Genomics of Pseudomonas aeruginosa isolated from surgical site infections at a teaching and referral hospital in Kenya.

Kindiki, S.*

Masinde Muliro University of Science and Technology

There is limited genomic data on Pseudomonas aeruginosa (PA) pathogens involved in surgical site infections (SSIs) in sub-Saharan Africa. PA is a notorious pathogen known for its ability to develop antimicrobial resistance (AMR) and its possession of various virulence factors that enhance its pathogenicity. The increasing resistance of PA to antibiotics, including highly effective antimicrobials, presents a significant challenge in the management of surgical site infections (SSI). In this study we report phenotypic and genotypic AMR patterns, genetic relatedness, and virulence determinants of PA isolated from SSIs. We characterized their antimicrobial resistance profiles, carried out whole genome sequencing and analyzed their genomes using standard software for identification of drug resistant genes and virulence determinants: Abricate, RGI, VDFB and SeqWord Genomic Island (GI) Sniffer. We also phenotypically characterized them for quorum-sensing (QS)-related virulence factors. Our study revealed diverse PA subtypes involved in SSIs at the facility. Ten (10) sequence types (ST) were identified with the biggest genome being of isolate ST 244 with biggest length of Genomic Islands (9.7%), while the smallest genome was of the isolate ST 870 with the smallest length (3.8%). The biggest horizontally acquired virulence genes are found in isolate ID014 with 31 genes. The study reports of a high–risk strain that was multidrug resistant and carried the largest number of antibiotic resistance genes in the GI which confer resistance to aminoglycosides, fluoroquinolones, disinfecting agents and antiseptics. Moreover, it is the only strain utilizing an antibiotic target alteration mechanism. Antibiotic efflux and beta-lactamase inhibition are the most utilized mechanisms accounting for 57% of the resistance mechanisms identified among the isolate. Horizontally acquired drug resistance determinants contributed to resistance against fluoroquinolones, aminoglycosides including other broad spectra of antibiotics. Notably, the study identified two previously unreported PA subtypes, perhaps specific to the region of Kenya. Several QS-related virulence factors were identified: proteases, pigment production and swarming motility, highlighting the pathogenic potential of the PA isolates infecting wounds. Our study shows that PA in Western Kenya are versatile, and some strains may be emerging as pathogens of public health concern. The two undocumented strains specific to Kenya underscores the importance of characterization and surveillance of local strains. However, there is an urgent need for strengthening infection control programs and antimicrobial stewardship to manage the emergence of multi-drug resistant microbes.

Keywords: Pseudomonas aeruginosa, surgical site infections, antimicrobial resistance, multidrug resistance, genetic relatedness, virulence factors