Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.

The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult.

Identification of Signatures of Positive Selection That Have Shaped the Genomic Landscape of South African Pig Populations.

South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer's extension of the statistic based on haplotype information (HapFLK) were utilised.

Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces.

The increasing prevalence of antimicrobial-resistant (AMR) pathogens has become a major global health concern. To address this challenge, innovative strategies such as bacteriophage therapy must be optimised. Genomic characterisation is a crucial step in identifying suitable phage candidates for combating AMR pathogens.

Characterization of the soil resistome and mobilome in Namib Desert soils.

The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics.

Resistome, mobilome, virulome analysis and phylogenomics of Enterococcus faecalis isolated from raw muscle foods of beef origin in Gauteng, South Africa.

Enterococcus faecalis is a ubiquitous bacterium found in various environments, including processed beef meat, and is known for its importance in both food safety and public health. This pivotal significance stems not solely from its virulence but also from its adeptness in eliciting multidrug-resistant infections in humans. The aim of this study was to investigate the population structure, resistome, mobilome, and virulome of E.

Genus-wide genomic characterization of : insights into evolution, population structure, and functional potential.

Introduction: species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be opportunistic pathogens in both veterinary and human clinical settings.

Genome sequence of an indole-3-acetic acid and siderophores producing SARCC-3054 with the potential as a microbial inoculant for enhanced crop production.

The genome of strain SARCC-3054 was sequenced after being confirmed as a potential plant growth-promoting rhizobacteria in both and assays. The 6.3 MB genome has a GC content of 60.

Draft Genome Sequence of Pectobacterium brasiliense Isolated from Potato in South Africa.

This study reports a draft genome of a phytopathogenic bacterium, Pectobacterium brasiliense, isolated from potato in South Africa. The total reported length of the genome is 4,897,858 bp, contained in 172 contigs with 4,378 genes. The GC content of the genome is 51.

Identification of and Multilocus Variable-Number Tandem Repeat Analysis (MLVA) Typing of and Isolates from Cattle Farms and Beef and Beef-Based Products from Retail Outlets in Mpumalanga and North West Provinces, South Africa.

In this study, Listeria isolates (214) were characterized as follows: L. innocua (77.10%), L.

Phylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago.

This study was conducted to determine the phylogenies of Salmonella strains isolated from cross-sectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016-2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness.

Botrytis cinerea expression profile and metabolism differs between noble and grey rot of grapes.

Botrytis cinerea, the pathogen causing grey rot (GR) with important economic losses in fruit crops, can also cause noble rot (NR) of grape berries under certain environmental conditions, leading to metabolic and physical changes necessary for producing highly regarded botrytized wines. The functional genes involved in biochemical processes in these harmful vs. beneficial berry rot types are still scarcely understood.

Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter- and Intranational Surveillance and Source Tracking.

Members of the Bacillus cereus sensu lato species complex, also known as the B. cereus group, vary in their ability to cause illness but are frequently isolated from foods, including meat products; however, food safety surveillance efforts that use whole-genome sequencing (WGS) often neglect these potential pathogens. Here, we evaluate the surveillance and source tracking potential of WGS as applied to B.

Metatranscriptomic Analyses Reveal the Functional Role of in Biochemical and Textural Changes during Noble Rot of Grapevines.

, can lead to the formation of noble rot (NR) of grape berries under certain environmental conditions, resulting in favored metabolic and physical changes necessary for producing highly regarded botrytized wines. The functional genes involved in the textural and biochemical processes are still poorly characterized. We generated and analyzed metatranscriptomic data from healthy (H) berries and from berries representing the four stages of NR from the Tokaj wine region in Hungary over three months.

Molecular Characterization of Detected along the Broiler Production Chain in Trinidad and Tobago.

This cross-sectional study determined the serovars, antimicrobial resistance genes, and virulence factors of isolated from hatcheries, broiler farms, processing plants, and retail outlets in Trinidad and Tobago. in silico serotyping detected 23 different serovars where Kentucky 20.5% (30/146), Javiana 19.

A 16S Next Generation Sequencing Based Molecular and Bioinformatics Pipeline to Identify Processed Meat Products Contamination and Mislabelling.

Processed meat is a target in meat adulteration for economic gain. This study demonstrates a molecular and bioinformatics diagnostic pipeline, utilizing the mitochondrial 16S ribosomal RNA (rRNA) gene, to determine processed meat product mislabeling through Next-Generation Sequencing. Nine pure meat samples were collected and artificially mixed at different ratios to verify the specificity and sensitivity of the pipeline.

Genomic Characterization of Endemic and Ecdemic Non-typhoidal Lineages Circulating Among Animals and Animal Products in South Africa.

In Africa, the burden of illness caused by non-typhoidal is disproportionally high; however, whole-genome sequencing (WGS) efforts are overwhelmingly concentrated in world regions with lower burdens. While WGS is being increasingly employed in South Africa to characterize , the bulk of these efforts have centered on characterizing human clinical strains. Thus, very little is known about lineages circulating among animals in the country on a genomic scale.

South African Buffalo-Derived Is Distinct From Other Buffalo and Cattle-Derived .

is a protozoan parasite transmitted by the brown-eared ticks, and . Buffaloes are the parasite's ancestral host, with cattle being the most recent host. The parasite has two transmission modes namely, cattle-cattle and buffalo-cattle transmission.

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.

Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime.