AUTHOR=Juma Meshack , Sankaradoss Arun , Ndombi Redcliff , Mwaura Patrick , Damodar Tina , Nazir Junaid , Pandit Awadhesh , Khurana Rupsy , Masika Moses , Chirchir Ruth , Gachie John , Krishna Sudhir , Sowdhamini Ramanathan , Anzala Omu , Meenakshi Iyer S. 

TITLE=Antimicrobial Resistance Profiling and Phylogenetic Analysis of Neisseria gonorrhoeae Clinical Isolates From Kenya in a Resource-Limited Setting

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.647565

DOI=10.3389/fmicb.2021.647565

ISSN=1664-302X

ABSTRACT=<sec><title>Background</title><p>Africa has one of the highest incidences of gonorrhea. <italic>Neisseria gonorrhoeae</italic> is gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing (WGS) is an efficient way of predicting AMR determinants and their spread in the population. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. Increasing accuracy of base-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer MinION in remote areas lead to its adoption for routine microbial genome sequencing. To investigate whether MinION-only sequencing is sufficient for WGS and downstream analysis in resource-limited settings, we sequenced the genomes of 14 suspected <italic>N. gonorrhoeae</italic> isolates from Nairobi, Kenya.</p></sec><sec><title>Methods</title><p>Using WGS, the isolates were confirmed to be cases of <italic>N. gonorrhoeae</italic> (<italic>n</italic> = 9), and there were three co-occurrences of <italic>N. gonorrhoeae</italic> with <italic>Moraxella osloensis</italic> and <italic>N. meningitidis</italic> (<italic>n</italic> = 2). <italic>N. meningitidis</italic> has been implicated in sexually transmitted infections in recent years. The near-complete <italic>N. gonorrhoeae</italic> genomes (<italic>n</italic> = 10) were analyzed further for mutations/factors causing AMR using an in-house database of mutations curated from the literature.</p></sec><sec><title>Results</title><p>We observe that ciprofloxacin resistance is associated with multiple mutations in both gyrA and parC. Mutations conferring tetracycline (<italic>rpsJ</italic>) and sulfonamide (<italic>folP</italic>) resistance and plasmids encoding beta-lactamase were seen in all the strains, and <italic>tet(M)</italic>-containing plasmids were identified in nine strains. Phylogenetic analysis clustered the 10 isolates into clades containing previously sequenced genomes from Kenya and countries across the world. Based on homology modeling of AMR targets, we see that the mutations in GyrA and ParC disrupt the hydrogen bonding with quinolone drugs and mutations in FolP may affect interaction with the antibiotic.</p></sec><sec><title>Conclusion</title><p>Here, we demonstrate the utility of mobile DNA sequencing technology in producing a consensus genome for sequence typing and detection of genetic determinants of AMR. The workflow followed in the study, including AMR mutation dataset creation and the genome identification, assembly, and analysis, can be used for any clinical isolate. Further studies are required to determine the utility of real-time sequencing in outbreak investigations, diagnosis, and management of infections, especially in resource-limited settings.</p></sec>