Genomic diversity and antimicrobial resistance in Salmonella isolates recovered from diverse sources in Nigeria
Antimicrobial Resistance (AMR) jeopardises the gains of modern medicine and is therefore considered a global public health threat. It has been predicted to cause up to 10 million deaths by 2050 if no serious actions are taken. AMR threatens people's lives worldwide but with a significantly higher burden in low and middle-income countries (LMICs), where it is challenging to determine the exact burden of bacterial AMR due to gaps in surveillance. Salmonella is an important zoonotic gram-negative pathogen that may be categorised into serovars and sequence types (STs) based on seven housekeeping genes. The Salmonella isolates that cause problems vary for geographical regions and have different antimicrobial susceptibility patterns. This is likely to be driven by the antimicrobials that are in use in these regions. Fluoroquinolone and cephalosporins are important antimicrobials for treating salmonellosis, but due to growing resistance, the World Health Organisation now considers fluoroquinolone-resistant (FQR) Salmonella a critically important pathogen. The central hypothesis of this thesis is that a better understanding of the genetic diversity, and sources, of antibiotic resistant Salmonella spp in Nigeria, and of markers of emergent antibiotic resistance will inform and encourage the development of integrated interventions to reduce the impact of Salmonella in this country. Whole-genome sequences of the sampled dataset combined with publicly available Nontyphoidal Salmonella (NTS) genomes (Nigeria NTS collection) recovered from various sources revealed the diversity of NTS in Nigeria. One hundred and twenty-one unique serovars belonging to 167 STs were identified within the dataset, with some serovars having more than one ST. An eBURST diagram confirmed that the majority of the Nigeria NTS collection were not closely related. S. enterica Kentucky (ST198) was the most common strain in poultry, while S. enterica Enteritidis (ST11) was the most common human serovar. Phenotypic and genotypic analyses were performed on the isolates. The highest level of resistance (57%) was observed for nalidixic acid, followed by 36.2% and 35% resistance to ciprofloxacin and gentamicin, respectively, on Disc Diffusion (DD); while VITEK-2 identified 32% of the strains to be resistant to enrofloxacin and marbofloxacin and 34% to gentamicin. Multidrug resistance to other antimicrobials was found in some serovars, and poultry isolates had higher resistance than other species, probably due to greater use of antimicrobials in these species. The tet(A) gene was the most common single resistance gene identified in the collection. In strains that showed resistance to the fluoroquinolones, 15% had the qnr gene. FQR in NTS was largely mediated by amino acid substitutions in the clinically significant positions of Ser83 and Asp87 of gyrA. Col(pHAD28) was the most common plasmid identified in the Nigeria NTS collection. My study showed that FQR could not be simply predicted from the presence of resistance genes and demonstrated that SNPs associated with FQR were the primary indicators of phenotypic resistance. FQR was poorly predicted in S. Kentucky, and more sulphonamide genes were predicted compared to phenotypic methods. Three genes conferring resistance to the β-lactams were detected, with TEM-1 β-lactamase being the most common β-lactamase found, and S. Schwarzengrund isolates with a variant of blaTEM-215 were the only isolates with an amino acid change from Histidine to Arginine at position 151 of TEM-1. Antimicrobial stewardship was worryingly low amongst poultry farmers. In particular, critically important antimicrobial such as colistin was reported to be used on farms. The antimicrobial for which resistance was found matched those for which high usage was reported. Findings from this research indicate that the burden of AMR is high in Nigeria as up to 44% of isolates in the collection carried at least one AMR gene. Although the dataset used in this study is only a fraction of the larger Salmonella population and does not consider other bacterial pathogens, the findings here might suggest a broader AMR problem in the larger population. The ease of access and misuse of important antimicrobials might contribute to the high AMR observed. This study also suggests a high-level diversity of NTS in Nigeria identified from multiple hosts, with isolates from Nigeria sharing some similarities with strains from neighbouring African countries, suggesting that trade and travel might play an important role in the transmission of pathogens and possibly resistance. A One-Health approach and regional effort are needed to tackle NTS and AMR's spread within Nigeria and the African region, considering the overlap of strains from various sources.
Antimicrobial Resistance, Salmonella, Nigeria, Genomic diversity
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