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Frontiers in Microbiology 2023species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be...
INTRODUCTION
species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.
METHODS
All high-quality, publicly available genomes ( = 104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).
RESULTS
Overall, the 110 genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across included macrolides, beta-lactams, and aminoglycosides ( = 81, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively). Genes showing homology to exoenzyme aureolysin were detected across multiple species (using 90% coverage, = 40 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). Panton-Valentine leucocidin toxin-associated and homologs were identified in eight genomes (≥40% AA identity, >85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species ( and ) were composed of multiple within-species populations. Notably, was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT < 0.05).
DISCUSSION
Overall, this study leverages all publicly available genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.
PubMed: 37547688
DOI: 10.3389/fmicb.2023.1181376 -
Antonie Van Leeuwenhoek Oct 2023The family Staphylococcacae and genus Gemella contain several organisms of clinical or biotechnological importance. We report here comprehensive phylogenomic and...
Phylogenomic and molecular markers based studies on Staphylococcaceae and Gemella species. Proposals for an emended family Staphylococcaceae and three new families (Abyssicoccaceae fam. nov., Salinicoccaceae fam. nov. and Gemellaceae fam. nov.) harboring four new genera, Lacicoccus gen. nov.,...
The family Staphylococcacae and genus Gemella contain several organisms of clinical or biotechnological importance. We report here comprehensive phylogenomic and comparative analyses on 112 available genomes from species in these taxa to clarify their evolutionary relationships and classification. In a phylogenomic tree based on 678 core proteins, Gemella species were separated from Staphylococcacae by a long branch indicating that they constitute a distinct family (Gemellaceae fam. nov.). In this tree, Staphylococcacae species formed two main clades, one encompassing the genera Aliicoccus, Jeotgalicoccus, Nosocomiicoccus and Salinicoccus (Family "Salinicoccaceae"), while the other clade consisted of the genera Macrococcus, Mammaliicoccus and Staphylococcus (Family Staphylococcaceae emend.). In this tree, species from the genera Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus each formed two distinct clades. Two species clades for these genera are also observed in 16S rRNA gene trees and supported by average amino acid identity analysis. We also report here detailed analyses on protein sequences from Staphylococcaceae and Gemella genomes to identify conserved signature indels (CSIs) which are specific for different genus and family-level clades. These analyses have identified 120 novel CSIs robustly demarcating different proposed families and genera. The identified CSIs provide independent evidence that the genera Gemella, Jeotgalicoccus, Macrococcus and Salinicoccus consist of two distinct clades, which can be reliably distinguished based on multiple exclusively shared CSIs. We are proposing transfers of the species from the novel clades of the above four genera into the genera Gemelliphila gen. nov., Phocicoccus gen. nov., Macrococcoides gen. nov. and Lacicoccus gen. nov., respectively. The identified CSIs also provide strong evidence for division of Staphylococcaceae into an emended family Staphylococcaceae and two new families, Abyssicoccaceae fam. nov. and Salinicoccaceae fam. nov. All of these families can be reliably demarcated based on several exclusively shared CSIs.
Topics: Humans; Gemella; Sequence Analysis, DNA; Staphylococcaceae; Phylogeny; RNA, Ribosomal, 16S; DNA, Bacterial; Bacterial Typing Techniques
PubMed: 37523090
DOI: 10.1007/s10482-023-01857-6 -
Environmental Monitoring and Assessment Jun 2023Environmental pollution is a serious issue all around the world, especially when it is caused by metal(oid)s and pathogenic microorganisms. This study reports here for...
Environmental pollution is a serious issue all around the world, especially when it is caused by metal(oid)s and pathogenic microorganisms. This study reports here for the first time on the contamination of soil and water with metal(oid)s and pathogenic bacteria directly resulting from the Soran Landfill Site. Soran landfill is a level 2 solid waste disposal site that lacks leachate collection infrastructure. The site is potentially an environmental and public hazard caused by metal(oid)s content and significantly dangerous pathogenic microorganisms through leachate release into the soil and nearby river. This study reports on the levels of the metal(oid)s content of As, Cd, Co, Cr, Cu, Mn, Mo, Pb, Zn, and Ni obtained by inductively coupled plasma mass spectrometer in soil, leachate stream mud, and leachate samples. Five pollution indices are used to assess potential environmental risks. According to the indices, Cd and Pb contamination is significant, whereas As, Cu, Mn, Mo, and Zn pollution is moderate. A total of 32 isolates of bacteria were defined from soil, leachate stream mud, and liquid leachate samples: 18, 9, and 5, respectively. Moreover, 16 s rRNA analysis suggested that the isolates belong to three enteric bacterial phyla of Proteobacteria, Actinobacteria, and Firmicutes. The closest GenBank matches of 16S rDNA sequences indicated the presence of the genera: Pseudomonas, Bacillus, Lysinibacillus, Exiguobacterium, Trichococcus, Providencia, Enterococcus, Macrococcus, Serratia, Salinicoccus, Proteus, Rhodococcus, Brevibacterium, Shigella, Micrococcus, Morganella, Corynebacterium, Escherichia, and Acinetobacter. The identity percentage was mostly between 95%-100%. The results of this study show the levels of microbiological and geochemical contamination of soils, surface and potentially ground water with harmful microorganisms and toxic metal(oid)s originating specifically from Soran landfill leachate which subsequently incorporated into the surrounding environment, creating thus a considerable health and environmental risk.
Topics: Bacteria; Cadmium; Environmental Monitoring; Environmental Pollution; Iraq; Lead; Metals, Heavy; Soil; Waste Disposal Facilities; Water Pollutants, Chemical; Soil Microbiology
PubMed: 37284886
DOI: 10.1007/s10661-023-11352-0 -
Fish & Shellfish Immunology May 2023In this study, the growth performance, health status and intestinal microbiota of juvenile Asian seabass, Lates calcarifer, were assessed after dietary administration of...
In this study, the growth performance, health status and intestinal microbiota of juvenile Asian seabass, Lates calcarifer, were assessed after dietary administration of a prebiotic product obtained from fermented Aspergillus orizae, Fermacto®. Asian seabass were fed three diets; control (without Aspergillus-meal prebiotic), 0.2% and 0.3% Aspergillus-meal prebiotic for 56 days. Fish were raised in freshwater with acceptable water quality. No significant differences were found in the growth performance and composition of dorsal fish muscle among all groups. Fish fed diets supplemented with 0.3% of Aspergillus-meal prebiotic had a significantly higher survival rate after being challenged with V. alginolyticus than fish fed with the control diet. Supplementation of the Aspergillus-meal prebiotic significantly improved immune responses by inducing higher respiratory burst, superoxide dismutase, phagocytic and lysozyme activity compared to the control group. In addition, prebiotic doses significantly induced an up-regulation of heat shock cognate 70 kDa protein (hsp70) in the liver compared to the control group. Signaling pathways were also affected with significantly higher gene expression of complement c-3 (c3), mechanistic target of rapamycin (mtor), and mammalian lethal with SEC13 protein 8 (mlst-8) in the liver of fish fed 0.3% Aspergillus prebiotic. The pro-inflammatory gene, tumor necrosis factor (tnf) and anti-inflammatory gene, transforming growth factor beta-1 (tfg-β1) were significantly higher in the head kidney of fish offered prebiotic diets. Fish receiving Aspergillus-meal prebiotic revealed significantly higher expression of Mx gene 24 h post nervous necrosis virus injection compared to the control. Additionally, the α-diversity of gut microbiota, including genus, Pielou's evenness, Shannon diversity index, and Margalef's species richness were significantly higher in fish fed 0.3% Aspergillus-meal prebiotic than the control group. The principal component analysis eigenvector plots showed that a high abundance of beneficial bacteria, such as Entercoccus faecium, Lactococcus lactis, Macrococcus caseolyticus and Vagococcus fluvialis, along with potentially pathogenic bacteria, such as Staphylococcus sciuri and L. garvieae subsp. garvieae were present in fish treated with Aspergillus-meal prebiotic. Although dietary Aspergillus-meal prebiotic did not improve the growth performance of Asian seabass, 0.3% of Aspergillus-meal prebiotic is recommended to elevate the immunological status of fish.
Topics: Animals; Prebiotics; Gastrointestinal Microbiome; Multilocus Sequence Typing; Diet; Perciformes; Fishes; Health Status; Animal Feed; Mammals
PubMed: 36935042
DOI: 10.1016/j.fsi.2023.108696 -
Microbial Drug Resistance (Larchmont,... Feb 2023
Topics: Humans; Methicillin Resistance; Anti-Bacterial Agents; Microbial Sensitivity Tests; Genes, Bacterial; Anti-Infective Agents; Methicillin-Resistant Staphylococcus aureus; Staphylococcal Infections
PubMed: 36802274
DOI: 10.1089/mdr.2022.0162 -
Environmental Science and Pollution... Mar 2023This study evaluated the effectiveness of using organic carbon materials (i.e., woodchips) to remove nitrate from groundwater. The results of our flow-through column...
This study evaluated the effectiveness of using organic carbon materials (i.e., woodchips) to remove nitrate from groundwater. The results of our flow-through column experiment, which was conducted over 1.6 years, suggested that denitrifying bacteria reduce nitrate by using it as an electron acceptor and woodchips as an electron donor. The nitrate removal rates were sufficiently high (0.39-1.04 mmol L day) during the operation of the column. Denitrification process was supported by fractionation of nitrogen and oxygen isotopes (δN and δO), with the δN and δO values enriched from 7.4‰ and 22.3‰ to 21.2‰ and 30.4‰, respectively. Enrichment factors ([Formula: see text]) for N and O were calculated using the Rayleigh fractionation model, with values of - 13.2‰ for εN and - 7.1‰ for εO. The fractionation ratio of N to O was 1.9:1, confirming denitrification. The most abundant bacterial genera in the soil used for inoculation were Enterobacter (86.7%), Nitrospira (1.8%), and Arthrobacter (1.5%), while those in the column effluent were Macrococcus (37.1%), Escherichia (14.7%), and Shigella (14.6%), indicating that bacterial communities changed in response to geochemical conditions in the column. This study suggests that nitrate in groundwater can be effectively removed using woodchip-based passive treatment systems and that information on isotopic fractionation and denitrifying bacteria can be key tools to understand denitrification.
Topics: Bacteria; Denitrification; Groundwater; Nitrates; Nitrogen; Nitrogen Isotopes; Organic Chemicals; Water Purification
PubMed: 36547843
DOI: 10.1007/s11356-022-24826-4 -
Current Research in Food Science 2022A microbial starter culture is expected to improve the quality of traditional fermented fish products. was selected for grass carp fermentation due to its high...
Proteomics and metagenomics reveal the relationship between microbial metabolism and protein hydrolysis in dried fermented grass carp using a lactic acid bacteria starter culture.
A microbial starter culture is expected to improve the quality of traditional fermented fish products. was selected for grass carp fermentation due to its high proteolytic activity. To investigate its effects on muscle proteolysis of dried fermented fish, the protein profile and microbial community were analysed by using proteomics and metabolomics. The myofibrillar protein and collagen profiles showed remarkable variation after processing, changes that were related to the development of flavour and texture in fish samples. The starter culture had a marked effect on the microbial composition. and were the dominant genera, with a relative abundance of 24.79% and 12.53%, respectively. There were significant correlations (P < 0.05) between the dominant genera and the major peptidase genes and quality-related proteins. These findings suggest that microbial activity is involved in proteolysis and affects the flavour and texture of dried fermented fish.
PubMed: 36467746
DOI: 10.1016/j.crfs.2022.11.016 -
International Journal of Food... Feb 2023Food-derived Staphylococcaceae species with severe antimicrobial resistance, especially Staphylococcus aureus, is a major threat to public health. Macrococcus...
Food-derived Staphylococcaceae species with severe antimicrobial resistance, especially Staphylococcus aureus, is a major threat to public health. Macrococcus caseolyticus (M. caseolyticus) is a member of the Staphylococcaceae family which plays a vital role in fermented products and disease causation in animals. In our previous study, several Staphylococcus aureus antibiotic-resistant island msr (SaRI) were found in multidrug-resistant S. aureus. In this study, novel SaRI, SaRI-III emerged from S. aureus. Another novel SaRI-like further emerged in M. caseolyticus from food. These isolates' prevalence and genetic environment were investigated and characterized to understand the distribution and transmission of these novel SaRI strains. All SaRI-positive S. aureus isolates exhibited a multidrug resistance (MDR) phenotype, within which a series of antimicrobial resistance genes (ARGs) and virulence factor genes (VFs) were identified. In addition, three SaRI types, SaRI-I (15.1 kb), SaRI-II (16-17 kb), and SaRI-III (18 kb) carrying mef(D)-msr(F), were identified in these isolates' chromosomes. SaRI-(I-III) contains a site-specific integrase gene int and operon mef(D)-msr(F). SaRI-III has an additional orf3-orf4-IS30 arrangement downstream of mef(D) and msr(F). Moreover, the SaRI-like and macrolide-resistant transposon Tn6776 forming a novel mosaic structure coexisted in one M. caseolyticus isolate. Within this mosaic structure, the macrolide-resistant genes mef(D)-msr(F) were absent in SaRI-like, whereas an operon, mef(F)-msr(G), was identified in Tn6776. The SaRI-(I-III) and SaRI-like structure were inserted into the rpsI gene encoding the 30S ribosomal protein S9 in the chromosome. Excision and cyclisation of SaRI-III, SaRI-like, operon mef(D)-msr(F), and orf3-orf4-IS30 arrangements were confirmed using two-step PCR. This study is the first to report MDR S. aureus harbouring novel SaRI-III and M. caseolyticus containing novel mosaic structures isolated from retail foods. Similar SaRI-type resistant islands' occurrence and propagation in Staphylococcaceae species require continuous monitoring and investigation.
Topics: Animals; Anti-Bacterial Agents; Staphylococcus aureus; Macrolides; Methicillin-Resistant Staphylococcus aureus; Drug Resistance, Bacterial; Staphylococcaceae; Staphylococcal Infections; Microbial Sensitivity Tests
PubMed: 36427466
DOI: 10.1016/j.ijfoodmicro.2022.110020 -
Frontiers in Microbiology 2022The influence of microbiota composition and metabolisms on the safety and quality of fermented fish products is attracting increasing attention. In this study, the total...
The influence of microbiota composition and metabolisms on the safety and quality of fermented fish products is attracting increasing attention. In this study, the total viable count (TVC), pH, total volatile base nitrogen (TVB-N) as well as biogenic amines (BAs) of traditional fermented () were quantitatively determined. To comprehend microbial community variation and predict their functions during fermentation, 16S rRNA-based high-throughput sequencing (HTS) and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were employed, respectively. The fresh samples stored without fermentation were used as controls. TVC and TVB-N values increased rapidly, and the content of BAs exceeded the permissible limit on day 2 in the controls, indicating serious spoilage of the fish. In contrast, a slower increase in TVC and TVB-N was observed and the content of BAs was within the acceptable limit throughout the fermentation of . Significant differences in microbiota composition were observed between and the controls. The bacterial community composition of was relatively simple and was identified as the dominant microbial group. The accumulation of histamine was inhibited in which was positively correlated with the relative abundance of , , , , et al. based on Redundancy analysis (RDA), while showed a positive correlation with tyramine, cadaverine, and putrescine. Functional predictions, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis, revealed that the relative abundance of metabolic function exhibited a decreasing trend with prolonged fermentation time and the abundance of metabolism-related genes was relatively stable in the later stage of fermentation. Those metabolisms related to the formation of BAs like histidine metabolism and arginine metabolism were inhibited in . This study has accompanied microbiota analysis and functional metabolism with the accumulation of BAs to trace their correspondences, clarifying the roles of microorganisms in the inhibition of BAs during fermentation of
PubMed: 36406411
DOI: 10.3389/fmicb.2022.1030789 -
BMC Microbiology Nov 2022Macrococcus caseolyticus is an opportunistic pathogen that is frequently isolated from dairy products and veterinary infections. Recent studies have reported the...
Macrococcus caseolyticus is an opportunistic pathogen that is frequently isolated from dairy products and veterinary infections. Recent studies have reported the possibility of methicillin resistance that be transferred among staphylococcal species in foods. The present study examined the population structure, antimicrobial resistance, virulence factors, and morphology of methicillin-resistant M. caseolyticus by investigation of 94 genomes derived from both isolates in beef (n = 7) and pork (n = 2) at Shanghai and those deposited in public domain (n = 85). Phylogenetically, M. caseolyticus were divided into four clades, which each consisted of genomes isolated from continent of European countries (82.4%, n = 78), Asian countries (11.3%, n = 10), United States (4.1%, n = 4), Australia (1%, n = 1), and Sudan (1%, n = 1). The M. caseolyticus isolated from present study formed a genetically distinguished clade, which was characterized by novel alleles in the traditional 7-gene MLST scheme. Furthermore, we identified 24 AMR genes that were associated with 10 classes of antimicrobial agents in M. caseolyticus. Most AMR genes were carried by dominant plasmids such as rep7a, rep22 and repUS56. The genomes in the global clades carried significantly less AMR genes (p < 0.05) and more virulence factors (p < 0.001) than present clade. Virulence factors were detected in methicillin resistant M. caseolyticus including genes coding hemolysin, adherence, biofilm formation, exotoxin, and capsule that associated to human health and infection. Finally, as the close relative of the genus Staphylococcus, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were performed for morphological comparison that M. caseolyticus has a larger diameter and thicker cell wall compared with S. aureus ATCC 25,923. Taken together, our study suggested that M. caseolyticus mediating divergent antimicrobial resistance and virulence factors could serve as the vector for methicillin resistance habitats in foodborne microorganisms.
Topics: Cattle; Animals; Humans; Methicillin Resistance; Anti-Bacterial Agents; Multilocus Sequence Typing; Virulence Factors; Staphylococcus aureus; Drug Resistance, Bacterial; Phylogeny; China; Staphylococcus; Staphylococcal Infections; Methicillin-Resistant Staphylococcus aureus; Microbial Sensitivity Tests
PubMed: 36335318
DOI: 10.1186/s12866-022-02679-8