Metagenomics analysis of pathogens in rodents in selected human-wildlife Interfaces in Tanzania

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Sokoine University of Agriculture


Rodents belongs to the order Rodentia, which comprise the largest proportions of all of the terrestrial mammals in the world. In Africa, rodents occur in 14 families, 89 genera and 290 species, East African region contains 14 families, 62 genera and 161 species of rodents. Over decades, rodents have been reported to harbor more than 60% of emerging zoonotic pathogens including viruses, bacteria and a number of parasites. Several human diseases including the most devastating in the history of mankind Plague‖ have been reported to have originated from rodents. Rodent borne diseases are transmitted either directly (Hantavirus, Lassa fever, Lymphocytic choriomeningitis) or indirectly through consumption of foods and water contaminated with rodent feces and urine (Leptospirosis, tularemia) or through ectoparasites carried by rodents (leishmaniasis, Lyme disease). Risks of human infection is linked to the possibility of contact between rodents, humans and animals, along with the closeness between rodent and human lives. Since there is constant interaction between humans, animals and rodents; it is therefore, essential to understand patterns of pathogen diversity and focusing surveillance in rodents in order to identify zoonotic potential pathogens prior to spill over to humans. Rodents were captured in Kibondo, Kyerwa and Uvinza in 2018. Trapping of rodents was done in peri-domestic areas by using Sherman box and Tomahawk traps added with peanut butter mixed with maize bran as baits. They were anaesthetized by using Isoflurane, and species identification was done by using morphological identification keys. In metagenomics sequencing a total of 116 rodents archived oral- pharyngeal and rectal swabs were subjected to RNA extraction and the products were pooled into twelve pools based on species of rodents, locations and swab types. There were eleven pools of oral- pharyngeal swabs and a single pool of rectal swabs. Pooled samples were sequenced on oxford Nanopore MinIon sequencing platform. This study employed 16S rRNA metagenomics sequencing analysis. Sequences were analyzed by using Kraken 2 classification and Kaiju software. A total of 5263 small mammals were trapped from Kibondo, Uvinza and Kyerwa during the three years of data collection. Majority (87.6%, n=4613) were rodents and 650 (12.4%) were shrews. Among the rodents, rats were the majority (70.0%; n=3683) while mice were 873 (16.6%) and squirrels were only 44 (0.8%). The dominant species in the group of rodents were Mastomys natalensis which constituted 63.6% (n=3346). Among the mice, Arvicanthis spp. were the majority as they constituted 7.1% (n=373) of all small mammals trapped. A total of 13 (0.3%) small mammals identified as rodents their genus was not established. In a metagenomics analysis, 44 bacteria species of public health, veterinary and environmental health importance were identified. They were detected in eight pools, while there was no detection in four pools. A total of 10 (22.7%) bacteria species including H. pylori were detected in the rectal swabs pool and the remaining 34 (77.3%) were distributed among the pools of oral-pharyngeal swabs. A total of 15 potentially pathogenic, zoonotic and bacteria of unknown zoonotic potential including Mycobacterium tuberculosis, Helicobacter pylori, Vibrio cholerae, Vibrio parahaemolyticus, Haemophilus influenzae, Klebsiella pneumonae, Staphylococcus aureus, Streptococcus mutans, Escherichia coli, Chlamydia psittaci, Campylobacter sputorum, Acinetobacter baumannii and Acinetobacter pitti were identified in this study. The findings of this study are in line with several previous studies that have reported a number of rodent species in western Tanzania; also, citing rodents as reservoirs of disease-causing agents; and has the potential to spread and maintain transmission cycles of human and livestock diseases. This study presents the first reports of natural infection of rodents with Helicobacter pylori and Mycobacterium tuberculosis. These findings provide baseline information to inform surveillance systems and the public in general on potential health risks that are associated with interaction between rodents, humans and livestock. Furthermore, it gives insight on the potential of using a unified approach One Health‖ between sectors in order to achieve better health and a safer community. However, since the findings of this study do not explain pathogen transmission from rodents to humansand vice versa, we recommend further studies to characterize them and understand their transmission dynamics.


Degree of Masters of Science in Public Health Pest Management


Rodents, Zoonotic, interfaces, bacteria Metagenomics, human-wildlife