Phenotypic and genotypic characterization of clinical Staphylococcus aureus isolates from Kenya

Abstract

BackgroundThe increase and spread of virulent-outbreak associated, methicillin and vancomycin resistant (MRSA/VRSA) Staphylococcus aureus require a better understanding of the resistance and virulence patterns of circulating and emerging strains globally. This study sought to establish the resistance phenotype, and strains of 32 non-duplicate clinical MRSA and MSSA S. aureus isolates from four Kenyan hospitals, identify their resistance and virulence genes and determine the genetic relationships of MRSA with global strains.MethodsAntimicrobial susceptibility profiles were determined on a Vitek 2, genomic DNA sequenced on an Illumina Miseq and isolates typed in-silico. Resistance and virulence genes were identified using ARIBA and phylogenies generated using RAxML.ResultsThe MRSA isolates were 100% susceptible to vancomycin, teicoplanin, linezolid, and tigecycline. Nine distinct CC, 12 ST and 15 spa types including the novel t17826 and STs (4705, 4707) were identified with CC8 and CC152 predominating. MRSA isolates distributed across 3 CCs; CC5-ST39 (1), CC8 – ST241 (4), a novel CC8-ST4705 (1), ST8 (1) and CC152 (1). There was > 90% phenotype-genotype concordance with key resistance genes identified only among MRSA isolates: gyrA, rpoB, and parC mutations, mecA, ant (4′)-lb, aph (3′)-IIIa, ermA, sat-4, fusA, mphC and msrA. Kenyan MRSA isolates were genetically diverse and most closely related to Tanzanian and UK isolates. There was a significant correlation between map, hlgA, selk, selq and cap8d virulence genes and severe infections.ConclusionThe findings showed a heterogeneous S. aureus population with novel strain types. Though limited by the low number of isolates, this study begins to fill gaps and expand our knowledge of S. aureus epidemiology while uncovering interesting patterns of distribution of strain types which should be further explored. Although last-line treatments are still effective, the potential for outbreaks of both virulent and resistant strains remain, requiring sustained surveillance of S. aureus populations.

Epidemiology of <i>Staphylococcus aureus</i> Infections in Kenya: Current State, Gaps and Opportunities

“…An evaluation of resistance profiles of isolates from the internal medicine department of Kenyatta National Hospital between 2014 and 2016 revealed an MRSA detection rate of 53.5% [24] while K'yanya et al recently analyzed the susceptibility profiles of 32 clinical isolates from four hospitals across Kenya where higher susceptibilities to vancomycin, teicoplanin, tigecycline and linezolid were observed [25]. However, there were decreased susceptibilities to trimethoprim-sulfamethoxazole, tetracycline and ciprofloxacin and complete resistance to penicillin [25]. The authors applied whole genome sequencing (WGS) to uncover both known and novel mechanisms of resistance which marked the first Kenyan study employing genomic approaches to characterize the genetic basis of resistance in clinical staphylococcal isolates [25].…”

“…However, there were decreased susceptibilities to trimethoprim-sulfamethoxazole, tetracycline and ciprofloxacin and complete resistance to penicillin [25]. The authors applied whole genome sequencing (WGS) to uncover both known and novel mechanisms of resistance which marked the first Kenyan study employing genomic approaches to characterize the genetic basis of resistance in clinical staphylococcal isolates [25]. Overall, the resistance ranges for seven most commonly tested drugs were: tetracycline (15.5% -35.5%), trimethoprim-sulfamethoxazole (19% -75.6%), erythromycin (11.9% -81.7%), clindamycin (2% -37.8%), gentamicin (1% -84.1%) and ciprofloxacin (7% -74.4%).…”

“…Overall, the resistance ranges for seven most commonly tested drugs were: tetracycline (15.5% -35.5%), trimethoprim-sulfamethoxazole (19% -75.6%), erythromycin (11.9% -81.7%), clindamycin (2% -37.8%), gentamicin (1% -84.1%) and ciprofloxacin (7% -74.4%). A major observation was the diminished efficacy of penicillin which varied from 66% in [21] to 100% in [25].…”

“…Many studies did not distinguish between community and hospital acquired infections. However, Kyany'a et al and Nyasinga et al reported such delineation where the bulk of skin and soft tissue infections caused by S. aureus were community acquired [9] [25]. The distinction between community and healthcare associated infections is important especially with regards to MRSA strains which display multidrug resistance.…”

“…In many studies, data was analyzed retrospectively and inevitably, there were gaps in clinical and socio-demographic data which may be useful in the estimation of risk factors for infection or AMR spread. However, data from prospective, multicenter studies covering other areas of the country are increasingly being reported [9] [25]. Further, the establishment of a national surveillance and reporting framework will enable more accurate estimations of the extent of infections caused by S. aureus.…”