2021 Fiscal Year Research-status Report
Pathogenomics and eco-epidemiology of Mycobacterium orygis, an emerging zoonotic tuberculosis organism
| Project/Area Number |
21K14969
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| Research Institution | Hokkaido University |
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Principal Investigator |
THAPA JEEWAN 北海道大学, 人獣共通感染症国際共同研究所, 助教 (40837449)
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| Project Period (FY) |
2021-04-01 – 2023-03-31
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| Keywords | tuberculosis / Mycobacterium orygis / Pathogenomics / molecular epidemiology / Nepal |
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| Outline of Annual Research Achievements |
This project aims to explore the unique pathogenomic features of Mycobacterium tuberculosis complex (MTBC) by taking M. orygis as a model and understand the eco-epidemiology of M. orygis by performing field surveillance in Nepal. The whole genome of M. orygis of a rhinoceros in Nepal was sequenced. The draft genome consisted of 4.2 Mb with 3,859 coding sequences. Preliminary analysis has shown that M. orygis has unique signature genetic features. Comparative genome analysis with other members of MTBCs is in progress. This project aims to import live M. orygis and M. tuberculosis bacteria isolated from wildlife in Nepal and perform in vitro and in vivo studies to explore pathogenomics of MTBCs. During last year field trip to Nepal, the viability of these bacteria was confirmed. An application to import these live bacteria was submitted to the Nepal government but final approval has yet to be obtained. We are developing a magnetic beads based fecal mycobacteria assay to detect tuberculosis (TB) bacteria from feces so that it can be used for noninvasive surveillance of TB in the wildlife of Nepal. We have developed and optimized sandwich ELISA system to detect TB in elephants and cattle but yet to be validated in field conditions. Furthermore, a TB serosurveillence study in captive elephants of Nepal showed that TB is now endemically distributed. We have collected TB suspected samples from animals including elephants in Nepal. We did not detect M. orygis from human TB samples in Nepal. We showed that Xpert MTB/RIF is an effective diagnostic method for human TB in Nepal.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
As previously planned, we were planning to import live M. orygis and M. tuberculosis bacteria that were isolated from wildlife from Nepal to Hokkaido University, Japan. Although we have applied for permission to import these bacteria to Japan and also performed a detailed presentation to the Nepal government, approval is yet to be granted. This has hindered our planned in vitro and in vivo research works. Some of the important reasons for this delay may be because Covid-19 has slowed research works mainly in Nepal due to travel restrictions and lockdowns. Since our TB isolates are from the wildlife of Nepal, the Nepal government is taking time to evaluate our application by considering legal issues. In the meantime, we have set up of laboratory facility at Hokkaido University and are ready to perform planned research works once we obtain the samples. We have tested our facility with invitro research works using M. bovis BCG reference strain and M. avium. Apart from this, our work has progressed smoothly. We have developed a model to perform molecular surveillance of TB across the wildlife/livestock/human interface in Nepal using PCR and LAMP based technologies. The developed fecal mycobacteria assay and ELISA system will be validated for TB surveillance in Nepal.
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| Strategy for Future Research Activity |
We are optimistically looking forward to receiving M. orygis and M. tuberculosis from Nepal this fiscal year. As soon as we receive them, we will start our comparative in-vitro and in-vivo experimental studies to identify pathogenomic features of M. orygis. The comparative genome analysis of the rhinoceros M. orygis will be expanded by including all the M. orygis isolates from the database. Altogether publicly available genome of 40 M. orygis has been collected for comparative analysis. We will identify why and how this M. orygis has evolved and been established to cause tuberculosis specifically in the South Asian region. Furthermore, the developed molecular TB diagnostic model (elephant and bovine sandwich ELISA, fecal mycobacteria assay, and dry-LAMP) will be evaluated for the routine surveillance of TB across the wildlife/livestock/human interface in Nepal. These simple diagnostic methods will help to understand eco-epidemiology of TB wildlife/livestock/human interface in Nepal.
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| Causes of Carryover |
I was able to use the existing consumables of the laboratory for experiments related to next-generation sequencing and molecular assays related to this project. In the next fiscal year, we plan to use our technology and resources for fieldwork in Nepal. We will also import live TB bacteria and Nepal and perform pathogenomics experiments.
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[Journal Article] Genetic Diversity and Transmission of Multidrug-Resistant Mycobacterium tuberculosis strains in Lusaka, Zambia2022
Author(s)
Joseph Yamweka Chizimu, Eddie Samuneti Solo, Precious Bwalya, Thoko Flav Kapalamula, Mwangala Lohah Akapelwa, Partick Lungu, Dipti Shrestha, Yukari Fukushima, Victor Mukonka, Jeewan Thapa, Chie Nakajima, Yasuhiko Suzuki
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Journal Title
International Journal of Infectious Diseases
Volume: 114
Pages: 142-150
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Whole-Genome Sequencing Reveals Recent Transmission of Multidrug-Resistant Mycobacterium tuberculosis CAS1-Kili Strains in Lusaka, Zambia2022
Author(s)
Joseph Yamweka Chizimu, Eddie Samuneti Solo, Precious Bwalya, Wimonrat Tanomsridachchai, Herman Chambaro, Misheck Shawa, Thoko Flav Kapalamula, Partick Lungu, Yukari Fukushima, Victor Mukonka, Jeewan Thapa, Chie Nakajima, Yasuhiko Suzuki
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Journal Title
Antibiotics (Basel)
Volume: 11
Pages: 29
DOI
Peer Reviewed / Open Access / Int'l Joint Research
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