Plasmid-mediated quinolone resistance genes detected in Ciprofloxacin non-susceptible Escherichia coli and Klebsiella isolated from children under five years at hospital discharge, Kenya.

BACKGROUND: The increasing spread of fluoroquinolone resistant enteric bacteria is a global public health concern. Children recently discharged from the hospital are at high risk of carriage of antimicrobial resistance (AMR) due to frequent exposure to antimicrobials during inpatient stays. This study aimed to determine the prevalence, correlates of ciprofloxacin (CIP) non-susceptibility, and distribution of plasmid-mediated quinolone resistance (PMQR) genes in Escherichia coli (E. coli) and Klebsiella spp isolated from children under five years being discharged from two Kenyan Hospitals. METHODS: E. coli and Klebsiella spp were isolated from fecal samples from children discharged from hospital and subjected to antimicrobial susceptibility testing (AST) by disc diffusion and E-test. CIP non-susceptible isolates were screened for seven PMQR genes using multiplex polymerase chain reaction (PCR). Poisson regression was used to determine the association between the carriage of CIP non-susceptible isolates and patient characteristics. RESULTS: Of the 280 CIP non-susceptible isolates: 188 E. coli and 92 Klebsiella spp isolates identified among 266 discharged children, 195 (68%) were CIP-non-susceptible with minimum inhibitory concentrations (MICs) of ≥ 1 µg/mL. Among these 195 isolates, 130 (67%) had high-level CIP MIC = ≥ 32 µg/mL). Over 80% of the isolates had at least one PMQR gene identified: aac(6')lb-cr (60%), qnrB (24%), oqxAB (22%), qnrS (16%), and qepA (6%), however, qnrA was not identified in any isolates tested. Co-carriage of qnrB with acc(6')-lb-cr was the most predominant accounting for 20% of all the isolates. Ceftriaxone use during hospital admission and the presence of extended spectrum beta-lactamase (ESBL) production were significantly associated with the carriage of CIP non-susceptible E. coli and Klebsiella spp. CONCLUSION: CIP non-susceptibility is common among E. coli and Klebsiella spp isolated from hospital discharged children in Kenya. Carriage and co-carriage of PMQR, including the newly identified qepA gene, were frequently observed. These findings suggest that children leaving the hospital may serve as an important reservoir for transmission of resistant E. coli and Klebsiella spp to the community. Enhanced surveillance for AMR determinants is critical to inform interventions to control antimicrobial-resistant bacteria.

Secondary malaria vectors in western Kenya include novel species with unexpectedly high densities and parasite infection rates.

BACKGROUND: Malaria vector control has been implemented chiefly through indoor interventions targeting primary vectors resulting in population declines-pointing to a possible greater proportional contribution to transmission by secondary malaria vectors with their predominant exophagic and exophilic traits. With a historical focus on primary vectors, there is paucity of data on secondary malaria vectors in many countries in Africa. This study sought to determine the species compositions and bionomic traits, including proportions infected with Plasmodium falciparum and phenotypic insecticide resistance, of secondary vectors in three sites with high malaria transmission in Kisumu County, western Kenya. METHODS: Cross-sectional sampling of adult Anopheles was conducted using indoor and outdoor CDC light traps (CDC-LT) and animal-baited traps (ABTs) in Kakola-Ombaka and Kisian, while larvae were sampled in Ahero. Secondary vectors captured were exposed to permethrin using WHO bioassays and then analyzed by ELISA to test for proportions infected with P. falciparum sporozoites. All Anopheles were identified to species using morphological keys with a subset being molecularly identified using ITS2 and CO1 sequencing for species identification. RESULTS: Two morphologically identified secondary vectors captured-An. coustani and An. pharoensis-were determined to consist of four species molecularly. These included An. christyi, An. sp. 15 BSL-2014, an unidentified member of the An. coustani complex (An. cf. coustani) and a species similar to that of An. pharoensis and An. squamosus (An. cf. pharoensis). Standardized (Anopheles per trap per night) capture rates demonstrate higher proportions of secondary vectors across most trapping methods-with overall indoor and outdoor CDC-LTs and ABT captures composed of 52.2% (n = 93), 78.9% (n = 221) and 58.1% (n = 573) secondary vectors respectively. Secondary vectors were primarily caught outdoors. The overall proportion of secondary vectors with P. falciparum sporozoite was 0.63% (n = 5), with the unidentified species An. cf. pharoensis, determined to carry Plasmodium. Overall secondary vectors were susceptible to permethrin with a > 99% mortality rate. CONCLUSIONS: Given their high densities, endophily equivalent to primary vectors, higher exophily and Plasmodium-positive proportions, secondary vectors may contribute substantially to malaria transmission. Unidentified species demonstrate the need for further morphological and molecular identification studies towards further characterization. Continued monitoring is essential for understanding their temporal contributions to transmission, the possible elevation of some to primary vectors and the development of insecticide resistance.

A six-member SNP assay on the iPlex MassARRAY platform provides a rapid and affordable alternative for typing major African Staphylococcus aureus types.

PURPOSE: Data on the clonal distribution of Staphylococcus aureus in Africa are scanty, partly due to the high costs and long turnaround times imposed by conventional genotyping methods such as spa and multilocus sequence typing (MLST), which means there is a need for alternative typing approaches. This study evaluated the discriminatory power, cost of and time required for genotyping Kenyan staphylococcal isolates using iPlex MassARRAY compared to conventional methods. METHODOLOGY: Fifty-four clinical S. aureus isolates from three counties were characterized using iPlex MassARRAY, spa and MLST typing methods. Ten single-nucleotide polymorphisms (SNPs) from the S. aureus MLST loci were assessed by MassARRAY. >RESULTS: The MassARRAY assay identified 14 unique SNP genotypes, while spa typing and MLST revealed 22 spa types and 21 sequence types (STs) that displayed unique regional distribution. spa type t355 (ST152) was the dominant type overall while t037/t2029 (ST 241) dominated among the methicillin-resistant S. aureus (MRSA) isolates. MassARRAY showed 83 % and 82 % accuracy against spa typing and MLST, respectively, in isolate classification. Moreover, MassARRAY identified all MRSA strains and a novel spa type. MassARRAY had a reduced turnaround time (<12 h) compared to spa typing (4 days) and MLST (20 days). The MassARRAY reagent and consumable costs per isolate were approximately $18 USD compared to spa typing ($30 USD) and MLST ($126 USD). CONCLUSION: This study demonstrated that iPlex MassARRAY can be adapted as a useful surveillance tool to provide a faster, more affordable and fairly accurate method for genotyping African S. aureus isolates to identify clinically significant genotypes, MRSA strains and emerging strain types.