Globally emphasis has been given to identify emerging and re-emerging pathogens. Rapid urban
expansion creates a problem which is two-fold. Firstly, increasing slum living conditions due to
inadequate rate of infrastructure development results in an increased reliance on natural resources,
including the capture and consumption of surrounding wildlife to subsist, thereby facilitating the transfer
of emergent zoonotic pathogens. Secondly, through activities such as pollution or alien species
introductions, the rapid transformation of once pristine environments, alters natural systems, potentially
exposing these environments to new bacterial pathogens. Therefore, the main aim of this study was to
assess overlooked bacterial species harboured by four host species (Bathyergus suillus, Georychus
capensis, Cryptomys hottentotus hottentotus and Fukomys damarensis) belonging to the subterranean
rodent family Bathyergidae, which inhabit an environment well-suited for an array of bacterial species,
and which varied in their exposure to human settlements. Bacterial prevalence and diversity was initially
evaluated using broad-range PCR techniques in combination with nucleotide sequencing. This revealed
high levels of bacterial prevalence (82.91%) and mixed infections (22.60%) in bathyergid species. Two
bacterial groups, the Bacillus cereus complex (a group of soil-dwelling bacterial strains with pathogenic
potential with an overall prevalence of 8.55%) and haemotropic Mycoplasma strains (vector-borne
bacterial strains of zoonotic potential with an overall prevalence of 1.28%) were subsequently selected for
further genetic analysis with genus and species-specific PCRs. Bacillus molecular screening and
phylogenetic analyses was achieved by targeting four gene regions with seven published primer assays
and two novel PCR assays. This enabled identification of two B. cereus complex strains in bathyergid
lungs and revealed an overall B. cereus complex prevalence of 17.95% for the 234 bathyergid lung
samples screened. Bacillus genome prevalence was significantly higher in B. suillus individuals (45.35%),
sampled in a peri-urban environment, compared to the other bathyergid species sampled from pristine
habitats (ranging from 0% - 4.44%). Anthropogenic activities in the area where B. suillus was sampled
could, at least partially, attribute to the perceived difference between urban and naturally sampled
bathyergid species, highlighting the role of B. suillus to act as both a reservoir of potentially zoonotic
pathogens and as a sentinel for anthropogenic soiling. Mycoplasma molecular screening using three
different PCR assays, all targeting the 16S rRNA gene region, confirmed an overall haemotropic
Mycoplasma prevalence of 24.13% in the 286 bathyergid organs (lung, spleen and liver) screened. A
significantly higher prevalence and diversity of haemotropic Mycoplasma strains was found in B. suillus
lungs (41.86%) compared to its naturally occurring relatives (ranging from 0%-36%). Phylogenetic analyses identified six novel haemotropic Mycoplasma strains, all grouping within a discrete
monophyletic cluster, sister to Mycoplasma coccoides, and comprising two well-supported sub-clusters.
The human introduction of commensal rodents harbouring Mycoplasma strains transferred through
cosmopolitan arthropod vectors to indigenous bathyergids, likely underlies the higher prevalence in urban
areas, although other biotic and abiotic factors affecting ectoparasite load also merit consideration. The
data generated by the current study indicate the need to identify largely overlooked and potentially
zoonotic bacterial pathogens in subterranean mammals and emphasises the importance of monitoring
anthropogenically-introduced, opportunistic pathogens and the threats they pose to vulnerable
communities and co-occurring, free-living animal species / Dissertation (MSc)--University of Pretoria, 2017. / Airports Company of South Africa (ACSA) / National Research Foundation (NRF) / Zoology and Entomology / MSc / Unrestricted
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:up/oai:repository.up.ac.za:2263/67139 |
| Date | January 2017 |
| Creators | Retief, Liezl |
| Contributors | Bastos, Armanda D.S., Bennett, Nigel C., 1961- |
| Publisher | University of Pretoria |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Type | Dissertation |
| Rights | © 2018 University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. |
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