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Microbiology Spectrum Feb 2023We found a new gene, , carried by a multidrug resistance plasmid in a clinical Vibrio furnissii isolate. QnrVF1 exhibits 44.6% to 72.5% similarity in identity with...
We found a new gene, , carried by a multidrug resistance plasmid in a clinical Vibrio furnissii isolate. QnrVF1 exhibits 44.6% to 72.5% similarity in identity with other Qnr family proteins. alleles are mainly encoded by chromosomes of V. furnissii and Vibrio fluvialis. Phylogenic analysis showed that QnrVF1 and QnrVF2 form a distinct clade in Qnr proteins. Thus, represents a new family. In addition, the gene is often flanked by the mobile element IS. Thus, it is likely that is mobilized by IS from chromosome to plasmid in V. furnissii. Quinolones are widely used drugs. Bacteria contain a quinolone resistance gene, which mediates resistance to quinolones. Currently, seven families of Qnr proteins, QnrVC, QnrA, QnrB, QnrC, QnrD, QnrE, and QnrS, have been identified. However, it is unclear whether there are any other families. In this study, we identified a new family, . We found many V. furnissii and V. fluvialis strains that possess chromosomal alleles, suggesting that V. furnissii and V. fluvialis are the reservoirs of . We also found that QnrVF1 confers low-level resistance to quinolones. IS may facilitate the spread of . The emergence and spread of may pose a considerable threat to public health.
Topics: Anti-Bacterial Agents; Drug Resistance, Bacterial; Quinolones; Plasmids; Microbial Sensitivity Tests
PubMed: 36656040
DOI: 10.1128/spectrum.01934-22 -
Microbiology Spectrum Feb 2023Vibrio cholerae can utilize a type VI secretion system (T6SS) to increase its intra- and interspecies competition. However, much still remains to be understood about the...
Vibrio cholerae can utilize a type VI secretion system (T6SS) to increase its intra- and interspecies competition. However, much still remains to be understood about the underlying mechanism of this intraspecies competition. In this study, we isolated an environmental V. cholerae strain E1 that lacked the typical virulence factors toxin-coregulated pilus and cholera toxin and that encoded a functional T6SS. We identified an evolved VgrG3 variant with a predicted C-terminal pesticin-like domain in V. cholerae E1, designated VgrG3. Using heterologous expression, protein secretion, and peptidoglycan-degrading assays, we demonstrated that VgrG3 is a T6SS-dependent effector harboring cell wall muramidase activity and that its toxicity can be neutralized by cognate immunity protein TsiV3. Site-directed mutagenesis proved that the aspartic acid residue at position 867 is crucial for VgrG3-mediated antibacterial activity. Bioinformatic analysis showed that genes encoding VgrG3-like homologs are distributed in species, are linked with T6SS structural genes and auxiliary genes, and the gene pair of V. cholerae probably evolved from Vibrio anguillarum and Vibrio fluvialis via homologous recombination. Through a time-lapse microscopy assay, we directly determined that cells accumulating VgrG3 disrupted bacterial division, while the cells continued to increase in size until the loss of membrane potential and cell wall breakage and finally burst. The results of the competitive killing assay showed that VgrG3 contributes to V. cholerae interspecies competition. Collectively, our study revealed a novel T6SS E-I pair representing a new T6SS toxin family which allows V. cholerae to gain dominance within polymicrobial communities by T6SS. The type VI secretion system used by a broad range of Gram-negative bacteria delivers toxic proteins to target adjacent eukaryotic and prokaryotic cells. Diversification of effector proteins determines the complex bacterium-bacterium interactions and impacts the health of hosts and environmental ecosystems in which bacteria reside. This work uncovered an evolved valine-glycine repeat protein G3, carrying a C-terminal pesticin-like domain (VgrG3), which has been suggested to harbor cell wall hydrolase activity and is able to affect cell division and the integrity of cell wall structure. Pesticin-like homologs constitute a family of T6SS-associated effectors targeting bacterial peptidoglycan which are distributed in species, and genetic loci of them are linked with T6SS structural genes and auxiliary genes. T6SS-delivered VgrG3 mediated broad-spectrum antibacterial activity for several microorganisms tested, indicating that VgrG3-mediated antimicrobial activity is capable of conferring bacteria a competitive advantage over competitors in the same niches.
Topics: Type VI Secretion Systems; Vibrio cholerae; Peptidoglycan; Ecosystem; Bacterial Proteins; Anti-Bacterial Agents; Cell Wall
PubMed: 36625646
DOI: 10.1128/spectrum.04267-22 -
Tropical Biomedicine Dec 2022Some of Vibrio species is well known as pathogenic bacteria in aquaculture and the marine industry. Its infection is able to generate a massive outbreak and affect the...
Some of Vibrio species is well known as pathogenic bacteria in aquaculture and the marine industry. Its infection is able to generate a massive outbreak and affect the fish population, especially for net caged fish such as seabass. This study was conducted to investigate the prevalence of Vibrio spp. isolated from seabass (Lates calcarifer) in Sri Tujuh Lagoon, Tumpat, Kelantan. Then, to determine the antibiotic resistance in Vibrio isolates. Polymerase chain reaction (PCR) was used to detect Vibrio species using specific primer VR169 and VR744 with estimation base pair size band, 597 bp and further identified by sequencing. On the other hand, antibiotic susceptibility tests were continued by using 13 types of antibiotics; kanamycin (K30), chloramphenicol (C30), neomycin (N10), ampicillin (AMP10), nitrofurantoin (F300), tetracycline (TE30), streptomycin (S10), norfloxacin (NOR10), ciprofloxacin (CIP5), nalidixic acid (NA30), gentamicin (CN10), doxycycline (DO30) and sulfamethoxazole (SXT100). As a result, 14 Vibrio isolates were identified, including Vibrio fluvialis (n=6), Vibrio parahaemolyticus (n=3), Vibrio harveyi (n=2) and each isolate for Vibrio vulnificus, Vibrio alginolyticus and Vibrio spp. The results showed that all isolates were sensitive to most antibiotics except ampicillin, neomycin and streptomycin. The MAR index value was ranging from 0 to 0.31. This study demonstrates the prevalence of Vibrio spp. in seabass and the report on multidrug resistance strains that could be of concern to the fish farmers. In addition, data from this study can be further used in fish disease management plans.
Topics: Animals; Vibrio; Microbial Sensitivity Tests; Bass; Anti-Bacterial Agents; Neomycin; Ampicillin; Streptomycin
PubMed: 36602217
DOI: 10.47665/tb.39.4.013 -
Iranian Journal of Microbiology Oct 2022is a Gram-negative, bacillus-shaped, curved bacterium known as an emerging pathogen. There are reports of outbreaks caused by this bacterium worldwide. Iran, especially...
BACKGROUND AND OBJECTIVES
is a Gram-negative, bacillus-shaped, curved bacterium known as an emerging pathogen. There are reports of outbreaks caused by this bacterium worldwide. Iran, especially Qom province, is an endemic region for gastrointestinal diseases caused by species. So, the aim was to isolate from clinical and environmental samples.
MATERIALS AND METHODS
During six months, 363 clinical and surface water samples were evaluated. The samples were cultured on specific media, and all incubated for 24 hours at 37°C. Suspicious colonies were evaluated by Gram staining and biochemical tests. The BD Phoenix automated microbiology system was used for the final confirmation of the isolated bacteria. Evaluation of antibiotic resistance of isolated strains was also performed according to CLSI standard.
RESULTS
Eight cases (2.2%) of , including seven from surface water samples (87.5%) and one from clinical samples (12.5%), were isolated. Based on antimicrobial susceptibility testing, all isolates were susceptible to amikacin, gentamicin, trimethoprim/sulfamethoxazole, ciprofloxacin, tetracycline, ceftazidime, and chloramphenicol. High-level resistance to ampicillin and amoxicillin/clavulanate was also observed. -infected patient had a mild fever, watery diarrhea, vomiting, nausea, and abdominal cramps that were manifested after drinking contaminated water or eating contaminated vegetables. The patient's symptoms recovered without antibiotic therapy after four days, resulting in self-limiting disease.
CONCLUSION
The current study is the first human case of infection isolated in Iran. Therefore, monitoring of water and food samples should be done routinely.
PubMed: 36531817
DOI: 10.18502/ijm.v14i5.10962 -
Journal of Dairy Science Jan 2023Composting is a common practice used for treating animal manures before they are used as organic fertilizers for crop production. Whether composting can effectively...
Composting is a common practice used for treating animal manures before they are used as organic fertilizers for crop production. Whether composting can effectively reduce microbial pathogens and antibiotic resistance genes remain poorly understood. In this study, we compared 3 different dairy manure composting methods-anaerobic fermentation (AF), static compost (SC), and organic fertilizer production (OFP)-for their effects on antibiotic-resistant bacteria, antibiotic resistance genes, and microbial community diversity in the treated manures. The 3 composting methods produced variable and distinct effects on antibiotic-resistant bacteria, zoonotic bacteria, and resistance genes, some of which were decreased and others of which showed no significant changes during composting. Particularly, SC and OFP reduced chloramphenicol resistance gene fexA and opportunistic pathogen Vibrio fluvialis, whereas AF significantly reduced tetracycline resistance gene tetB and opportunistic pathogens Enterococcus faecium and Escherichia fergusonii. The compositions of microbial communities varied significantly during the composting processes, and there were significant differences between the 3 composting methods. In all 3 composts, the dominant phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Interestingly, Firmicutes, Proteobacteria, and Bacteroidetes remained stable in the entire AF process, whereas they were dominated at the beginning, decreased at the early stage of composting, and rebounded at the later stage during SC and OFP. In general, SC and OFP produced a more profound effect than AF on microbial community diversities, pathogens, and dominant species. Additionally, Enterococcus aquimarinus was isolated from AF for the first time. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States function prediction analysis indicated that the genes related to membrane transport and amino acid metabolism were abundant in the 3 composts. The metabolism of amino acids, lipids, and carbohydrates increased as composting progressed. The biosynthesis of antibiotics was enhanced after fermentation in the 3 composting methods, and the increase in the SC was the most obvious. These results reveal dynamic changes in antibiotic-resistant bacteria, antibiotic resistance genes, microbial community composition, and function succession in different dairy manure composts and provide useful information for further optimization of composting practices.
Topics: Cattle; Animals; Composting; Manure; Anti-Bacterial Agents; Phylogeny; Soil Microbiology; Drug Resistance, Microbial; Bacteria; Genes, Bacterial; Soil
PubMed: 36333143
DOI: 10.3168/jds.2022-22193 -
Gut Microbes 2022is a halophilic Gram-negative bacterium regarded as an emerging unusual enteric pathogen of increasing public health concern. Our previous work has identified two type...
is a halophilic Gram-negative bacterium regarded as an emerging unusual enteric pathogen of increasing public health concern. Our previous work has identified two type VI secretion systems (T6SSs) in , VflT6SS1, and VflT6SS2, and the latter is functional in mediating interbacterial competitiveness. However, its antibacterial effectors remain to be clarified. In this work, we focused on a new potential effector/immunity pair TssI2/TsiI2. Bioinformatics analysis revealed that the C-terminal domain of TssI2 belongs to a widespread family of pesticin, and its antibacterial toxicity and corresponding protection by TsiI2 were proved via bacterial killing assays, and their action sites were localized to the periplasm of bacterial cells. The interaction of TssI2 and TsiI2 was demonstrated by the bacterial adenylate cyclase two-hybrid, protein pull-down and isothermal titration calorimetry assays. Site-directed mutagenesis demonstrated that, in addition to Glu-844, Thr-863, and Asp-869, which correspond to three reported residues in pesticin of , additional residues including Phe-837, Gly-845, Tyr-851, Gly-867, Gln-963, Trp-975, and Arg-1000 were also proved to be crucial to the bactericidal activity of TssI2. Muramidase/lysozyme-related peptidoglycan (PG) hydrolase activities of TssI2 and its variants were validated with permeabilized cells and purified PG substrate. Based on sequence homologies at C-terminals in various isolates, TssI2 was subdivided into five clusters (12-22% identity among them), and the antibacterial activities of representative effectors from other four Clusters were also confirmed through periplasmic over-expression in host. Two selected cognate immunities were proved to confer protection against the toxicities of their effectors. Additionally, TsiI2, which belongs to Cluster I, exhibited cross-protection to effector from Cluster V. Together, current findings expand our knowledge of the diversity and consistency of evolved VgrG effectors in and on how VflT6SS2 mediates a competitive advantage to gain a better survival.
Topics: Type VI Secretion Systems; Periplasm; Muramidase; Escherichia coli; Peptidoglycan; Adenylyl Cyclases; Gastrointestinal Microbiome; Bacterial Proteins; Anti-Bacterial Agents
PubMed: 36288406
DOI: 10.1080/19490976.2022.2136460 -
International Journal of Systematic and... Oct 2022A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic motile bacterium, designated strain OG9-811, was isolated from the gut of an oyster...
A Gram-stain-negative, oxidase- and catalase-positive, facultative anaerobic motile bacterium, designated strain OG9-811, was isolated from the gut of an oyster collected in the Yellow Sea, Republic of Korea. The strain grew at 10-37 °C, pH 6.0-9.0 and with 0.5-10% (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain OG9-811 affiliated with the genus , with the highest sequence similarity of 98.2% to ATCC BAA-450 followed by R-40492 (98.0 %), LMG 20362 (97.7 %) and LMG 20536 (97.6 %); other relatives were JCM 16456 (97.4 %), NBRC 103150 (97.0 %) and CIP 102972 (97.0 %). The complete genome of strain OG9-811 comprised two chromosomes of a total 4 807 684 bp and the G+C content was 50.2 %. Results of analysis based on the whole genome sequence showed the distinctiveness of strain OG9-811. The average nucleotide identity (ANI) values between strain OG9-811 and the closest strains ATCC BAA-450, R-40492, LMG 20362, KCTC 12702 JCM 16456, ATCC 33809 and CIP 102972 were 73.0, 72.6, 73.3, 73.0, 72.7, 78.5 and 77.8 %, respectively, while the digital DNA-DNA hybridization values between strain OG9-811 and the above closely related strains were 20.8, 21.2, 20.8, 21.7, 20.7, 23.2 and 22.4 %, respectively. The major fatty acids of strain OG9-811 were summed feature 3 (C 7 and/or C 6), summed feature 8 (C c and/or C 7) and C. The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain OG9-811 contained Q-8 as a quinone. On the basis of polyphasic taxonomic characteristics, strain OG9-811 is considered to represent a novel species, for which the name sp. nov. is proposed. The type strain is OG9-811 (=KCTC 72623=GDMCC 1.2610).
Topics: Animals; Bacterial Typing Techniques; Base Composition; Cardiolipins; Catalase; DNA, Bacterial; Fatty Acids; Nucleotides; Ostreidae; Phosphatidylethanolamines; Phospholipids; Phylogeny; Quinones; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sodium Chloride; Vibrio
PubMed: 36269578
DOI: 10.1099/ijsem.0.005586 -
Marine Pollution Bulletin Nov 2022Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined...
Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics.
Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined the abundance of genes associated with resistance and tolerance to heavy metals in the rhizosphere microbiome of Avicennia germinans from a semi-arid mangrove of La Guajira-Colombia by metagenomics and genomics approach. Twenty-eight genes associated with tolerance and 49 genes related to resistance to heavy metals were detected. Genes associated with tolerance and resistance to Cu, especially cusA and copA, were the most abundant. The highest number of genes for tolerance and resistance were for Zn and Co, respectively. The isolate Vibrio fluvialis showed the ability to tolerate Cu, Ni, Zn, and Cd. This work used a complementary approach of metagenomics and genomics to characterize the potential of mangrove microorganisms to tolerate and resist heavy metals and the influence of salinity on their abundance.
Topics: Avicennia; Wetlands; Rhizosphere; Metagenomics; Cadmium; Metals, Heavy; Microbiota
PubMed: 36219973
DOI: 10.1016/j.marpolbul.2022.114204 -
Heliyon Oct 2022This study investigated the bacteriological quality of ready-to-eat (RTE) African salads in Enugu metropolis, Enugu, Nigeria. A total of 10 samples of African salad were...
Culture-dependent examination of the bacteriological quality of ready-to-eat African salads in Enugu metropolis, Nigeria and antibiotic resistance profile of associated bacteria.
This study investigated the bacteriological quality of ready-to-eat (RTE) African salads in Enugu metropolis, Enugu, Nigeria. A total of 10 samples of African salad were purchased from 10 different vendors in Enugu metropolis. The samples were purchased from Agbani Road, Ogbete, Mayor, Uwani, Kenyatta, Achara Layout, Obiagu and Timber. Isolation and enumeration of bacterial isolates were done using Nutrient agar, Eosin Methylene Blue (EMB) agar, Thiosulphate-citrate-bile salts-sucrose (TCBS) agar, Salmonella-Shigella Agar (SSA) and MacConkey agar, following standard methods. Identification of the bacterial isolates were done through biochemical tests and the Analytical Profile Index (API 20E) test kit. The antibiotic sensitivity of the bacterial isolates was also done using the Kirby Bauer disc diffusion method. Total culturable heterotrophic count was above 300 colonies across the samples. The highest bacterial counts recorded on EMB, SSA and TCBS across the samples were 6.3 × 10 CFU/g, 7.4 × 10 CFU/g and 1.21 × 10 CFU/g respectively. The identities of the organisms were; spp., , , , , and . The prevalent organism across the samples was spp. The antibiotic sensitivity test suggested that spp. was resistant to Ampiclox and Amoxycillin but sensitive to Erythromycin, Pefloxacin and Septrin. From this study, it was discovered that consumers of RTE African salad from majority of the vendors across Enugu metropolis are at risk of severe food poisoning.
PubMed: 36212018
DOI: 10.1016/j.heliyon.2022.e10782 -
Plants (Basel, Switzerland) Aug 2022L. essential oil (cumin EO) was studied for its chemical composition, antioxidant and vibriocidal activities. Inhibition of biofilm formation and secretion of some...
L. essential oil (cumin EO) was studied for its chemical composition, antioxidant and vibriocidal activities. Inhibition of biofilm formation and secretion of some virulence properties controlled by the quorum sensing system in and strains were also reported. The obtained results showed that cuminaldehyde (44.2%) was the dominant compound followed by β-pinene (15.1%), γ-terpinene (14.4%), and -cymene (14.2%). Using the disc diffusion assay, cumin EO (10 mg/disc) was particularly active against all fifteen species, and the highest diameter of growth inhibition zone was recorded against (41.33 ± 1.15 mm), (39.67 ± 0.58 mm), and (36.67 ± 0.58 mm). At low concentration (MICs value from 0.023-0.046 mg/mL), cumin EO inhibited the growth of all strains, and concentrations as low as 1.5 mg/mL were necessary to kill them (MBCs values from 1.5-12 mg/mL). Using four antioxidant assays, cumin EO exhibited a good result as compared to standard molecules (DPPH = 8 ± 0.54 mg/mL; reducing power = 3.5 ± 0.38 mg/mL; β-carotene = 3.8 ± 0.34 mg/mL; chelating power = 8.4 ± 0.14 mg/mL). More interestingly, at 2x MIC value, cumin EO inhibited the formation of biofilm by (9.96 ± 1%), (15.45 ± 0.7%), (14.9 ± 0.4%), and (18.14 ± 0.3%). In addition, cumin EO and cuminaldehyde inhibited the production of violacein on Lauria Bertani medium (19 mm and 35 mm, respectively). Meanwhile, 50% of violacein inhibition concentration (VIC) was about 2.746 mg/mL for cumin EO and 1.676 mg/mL for cuminaldehyde. Moreover, elastase and protease production and flagellar motility in were inhibited at low concentrations of cumin EO and cuminaldehyde. The adopted in-silico approach revealed good ADMET properties as well as a high binding score of the main compounds with target proteins (1JIJ, 2UV0, 1HD2, and 3QP1). Overall, the obtained results highlighted the effectiveness of cumin EO to prevent spoilage with species and to interfere with the quorum sensing system in Gram-negative bacteria by inhibiting the flagellar motility, formation of biofilm, and the secretion of some virulence enzymes.
PubMed: 36079620
DOI: 10.3390/plants11172236