistance to H. pylori is increasing over time and affects the effectiveness of H. pylori eradication.
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Affiliation(s)
- Vu Van Khien
- Departments of GI Endoscopy, 108 Central Hospital, Hanoi, Vietnam
| | - Duong Minh Thang
- Departments of GI Endoscopy, 108 Central Hospital, Hanoi, Vietnam
| | - Tran Manh Hai
- Departments of Molecular Biology, 108 Central Hospital, Hanoi, Vietnam.,University of Science and Technology of Hanoi, Hanoi, Vietnam
| | | | - Pham Hong Khanh
- Department of Gastroenterology, 103 Hospital, Hanoi, Vietnam
| | - Dang Thuy Ha
- Department of Gastroenterology, National Children Hospital, Hanoi, Vietnam
| | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Ho Dang Quy Dung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | | | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
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Tuan VP, Narith D, Tshibangu-Kabamba E, Dung HDQ, Viet PT, Sokomoth S, Binh TT, Sokhem S, Tri TD, Ngov S, Tung PH, Thuan NPM, Truc TC, Phuc BH, Matsumoto T, Fauzia KA, Akada J, Trang TTH, Yamaoka Y. A Next-Generation Sequencing-Based Approach to Identify Genetic Determinants of Antibiotic Resistance in Cambodian Helicobacter pylori Clinical Isolates. J Clin Med 2019; 8:jcm8060858. [PMID: 31208076 PMCID: PMC6617194 DOI: 10.3390/jcm8060858] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022] Open
Abstract
We evaluated the primary resistance of Helicobacter pylori (H. pylori) to routinely used antibiotics in Cambodia, an unexplored topic in the country, and assessed next-generation sequencing’s (NGS) potential to discover genetic resistance determinants. Fifty-five H. pylori strains were successfully cultured and screened for antibiotic susceptibility using agar dilution. Genotypic analysis was performed using NGS data with a CLC genomic workbench. PlasmidSeeker was used to detect plasmids. The correlation between resistant genotypes and phenotypes was evaluated statistically. Resistances to metronidazole (MTZ), levofloxacin (LVX), clarithromycin (CLR), and amoxicillin (AMX) were 96.4%, 67.3%, 25.5%, and 9.1%, respectively. No resistance to tetracycline (TET) was observed. Multi-drug resistance affected 76.4% of strains. No plasmids were found, but genetic determinants of resistance to CLR, LVX, and AMX were 23S rRNA (A2146G and A2147G), GyrA (N87K and D91Y/N/G), and pbp1 (P473L), respectively. No determinants were genetically linked to MTZ or TET resistance. There was high concordance between resistant genotypes and phenotypes for AMX, LVX, and CLR. We observed high antibiotic resistance rates of CLR, MTZ, and LVX, emphasizing the need for periodic evaluation and alternative therapies in Cambodia. NGS showed high capability for detecting genetic resistance determinants and potential for implementation in local treatment policies.
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Affiliation(s)
- Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu 879-5593, Japan.
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
| | - Dou Narith
- Department of Endoscopy, Cho Ray Phnom Penh Hospital, Phnom Penh 12357, Cambodia.
| | - Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu 879-5593, Japan.
| | - Ho Dang Quy Dung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
| | - Pham Thanh Viet
- Department of Integrated Planning, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
| | - Sin Sokomoth
- Department of Integrated Planning, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
- Department of Cardiovascular Surgery, Cho Ray Phnom Penh Hospital, Phnom Penh 12357, Cambodia.
| | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
| | - Sok Sokhem
- Department of Endoscopy, Cho Ray Phnom Penh Hospital, Phnom Penh 12357, Cambodia.
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
| | - Seng Ngov
- Department of General Internal Medicine, Cho Ray Phnom Penh Hospital, Phnom Penh 12357, Cambodia.
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
| | | | - Tran Cong Truc
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh 749000, Vietnam.
| | - Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu 879-5593, Japan.
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu 879-5593, Japan.
| | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu 879-5593, Japan.
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu 879-5593, Japan.
| | - Tran Thi Huyen Trang
- Department of Molecular Biology, 108 Military Central Hospital, Hanoi 113601, Vietnam.
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu 879-5593, Japan.
- Global Oita Medical Advanced Research Center for Health, Yufu 879-5593, Japan.
- Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX 77030, USA.
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Affiliation(s)
- Ichiro Yasuda
- Third Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Shomei Ryozawa
- Department of Gastroenterology, Saitama Medical University International Medical Center, Hidaka, Japan
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Binh TT, Tuan VP, Dung HDQ, Tung PH, Tri TD, Thuan NPM, Khien VV, Hoan PQ, Suzuki R, Uchida T, Trang TTH, Yamaoka Y. Advanced non-cardia gastric cancer and Helicobacter pylori infection in Vietnam. Gut Pathog 2017; 9:46. [PMID: 28824711 PMCID: PMC5561603 DOI: 10.1186/s13099-017-0195-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/06/2017] [Indexed: 02/06/2023] Open
Abstract
Background The incidence of gastric cancer in the Northern city, Hanoi is higher than in the Southern city, Ho Chi Minh, Vietnam. We previously reported that Helicobacter pylori vacA m1 genotype might be responsible for the difference between the two cities, however, the study only included non-cancer patients. The aim of this study is to investigate the non-cardia gastric cancer characteristics and the role of H. pylori virulence on different non-cardia gastric cancer incidence between two cities in Vietnam. Methods and Results We recruited 282 non-cardia gastric cancer patients that had undergone gastroscopy in two cities, Ho Chi Minh and Hanoi, Vietnam. Characteristics of non-cardia gastric cancer were late age of onset (mean age, 62.5 years), predominance in males (ratio of males/females; 3.9:1), diffuse type (55.3%), and high prevalence of H. pylori infection (79.4%). H. pylori infection and the vacA m1 genotype conferred an increased risk for GC (OR, 2.02; 95% CI 1.4–3.0; P = 0.0003 and OR, 2.7; 95% CI 1.5–4.7; P = 0.001, respectively). Interestingly, the presence of vacA m1 genotype in the gastric cancer group was significantly higher than that in the non-cancer group (68.8% vs 44.9%, P = 0.001) and the significant tendency still observed in Ho Chi Minh (67.6% vs 31.9%, P < 0.0001). Conclusion We first describe the characteristics of non-cardia gastric cancer in Vietnam. Helicobacter pylori infection was associated with the development of non-cardia GC. vacA m1 genotype might contribute to incidence differences between the two cities. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0195-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tran Thanh Binh
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan.,Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Vo Phuoc Tuan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan.,Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Vu Van Khien
- Department of Hepatogastroenterology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Phan Quoc Hoan
- Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Oita University Faculty of Medicine, Yufu, Japan
| | - Tran Thi Huyen Trang
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan.,Department of Molecular Biology, 108 Military Central Hospital, Hanoi, Vietnam
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan.,Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, TX USA
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