The phylogenomic landscape of extended-spectrum ß-lactamase producing Citrobacter species isolated from surface water.

BACKGROUND: Citrobacter species are Gram-negative opportunistic pathogens commonly reported in nosocomial-acquired infections. This study characterised four Citrobacter species that were isolated from surface water in the North West Province, South Africa. RESULTS: Phenotypic antimicrobial susceptibility profiles of the isolates demonstrated their ability to produce the extended-spectrum ß-lactamase (ESBL). Whole genomes were sequenced to profile antibiotic resistance and virulence genes, as well as mobile genetic elements. In silico taxonomic identification was conducted by using multi-locus sequence typing and average nucleotide identity. A pangenome was used to determine the phylogenomic landscape of the Citrobacter species by using 109 publicly available genomes. The strains S21 and S23 were identified as C. braakii, while strains S24 and S25 were C. murliniae and C. portucalensis, respectively. Comparative genomics and sequenced genomes of the ESBL-producing isolates consisted of n = 91; 83% Citrobacter species in which bla-CMY-101 (n = 19; 32,2%) and bla-CMY-59 (n = 12; 38,7%) were prevalent in C. braakii, and C. portucalensis strains, respectively. Macrolide (acrAB-TolC, and mdtG) and aminoglycoside (acrD) efflux pumps genes were identified in the four sequenced Citrobacter spp. isolates. The quinolone resistance gene, qnrB13, was exclusive to the C. portucalensis S25 strain. In silico analysis detected plasmid replicon types IncHI1A, IncP, and Col(VCM04) in C. murliniae S24 and C. portucalensis S25, respectively. These potentially facilitate the T4SS secretion system in Citrobacter species. In this study, the C. braakii genomes could be distinguished from C. murliniae and C. portucalensis on the basis of gene encoding for cell surface localisation of the CPS (vexC) and identification of genes involved in capsule polymer synthesis (tviB and tviE). A cluster for the salmochelin siderophore system (iro-BCDEN) was found in C. murliniae S24. This is important when it comes to the pathogenicity pathway that confers an advantage in colonisation. CONCLUSIONS: The emerging and genomic landscapes of these ESBL-producing Citrobacter species are of significant concern due to their dissemination potential in freshwater systems. The presence of these ESBL and multidrug-resistant (MDR) pathogens in aquatic environments is of One Health importance, since they potentially impact the clinical domain, that is, in terms of human health and the agricultural domain, that is, in terms of animal health and food production as well as the environmental domain.

Bacterial Communities Associated with Houseflies (Musca domestica L.) Inhabiting Hospices in South Africa.

Houseflies are alleged reservoirs as well as vectors of human and animal pathogens, including bacteria, because they frequently have contact with animal excreta and decaying organic substances. The rapid adaptation process of ingested microbes in the insect gut may involve gene transfer, including antibiotic resistance determinants among different bacterial strains. Six hundred and fifty-seven (n = 657) houseflies were collected from hospices and were identified morphologically and genetically using the 16S rRNA, CO1, and ITS2 barcoding genes. This study also characterized the bacterial communities harboured by the captured houseflies using 16S rRNA metabarcoding on the next-generation sequencing (NGS) platform and further sought to detect antibiotic resistance traits by using gene-specific PCR assays. Generated sequences for the targeted gene fragments matched with Musca domestica and all the sequences were deposited to the GenBank database. The 16S rRNA metabarcoding analysis revealed that the most abundant phyla detected with variable abundance observed among all the houseflies were Proteobacteria, followed by Firmicutes, and Bacteroidetes. Furthermore, the NGS data revealed the presence of multiple bacterial genera, including Providencia, Enterobacter, Dysgonomonas, Escherichia-Shigella, Klebsiella, Pseudomonas, and Streptococcus, which are known to harbour potentially pathogenic species of animals and humans. Antibiotic resistance genes detected from the housefly DNA in this study included ermB, tetA, blaSHV, and blaTEM. Moreover, these genes are associated with resistance to erythromycin, tetracycline, and beta-lactams antibiotics, respectively. The presence of bacterial pathogens and the detection of antibiotic resistance genes from the houseflies collected from the hospices indicates the possible health risk to patients in hospices and the surrounding community. Therefore, it is imperative to keep high standards of hygiene, food preparation, safety, and control of houseflies in hospices.

Draft Genome Sequences of Multidrug-Resistant Shiga Toxin-Producing Escherichia coli O116:H25 Strains from Ready-to-Eat Foods Sold in Lagos, Nigeria.

Draft genomes of multidrug-resistant Shiga toxin-producing Escherichia coli (STEC) strains IPK9(1) and IKS1(2), which were isolated from ready-to-eat foods (kokoro and shawarma) sold in Lagos, Nigeria, are reported. The genomes possessed genetic determinants for virulence and the antibiotic resistance gene for macrolide-associated resistance mdf(A). Ready-to-eat foods increase public health threats in Nigeria.

Draft Genome Sequences of Three Identified Rhizobacteria Associated with Maize Rhizosphere.

In this study, we sequenced the entire genomes of three identified rhizobacterial strains associated with maize plantation. Genome annotation of the sequenced data revealed several putative growth-promoting proteins associated with the production of indoleacetic acids and siderophore, the assimilation of nitrogen, and phosphorus solubilization.

Antifungal agents, yeast abundance and diversity in surface water: Potential risks to water users.

South African surface waters are subject to various forms of pollution. Recent findings in aquatic systems suggest an association exists between yeast diversity, chemical pollutants and land coverage, which are important water quality determinants. Yeast abundance and diversity, as well as antifungal agents in two river systems in South Africa, were investigated and related to the existing land coverage. Yeast abundance and diversity were determined from environmental DNA by quantitative polymerase chain reaction and next-generation sequencing, respectively, of the 26S ribosomal ribonucleic acid (rRNA) gene. Antifungal agents were qualitatively and/or quantitatively detected by ultra-high-pressure liquid chromatography-mass spectrometry. Analyses of 2 031 714 high-quality 26S rRNA sequences yielded 5554 amplicon sequence variants (ASVs)/species. ASV richness and Shannon-Wiener index of diversity reflected the southward flow of the river with higher values observed downstream compared to the upstream. Fluconazole concentrations were quantifiable in only two samples; 178 and 271 ng L-1. Taxonomically, at least 20 yeast species were detected, including the dominant Candida tropicalis, Cryptococcus spp. as well as the lesser dominant Bensingtonia bomiensis, Fereydounia khargensis, Hericium erinaceus, Kondoa changbaiensi, Pseudozyma spp. and Sphacelotheca pamparum. The two dominant species are known opportunistic pathogens which had antifungal resistant traits in previous studies from the same rivers and therefore is a public health threat. The present study provides further evidence that yeasts should be included as part of water quality parameters, especially in developing countries where much of the population are economically disadvantaged, and also immunocompromised due to age and disease.

High-Throughput Sequence Analyses of Bacterial Communities and Multi-Mycotoxin Profiling During Processing of Different Formulations of Kunu, a Traditional Fermented Beverage.

Kunu is a traditional fermented single or mixed cereals-based beverage popularly consumed in many parts of West Africa. Presently, the bacterial community and mycotoxin contamination profiles during processing of various kunu formulations have never been comprehensively studied. This study, therefore, investigated the bacterial community and multi-mycotoxin dynamics during the processing of three kunu formulations using high-throughput sequence analysis of partial 16S rRNA gene (hypervariable V3-V4 region) and liquid chromatography tandem mass spectrometry (LC-MS/MS), respectively. A total of 2,303 operational taxonomic units (OTUs) were obtained across six processing stages in all three kunu formulations. Principal coordinate analysis biplots of the Bray-Curtis dissimilarity between bacterial communities revealed the combined influences of formulations and processing steps. Taxonomically, OTUs spanned 13 phyla and 486 genera. Firmicutes (phylum) dominated (relative abundance) most of the processing stages, while Proteobacteria dominated the rest of the stages. Lactobacillus (genus taxa level) dominated most processing stages and the final product (kunu) of two formulations, whereas Clostridium sensu stricto (cluster 1) dominated kunu of one formulation, constituting a novel observation. We further identified Acetobacter, Propionibacterium, Gluconacetobacter, and Gluconobacter previously not associated with kunu processing. Shared phylotypes between all communities were dominated by lactic acid bacteria including species of Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, and Weissella. Other shared phylotypes included notable acetic acid bacteria and potential human enteric pathogens. Ten mycotoxins [3-Nitropropionic acid, aflatoxicol, aflatoxin B1 (AFB1), AFB2, AFM1, alternariol (AOH), alternariolmethylether (AME), beauvericin (BEAU), citrinin, and moniliformin] were quantified at varying concentrations in ingredients for kunu processing. Except for AOH, AME, and BEAU that were retained at minimal levels of < 2 µg/kg in the final product, most mycotoxins in the ingredients were not detectable after processing. In particular, mycotoxin levels were substantially reduced by fermentation, although simple dilution and sieving also contributed to mycotoxin reduction. This study reinforces the perception of kunu as a rich source of bacteria with beneficial attributes to consumer health, and provides in-depth understanding of the microbiology of kunu processing, as well as information on mycotoxin contamination and reduction during this process. These findings may aid the development of starter culture technology for safe and quality kunu production.

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and ß-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type.