Farm-to-fork changes in poultry microbiomes and resistomes in Maputo City, Mozambique.

Unlabelled: Increasing demand for poultry has spurred poultry production in low- and middle-income countries like Mozambique. Poultry may be an important source of foodborne, antimicrobial-resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways (ChEEP ChEEP) study was conducted in Maputo City, Mozambique from 2019 to 2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.

Accumulation of microbial hazards and assessment of food hygiene associated with broiler chicken processing at open air food markets in Maputo, Mozambique.

The burden of foodborne disease due to the consumption of animal-sourced foods is substantial in low- and middle-income countries (LMICs). Open air markets, while providing fresh and affordable foods, often have unhygienic practices that may contribute to contamination during the slaughter and processing of chicken meat. This study examines whether and how the common practice of rinse water (stored water used for rinsing broiler carcasses during processing) reuse leads to accumulation of pathogens, with potential cross contamination of chicken meat.

Multiplex PCR detection of enteric pathogens in a community-based birth cohort in Ecuador: comparison of xTAG-GPP and TaqMan array card assays.

We compared the performance of two multiplex platforms, Luminex xTAG Gastrointestinal Pathogen PanelⓇ and TaqMan Array Card, against a panel of 14 enteric pathogen targets in a community-based birth cohort in Ecuador. We found high levels of agreement and similar prevalence estimates across most pathogens.

Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic in northern Ecuador.

A high proportion of enteric infections, including those caused by diarrheagenic (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage.

Quantifying Enteropathogen Contamination along Chicken Value Chains in Maputo, Mozambique: A Multidisciplinary and Mixed-Methods Approach to Identifying High Exposure Settings.

Background: Small-scale poultry production is widespread and increasing in low- and middle-income countries (LMICs). Exposure to enteropathogens in poultry feces increases the hazard of human infection and related sequela, and the burden of disease due to enteric infection in children y in particular is substantial. Yet, the containment and management of poultry-associated fecal waste in informal settings in LMICs is largely unregulated.

Distribution of Escherichia coli Pathotypes along an Urban-Rural Gradient in Ecuador.

Diarrheal diseases are a leading cause of mortality and morbidity in low- and middle-income countries. Diarrhea is associated with a wide array of etiological agents including bacterial, viral, and parasitic enteropathogens. Previous studies have captured between- but not within-country heterogeneities in enteropathogen prevalence and severity.

Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador.

Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E.

Gut microbiome, enteric infections and child growth across a rural-urban gradient: protocol for the ECoMiD prospective cohort study.

Introduction: The functional consequences of the bacterial gut microbiome for child health are not well understood. Characteristics of the early child gut microbiome may influence the course of enteric infections, and enteric infections may change the composition of the gut microbiome, all of which may have long-term implications for child growth and development.

Methods And Analysis: We are conducting a community-based birth cohort study to examine interactions between gut microbiome conditions and enteric infections, and how environmental conditions affect the development of the gut microbiome.

Updates on defining and detecting diarrheagenic Escherichia coli pathotypes.

Purpose Of Review: Several types of Escherichia coli cause acute diarrhea in humans and are responsible for a large burden of disease globally. The purpose of this review is to summarize diarrheagenic Escherichia coli (DEC) pathotype definitions and discuss existing and emerging molecular, genomic, and gut microbiome methods to detect, define, and study DEC pathotypes.

Recent Findings: DEC pathotypes are currently diagnosed by molecular detection of unique virulence genes.

Clustering of Isolates Using MLST and Whole-Genome Phylogenetics and Protein Motif Fingerprinting.

is a ubiquitous and abundant member of native microbial assemblages in coastal waters and shellfish. Though is predominantly environmental, some strains have infected human hosts and caused outbreaks of seafood-related gastroenteritis. In order to understand differences among clinical and environmental strains, we used high quality DNA sequencing data to compare the genomes of isolates ( = 43) from a variety of geographic locations and clinical and environmental sample matrices.

Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 ().

Of marine eubacteria, the genus is intriguing because member species are relevant to both marine ecology and human health. Many studies have touted the relationships of to environmental factors, especially temperature and salinity, to predict total abundance but lacked the taxonomic resolution to identify the relationships among species and the key drivers of dynamics. To improve next-generation sequencing (NGS) surveys of , we have conducted both 16S small subunit rRNA and heat shock protein 60 () amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC.

Quantitative PCR analysis of functional genes in iron-rich microbial mats at an active hydrothermal vent system (Lō'ihi Seamount, Hawai'i).

The chemolithotrophic Zetaproteobacteria represent a novel class of Proteobacteria which oxidize Fe(II) to Fe(III) and are the dominant bacterial population in iron-rich microbial mats. Zetaproteobacteria were first discovered at Lō'ihi Seamount, located 35 km southeast off the big island of Hawai'i, which is characterized by low-temperature diffuse hydrothermal venting. Novel nondegenerate quantitative PCR (qPCR) assays for genes associated with microbial nitrogen fixation, denitrification, arsenic detoxification, Calvin-Benson-Bassham (CBB), and reductive tricarboxylic acid (rTCA) cycles were developed using selected microbial mat community-derived metagenomes.