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Title: Thermophilic Campylobacter in Nigeria and a comparison to isolates globally
Author: Audu, Benshak John
ISNI:       0000 0004 7961 2594
Awarding Body: University of Aberdeen
Current Institution: University of Aberdeen
Date of Award: 2019
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The occurrence and epidemiology of Campylobacter was investigated with a focus on C. jejuni and C. coli in humans and livestock from Plateau State, Nigeria. Campylobacter species are zoonotic pathogens, widely distributed in many animals such as poultry, pigs, cattle, sheep, dogs from which they are transmitted to humans directly or through animal products. Human campylobacteriosis is of public health significance but lack of a national surveillance programme in Nigeria hinders an accurate estimation of incidence. In livestock, C. jejuni and C. coli are ubiquitous and are found naturally as commensals in many animals. To understand the human epidemiology of Campylobacter in Nigeria, the dynamics of the organism within their hosts, identification of putative sources of infection and risk factors must be determined. Stool and faecal samples from humans and livestock were cultured for Campylobacter species on modified charcoal cefoperazone deoxycholate agar (mCCDA). Culture in combination with molecular techniques identified and confirmed the presence of Campylobacter in humans and animals from the study area. 586 human stool samples were tested with 50 (9%) being positive of which 33 (66%) were C. jejuni, 14 (28%) were C. coli while 3 (6%) were C. hyointestinalis. From poultry, 312 samples were tested with 124 (40%) being positive. Thirty one (25%) were C. jejuni while 93 (75%) were C. coli. In cattle, 160 samples were tested with all the eight (5%) positives being C. coli. This result confirms chicken as a major reservoir for Campylobacter species in Nigeria. From questionnaires from human volunteers, a number of risk factors were observed to be associated with human campylobacteriosis in Nigeria and these included ownership of poultry and other animals, private water supply as a source of water for the household and young age of the study participant. The age of infection was also found to be highest in children below six who were mostly asymptomatic. Multilocus Sequence Typing (MLST) was used to genotype the isolates and characterise the population structure of isolates from humans and livestock. A total of 32 sequence types (STs) were identified from 47 human isolates while 48 STs were identified in 124 chicken and eight cattle isolates. This indicated a population which was overall, genetically diverse with a few more dominant strains. Comparison of genetic diversity in Nigeria with Africa and other parts of the world revealed clustering behaviour of the isolates to be largely regional which might reflect the influence of local genetic evolutionary trends and adaption to local environmental conditions. STs from other parts of the world though, which were closely associated and formed phylogenetic clusters with STs from Nigeria likely had similar ancestry with divergence occurring possibly due to fitness requirements. Nigerian Campylobacter isolates attributed more to Scottish wild bird isolates than to other livestock. This may be an indication of how farming practices, environmental contamination and human habits can modify the importance of an infection source. Chicken and other livestock sources though, remain important as significant sources of infection. The antimicrobial resistance profiles of the isolates to fluoroquinolone, betalactam, tetracycline and macrolide classes of antimicrobials indicated an overall higher prevalence of resistance in Campylobacter in poultry and other livestock than in humans. Resistance in all the isolates was greatest for betalactams (42%) followed by fluoroquinolones (41%), tetracyclines (15%) and lastly macrolides (2%). Multidrug resistance to three or more antimicrobials was observed in 24 (13%) Campylobacter isolates from humans (n=1, 4%) and chicken (n=23, 96%). Comparison between antimicrobial resistance profiles and MLST subtypes was investigated and revealed no overall correlation which suggests multiple separate evolutionary processes. While MLST uses housekeeping genes, which are stable and evolve slowly, resistance can be acquired from the transfer of plasmids and mutations in target gene locations and which occur rapidly depending on selection pressure. Individual strains would be assumed to have acquired resistance to a particular, or many antimicrobials, independently and not through the branching out of a single clone. This study has contributed information about the epidemiology of Campylobacter in humans, poultry and cattle in Nigeria with certain identified risk factors being associated with human infection. Further characterization of the study isolates has also revealed a diverse population structure within each of the hosts. These findings will provide useful information and contribute to the overall surveillance of Campylobacter in humans and its distribution in different hosts. From known records, whole genome sequencing of Campylobacter isolates carried out in this study is the first to be done on a substantial number of isolates from Nigeria. This opens up numerous possibilities to closely examine genetic information of these organisms from this geographical location and to use this same genetic information to compare with gene sequences from other countries for phenotypic characteristics like virulence, pathogenicity and antimicrobial resistance.
Supervisor: Forbes, Kenneth. ; Strachan, Norval J. C. Sponsor: University of Aberdeen (Elphinstone Institute)
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: Thermophilic bacteria ; Campylobacter infections ; Pathogenic microorganisms