Enteric Pathogens in Humans, Domesticated Animals, and Drinking Water in a Low-Income Urban Area of Nairobi, Kenya.

To explore the sources of and associated risks with drinking water contamination in low-income, densely populated urban areas, we collected human feces, domesticated animal feces, and source and stored drinking water samples in Nairobi, Kenya in 2019; and analyzed them using microbial source tracking (MST) and enteric pathogen TaqMan Array Cards (TACs). We established host-pathogen relationships in this setting, including detecting and Norovirus─which are typically associated with humans─in dog feces. We evaluated stored and source drinking water quality using indicator (), MST markers, and TACs, detecting pathogen targets in drinking water that were also detected in specific animal feces.

Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance.

Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species.

Evaluation of a modified quantitative polymerase chain reaction assay for genus Schistosoma detection using stool and urine samples from schistosomiasis endemic areas in Kenya.

Introduction: The microscopy-based Kato-Katz and urine filtration techniques have traditionally faced challenges in the detection of schistosomiasis in areas with low infection levels. A modified singleplex Schistosoma genus-specific quantitative real-time polymerase chain reaction (qPCR) assay was therefore evaluated as a sensitive and confirmatory schistosomiasis diagnostic test.

Methodology: The qPCR assay utilized primers and probe targeting internal transcribed spacer- 2 (ITS2) sequence of S.

Bacterial strain sharing between humans, animals, and the environment among urban households.

Identifying bacterial transmission pathways is crucial to inform strategies aimed at curbing the spread of pathogenic and antibiotic-resistant bacteria, especially in rapidly urbanizing low- and middle-income countries. In this study, we assessed bacterial strain-sharing and dissemination of antibiotic resistance across humans, domesticated poultry, canines, household soil, and drinking water in urban informal settlements in Nairobi, Kenya. We collected 321 samples from 50 households and performed Pooling Isolated Colonies-seq (PIC-seq) by sequencing pools of up to five colonies per sample to capture strain diversity, strain-sharing patterns, and overlap of antibiotic-resistant genes (ARGs).