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Chua EG, Debowski AW, Webberley KM, Peters F, Lamichhane B, Loke MF, Vadivelu J, Tay CY, Marshall BJ, Wise MJ. Analysis of core protein clusters identifies candidate variable sites conferring metronidazole resistance in Helicobacter pylori. Gastroenterol Rep (Oxf) 2019; 7:42-49. [PMID: 30792865 PMCID: PMC6375344 DOI: 10.1093/gastro/goy048] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 06/28/2018] [Revised: 09/19/2018] [Accepted: 09/26/2018] [Indexed: 01/10/2023] Open
Abstract
Background Metronidazole is one of the first-line drugs of choice in the standard triple therapy used to eradicate Helicobacter pylori infection. Hence, the global emergence of metronidazole resistance in Hp poses a major challenge to health professionals. Inactivation of RdxA is known to be a major mechanism of conferring metronidazole resistance in H. pylori. However, metronidazole resistance can also arise in H. pylori strains expressing functional RdxA protein, suggesting that there are other mechanisms that may confer resistance to this drug. Methods We performed whole-genome sequencing on 121 H. pylori clinical strains, among which 73 were metronidazole-resistant. Sequence-alignment analysis of core protein clusters derived from clinical strains containing full-length RdxA was performed. Variable sites in each alignment were statistically compared between the resistant and susceptible groups to determine candidate genes along with their respective amino-acid changes that may account for the development of metronidazole resistance in H. pylori. Results Resistance due to RdxA truncation was identified in 34% of metronidazole-resistant strains. Analysis of core protein clusters derived from the remaining 48 metronidazole-resistant strains and 48 metronidazole-susceptible identified four variable sites significantly associated with metronidazole resistance. These sites included R16H/C in RdxA, D85N in the inner-membrane protein RclC (HP0565), V265I in a biotin carboxylase protein (HP0370) and A51V/T in a putative threonylcarbamoyl–AMP synthase (HP0918). Conclusions Our approach identified new potential mechanisms for metronidazole resistance in H. pylori that merit further investigation.
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Affiliation(s)
- Eng-Guan Chua
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia
| | - Aleksandra W Debowski
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia.,School of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - K Mary Webberley
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia
| | - Fanny Peters
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia
| | - Binit Lamichhane
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia
| | - Mun-Fai Loke
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Jamuna Vadivelu
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Chin-Yen Tay
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia.,Shenzhen Dapeng New District Kuichong People Hospital, Shenzhen, Guangdong, China
| | - Barry J Marshall
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia.,Shenzhen Dapeng New District Kuichong People Hospital, Shenzhen, Guangdong, China.,UM Marshall Centre, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Perth, Western Australia, Australia.,School of Computer Science and Software Engineering, University of Western Australia, Perth, Western Australia, Australia
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