Department of Biochemistry, Cell and Molecular Biology

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Start date: 2020End date: 2021Author: search.filters.author.Agbodzi, B.

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    Pathogenomics And Antimicrobial Resistance Analysis In Neisseria Gonorrhoeae
    (University Of Ghana, 2021-01) Agbodzi, B.
    Gonorrhoea is a poorly controlled public health problem. With the global emergence of resistance to first line antibiotic treatment options, the infection has been predicted to be untreatable in the near future. This emerging trend highlights the need for constant genetic surveillance to unravel the mechanisms of resistance and inform therapy. This study therefore, sought to perform whole genome characterization of N. gonorrhoeae collected in Ghana to identify lineages of circulating strains, their antimicrobial resistance (AMR) and some virulence determinants. Gonococci isolates were cultured on gonococcal (GC) medium and identified using the API NH kit (Biomerieux, France). Genomic DNA was extracted from N. gonorrhoeae isolates using the QIAamp® DNeasy Ultraclean Microbial kit (Qiagen, Hilden, Germany). Whole genome sequencing (WGS) was performed on 56 isolates using both the Oxford Nanopore MinION and Illumina MiSeq sequencing platforms. The Comprehensive Antimicrobial Resistance Database (CARD) and PubMLST Neisseria database were used to catalogue chromosomal and plasmid genes implicated in AMR and assign sequence types (STs). The core genome MLST (cgMLST) approach was used for comparative genomics. The Virulence Factors of Pathogenic Bacteria Database (VFDB) was used to annotate virulence factors. In vitro resistance measured by disc diffusion revealed that (56)100%, (51)91% and (50)89.3% of the isolates were resistant to tetracycline, penicillin and ciprofloxacin respectively, while for the E-test method, (54)96.4%, (51)91% and (49)87.5% respectively were recorded. Four isolates exhibited reduced susceptibility to both cefixime and ceftriaxone as measured by disc diffusion. For these isolates, MIC ranges of 0.004 – 0.016 μg/ml and 0.016 - 0.75 μg/ml for ceftriaxone and cefixime respectively were recorded. No spectinomycin and azithromycin resistance was recorded using the E-test method. A total of 22 STs were identified by Multi-Locus Sequence Typing (MLST), with ST-14422 (n=10), ST-1927 (n=8) and ST-11210 (n=7) being the most prevalent. Six novel STs were also identified and submitted for the assignment of new sequence types (ST-15634-115641). Seven clusters of isolates with distinct AMR genotypes were identified after the cgMLST analysis, highlighting the presence of genome wide genetic variation. All isolates harboured chromosomal AMR determinants that confer resistance to beta-lactam antimicrobials and tetracycline. A total of (49)87.5% and (13)23% isolates contained fluoroquinolone and macrolide resistance markers respectively. Plasmids were highly prevalent: pTetM and pBlaTEM were found in 96%, and 92% of isolates, respectively. All isolates possessed the PI (B) variant of the porB gene which is associated with localized infection while high antigenic variations in the pillin genes was also detected. The study highlighted the need for constant genomic surveillance with the looming possible emergence of cephalosporin resistant isolates and isolates with highly variable antigens which could severely impact disease treatment.