Expediting pathogen genomics adoption for enhanced foodborne disease surveillance in Africa.

The role of genomics in public health surveillance has been accentuated by its crucial contributions during the COVID-19 pandemic, demonstrating its potential in addressing global disease outbreaks. While Africa has made strides in expanding multi-pathogen genomic surveillance, the integration into foodborne disease (FBD) surveillance remains nascent. Here we highlight the critical components to strengthen and scale-up the integration of whole genome sequencing (WGS) in foodborne disease surveillance across the continent.

The dynamics of bla resistance genes in Salmonella Typhi.

Salmonella Typhi (S. Typhi) is an important pathogen causing typhoid fever worldwide. The emergence of antibiotic resistance, including that of bla genes encoding to TEM [Formula: see text]-lactamases has been observed.

Molecular Epidemiology and AMR Perspective of Diarrhoeagenic Escherichia coli in Africa: A Systematic Review and Meta-analysis.

Introduction: Diarrhoeagenic Escherichia coli (DEC) persistently challenges public health in Africa, contributing substantially to the diarrhoeal disease burden. This systematic review and meta-analysis illuminate the distribution and antimicrobial resistance (AMR) patterns of DEC pathotypes across the continent.

Methods: The review selectively focused on pathotype-specific studies reporting prevalence and/or AMR of human-derived DEC pathotypes from African nations, excluding data from extra-intestinal, animal, and environmental sources and studies focused on drug and mechanism experiments.

Predicting Listeria monocytogenes virulence potential using whole genome sequencing and machine learning.

Contamination with food-borne pathogens, such as Listeria monocytogenes, remains a big concern for food safety. Hence, rigorous and continuous microbial surveillance is a standard procedure. At this point, however, the food industry and authorities only focus on detection of Listeria monocytogenes without characterization of individual strains into groups of more or less concern.

Association of health, nutrition, and socioeconomic variables with global antimicrobial resistance: a modelling study.

Background: Although antimicrobial use is a key selector for antimicrobial resistance, recent studies have suggested that the ecological context in which antimicrobials are used might provide important factors for the prediction of the emergence and spread of antimicrobial resistance.

Methods: We used 1547 variables from the World Bank dataset consisting of socioeconomic, developmental, health, and nutritional indicators; data from a global sewage-based study on antimicrobial resistance (abundance of antimicrobial resistance genes [ARGs]); and data on antimicrobial usage computed from the ECDC database and the IQVIA database. We characterised and built models predicting the global resistome at an antimicrobial class level.

An Overview of Antimicrobial Resistance Profiles of Publicly Available Genomes with Sufficient Quality and Metadata.

(. ) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns.

Comparison of Source Attribution Methodologies for Human Campylobacteriosis.

spp. are the most common cause of bacterial gastrointestinal infection in humans both in Denmark and worldwide. Studies have found microbial subtyping to be a powerful tool for source attribution, but comparisons of different methodologies are limited.

The Microbial Genetic Diversity and Succession Associated with Processing Waters at Different Broiler Processing Stages in an Abattoir in Australia.

The high organic content of abattoir-associated process water provides an alternative for low-cost and non-invasive sample collection. This study investigated the association of microbial diversity from an abattoir processing environment with that of chicken meat. Water samples from scalders, defeathering, evisceration, carcass-washer, chillers, and post-chill carcass rinsate were collected from a large-scale abattoir in Australia.

Source Attribution of Human Campylobacteriosis Using Whole-Genome Sequencing Data and Network Analysis.

spp. are a leading and increasing cause of gastrointestinal infections worldwide. Source attribution, which apportions human infection cases to different animal species and food reservoirs, has been instrumental in control- and evidence-based intervention efforts.

Potential Influence of Regulation of the Food Value Chain on Prevalence and Patterns of Antimicrobial Resistance: the Case of Tilapia (Oreochromis niloticus).

The current study was designed to evaluate the potential impact of the level of regulation on the prevalence and patterns of antimicrobial agent resistance in bacteria isolated from fish. The study sites included two large lakes and both semiregulated and unregulated fish value chains. A total of 328 bacterial isolates belonging to 11 genera were evaluated for antimicrobial susceptibility testing using the disk diffusion method.

Prevalence and epidemiological distribution of selected foodborne pathogens in human and different environmental samples in Ethiopia: a systematic review and meta-analysis.

Bacterial Foodborne Pathogens (FBP) are the commonest cause of foodborne illness or foodborne diseases (FBD) worldwide. They contaminate food at any stages in the entire food chain, from farm to dining-table. Among these, the Diarrheagenic Escherichia coli (DEC), Non typhoidal Salmonella (NTS), Shigella spp.

Quantitative Microbial Risk Assessment Based on Whole Genome Sequencing Data: Case of .

The application of high-throughput DNA sequencing technologies (WGS) data remain an increasingly discussed but vastly unexplored resource in the public health domain of quantitative microbial risk assessment (QMRA). This is due to challenges including high dimensionality of WGS data and heterogeneity of microbial growth phenotype data. This study provides an innovative approach for modeling the impact of population heterogeneity in microbial phenotypic stress response and integrates this into predictive models inputting a high-dimensional WGS data for increased precision exposure assessment using an example of .

The Analysis of Field Strains Isolated From Food, Animal and Clinical Sources Uncovers Natural Mutations in Nisin Resistance Genes.

Nisin is a commonly used bacteriocin for controlling spoilage and pathogenic bacteria in food products. Strains possessing high natural nisin resistance that reduce or increase the potency of this bacteriocin against have been described. Our study sought to gather more insights into nisin resistance mechanisms in natural populations by examining a collection of 356 field strains that were isolated from different foods, food production environments, animals and human infections.

Application of Whole-Genome Sequences and Machine Learning in Source Attribution of Salmonella Typhimurium.

Prevention of the emergence and spread of foodborne diseases is an important prerequisite for the improvement of public health. Source attribution models link sporadic human cases of a specific illness to food sources and animal reservoirs. With the next generation sequencing technology, it is possible to develop novel source attribution models.

A High Resolution DNA Melting Curve Analysis for the Rapid and Efficient Molecular Diagnostics of Extended Spectrum β-Lactamase Determinants from Foodborne .

The accurate identification of Extended-Spectrum β-Lactamase (ESBL) genes in Gram-negative bacteria is necessary for surveillance and epidemiological studies of transmission through foods. We report a novel rapid, cheap, and accurate closed tube molecular diagnostic tool based on two multiplex HRM protocols for analysis of the predominant ESBL families encountered in foods. The first multiplex PCR assay targeted blaCTX-M including phylogenetic groups 1 (CTX-M-1-15, including CTX-M-1, CTX-M-3 and CTX-M-15), 2 (CTX-M-2), and 9 (CTX-M-9-14, including CTX-M-9 and CTX-M-14).

Meta-Analysis and Meta-Regression Indicate Dynamic Prevalence and Moderators of Foodborne Pathogens in African Indigenous Fermented Milk.

As more microbiological data for indigenous fermented milk (IFM) becomes available, concern about their microbial safety becomes eminent. Nonetheless, these data are highly fragmented, and a tool is required to integrate existing data and to provide a basis for data-driven decision making for IFM's safety. Therefore, meta-analysis and meta-regression were conducted to estimate the prevalence of foodborne pathogens in IFM and to determine factors influencing the estimated values.

Improving hazard characterization in microbial risk assessment using next generation sequencing data and machine learning: Predicting clinical outcomes in shigatoxigenic Escherichia coli.

The ever decreasing cost and increase in throughput of next generation sequencing (NGS) techniques have resulted in a rapid increase in availability of NGS data. Such data have the potential for rapid, reproducible and highly discriminative characterization of pathogens. This provides an opportunity in microbial risk assessment to account for variations in survivability and virulence among strains.

Machine Learning Methods as a Tool for Predicting Risk of Illness Applying Next-Generation Sequencing Data.

Next-generation sequencing (NGS) data present an untapped potential to improve microbial risk assessment (MRA) through increased specificity and redefinition of the hazard. Most of the MRA models do not account for differences in survivability and virulence among strains. The potential of machine learning algorithms for predicting the risk/health burden at the population level while inputting large and complex NGS data was explored with Listeria monocytogenes as a case study.

Microbiological Safety of Fresh Tilapia ( Oreochromis niloticus) from Kenyan Fresh Water Fish Value Chains.

This study evaluated the microbiological safety of fresh Nile tilapia ( Oreochromis niloticus) from Kenyan fresh water fish value chains. One hundred seventy-six fish samples were analyzed. The microbial counts of hygiene indicators, total viable aerobic count (TVC), total coliforms, and fecal coliforms isolated by using culture techniques were enumerated, and microbial pathogens present in the fish samples were identified and characterized by using molecular methods.

Species Distribution and Antimicrobial Profiles of Enterococcus spp. Isolates from Kenyan Small and Medium Enterprise Slaughterhouses.

The present study aimed at identifying and assessing antimicrobial resistance of Enterococcus spp. isolated from small and medium enterprise slaughterhouses in Kenya. In total, 67 isolates were recovered from 48 of 195 samples examined from beef carcasses, personnel, and cutting equipment in five small and medium enterprise slaughterhouses.

The Impact of Cooling Rate on the Safety of Food Products as Affected by Food Containers.

In recent decades, the demand for ready-to-eat (RTE) food items prepared by the food catering sector has increased together with the value of cook-serve, cook-chill, and cook-freeze food products. The technologies by which foods are cooked, chilled, refrigerated for storage, and reheated before serving are of prime importance to maintain safety. Packaging materials and food containers play an important role in influencing the cooling rate of RTE foods.

Draft Genome Sequences of Enterococcus mundtii Strains Isolated from Beef Slaughterhouses in Kenya.

We present here draft genome sequences of strains K7-EM, P2-EM, C11-EM, and H18-EM, which were isolated from slaughterhouse equipment, carcasses, and personnel of small- and medium-sized beef slaughterhouses in Kenya.

Microbial Contamination Level Profiles Attributed to Contamination of Beef Carcasses, Personnel, and Equipment: Case of Small and Medium Enterprise Slaughterhouses.

The microbial contamination level profiles (MCLPs) attributed to contamination of beef carcasses, personnel, and equipment in five Kenyan small and medium enterprise slaughterhouses were determined. Aerobic plate counts, Enterobacteriaceae, Staphylococcus, and Salmonella were used to determine contamination at four different slaughter stages, namely, dehiding, evisceration, splitting, and dispatch. Microbiological criteria of the four microorganisms were used to score contamination levels (CLs) as poor (0), poor to average (1), average (2), or good (3).

Quantitative Risk Assessment of Hemolytic Uremic Syndrome Associated with Consumption of Bulk Milk Sold Directly from Producer to Consumer in South Africa.

This study was conducted to estimate the hemolytic uremic syndrome (HUS) risk associated with consumption of producer-distributor bulk milk (PDBM) contaminated with Shiga toxin-producing Escherichia coli (STEC) in South Africa. Data were obtained from recently completed studies in South Africa taking into account prior collected prevalence data of STEC in raw and pasteurized PDBM and survey information from producer-distributor outlets and households. Inputs for the models were complemented with data from published and unpublished literature.

Microbial Performance of Food Safety Control and Assurance Activities in a Fresh Produce Processing Sector Measured Using a Microbial Assessment Scheme and Statistical Modeling.

Current approaches such as inspections, audits, and end product testing cannot detect the distribution and dynamics of microbial contamination. Despite the implementation of current food safety management systems, foodborne outbreaks linked to fresh produce continue to be reported. A microbial assessment scheme and statistical modeling were used to systematically assess the microbial performance of core control and assurance activities in five Kenyan fresh produce processing and export companies.