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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. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies. [ABSTRACT FROM AUTHOR]

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. The aim of this study was to characterise seven phages that infect the Escherichia coli O177 strain using a whole genome sequencing. The analysis of genome sequences revealed that these phages had linear dsDNA, with genome sizes spanning from 136, 483 to 166,791 bp and GC content varying from 35.39 to 43.63%. Taxonomically, the phages were classified under three different subfamilies (Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae) and three genera (Phapecoctavirus, Tequatrovirus, and Vequintavirus) within the class Caudoviricetes. In silico PhageAI analysis predicted that all the phages were virulent, with confidence levels between 96.07 and 97.26%. The phage genomes contained between 66 and 82 ORFs, which encode hypothetical and putative functional proteins. In addition, the phage genomes contained core genes associated with molecular processes such as DNA replication, transcription modulation, nucleotide metabolism, phage structure (capsid and tail), and lysis. None of the genomes carried genes associated with undesirable traits such as integrase, antimicrobial resistance, virulence, and toxins. The study revealed high genome and proteome homology among E. coli O177 phages and other known Escherichia phages. The results suggest that the seven phages are new members of the genera Phapecoctavirus, Tequatrovirus, and Vequintavirus under the subfamilies Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae, respectively. [ABSTRACT FROM AUTHOR]

This study was conducted within 2 months by sampling chicken batches from a broiler farm, a plant processing plant, and supermarket retail. The overall frequency of isolation of Salmonella was 50% (16/32), 17.5% (7/40), and 40% (4/10) for the samples collected from the broiler farm, processing plant, and retail outlet, respectively. Serovar Infantis was the predominantly isolated serovar at the 3 sampling sites. Resistance genes aac(3)IV, aph(4)Ia, blaCTX-M65, and qacEdelta1 were detected in 84.6% (11/13) of the isolates subjected to whole genome sequencing. S. Infantis strains were clustered within and across the 3 sampling sites. This study demonstrates a direct measure of the transmission dynamics of Salmonella during a farm-to-fork approach. [ABSTRACT FROM AUTHOR]

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. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils. [ABSTRACT FROM AUTHOR]

Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic distribution in Australia. These accessions were subsequently bred, cloned and exported across the world to start local macadamia industries. The South African macadamia industry was established with pre-commercial and commercial macadamia from different parts of the world, and local selections were also performed. Many of these accessions have unique genetic compositions that have not been characterized yet. We used 13 nuclear microsatellite markers to study the genetic diversity and structure of macadamia germplasm cultivated in South Africa. We compared four groups of accessions including 31 originating from the Hawaiian Agricultural Experimental Station (HAES), 19 from Australia (AUS), two from California and one from Israel (OTH), 31 from South Africa's locally selected accessions (SA) and 26 from two local Farmers (FARM). We used STRUCTURE, PCoA and neighbour-joining phylogenetic analyses to show that the South African selected accessions include diverse hybrid genotypes with strong Macadamia tetraphylla composition, unlike the Hawaiian commercially released and Australian representative collections that mostly have M. integrifolia or hybrid composition. Our results suggest that the South African selections represent a unique and diverse set of germplasm for future macadamia improvement efforts that will benefit from genomic breeding technologies. [ABSTRACT FROM AUTHOR]

Maize yellow mosaic virus (MaYMV) is a single-stranded RNA polerovirus first identified in China. MaYMV was recently reported from West and East Africa, however it had not yet been reported from southern Africa. RNA-seq data from South African field-grown fungal-infected maize was mined for viral sequences by de novo assembly of reads that did not map to the maize or fungal genomes. Predicted proteins from the de novo-assembled unmapped reads matched MaYMV proteins with regions of 96–100% identity. MaYMV was detected in maize RNAseq data from 2009, 2012 and 2013. Complete South African MaYMV genome sequences (5642 nt) were determined by RT-PCR and Sanger sequencing of samples from two different maize genotypes, years, and sites. Phylogenetic analysis confirmed the species identity as MaYMV, and showed separate clustering of isolates between Africa, Asia and South America. Some MaYMV positive samples had reads matching Potyviridae (Johnson grass mosaic virus and Sugarcane mosaic virus), and mycoviruses (Setosphaeria turcica hypovirus 1, Bipolaris maydis partitivirus 1, and Pleospora typhicola fusarivirus 1). A 2016/2017 RT-PCR survey of maize plants exhibiting virus-like symptoms, such as yellowing and streaking patterns, revealed MaYMV in 39 samples from six provinces in South Africa. This report documents the earliest known MaYMV infection world-wide, and indicates that the virus is widespread throughout Africa. [ABSTRACT FROM AUTHOR]

It has recently been shown that Pseudomonas syringae strains pathogenic to woody hosts belonging to phylogroup (PG) 2 lack phenolic compound degradation pathways such as the beta-ketoadipate and protocatechuate pathways. The aim of this study was to analyse a selection of P. syringae PG 2 genomes, including those used previously to determine if they had other phenolic compound degradation pathways and to determine whether or not they were functional. Twenty-one publicly available genomes of PG 2 strains were analyzed. These strains had previously been isolated from both woody and herbaceous hosts. Phenolic degradation enzymes were present in 5 (23%) of the strains analysed, originating from both woody and herbaceous hosts. Hypothetical pathways were proposed to determine if catechol, anthranilate and benzoic acid were degraded by these strains. Both spectrophotometric and HPLC were used to determine phenolic compound degradation. The five strains with phenolic degradation enzymes were able to metabolize catechol, and HRI-W 7924 and MAFF 301072 could also metabolize anthranilate and benzoate, respectively. The study showed that even though some PG 2 strains lack the beta-ketoadipate and protocatechuate pathways, they still have phenolic compound degrading enzymes that may play a role in virulence. [ABSTRACT FROM AUTHOR]

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. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics., (© 2023. The Author(s).)