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Journal of Veterinary Research Sep 2023Universally, in microbiological diagnostics the detection of live bacteria is essential. Rapid identification of pathogens enables appropriate remedial measures to be...
INTRODUCTION
Universally, in microbiological diagnostics the detection of live bacteria is essential. Rapid identification of pathogens enables appropriate remedial measures to be taken. The identification of many bacteria simultaneously facilitates the determination of the characteristics of the accompanying microbiota and/or the microbiological complexity of a given environment.
MATERIAL AND METHODS
The effectiveness of the VITEK2 Compact automated microbial identification system and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS), analytical profile index (API) and Remel RapID tests were compared in identification of bacteria isolated from the alpaca gastrointestinal tract.
RESULTS
Most isolates were Gram-positive, such as and and , , and ; ; ; ; ; , , and (the last only isolated manually by API Coryne and the VITEK2 system and (CBC) card). was misidentified by MALDI-TOF MS as (currently ). Gram-positive and Gram-variable were also isolated. Gram-negative , , and ; ; subsp. ; and ; , and ; subsp. ; ; ; ; ; and were also found. The yeasts and were also present.
CONCLUSION
MALDI-TOF MS enabled the identification of pathogens and opportunistic pathogens from the alpaca gut which may represent a high risk to human and animal health.
PubMed: 37786852
DOI: 10.2478/jvetres-2023-0051 -
Frontiers in Microbiology 2021Africa has one of the highest incidences of gonorrhea. is gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome...
BACKGROUND
Africa has one of the highest incidences of gonorrhea. is gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing (WGS) is an efficient way of predicting AMR determinants and their spread in the population. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. Increasing accuracy of base-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer MinION in remote areas lead to its adoption for routine microbial genome sequencing. To investigate whether MinION-only sequencing is sufficient for WGS and downstream analysis in resource-limited settings, we sequenced the genomes of 14 suspected isolates from Nairobi, Kenya.
METHODS
Using WGS, the isolates were confirmed to be cases of ( = 9), and there were three co-occurrences of with and ( = 2). has been implicated in sexually transmitted infections in recent years. The near-complete genomes ( = 10) were analyzed further for mutations/factors causing AMR using an in-house database of mutations curated from the literature.
RESULTS
We observe that ciprofloxacin resistance is associated with multiple mutations in both gyrA and parC. Mutations conferring tetracycline () and sulfonamide () resistance and plasmids encoding beta-lactamase were seen in all the strains, and -containing plasmids were identified in nine strains. Phylogenetic analysis clustered the 10 isolates into clades containing previously sequenced genomes from Kenya and countries across the world. Based on homology modeling of AMR targets, we see that the mutations in GyrA and ParC disrupt the hydrogen bonding with quinolone drugs and mutations in FolP may affect interaction with the antibiotic.
CONCLUSION
Here, we demonstrate the utility of mobile DNA sequencing technology in producing a consensus genome for sequence typing and detection of genetic determinants of AMR. The workflow followed in the study, including AMR mutation dataset creation and the genome identification, assembly, and analysis, can be used for any clinical isolate. Further studies are required to determine the utility of real-time sequencing in outbreak investigations, diagnosis, and management of infections, especially in resource-limited settings.
PubMed: 34385981
DOI: 10.3389/fmicb.2021.647565 -
Frontiers in Microbiology 2022The intestinal microbiota of marine animals was influenced by the water and environment in which they live. The Amur ide () adapts to extremely high alkalinity and is an...
The intestinal microbiota of marine animals was influenced by the water and environment in which they live. The Amur ide () adapts to extremely high alkalinity and is an ideal material for aquacultural studies of alkaline adaptation. In this study, we screened intestinal indicator flora and functional redundancy of intestinal colonies in alkaline-water species (AW) and freshwater species (FW) of Amur ide () in these different aquatic environments. The available vs. community composition correlations were then predicted by contrasting each other with the flora contained in environmental water samples. Here, five microbial species and six genera were identified owing to the classifiable sequence. The intestinal microbiota that existed in AW and FW had approximately 1/3 of the operational taxonomic units in the respective living water environments, meaning gut microbes in the aqueous habitats will have an influential association with gut microbes in AW and FW. Compared to the bacterial composition of the FW intestine and that present in freshwater, , and were significantly enriched in the intestine of AW and alkaline water samples. In the FW intestine and freshwater samples, however, and were highly improved, which can be summarized as ., the predominant population in the AW gut, while and being primarily present in FW intestines. Photosynthetic bacteria were most significant in both water samples. The results indicated that the intestinal microbiota composition, abundance, and diversity of AW and FW were quite different. In contrast, the microbial composition of the additional alkaline water and freshwater environments showed slight differences. This study expects to enhance our understanding of the alkalinity tolerance of , which will be provided for the breeding of fish living in alkaline water, and push the development of alkaline water resources with increased efficiency.
PubMed: 35602074
DOI: 10.3389/fmicb.2022.881132 -
Molecules (Basel, Switzerland) Apr 2020The purpose of this study was to investigate the composition of leaf extracts from , , and , and their antimicrobial activity against typical spoilage-causing and...
The purpose of this study was to investigate the composition of leaf extracts from , , and , and their antimicrobial activity against typical spoilage-causing and pathogenic bacteria found in meat and meat products. The highest total phenolic content (TPC) was detected in extract, followed by and extracts. The antioxidant capacity of the extracts was measured by DPPH and ABTS assays. The lowest IC values were found for extract, followed by and extracts. LC-MS and HPLC analysis revealed that and extracts contained hydroxycinnamic acid derivatives and flavonoids (mainly flavonols). Hydroxycinnamic acid derivatives were detected in the extract, as well as flavonols, ellagitannins, and iridoids. The antibacterial activity of the plant extracts was tested against Gram-negative bacteria (, , , , , ) and Gram-positive bacteria (, , , , ) using the microculture method. The extracts acted as bacteriostatic agents, decreasing the growth rate (µ) and extending the lag phase (t). showed most potent antibacterial activity, as confirmed by principal component analysis (PCA).
Topics: Anti-Bacterial Agents; Antioxidants; Dose-Response Relationship, Drug; Microbial Sensitivity Tests; Photinia; Phytochemicals; Plant Extracts; Plant Leaves; Polyphenols
PubMed: 32344904
DOI: 10.3390/molecules25092011 -
Frontiers in Microbiology 2022Nematodes in the genus can infect and kill slugs and snails, which are important agricultural pests. This useful trait has been commercialized by the corporation BASF...
Nematodes in the genus can infect and kill slugs and snails, which are important agricultural pests. This useful trait has been commercialized by the corporation BASF after they mass produced a product labeled Nemaslug®. The product contains , which has been cultured with , a bacterial strain that was originally thought to be responsible for causing mortality in slugs and snails. The exact mechanism leading to death in a infected host is unknown but may involve contributions from nematode-associated bacteria. The naturally occurring microbial community of is unexplored; the previous microbial community studies have focused on laboratory grown or commercially reared nematodes, and in order to obtain a deeper understanding of the parasite and its host interactions, it is crucial to characterize the natural microbial communities associated with this organism in the wild. We sampled , , and directly from their habitats in Central and Southern California nurseries and garden centers and identified their native microbial community 16S amplicon sequencing. We found that the microbial community was influenced by species, location, and possibly gastropod host from which the nematode was collected. The predominant bacteria of the isolates collected included , , Aeromonadaceae, Pseudomonadaceae, and . isolates exhibited an enrichment with species belonging to Acinetobacter or Pseudomonadaceae. However, further research must be performed to determine if this is due to the location of isolate collection or a species specific microbial community pattern. More work on the natural microbial community of is needed to determine the role of bacteria in nematode virulence.
PubMed: 35910595
DOI: 10.3389/fmicb.2022.903136 -
Frontiers in Microbiology 2022To understand the role of the skin commensal bacterial community in skin health and the spread of pathogens, it is crucial to identify genetic differences in the...
To understand the role of the skin commensal bacterial community in skin health and the spread of pathogens, it is crucial to identify genetic differences in the bacterial strains corresponding to human individuals. A culture-independent genomics approach is an effective tool for obtaining massive high-quality bacterial genomes. Here we present a single-cell genome sequencing to obtain comprehensive whole-genome sequences of uncultured skin bacteria from skin swabs. We recovered 281 high-quality (HQ) and 244 medium-quality single-amplified genomes (SAGs) of multiple skin bacterial species from eight individuals, including cohabiting group. Single-cell sequencing outperformed in the genome recovery from the same skin swabs, showing 10-fold non-redundant strain genomes compared to the shotgun metagenomic sequencing and binning approach. We then focused on the abundant skin bacteria and identified intra-species diversity, especially in 47 derived HQ SAGs, characterizing the strain-level heterogeneity at mobile genetic element profiles, including plasmids and prophages. Even between the cohabiting individual hosts, they have unique skin bacterial strains in the same species, which shows microdiversity in each host. Genetic and functional differences between skin bacterial strains are predictive of competition to adapt bacterial genome to utilize the sparse nutrients available on the skin or produce molecules that inhibit the colonization of other microbes or alter their behavior. Thus, single-cell sequencing provides a large number of genomes of higher resolution and quality than conventional metagenomic analysis and helps explore the skin commensal bacteria at the strain level, linking taxonomic and functional information.
PubMed: 35992707
DOI: 10.3389/fmicb.2022.955404 -
Journal of Insect Science (Online) Jul 2021The gut microbiota of insects usually plays an important role in the development and reproduction of their hosts. The fecundity of Henosepilachna vigintioctopunctata...
The gut microbiota of insects usually plays an important role in the development and reproduction of their hosts. The fecundity of Henosepilachna vigintioctopunctata (Fabricius) varies greatly when they develop on different host plants. Whether and how the gut microbiota regulates the fecundity of H. vigintioctopunctata was unknown. To address this question, we used 16S rRNA sequencing to analyze the gut microbiomes of H. vigintioctopunctata adults fed on two host plant species (Solanum nigrum and Solanum melongena) and one artificial diet. The development of the ovaries and testes was also examined. Our results revealed that the diversity and abundance of gut microorganisms varied significantly in insects reared on different diets. The gut microbiota of H. vigintioctopunctata raised on the two host plants was similar, with Proteobacteria being the dominant phylum in both groups, whereas Firmicutes was the dominant phylum in the group reared on the artificial diet. The predominant microbiota in the S. nigrum group were Acinetobacter soli and Acinetobacter ursingii (Acinetobacter, Moraxellaceae); Moraxella osloensis (Enhydrobacter, Moraxellaceae); and Empedobacter brevis (Empedobacter, Weeksellaceae). The microbiota in this group are associated with high lipid metabolism. In addition, the beetles' ovaries and testes were more highly developed in the S. nigrum group than in the other two groups. These findings provide valuable information for elucidating the complex roles the gut microbiota play in the fecundity of H. vigintioctopunctata, and may also contribute to developing future novel control strategies involving this economically important pest.
Topics: Animals; Bacteria; Coleoptera; DNA, Bacterial; Diet; Female; Fertility; Gastrointestinal Microbiome; Lipid Metabolism; Male; Metagenomics; Ovary; Pest Control; RNA, Ribosomal, 16S; Testis
PubMed: 34415303
DOI: 10.1093/jisesa/ieab061 -
Frontiers in Immunology 2022Nematodes and bacteria are prevalent in soil ecosystems, and some have evolved symbiotic relationships. In some cases, symbionts carry out highly specialized functions:...
Nematodes and bacteria are prevalent in soil ecosystems, and some have evolved symbiotic relationships. In some cases, symbionts carry out highly specialized functions: a prime example being entomopathogenic nematodes (EPNs), which vector bacteria ( or ) into insect hosts, killing them to provide a food source for the nematodes. It is thought that the commercially available malacopathogenic (kills slugs and snails) biocontrol nematode vectors a bacterium () into slugs to kill them. To investigate this further we used a metagenomic approach to profile the bacteria present in the commercial strain of , a wild strain of and two other species ( and ), after they had killed their slug host (). We show that these nematodes do not exclusively associate with one bacterium but a range of species, with members of the phyla Pseudomonadota, Bacillota, Actinobacteriota and Bacteroidota the most prevalent. The commercial strain of had the least diverse bacterial community. Furthermore, we found that the bacterium has been cultured on for 25 years is not the expected species but is spp. and the only strain of the species to associate with spp. was the commercial strain of . In summary, we found no evidence to show that rely exclusively on one bacterium to cause host mortality but found variable and diverse bacterial communities associated with these nematodes in their slug hosts.
Topics: Animals; Microbiota; Nematoda; Rhabditoidea; Snails; Soil
PubMed: 35515005
DOI: 10.3389/fimmu.2022.878783 -
Frontiers in Public Health 2024Given the dense population on university campuses, indoor and outdoor airborne bacterial contamination may lead to the rapid spread of diseases in a university...
Given the dense population on university campuses, indoor and outdoor airborne bacterial contamination may lead to the rapid spread of diseases in a university environment. However, there are few studies of the characteristics of airborne and pathogenic bacterial communities in different sites on a university campus. In this study, we collected particulate matter samples from indoor and outdoor locations at a university in Bengbu City, Anhui Province, China, and analyzed the community characteristics of airborne and pathogenic bacteria using a high-throughput sequencing technique. The results showed that the composition of the dominant airborne and pathogenic bacterial communities was consistent among sites at the phylum and genus levels, with differences in their relative abundance. There were significant differences in the structure of the airborne and pathogenic bacterial communities between indoor and outdoor sites ( < 0.05). An analysis of similarities (ANOSIM) indicated that the structure of airborne bacterial communities in indoor sites was influenced by the room occupancy rate, ventilation conditions, and the extent of indoor furnishing ( < 0.05), while the structure of pathogenic bacterial communities was influenced by the number of individuals and spatial dimensions ( < 0.05). The impact of particle size on the structure of airborne and pathogenic bacterial communities was relatively minor. A total of 194 suspected pathogenic bacterial species were identified, accounting for 0.0001-1.3923% of the total airborne bacteria, all of which were conditional pathogens. Among them, , , and exhibited relatively high relative abundance, accounting for 24.40, 16.22, and 8.66% of the total pathogenic bacteria, respectively. Moreover, 18 emerging or re-emerging pathogenic bacterial species with significant implications for human health were identified, although their relative abundance was relatively low (0.5098%). The relative abundance of pathogenic bacteria in indoor environments was significantly higher than outdoors, with the laboratory and dormitory having the highest levels. The findings of this study provide valuable guidance for the prevention and control of airborne bacterial contamination and the associated health risks in both a campus environment and other public spaces with high occupancy rates.
Topics: Universities; Air Microbiology; China; Bacteria; Humans; Particle Size; Air Pollution, Indoor; Particulate Matter; Environmental Monitoring
PubMed: 38651126
DOI: 10.3389/fpubh.2024.1371656 -
World Journal of Clinical Oncology Dec 2020The gram-negative aerobic bacterium is an opportunistic pathogen in brain tissues.
BACKGROUND
The gram-negative aerobic bacterium is an opportunistic pathogen in brain tissues.
CASE SUMMARY
The gram-negative aerobic bacterium was isolated from a patient's brain tissue during a stereotactic biopsy.
CONCLUSION
This is the first report of a brain tissue infection with possibly causing brain gliomatosis.
PubMed: 33437667
DOI: 10.5306/wjco.v11.i12.1064