Aim: This study aimed to develop a multiplex PCR assay for simultaneous detection of major Gram-negative etiologies of septicemia and evaluate its performance.

Methods: Multiplex PCR (mPCR) assays were developed targeting 11 bacterial strains. Species-specific primers were confirmed using known clinical isolates and standard strains. Gradient PCR was performed on each primer against its target bacterial gene to determine its optimal amplification condition. The minimum detectable DNA concentration of the two assays was evaluated by adjusting bacterial DNA concentration to 100 ng/μL and, tenfold serially diluting it up to 10 pg/μL with DNAse-free water. The diagnostic accuracy of mPCR assays was established by subjecting the assays to 60 clinical blood samples.

Results: Two mPCR assays were developed. Optimal primer annealing temperature of 55 °C was established and utilized in the final amplification conditions. The assays detected all targeted bacteria, with a 100 pg minimum detectable DNA concentration. Pathogens were not detected directly from whole blood, but after 4 h and 8 h of incubation, 41% (5/12) and 100% (12/12) of the bacteria were detected in culture fluids, respectively. The assays also identified Salmonella spp. and Klebsiella pneumoniae co-infections and extra pathogens (1 E. coli and 2 K. pneumoniae) compared with culture. The sensitivity and specificity of the mPCR were 100.0% (71.7-100.0) and 98.0% (90.7-99.0), respectively. The area under the ROC curve was 1.00 (1.00-1.00).

Conclusions: The mPCR assays demonstrated substantial potential as a rapid tool for septicemia diagnosis alongside the traditional blood culture method. Notably, it was able to identify additional isolates, detect co-infections, and efficiently detect low bacterial DNA loads with high sensitivity, implying its value in enhancing efficiency of diagnosis of septicemia.

In Kenya, food screening exercises mostly applies to bacterial and parasitic agents, with enteric viral detection neglected. The aim of this study was to investigate the prevalence and molecular characterization of rotavirus in beef and pork cuts, as well as among handlers, in four selected abattoirs in Nairobi. Rotavirus was preferred because of its high prevalence rates and its ability to cause pathophysiologic infective gastroenteritis in humans. It has diverse strains characterized as P and G genotypes based on the VP7 and VP4 proteins, respectively. This cross-section study involved the collection of a total of 467, (165) beef/pork cuts and (302) handlers’ fecal samples. Collected samples were prepared before rotavirus identification. Prepared meat and stool suspensions were subjected to direct RNA extraction and EIA detection respectively. All the stool suspensions and RNA extracted meat suspensions subjected to EIA and Two step RT-PCR were all non-reactive respectively. Therefore, there was no VP4 and VP7 genotyping for characterization purposes on confirmed primary PCR products. Eppicollect5 was also used to collect and store the descriptive data of study participants, and the analysis conducted using Power BI statistical software application. The study’s findings, indicating no human viral infections in meat cuts, enhance public health by reassuring consumers, guiding regulatory policies, emphasizing the need for ongoing surveillance, directing resources to pressing concerns, supporting safe food handling campaigns, establishing baseline data for future assessments, and encouraging best practices in both formal and informal markets.

Objective This study analyzed the metatranscriptome of wastewater samples from different sites with a focus of identifying antibiotic resistance genes and the bacterial community.

Methods Twenty-four wastewater samples were collected from a hospital, university sewer, and the influent and effluent of a wastewater treatment plant (WWTP). The metatranscriptome was sequenced to identify antimicrobial resistance genes (ARGs), mobile genetic elements, and bacterial community composition.

Results Metatranscriptome analysis revealed varying abundances of ARG transcripts across different sites, with 84, 27, 14, and 9 ARG transcripts identified in wastewater collected from the hospital, university, influent, and effluent of a WWTP, respectively. Notably, hospital wastewater contained clinically relevant beta-lactam ARGs, including bla-NDM-1 and several blaOXA transcripts. Four core ARGs, against sulfonamides sul1 and sul2 and aminoglycosides aph(6)-ld and aph(’3’)-lb were also identified. The predominant bacterial community comprised of Gammaproteobacteria, with priority pathogens like Neisseria gonorrhea and Helicobacter pylori present in hospital wastewater and WWTP influent.

Conclusion These findings provide insights into the wastewater resistome and how meta-transcriptomic data can be utilized for the surveillance of antibiotic resistance. Overall, our study highlights the utility of wastewater surveillance in understanding and addressing the dissemination of antibiotic resistance and emphasizes the crucial role of proper wastewater management in protecting public and environmental health.

Background: Kenya introduced a monovalent rotavirus vaccine administered orally at 6 and 10 weeks of age into her National Immunization Program in July 2014. The study evaluated the long-term impact of the vaccine on hospitalization for all-cause and rotavirus-specific acute gastroenteritis (AGE) and strain epidemiology in Kenya.

Methods: Data on all-cause and rotavirus-specific AGE and strain distribution were derived from an eleven-year hospital-based surveillance of AGE among children aged <5 years at Kiambu County Teaching and Referral Hospital (KCTRH) in Central Kenya between 2009 and 2020. Fecal samples were screened for group A rotavirus using ELISA and genotyped using multiplex semi-nested RT-PCR. Trends in all-cause and rotavirus-related AGE and strain distribution were compared between the pre-vaccine (July 2009-June 2014), early post-vaccine (July 2014-June 2016) and late post-vaccine (February 2019-October 2020) periods.

Results: Rotavirus-specific AGE was detected at 27.5% (429/1546, 95% CI: 25.5-30.1%) in the pre-vaccine period; 13.8% (91/658, 95% CI: 11.3-16.6%) in the early post-vaccine period (July 2014-June 2016); and 12.0% (229/1916, 95% CI: 10.6-13.5%) in the late post-vaccine period (February 2019-October 2020). This amounted to a decline of 49.8% (95% CI: 34.6%-63.7%) in rotavirus-specific AGE in the early post-vaccine period and 53.4% (95% CI: 41.5-70.3%) in the late post-vaccine period when compared to the pre-vaccine period. All-cause AGE hospitalizations declined by 40.2% (95% CI: 30.8%-50.2%) and 75.3% (95% CI: 65.9-83.1%) in the early post-vaccine and late post-vaccine periods, respectively, when compared to the pre-vaccine period. G3P [8] was the predominant strain in the late post-vaccine period, replacing G1P[8] which had predominated in the pre-vaccine and early post-vaccine periods. Additionally, we detected considerable proportions of uncommon strains G3P[6] (4.8%) and G12P[6] (3.5%) in the post-vaccine era.

Conclusion: Rotavirus vaccination has resulted in a significant decline in all-cause and rotavirus-specific AGE, and thus, provides strong evidence for public health policy makers in Kenya to support the sustained use of the rotavirus vaccine in routine immunization. However, the shift in strain dominance and age distribution of rotavirus AGE in the post-vaccine era underscores the need for continued surveillance to assess any possible vaccine-induced selective pressure that could diminish the vaccine effectiveness over time.