Search

The global antibiotic resistance crisis, driven by overuse and misuse of antibiotics, is multifaceted. This study aimed to assess the microbiological and genetic characteristics of raw retail pork meat through various methods, including the isolation, antibiotic susceptibility testing (AST), whole-genome sequencing (WGS) of selected indicator bacteria, antibiotic residue testing, and metagenomic sequencing. Samples were purchased from 10 pre-selected retail stores in Gauteng, South Africa. The samples were aseptically separated, with portions sent to an external laboratory for isolating indicator bacteria and testing for antibiotic residues. Identification of the isolated bacteria was reconfirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). AST was performed using the Microscan Walkaway system (Beckman Coulter, Brea, CA, USA). WGS and metagenomic sequencing were performed using the Illumina NextSeq 550 instrument (San Diego, CA, USA). The isolated E. coli and E. faecalis exhibited minimal phenotypic resistance, with WGS revealing the presence of tetracycline resistance genes. Both the isolated bacteria and meat samples harboured tetracycline resistance genes and the antibiotic residue concentrations were within acceptable limits for human consumption. In the metagenomic context, most identified bacteria were of food/meat spoilage and environmental origin. The resistome analysis primarily indicated beta-lactam, tetracycline and multidrug resistance genes. Further research is needed to understand the broader implications of these findings on environmental health and antibiotic resistance. [ABSTRACT FROM AUTHOR]

Background: Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples. Methods: The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools. Results: The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242). Conclusion: The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics. [ABSTRACT FROM AUTHOR]

We present metagenomes of 16 samples of water and sediment from two lakes, collected from eutrophic and non-eutrophic areas, including pooled samples enriched with phosphate and nitrate. Additionally, we assembled 167 bacterial metagenome-assembled genomes (MAGs). These MAGs were de-replicated into 83 unique genomes representing different species found in the lakes. All the MAGs exhibited >70% completeness and <10% contamination, with 79 MAGs being classified as 'nearly complete' (completeness >90%), while 54 falling within 80–90% range and 34 between 75–80% complete. The most abundant MAGs identified across all samples were Proteobacteria (n = 80), Firmicutes_A (n = 35), Firmicutes (n = 13), and Bacteriodota (n = 22). Other groups included Desulfobacteria_I (n = 2), Verrucomicrobiota (n = 4), Campylobacterota (n = 4) and Actinobacteriota (n = 6). Importantly, phylogenomic analysis identified that approximately 50.3% of the MAGs could not be classified to known species, suggesting the presence of potentially new and unknown bacteria in these lakes, warranting further in-depth investigation. This study provides valuable new dataset on the diverse and often unique microbial communities living in polluted lakes, useful in developing effective strategies to manage pollution. [ABSTRACT FROM AUTHOR]

During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain. [ABSTRACT FROM AUTHOR]

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next‐generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real‐time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web‐based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co‐infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods. [ABSTRACT FROM AUTHOR]

Helianthus annus (sunflower) is a globally important oilseed crop whose survival is threatened by various pathogenic diseases. Agrochemical products are used to eradicate these diseases; however, due to their unfriendly environmental consequences, characterizing microorganisms for exploration as biocontrol agents are considered better alternatives against the use of synthetic chemicals. The study assessed the oil contents of 20 sunflower seed cultivars using FAMEs-chromatography and characterized the endophytic fungi and bacteria microbiome using Illumina sequencing of fungi ITS 1 and bacteria 16S (V3–V4) regions of the rRNA operon. The oil contents ranged between 41–52.8%, and 23 fatty acid components (in varied amounts) were found in all the cultivars, with linoleic (53%) and oleic (28%) acids as the most abundant. Ascomycota (fungi) and Proteobacteria (bacteria) dominated the cultivars at the phyla level, while Alternaria and Bacillus at the genus level in varying abundance. AGSUN 5102 and AGSUN 5101 (AGSUN 5270 for bacteria) had the highest fungi diversity structure, which may have been contributed by the high relative abundance of linoleic acid in the fatty acid components. Dominant fungi genera such as Alternaria, Aspergillus, Aureobasidium, Alternariaste, Cladosporium, Penicillium, and bacteria including Bacillus, Staphylococcus, and Lactobacillus are established, providing insight into the fungi and bacteria community structures from the seeds of South Africa sunflower. [ABSTRACT FROM AUTHOR]

• Gut microbial colonisation in infants is a crucial, yet intricate, process, characterised by minimal diversity at birth that increases with age. • The infant gut virome is dominated by eukaryotic viruses, consisting primarily of human enteric viruses and non-human dietary viruses. • The infants' gut haboured high abundance of gastroenteritis-associated viruses, despite the absence of clinical symptoms. • The presence of plant viruses in the gut of infants who are not exposed to solid food could suggest vertical transmission from mother to infant, or possibly, contact between infant and other family members. The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae , and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut. [ABSTRACT FROM AUTHOR]

Wild plant species play an important role in plant virus epidemiology, mainly by harbouring viruses pathogenic to cultivated plant species. The genus Solanum includes important crop species as well as some highly abundant and widely distributed wild plant species. The aim of the present study was to profile the viromes of 11 wild Solanum spp. found in five provinces of South Africa. Metatranscriptomic analysis of pooled RNA samples from each of the Solanum spp. detected viruses belonging to 13–19 families. Reverse transcription PCR confirmed the detection of potato virus Y (PVY), potato leaf roll virus (PLRV), tomato torrado virus (ToTV) and tomato chlorosis virus (ToCV) for the first time in some of the Solanum spp. studied. Phylogenetic analyses indicated that the PVY and PLRV strains from the wild Solanum spp. were divergent from those reported in cultivated crops, while there was limited divergence among ToTV and ToCV isolates. Viruses detected for the first time in South Africa included tobacco mild green mosaic virus, tomato matilda virus, a pepper enamovirus from Rwanda and a cytorhabdovirus from potato in Kenya. Potentially novel viruses were also detected in S. lichtensteinii, S. mauritianum and S. viarum. This study demonstrates the role of Solanum spp. in harbouring viruses pathogenic to solanaceous crops, and in the emergence of new virus strains. It may therefore inform strategies for virus disease management by control of wild solanums that harbour viruses pathogenic to important Solanum crops. [ABSTRACT FROM AUTHOR]

In July 2017, a family of three members, a 46-year-old male, a 45-year-old female and their 8-year-old daughter, returned to South Africa from Thailand. They presented symptoms consistent with mosquito-borne diseases, including fever, headache, severe body aches and nausea. Mosquito bites in all family members suggested recent exposure to arthropod-borne viruses. Dengue virus 1 (Genus Orthoflavivirus ) was isolated (isolate no. SA397) from the serum of the 45-year-old female via intracerebral injection in neonatal mice and subsequent passage in VeroE6 cells. Phylogenetic analysis of this strain indicated close genetic identity with cosmopolitan genotype 1 DENV1 strains from Southeast Asia, assigned to major lineage K, minor lineage 1 (DENV1I&#95;K.1), such as GZ8H (99.92%) collected in November 2018 from China, and DV1I-TM19-74 isolate (99.72%) identified in Bangkok, Thailand, in 2019. Serum samples from the 46-year-old male yielded a virus isolate that could not be confirmed as DENV1, prompting unbiased metagenomic sequencing for virus identification and characterization. Illumina sequencing identified multiple segments of a mammalian orthoreovirus (MRV), designated as Human/SA395/SA/2017. Genomic and phylogenetic analyses classified Human/SA395/SA/2017 as MRV-3 and assigned a tentative genotype, MRV-3d, based on the S1 segment. Genomic analyses suggested that Human/SA395/SA/2017 may have originated from reassortments of segments among swine, bat, and human MRVs. The closest identity of the viral attachment protein σ1 (S1) was related to a human isolate identified from Tahiti, French Polynesia, in 1960. This indicates ongoing circulation and co-circulation of Southeast Asian and Polynesian strains, but detailed knowledge is hampered by the limited availability of genomic surveillance. This case represents the rare concurrent detection of two distinct viruses with different transmission routes in the same family with similar clinical presentations. It highlights the complexity of diagnosing diseases with similar sequelae in travelers returning from tropical areas.

Arid regions harbor seasonal and permanent wetlands, as biodiversity hotspots crucial for ecosystem services despite harsh conditions. These wetlands, typically dependent on episodic intense rainfall, are understudied compared to their humid counterparts. While the diversity of plants and animals in these wetlands is well-known, the microbial communities remain largely unexplored. To address this knowledge gap, we employed metagenome sequencing technologies to profile protist communities, including pathogenic protozoa, and their associated functional pathways, in sediment of permanent and seasonal arid freshwater wetlands across northern South Africa. Results revealed a core community of protists dominated by phylum Apicomplexa (66.73 %), Euglenazoa (19.03 %), Bacillariophyta (5.44 %), Metamonada (4.65 %), Cryptophyta (1.90 %), and Amoebazoa (1.21 %). Seasonal wetlands showed significantly higher protist diversity compared to permanent wetlands (Shannon index, p = 0.019; Chao1, p = 0.0095). A high abundance and diversity of human and zoonotic pathogenic protists (87.67 %) was observed, with lower levels of photoautotrophs (6.69 %) and limited diversity of phagotrophs (5.64 %). Key photoautotrophs identified included diatoms (Thalassiosiraceae and Phaeodactylaceae) and cryptophytes (genus Hemiselmis and Cryptophyta), with consumers/phagotrophs exhibited a correlation with the bacterial community abundance (r 2  = 0.218, p < 0.001). Pathogenic protozoans identified, include malaria-causing Plasmodium, kinetoplastids (genus Besnoita, Theilleria, Neospora, Toxoplasma, Encephalitozoon, and Babesia) and waterborne protozoans of public health importance (such as Cryptosporidium parvum and Giardia lamblia). Furthermore, the enrichment of pathogenesis-associated pathways (amino acid biosynthesis, peptidoglycan maturation, heme biosynthesis and degradation, and the Calvin-Benson-Bassham cycle), along with virulence gene families identified, highlighted these wetlands as potential reservoirs for infectious diseases. Our results unveil a baseline protist taxonomic and functional composition within arid wetlands, including beneficial and pathogenic protozoa. The close proximity of these wetlands to human activity raises concern for local and transboundary spread of these pathogens. Thus, continued monitoring is vital for disease control and preserving these unique ecosystems., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Plant rhizosphere zones are hotspots for microbial diversity consisting of different communities when contrasted with surrounding bulk soils. Rhizosphere microorganisms play significant roles in plant development. We investigated the bacterial community and metabolic potentials of maize rhizosphere and bulk soils at two distant geographical locations in the North West Province of South Africa using shotgun metagenomics. We further characterized bacterial genes contributing to plant-beneficial functions present in the soils. Genes involved in plant-beneficial functions like nitrogen fixation and potassium transport were uncovered. Overall, 51 OTUs were identified in the soils. Shared OTUs between soils were 10.9% and 17.2% at Ventersdorp and Mafikeng, respectively. Significant differences in bacterial taxonomic composition and functional categories between soils (P < 0.05) were revealed. Acidobacteria and Firmicutes dominated the rhizosphere soils while Actinobacteria and Gemmatimonadetes were predominant in bulk soils. Proper understanding of soil indigenous microbiome can help ascertain prospective targets for imminent crop breeding and management. [ABSTRACT FROM AUTHOR]

Papillomaviruses (PV) infect epithelial cells and can cause hyperplastic or neoplastic lesions. In felids, most described PVs are from domestic cats ( Felis catus ; n = 7 types), with one type identified in each of the five wild felid species studied to date ( Panthera uncia , Puma concolor , Leopardus wiedii , Panthera leo persica and Lynx rufus ). PVs from domestic cats are highly diverse and are currently classified into three genera ( Lambdapapillomavirus , Dyothetapapillomavirus , and Taupapillomavirus ), whereas those from wild felids, although diverse, are all classified into the Lambdapapillomavirus genus. In this study, we used a metagenomic approach to identify ten novel PV genomes from rectal swabs of five deceased caracals ( Caracal caracal ) living in the greater Cape Town area, South Africa. These are the first PVs to be described from caracals, and represent six new PV types, i.e., Caracal caracal papillomavirus (CcarPV) 1-6. These CcarPV fall into two phylogenetically distinct genera: Lambdapapillomavirus , and Treisetapapillomavirus . Two or more PV types were identified in a single individual for three of the five caracals, and four caracals shared at least one of the same PV types with another caracal. This study broadens our understanding of wild felid PVs and provides evidence that there may be several wild felid PV lineages.

Waterborne pathogens are still considered a threat to human health. Wastewater treatment plants (WWTPs), contain a high populace and diversity of viruses that can significantly affect the aquatic ecosystem. Subsequently, the occurrence and recurrence of viral pathogens are alarming that exist in human populations, which are potentially discharged into sewage systems. This study investigated the distribution and diversity of the viral communities from three WWTPs in Gauteng Province, South Africa using next-generation sequencing technology. The results uncovered that most of the viral populaces in the wastewater plants belong to the families Siphoviridae, Microviridae, and Myoviridae of the order Caudovirales. Other families including Baculoviridae, Partitiviridae, Virgaviridae, and Tymoviridae were likewise recorded. On the other hand, enteric pathogens detected were Astroviridae, Reoviridae, and Coronaviridae. The predicted functional features for the viromes revealed that the DNA metabolism was the major function within the community followed by carbohydrate and amino acid metabolism, suggesting that the treatment plants provide a rich biological environment for the growth of diverse viral species and other processes. The overall results in this study highlight the biological significance of WWTPs as a hotspot for some viral agents. The contamination routes of these viral agents are needed for efficient and cost-effective management strategies in water systems. Further, viral metagenomics ought to be considered as a key approach for revealing the diversity and early warning of emerging disease outbreaks. [ABSTRACT FROM AUTHOR]

A metagenomic approach was used to study the gut microbiome of Haemonchus contortus field strains and that of its predilection site, the abomasum of Dohne Merino sheep. The abomasum contents and H. contortus were collected from 10 naturally infected Dohne Merino sheep. The H. contortus specimens were classified and sexually differentiated using morphometric characters and was further confirmed through molecular identification. We investigated differences and similarities between the bacterial composition of the adult male and female H. contortus gut microbiomes, which were both dominated by bacteria from the Escherichia, Shigella, Vibrio and Halomonas genera. Major abundance variations were identified between the shared adult male and female H. contortus microbiomes. The results also revealed that Succiniclasticum, Rikenellaceae RC9 gut group and Candidatus Saccharimonas were the predominant genera in the Dohne Merino abomasum. This study provides insight into the highly diverse bacterial composition of the H. contortus gut microbiome and the Dohne Merino abomasum which needs to be studied further to explore the complex interactions of different gastrointestinal nematode microbiomes with the host. [ABSTRACT FROM AUTHOR]

We conducted shotgun metagenomics sequencing of the maize rhizosphere and bulk soils in Ventersdorp, South Africa. Information on the structural composition and functional capabilities of microbial communities in the maize rhizosphere are provided by the data. Characterising the functional potentials of rhizosphere microbiomes gives an opportunity to link the microbiome to plant growth and health and provides the possibility of discovering new plant-beneficial genes that could enhance agricultural sustainability. [ABSTRACT FROM AUTHOR]

A serious factor hampering global maize production is gray leaf spot disease. Cercospora zeina is one of the causative pathogens, but population genomics analysis of C. zeina is lacking. We conducted whole-genome Illumina sequencing of a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe, and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the C. zeina isolates was done by (1) de novo assembly of the reads with SPAdes, (2) annotation with BRAKER, and (3) protein clustering with OrthoFinder. A published long-read assembly of C. zeina (CMW25467) from Zambia was included and annotated using the same pipeline. This analysis revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. Accessory gene content was largely shared between isolates from all countries, with a few genes unique to populations from Southern Africa (32) or East Africa (6). There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). PCA, ADMIXTURE, and phylogenetic analysis using a neighbor-net network indicated a population structure with a geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, possibly from 2 regional founder populations, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)

Limited studies have been undertaken with regard to virus complexes contributing to the aetiology of sweet potato virus disease (SPVD) in South Africa (SA). In this study, a metagenomic approach was adopted to reveal the genetic diversity of viruses infecting sweet potato. In order to undertake a comprehensive analysis of viral sequences, total RNA was isolated from 17 asymptomatic and symptomatic sweet potato plants that were collected from the Eastern (EC) and Western Cape (WC) provinces of SA. DNase-treated total RNA was depleted of ribosomal RNA (rRNA) and deep-sequenced using the Illumina MiSeq platform. Genomic DNA, isolated from the same plants, underwent rolling circle amplification (RCA) and deep sequencing. Sequence reads were analysed with the CLC Bio Genomics Workbench. Both de novo and reference-guided assemblies were performed resulting in four near full-length RNA virus genomes. BLAST searches using de novo assembled sequences against published virus genomes confirmed the presence of previously detected begomoviruses in the Western Cape (WC) province, namely Sweet potato mosaic virus (SPMaV) and Sweet potato leaf curl Sao Paulo virus (SPLCSPV). The begomoviruses were detected in mixed infections with two major disease-causing RNA viruses, Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV). The sequence data further demonstrated mixed infections of RNA and DNA viruses from 11 of the 17 sequenced samples. Metagenomics is a reliable diagnostic tool for virus diversity detection, in particular virus-complexes and synergies affecting disease aetiology. [ABSTRACT FROM AUTHOR]

Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard. [ABSTRACT FROM AUTHOR]

Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens. [ABSTRACT FROM AUTHOR]

Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the normal commensal respiratory virome in comparison to those in severe acute respiratory infections (SARIs) state. This study characterised the respiratory RNA virome in children ≤ 5 years with (n = 149) and without (n = 139) SARI during the summer and winter of 2020/2021 seasons in South Africa. Nasopharyngeal swabs were, collected, pooled, enriched for viral RNA detection, sequenced using Illumina MiSeq, and analysed using the Genome Detective bioinformatic tool. Overall, Picornaviridae , Paramoxyviridae , Pneumoviridae , Picobirnaviridae , Totiviridae , and Retroviridae families were the most abundant viral population in both groups across both seasons. Human rhinovirus and endogenous retrovirus K113 were detected in most pools, with exclusive detection of Pneumoviridae in SARI pools. Generally, higher viral diversity/abundance was seen in children with SARI and in the summer pools. Several plant/animal viruses, eukaryotic viruses with unclear pathogenicity including a distinct rhinovirus A type, were detected. This study provides remarkable data on the respiratory RNA virome in children with and without SARI with a degree of heterogeneity of known viruses colonizing their respiratory tract. The implication of the detected viruses in the dynamics/progression of SARI requires further investigations.

The emergence and spread of antibiotic resistance through insufficiently treated effluents from wastewater treatment systems are detrimental to the receiving environment and human health. Metagenomic and transcriptomic approaches were employed to assess the diversity and the removal of bacterial pathogens, antibiotic-resistant genes (ARGs) and mobile genetic elements (MGEs) in three wastewater treatment plants (WWTPs) in Durban, South Africa. In total, 23 pathogenic bacterial genera, including enteric and emerging opportunistic pathogens, were found abundant in the samples. Aeromonas and Acinetobacter spp were the most dominant pathogens detected in the influent metagenomes, while the influent transcripts showed Escherichia and Acinetobacter spp as the most dominant pathogens. Shannon-Wiener indices showed that the bacterial diversity increased from influents to final effluents in two selected treatment plants. ARG types, including those conferring resistance to aminoglycosides, beta-lactamases, tetracycline and sulfonamide were abundant in both influent and effluent samples. Results further exposed that MGE-ARGs associations were the main drivers of ARG persistence into final effluents. This included 5 plasmids: R338-R151 (sulI), pRH-1238 (strB), pPM91 (aadA), pRH-1238 (aadA4–5), pRH-1238 (sulII); two class 1 integrons (aadA and arr) and 1 transposon Tn4351(tetX). In transcripts, MGE-ARG association showed two plasmids: pRH-1238 (aadA) and pPM91(aadA) and one hybrid plasmid R338-R151 (sulI). It was apparent across all the WWTPs that chlorination had little or no effect on MGE-ARG association. Combined, this study has highlighted the presence of bacterial pathogens, ARGs and MGEs in treated effluents, which can encourage the propagation of antibiotic resistance and potential sharing of genes in the downstream environments. [Display omitted] • Metagenomic and transcriptomic profiling of pathogens and antibiotic resistant genes and MGEs in wastewater in South Africa. • Aeromonas and Acinetobacter spp were the most dominant pathogens detected in the influent metagenomes. • Escherichia and Acinetobacter were the most abundant in the trsncripts. • Antibiotic resistant genes aaminoglycosides, beta-lactamases, tetracycline and sulfonamide were the most abundant. • Chlorination has little or no effect on MGE-ARG association was apparent across all WWTPs. [ABSTRACT FROM AUTHOR]

Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographical history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographical regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonized environments., (© 2022 John Wiley & Sons Ltd.)

Streptococcus pneumoniae is a major human pathogen responsible for over 317000 deaths in children <5 years of age with the burden of the disease being highest in low- and middle-income countries including South Africa. Following the introduction of the 7-valent and 13-valent pneumococcal conjugate vaccine (PCV) in South Africa in 2009 and 2011, respectively, a decrease in both invasive pneumococcal infections and asymptomatic carriage of vaccine-type pneumococci were reported. In this study, we described the changing epidemiology of the pneumococcal carriage population in South Africa, by sequencing the genomes of 1825 isolates collected between 2009 and 2013. Using these genomic data, we reported the changes in serotypes, Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance before and after the introduction of PCV13. The pneumococcal carriage population in South Africa has a high level of diversity, comprising of 126 GPSCs and 49 serotypes. Of the ten most prevalent GPSCs detected, six were predominantly found in Africa (GPSC22, GPSC21, GPSC17, GPSC33, GPSC34 and GPSC52). We found a significant decrease in PCV7 serotypes (19F, 6B, 23F and 14) and an increase in non-vaccine serotypes (NVT) (16F, 34, 35B and 11A) among children <2 years of age. The increase in NVTs was driven by pneumococcal lineages GPSC33, GPSC34, GPSC5 and GPSC22. Overall, a decrease in antibiotic resistance for 11 antimicrobials was detected in the PCV13 era. Further, we reported a higher resistance prevalence among vaccine types (VTs), as compared to NVTs; however, an increase in penicillin resistance among NVT was observed between the PCV7 and PCV13 eras. The carriage isolates from South Africa predominantly belonged to pneumococcal lineages, which are endemic to Africa. While the introduction of PCV resulted in an overall reduction of resistance in pneumococcal carriage isolates, an increase in penicillin resistance among NVTs was detected in children aged between 3 and 5 years, driven by the expansion of penicillin-resistant clones associated with NVTs in the PCV13 era.

Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple "western-nonwestern" axis and contains undescribed microbial diversity., (© 2022. The Author(s).)

Background: The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies., Methodology: We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction., Results: We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168)., Conclusions: There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract., (© 2021. The Author(s).)

This study used conventional culturing and 16S rRNA metagenomics analyses to assess the diversity of bacterial communities in sediment samples obtained from the Berg River, Western Cape, South Africa. Samples were collected from six points: a residential and recreational area, an industrial area, an informal residential settlement, a point next to a wastewater treatment plant (WWTP), a pumping station, and a residential and agricultural farming area along the river. High bacterial counts recorded on general selective and differential culture media signify substantial microbial contamination along the sampling sites. The most prevalent bacterial phyla detected (through metagenomics analyses) along the sampling sites were Proteobacteria (61%), Planctomycetes (9.5%), Firmicutes (7.8%), Bacteroidetes (5%), Acidobacteria (4.6%), and Actinobacteria (4.6%). Some members of the identified predominant bacterial phyla, genera, and classes are important public health bacteria that have been implicated in human diseases and outbreaks, while some others are metal or hydrocarbon tolerant, indicating possible significant environmental pollution. Notable human pathogenic genera such as Bacillus, Clostridium, Shigella, Legionella, Mycobacterium, and Pseudomonas were identified in varying percentages at five of the six sampling areas. Fecal contamination was particularly rife at all residential areas, with the informal housing area being the most notably polluted. Diverse functional pathways were predicted for identified bacteria, such as those associated with different chronic and infectious human diseases as well as those related to hydrocarbon and metal remediation. The point next to a WWTP contained vastly diverse groups of bacterial contaminants as well as the most abundant pathway identities and titles., (© 2021. Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.)

Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings., (© 2021. The Author(s).)

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nif A, fix J, nor B, pst A, kef A and B, and ktr B were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO 3 ) was the most influential physicochemical parameter ( p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

This paper presents a review of synthetic polymer (notably plastic) wastes profiles in Africa, their current management status, and better options. Data revealed that of the approximated 86.14 million metric tonnes and 31.5 million metric tonnes of primary polymers and plastics, respectively, and an estimated 230 million metric tonnes of plastic components imported between 1990 and 2017, about 17 million metric tonnes are mismanaged. Leading African nations on the plastic wastes generator table in increasing order are Tunisia (6.9%), Morocco (9.6%), Algeria (11.2%), South Africa (11.6%), Nigeria (16.9%), and the chief is Egypt (18.4%). The volume of plastic wastes generated in Africa directly correlates with her increasing population status, however, the current treatment options have major drawbacks (high energy and technological input, high demand for space, and creation of obnoxious by-products). Ineffective regulations, poor monitoring, and slow adoption of veritable practices by governments are responsible for the steady increase in plastic volume in the African landscapes and environments. In Nigeria, only about 9% and 12% of the total generated wastes are recycled and incinerated. The remainder bulk is either discarded into waste dumps (and a few available landfills) or natural environments. There is a paucity of standard plastic biodegradative work by African scientists, and only a few works show detection of competent synthetic plastic degrading microbes globally. Asides from the ills of possible omission of core degraders, there is a need for researchers to follow standard degradation procedures to arrive at efficient, reproducible, and generally accepted outcomes utilizable on a larger scale. Thus, metagenomic search on the vast African urban and rural plastisphere is the best isolation option., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Consumption of food that is contaminated by microorganisms, chemicals, and toxins may lead to significant morbidity and mortality, which has negative socioeconomic and public health implications. Monitoring and surveillance of microbial diversity along the food value chain is a key component for hazard identification and evaluation of potential pathogen risks from farm to the consumer. The aim of this study was to determine the microbial diversity in meat and meat products from different enterprises and meat types in South Africa. Samples (n = 2017) were analyzed for Yersinia enterocolitica, Salmonella species, Listeria monocytogenes, Campylobacter jejuni, Campylobacter coli, Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, and Clostridium botulinum using culture-based methods. PCR was used for confirmation of selected pathogens. Of the 2017 samples analyzed, microbial ecology was assessed for selected subsamples where next generation sequencing had been conducted, followed by the application of computational methods to reconstruct individual genomes from the respective sample (metagenomics). With the exception of Clostridium botulinum, selective culture-dependent methods revealed that samples were contaminated with at least one of the tested foodborne pathogens. The data from metagenomics analysis revealed the presence of diverse bacteria, viruses, and fungi. The analyses provide evidence of diverse and highly variable microbial communities in products of animal origin, which is important for food safety, food labeling, biosecurity, and shelf life limiting spoilage by microorganisms. [ABSTRACT FROM AUTHOR]

The northwest (NW) province of South Africa is a semi-arid area, often disturbed by soil extremes such as drought and intense temperature. However, many functions possessed by the rhizosphere microbiome are still required, especially those inhabiting arid and semi-arid soils. This study involves a metagenomic comparison of the major metabolic attributes of two maize rhizosphere soils and their surrounding soils. Here, we hypothesized that there is a considerable difference between the functional diversity of maize rhizosphere and bulk soils and that the rhizosphere soil has distinct functional traits of agricultural importance. A high-throughput sequencing approach was used to assess the metabolic profile of rhizosphere soil microbiota of maize collected from the Gauteng and NW provinces of South Africa. The relative abundance of 13 functional hit categories was significantly different between the sampling sites. The diversity indices showed a considerable difference between the rhizosphere and surrounding soils. The difference in the chemical properties of the sampling sites was responsible for the variation in the microbial functional composition. Nevertheless, the presence of a high relative abundance of functional categories with unknown functions in SEED subsystem-2 coupled with the large number of functional hits conferring a response to soil stressors viz. oxidative stress, heat shock, osmotic stress, and cold shock noticed in the rhizosphere samples may indicate the presence of novel genes at the sampling sites. Exploring the plant growth-promoting traits of microorganisms present at these sites could eliminate the constraint posed by soil stressors on sustainable agriculture. [ABSTRACT FROM AUTHOR]

• Five complete crAssphage genomes from feces of South African woman and unrelated infants. • Elevated positive selection in RNA polymerase and phage tail protein genes. • Hotspots of selection may be mediated by selection pressure from bacterial partners. crAssphages are a broad group of diverse bacteriophages in the order Caudovirales that have been found to be highly abundant in the human gastrointestinal tract. Despite their high prevalence, we have an incomplete understanding of how crAssphages shape and respond to ecological and evolutionary dynamics in the gut. Here, we report genomes of crAssphages from feces of one South African woman and three infants. Across the complete genome sequences of the South African crAssphages described here, we identify particularly elevated positive selection in RNA polymerase and phage tail protein encoding genes, contrasted against purifying selection, genome-wide. We further validate these findings against a crAssphage genome from previous studies. Together, our results suggest hotspots of selection within crAssphage RNA polymerase and phage tail protein encoding genes are potentially mediated by interactions between crAssphages and their bacterial partners. [ABSTRACT FROM AUTHOR]

Studies in humans and laboratory animals link stable gut microbiome "enterotypes" with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease.

Little is known of the mycobiota present in ready-to-eat peanuts consumed in Southern Africa. Knowledge of the mycobiota and aflatoxigenic species can elucidate potential health risks associated with consumption of ready-to-eat peanuts sold by supermarkets and roadside vendors. We investigated the culturable mycobiota diversity in supermarket and roadside-vended peanuts as well as the presence of five aflatoxin biosynthesis pathway-related genes ( aflR, aflJ, aflM, aflD , and aflP ) in 15 suspected aflatoxigenic isolates, with a focus on Mafikeng, South Africa. Mean colony-forming unit (CFU) counts of 288.7 and 619.7 CFU/g were observed in supermarket and roadside-vended peanuts, respectively. A total of 145 fungal isolates comprising 26 distinct taxa (based on 97% internal transcribed spacer region [ITS1-5.8S-ITS2] sequence similarity) were obtained, including strains representing Aspergillus, Acremonium, Alternaria, Bipolaris, Chaetomium, Ectophoma, Epicoccum, Hamigera, Leancillium, Monascus, Penicillium, Periconia, Talaromyces , and Trichoderma . Phylogenetic analyses of concatenated sequences of the ITS1-5.8S-ITS2, β-tubulin, and calmodulin genes delineated the species of As pergillus , which included A. flavus, A. fumigatus, A. hiratsukae, A. niger , and A. parasiticus . Higher species richness was obtained from supermarket peanuts compared with roadside-vended peanuts, with eight species common to both sources. Across supermarket or roadside-vended peanuts, A. fumigatus, A. niger , and A. flavus were prevalent (>40% incidence). In contrast, strains related to or representing Ectophoma multirostata, Aspergillus hiratsukae, Bipolaris zeae, Chaetomium bostrychodes, Epicoccum nigrum, Hamigera paravellanea, Lecanicillium aphanocladii, Monascus ruber, Periconia macrospinosa, Periconia lateralis, Talaromyces funiculosus, Talaromyces minioluteus, Talaromyces wortmannii, Talaromyces spp., and Trichoderma sp. were detected in either supermarket or roadside-vended peanuts. Among the five aflatoxin biosynthesis pathway-related genes, aflD and aflM were more prevalent (87%) and aflR was the least prevalent (40%). Findings suggest that roasted peanuts meant for human consumption and sold at supermarkets and by roadside vendors are contaminated with potential toxin-producing fungi. Hence, proper processing and packaging of peanuts before vending is recommended.

Genomoviruses (family Genomoviridae) are circular single-stranded DNA viruses that have been mainly identified through metagenomics studies in a wide variety of samples from various environments. Here, we describe 98 genomes of genomoviruses found associated with members of 19 plant families from Australia, Brazil, France, South Africa and the USA. These 98 genomoviruses represent 29 species, 26 of which are new, in the genera Gemykolovirus (n = 37), Gemyduguivirus (n = 9), Gemygorvirus (n = 8), Gemykroznavirus (n = 6), Gemycircularvirus (n = 21) and Gemykibivirus (n = 17).

Introduction: Nasopharyngeal (NP) colonization with antimicrobial-resistant bacteria is a global public health concern. Antimicrobial-resistance (AMR) genes carried by the resident NP microbiota may serve as a reservoir for transfer of resistance elements to opportunistic pathogens. Little is known about the NP antibiotic resistome. This study longitudinally investigated the composition of the NP antibiotic resistome in Streptococcus-enriched samples in a South African birth cohort., Methods: As a proof of concept study, 196 longitudinal NP samples were retrieved from a subset of 23 infants enrolled as part of broader birth cohort study. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of streptococcal and non-streptococcal bacterial reads. Contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes., Results: AMR genes were detected in 64% (125/196) of the samples. A total of 329 AMR genes were detected, including 36 non-redundant genes, ranging from 1 to 14 genes per sample. The predominant AMR genes detected encoded resistance mechanisms to beta-lactam (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline antibiotics (12%, 38/329). MsrD, ermB, and mefA genes were only detected from streptococcal reads. The predominant genes detected from non- streptococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Different patterns of carriage of AMR genes were observed, with only one infant having a stable carriage of mefA, msrD and tetM over a long period., Conclusion: This study demonstrates that WMGS can provide a broad snapshot of the NP resistome and has the potential to provide a comprehensive assessment of resistance elements present in this niche., Competing Interests: The authors have no conflict of interest to declare related to the content of this paper.

Although exclusive breastfeeding has been linked to lower rates of postnatal HIV transmission compared to nonexclusive breastfeeding, mechanisms underlying this are unclear. Across a longitudinally sampled cohort of South African infants, we showed that exclusively breastfed (EBF) infants had altered gut bacterial communities when compared to nonexclusively breastfed (NEBF) infants, as well as reduced peripheral CD4 + T cell activation and lowered chemokine and chemokine receptor expression in the oral mucosa. We further demonstrated that the relative abundance of key taxa was correlated with peripheral CD4 + T cell activation. Here, we supplement those findings by using compositional data analyses to identify shifts in the abundance of several Bifidobacteria strains relative to select strains of Escherichia, Bacteroides , and others that are associated with the transition to NEBF. We illustrate that the abundance ratio of these taxa is tightly correlated with feeding modality and is a strong predictor of peripheral T cell activation. More broadly, we discuss our study in the context of novel developments and explore future directions for the field.

Recent studies have identified cemeteries as potential environmental reservoirs of multi-drug resistant pathogenic bacteria that could contaminate groundwater sources posing public health threats. However, these findings were based on the identification of culturable bacteria and at times not below burial grounds. Investigation on the bacterial diversity and functional profiles of bacterial communities above and below burial grounds in human cemeteries are few. The current study used high-throughput sequencing techniques to determine the bacterial composition and their associated functional profiles in cemetery soil samples collected at the surface and below burial ground in two South African cemeteries (Maitland Cemetery in Cape Town and Fontein Street Cemetery in Middelburg) to evaluate the potential health threat to surrounding populations through contamination of groundwater. Significant differences were observed between sample depths with the clustering of the surface (0 m) and the 2 m samples into separate groups. Pseudomonas and Corynebacterium were the most abundant genera across all samples. Pseudomonas and Rhodococcus were the dominant genera in the 2 m samples while Prauserella and Staphylococcus were dominant in the surface samples. The 2 m samples showed a lower alpha diversity but recorded higher proportions of human diseases functional classes compared to the surface samples. Human disease functional profiles revealed involvement, in infectious (cholera), neurodegenerative (Alzheimer's disease) cardiovascular (hypertrophic cardiomyopathy) immune system (Systemic lupus erythematosus) metabolic (Type I & II diabetes) diseases and cancer. Antibiotic resistance and antibiotics synthesis signatures were also identified. Thus, cemeteries could be potential sources of microbial and antibiotic pollution in groundwater, especially in areas with shallow water tables such as Maitland. Selection of sites for use as cemeteries should, therefore, require a proper understanding of the hydrogeological characteristics of the selected site. However, further studies are required to trace the actual movement of these pollutants into groundwater resources., (Copyright © 2018 Elsevier B.V. All rights reserved.)

A correction to the article "Diversity of dsDNA Viruses in a South African Hot Spring Assessed by Metagenomics and Microscopy" that was published on January 2, 2018, issue is presented.

Recent skin metagenomic studies have investigated the harbored viral diversity and its possible influence on healthy skin microbial populations, and tried to establish global patterns of skin-phage evolution. However, the detail associated with the phages that potentially play a role in skin health has not been investigated. While skin metagenome and -metavirome studies have indicated that the skin virome is highly site specific and shows marked interpersonal variation, they have not assessed the presence/absence of individual phages. Here, we took a semi-culture independent approach (metaviromic) to better understand the composition of phage communities on skin from South African study participants. Our data set adds over 130 new phage species of the skin to existing databases. We demonstrated that identical phages were present on different individuals and in different body sites, and we conducted a detailed analysis of the structural organization of these phages. We further found that a bacteriophage related to the Staphylococcus capitis phage Stb20 may be a common skin commensal virus potentially regulating its host and its activities on the skin.

A metagenomic approach was applied using 454-pyrosequencing data analysis for the profiling of bacterial communities in the brine samples of the water reclamation plant. Some physicochemical characteristics of brine samples were also determined using standard methods. Samples ranged from being lightly alkaline to highly alkaline (pH 7.40-10.91) throughout the various treatment stages, with the salinity ranging from 1.62 to 4.53 g L(-1) and dissolved oxygen concentrations ranging from 7.47 to 9.12 mg L(-1). Phenotypic switching was found to occur due to these physicochemical parameters. Microbial diversities increased from those present in Stage I reactor (six taxonomic groups) to those in Reverse Osmosis (RO) stage I (17 taxonomic groups), whereas in the second phase of the treatment, it increased in Stage II clarifier (14 taxonomic groups) followed by a decrease in RO stage II (seven taxonomic groups). Overall, seven phyla were detected, apart from many bacterial sequences that were unclassified at the phylum level. The most dominant phylum found was Proteobacteria accounting for 59% of the total sequences. A blastn sequence similarity search showed that the majority of the sequences (56%) were homologous to the uncultured bacterial species, underlining the vast untapped bacterial diversity., (© 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.)