Genetic Diversity, Distribution, and Genomic Characterization of Antibiotic Resistance and Virulence of Clinical Pseudomonas aeruginosa Strains in Kenya.

Shahiid Kiyaga,Cecilia Kyany'A,Hunter J Smith,Emma G Mills,Caleb Kibet,Angela W Muraya,Lillian Musila,Gerald Mboowa

doi:10.3389/fmicb.2022.835403

Abstract

Pseudomonas aeruginosa is a leading cause of nosocomial infections worldwide. It can produce a range of debilitating infections, have a propensity for developing antimicrobial resistance, and present with a variety of potent virulence factors. This study investigated the sequence types (ST), phenotypic antimicrobial susceptibility profiles, and resistance and virulence genes among clinical isolates from urinary tract and skin and soft tissue infections. Fifty-six P. aeruginosa clinical isolates were obtained from six medical centers across five counties in Kenya between 2015 and 2020. Whole-genome sequencing (WGS) was performed to conduct genomic characterization, sequence typing, and phylogenetic analysis of the isolates. Results showed the presence of globally distributed high-risk clones (ST244 and ST357), local high-risk clones (ST2025, ST455, and ST233), and a novel multidrug-resistant (MDR) clone carrying virulence genes (ST3674). Furthermore, 31% of the study isolates were found to be MDR with phenotypic resistance to a variety of antibiotics, including piperacillin (79%), ticarcillin-clavulanic acid (57%), meropenem (34%), levofloxacin (70%), and cefepime (32%). Several resistance genes were identified, including carbapenemases VIM-6 (ST1203) and NDM-1 (ST357), fluoroquinolone genes, crpP, and qnrVCi, while 14 and 22 different chromosomal mutations were detected in the gyrA and parC genes, respectively. All isolates contained at least three virulence genes. Among the virulence genes identified, phzB1 was the most abundant (50/56, 89%). About 21% (12/56) of the isolates had the exoU+/exoS- genotype, while 73% (41/56) of the isolates had the exoS+/exoU- genotype. This study also discovered 12 novel lineages of P. aeruginosa, of which one (ST3674) demonstrated both extensive antimicrobial resistance and the highest number of virulence genes (236/242, 98%). Although most high-risk clones were detected in Nairobi County, high-risk and clones of interest were found throughout the country, indicating the local spread of global epidemic clones and the emergence of new strains. Thus, this study illustrates the urgent need for coordinated local, regional, and international antimicrobial resistance surveillance efforts.

Highlights

Pseudomonas aeruginosa is a Gram-negative bacterium with a diverse genetic composition allowing it to colonize various environments such as water, soil, and humans (Stover et al, 2000)
Our study identified 41 sequence types (ST) among the P. aeruginosa isolates, which is consistent with other studies that have reported the non-clonal population structure of P. aeruginosa (Barrio-Tofiño et al, 2020)
It is primarily associated with O-antigen serotype O11, exoU+/exoS− T3SS genotype, and MBLs such as VIM-2, IMP-1,6, and OXA-1,2,10 (Mano et al, 2015; Oliver et al, 2015; MiyoshiAkiyama et al, 2017)

Summary

Introduction

Pseudomonas aeruginosa is a Gram-negative bacterium with a diverse genetic composition allowing it to colonize various environments such as water, soil, and humans (Stover et al, 2000) It is a leading cause of nosocomial infections and can lead to many debilitating infections, including wound infections, pneumonia, and keratitis (Stapleton and Carnt, 2012). The numerous resistance mechanisms, against lastresort drugs, make treating associated infections challenging, resulting in treatment failure, prolonged hospitalization, and high morbidity and mortality (Thuo et al, 2019) This penchant for developing multidrug resistance (MDR) and ability to cause life-threatening infections with high mortality rates (Farshadzadeh et al, 2014) earned P. aeruginosa the Priority 1: Critical designation among the World Health Organization’s (WHO) list of priority pathogens for antimicrobial research and development (World Health Organization, 2017). The innate resistance of P. aeruginosa to some antibiotics, accumulation of mutations, and horizontally acquired resistance mechanisms have led to the global distribution of high-risk MDR clones such as ST111, ST175, and ST235 (Barrio-Tofiño et al, 2017) due to global human travel

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Conclusion