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Virulence Jan 2018Non-fermenting Gram-negative bacteria are problematic in clinical locations, being one of the most prevalent causes of nosocomial infections. Many of these... (Review)
Review
Non-fermenting Gram-negative bacteria are problematic in clinical locations, being one of the most prevalent causes of nosocomial infections. Many of these non-fermenting Gram-negative bacteria are opportunistic pathogens that affect patients that are suffering with underlying medical conditions and diseases. Brevundimonas spp., in particular Brevundimonas diminuta and Brevundimonas vesicularis, are a genus of non-fermenting Gram-negative bacteria considered of minor clinical importance. Forty-nine separate instances of infection relating to Brevundimonas spp were found in the scientific literature along with two pseudo-infections. The majority of these instances were infection with Brevundimonas vesicularis (thirty-five cases - 71%). The major condition associated with Brevundimonas spp infection was bacteraemia with seventeen individual cases/outbreaks (35%). This review identified forty-nine examples of Brevundimonas spp. infections have been discussed in the literature. These findings indicate that infection review programs should consider investigation of possible Brevundimonas spp outbreaks if these bacteria are clinically isolated in more than one patient.
Topics: Bacteremia; Caulobacteraceae; Communicable Diseases, Emerging; Disease Outbreaks; Global Health; Gram-Negative Bacterial Infections; Humans; Opportunistic Infections
PubMed: 29484917
DOI: 10.1080/21505594.2017.1419116 -
Microbiology Spectrum Sep 2021is a genus of Gram-negative bacteria widely distributed in nature and is also an opportunistic pathogen causing health care-associated infections. strain 090558 was...
is a genus of Gram-negative bacteria widely distributed in nature and is also an opportunistic pathogen causing health care-associated infections. strain 090558 was recovered from a blood culture of a cancer patient and was subjected to genome sequencing and analysis. The average nucleotide identity and DNA-DNA hybridization values between 090558 and type strains of species were 78.76% to 93.94% and 19.8% to 53.9%, respectively, below the cutoff to define bacterial species. Detailed phenotypic tests were performed, suggesting that 090558 can be differentiated from other species by its ability to assimilate sodium acetate but not to utilize glucose, trypsin, or β-glucosidase. Strain 090558 (GDMCC 1.1871 or KCTC 82165) therefore represents a novel species, for which the name Brevundimonas huaxiensis sp. nov. is proposed. All genomes available in GenBank (accessed on 25 January 2021) were retrieved, discarding those labeled "excluded from RefSeq" by GenBank, and included 82 genomes for precise species curation. In addition to the 21 species with genomes of type strains available, we identified 29 taxa that either belong to the 12 species without available genomes of type strains or represent novel species. We found that more than half (57.3%) of the 82 genomes need to be corrected for species assignation, including species mislabeling of a type strain. Our analysis highlights the complexity of taxonomy. We also found that only some species are associated with human infections, and more studies are warranted to understand their pathogenicity and epidemiology. is a genus of the family and comprises 33 species. can cause various infections but remains poorly studied. In this study, we reported a novel species, , based on genome and phenotype studies of strain 090558 recovered from human blood. We then examined the species assignations of all genomes ( = 82) in GenBank and found that in addition to the known species with genome sequences of type strains available, there are 29 taxa based on genome analysis, which need to be further studied using phenotype-based methods to establish their species status. Our study significantly updates the taxonomy of and enhances our understanding of this genus of clinical relevance. The findings also encourage future studies on the characterization of novel species.
Topics: Caulobacteraceae; Genome, Bacterial; Glucose; Phenotype; Phylogeny; Sodium Acetate; Trypsin
PubMed: 34232096
DOI: 10.1128/Spectrum.00111-21 -
Scientific Reports Jun 2023The aim of this study was to evaluate the effect of Lactobacillus delbrueckii subsp. lactis (L.del) on vaginal microbiota (VM) dysbiosis and vaginal radiation injury in... (Randomized Controlled Trial)
Randomized Controlled Trial
The aim of this study was to evaluate the effect of Lactobacillus delbrueckii subsp. lactis (L.del) on vaginal microbiota (VM) dysbiosis and vaginal radiation injury in gynecologic cancer patients. The inhibitory effects of L.del on cervical cancer cells were also studied in vitro. Gynecologic cancer patients receiving radiotherapy were randomized into control and L.del intervention groups. The control group received radiotherapy, while the intervention group received radiotherapy and L.del intervention (1 capsule/day placed into the deep vagina from the first day of radiotherapy until the end of treatment). Vaginal swab samples were collected on the first day pre-treatment and the last day post-treatment. DNA from 54 patients was extracted and assessed by the 16S rRNA sequencing method. Radiotherapy resulted in vaginal microbiome dysbiosis characterized by increased phylogenetic diversity and increased abundance of Brevundimonas, Streptococcus and Prevotella, but a decreased abundance of Lactobacillus. Level 2 vaginal radiation injury was positively associated with the abundance of Brevundimonas and gram-negative non-fermenting bacteria. Administration of L.del attenuated the reduction of Lactobacillus while also inhibiting the abundance of Streptococcus and Prevotella, thereby ameliorating radiotherapy-related vaginal microbiota dysbiosis. CLD inhibited the in vitro proliferation of SiHa cells by altering the expression of BCL2, HPV16-E6, HPV16-E7, IL6, MAP7, BAX, Caspase-3, Caspase-9 and LTF. In conclusion, L. del application can alleviate radiation-induced vaginal dysbiosis and restore Lactobacillus dominance of the vaginal microbiome. Moreover, CLD was found to inhibit cell growth and promote the apoptosis of SiHa cells in vitro. The registration number for this clinical trial is ChiCTR1900021784.
Topics: Female; Humans; Dysbiosis; RNA, Ribosomal, 16S; Phylogeny; Vagina; Lactobacillus; Streptococcus; Neoplasms
PubMed: 37344615
DOI: 10.1038/s41598-023-37241-7 -
Microbiology Spectrum Apr 2022The genus consists of Gram-negative bacteria widely distributed in environment and can cause human infections. However, the genomic characteristics and pathogenicity of...
The genus consists of Gram-negative bacteria widely distributed in environment and can cause human infections. However, the genomic characteristics and pathogenicity of remain poorly studied. Here, the whole-genome features of 24 type strains were described. spp. had relatively small genomes (3.13 ± 0.29 Mb) within the family but high G+C contents (67.01 ± 2.19 mol%). Two-dimensional hierarchical clustering divided those genomes into 5 major clades, in which clades II and V contained nine and five species, respectively. Interestingly, phylogenetic analysis showed a one-to-one match between core and accessory genomes, which suggested coevolution of species within the genus . The unique genes were annotated to biological functions like catalytic activity, signaling and cellular processes, multisubstance metabolism, etc. The majority of spp. harbored virulence-associated genes , , , , and , which encoded isocitrate lyase, elongation factor, 2-dehydro-3-deoxyphosphooctonate aldolase, heat shock protein, and acyl carrier protein, respectively. In addition, genomic islands (GIs) and phages/prophages were identified within the genus. Importantly, a novel species was identified from the feces of a patient (suffering from diarrhea) by the analyses of biochemical characteristics, phylogenetic tree of 16S rRNA gene, multilocus sequence analysis (MLSA) sequences, and genomic data. The name sp. nov. was proposed, with type strain CHPC 1.3453 (= GDMCC 1.2503= KCTC 82824). spp. also showed obvious slow growth compared with that of Escherichia coli. Our study reveals insights into genomic characteristics and potential virulence-associated genes of spp., and provides a basis for further intensive study of the pathogenicity of . spp., a group of bacteria from the family , is associated with nosocomial infections, deserve widespread attention. Our study elucidated genes potentially associated with the pathogenicity of the genus. We also described some new characteristics of spp., such as small chromosome size, high G+C content, and slow-growth phenotypes, which made the genus a good model organism for in-depth studies of growth rate traits. Apart from the comparative analysis of the genomic features of the genus, we also reported a novel species, Brevundimonas pishanensis, from the feces of a patient with diarrhea. Our study promotes the understanding of the pathogenicity characteristics of species bacteria.
Topics: Bacteria, Aerobic; Bacterial Typing Techniques; Caulobacteraceae; DNA, Bacterial; Diarrhea; Fatty Acids; Genomics; Humans; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Virulence
PubMed: 35416704
DOI: 10.1128/spectrum.02468-21 -
Frontiers in Microbiology 2021A novel endophytic bacterial strain, designated GR-TSA-9, was isolated from surface-sterilized grape ( L.). 16S rRNA gene sequence analyses showed that the isolate was...
A novel endophytic bacterial strain, designated GR-TSA-9, was isolated from surface-sterilized grape ( L.). 16S rRNA gene sequence analyses showed that the isolate was grouped within the genus , displaying the highest similarity with DS-18 (97.9%) and KSL-102 (97.8%) and less than 97.5% similarity with other members of . The strain GR-TSA-9 was a gram negative, rod shaped, facultatively anaerobic, catalase and oxidase positive, and motile bacterium. Its growth occurred at 10-37°C (optimally 25-30°C), at pH 7.0-8.0, and in NaCl 0-1% (optimally 0%). It contained ubiquinone-10 as a respiratory quinone, and the major cellular fatty acids (>10% of the total) were C (14.2%) and summed feature 8 (Cω7 and/or Cω6c, 65.6%). The polar lipids present in the strain were phosphoglycolipids, phosphatidylglycerol, 1,2-di-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol, and unidentified lipids (L1, L2, and L4). The strain had one 2,976,716bp circular chromosome with a G+C content of 66.4%. The digital DNA-DNA hybridization value between strain GR-TSA-9 and DS-18 was 20.9%, while the average nucleotide identity value was 76.7%. In addition, the dDDH and ANI values to other members in this genus, whose genome sequences are available, are less than 21.1 and 77.6%. Genome annotation predicted the presence of some gene clusters related to tyrosine degradation and pyomelanin formation. Strain GR-TSA-9 produced a brown melanin-like pigment in the presence of L-tyrosine-containing media. The highest pigment production (0.19g/L) was observed in tryptic soy broth with 1.0mg/ml L-tyrosine at 25°C for 6days of culture. Biophysical characterization by ultraviolet (UV)-visible spectroscopy, Fourier-transform infrared spectroscopy, and electrospray ionization mass spectrometry confirmed that the pigment was pyomelanin. Additionally, melanized GR-TSA-9 cells could protect the cells against UVC exposure. The phylogenetic, genomic, phenotypic, and chemotaxonomic features indicated that strain GR-TSA-9 represents a novel melanin-producing species of . The type strain was GR-TSA-9 (KCTC 82386=CGMCC 1.18820).
PubMed: 34721332
DOI: 10.3389/fmicb.2021.733612 -
The EMBO Journal Mar 2023Glycosylation of surface structures diversifies cells chemically and physically. Nucleotide-activated sialic acids commonly serve as glycosyl donors, particularly...
Glycosylation of surface structures diversifies cells chemically and physically. Nucleotide-activated sialic acids commonly serve as glycosyl donors, particularly pseudaminic acid (Pse) and its stereoisomer legionaminic acid (Leg), which decorate eubacterial and archaeal surface layers or protein appendages. FlmG, a recently identified protein sialyltransferase, O-glycosylates flagellins, the subunits of the flagellar filament. We show that flagellin glycosylation and motility in Caulobacter crescentus and Brevundimonas subvibrioides is conferred by functionally insulated Pse and Leg biosynthesis pathways, respectively, and by specialized FlmG orthologs. We established a genetic glyco-profiling platform for the classification of Pse or Leg biosynthesis pathways, discovered a signature determinant of eubacterial and archaeal Leg biosynthesis, and validated it by reconstitution experiments in a heterologous host. Finally, by rewiring FlmG glycosylation using chimeras, we defined two modular determinants that govern flagellin glycosyltransferase specificity: a glycosyltransferase domain that either donates Leg or Pse and a specialized flagellin-binding domain that identifies the acceptor.
Topics: Flagellin; Stereoisomerism; Bacteria; Glycosyltransferases; Sialyltransferases; Archaea; Flagella; Bacterial Proteins
PubMed: 36636824
DOI: 10.15252/embj.2022112880 -
Frontiers in Microbiology 2023Focusing on visible plaques for phage isolation leaves the question if we miss the diversity of non-plaque forming phages. We addressed this question through direct...
Focusing on visible plaques for phage isolation leaves the question if we miss the diversity of non-plaque forming phages. We addressed this question through direct plaque-based isolation by employing the new hosts LVF1 and LVF3 dsDNA, ssDNA, dsRNA, and ssRNA host-associated metavirome analysis. Of the 25 distinctive dsDNA phage isolates, 14 were associated with and 11 with . TEM analysis revealed that 6 were myoviruses, 18 siphoviruses and 1 podovirus, while phages infecting belonged all to siphoviruses. The associated viromes suggested a higher phage diversity in summer than in winter, and dsDNA phages were the dominant group. Isolation of vB_SmaP-Kaonashi was possible after investigating the viromes associated with , demonstrating the great potential of accompanying host-associated metavirome analysis. The ssDNA virome analysis showed that the LVF1 host is associated with and phages, although none of them were isolated. The results demonstrated that the classical isolation technique is not exhausted, leading to the isolation of new dsDNA phages. It can be further improved by combination with metavirome techniques, which revealed further diversity.
PubMed: 37025643
DOI: 10.3389/fmicb.2023.1095850 -
Frontiers in Cellular and Infection... 2022Some spp. are globally emerging opportunistic pathogens that can be dangerous to individuals with underlying medical conditions and for those who are immunocompromised....
Some spp. are globally emerging opportunistic pathogens that can be dangerous to individuals with underlying medical conditions and for those who are immunocompromised. Gram-negative spp. can form resilient sessile biofilms and are found not only in different confined terrestrial settings (e.g., hospitals) but are also frequently detected in spacecraft which is inhabited by astronauts that can have altered immunity. Therefore, spp. pose a serious health hazard in different environments, especially in its biofilm form. Conventional antimicrobials applied to disrupt, inactivate, or prevent biofilm formation have limited efficiency and applicability in different closed-loop systems. Therefore, new, effective, and safe biofilm control technologies are in high demand. The present work aimed to investigate antimicrobial photoinactivation (API) of sp. ESA1 monocultural biofilms mediated by non-toxic, natural photosensitizers such as riboflavin (RF) and chlorophyllin (Chl) with an emphasis of this technology as an example to be safely used in closed-loop systems such as spacecraft. The present study showed that Chl-based API had a bactericidal effect on sp. ESA1 biofilms at twice the lower irradiation doses than was needed when applying RF-based API. Long-term API based on RF and Chl using 450 nm low irradiance plate has also been studied in this work as a more practically applicable API method. The ability of sp. ESA1 biofilms to reduce alamarBlue™ and regrowth analysis have revealed that after the applied photoinactivation, bacteria can enter a viable but non-culturable state with no ability to resuscitate in some cases.
Topics: Humans; Photosensitizing Agents; Biofilms; Anti-Bacterial Agents; Anti-Infective Agents; Riboflavin
PubMed: 36262183
DOI: 10.3389/fcimb.2022.1006723 -
Antioxidants (Basel, Switzerland) Feb 2021PON1, PON2, and PON3 belong to a family of lactone hydrolyzing enzymes endowed with various substrate specificities. Among PONs, PON2 shows the highest hydrolytic... (Review)
Review
PON1, PON2, and PON3 belong to a family of lactone hydrolyzing enzymes endowed with various substrate specificities. Among PONs, PON2 shows the highest hydrolytic activity toward many acyl-homoserine lactones (acyl-HL) involved in bacterial quorum-sensing signaling. Accordingly, defense against pathogens, such as (), was postulated to be the principal function of PON2. However, recent findings have highlighted the importance of PON2 in oxidative stress control, inhibition of apoptosis, and the progression of various types of malignancies. This review focuses on all of these aspects of PON2.
PubMed: 33562328
DOI: 10.3390/antiox10020256 -
Microbiology Spectrum Jun 2023To increase knowledge on pathogens, we conducted in-depth genomic and phenotypic characterization of a strain isolated from the cerebrospinal fluid of a patient...
To increase knowledge on pathogens, we conducted in-depth genomic and phenotypic characterization of a strain isolated from the cerebrospinal fluid of a patient admitted in a neonatal intensive care unit. The strain was identified as a member of the genus based on Vitek 2 system results and 16S rRNA gene sequencing and presented a multidrug resistance profile (MDR). Several molecular and biochemical tests were used to characterize and identify the species for in-depth results. The draft genome assembly of the isolate has a total length of 3,261,074 bp and a G+C of 66.86%, similar to other species of the genus. Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the sp. studied represents a distinct species, for which we propose the name sp. nov. analysis detected antimicrobial resistance genes (AMRGs) mediating resistance to β-lactams (, , and ) and aminoglycosides [, , , and ]. We also found AMRGs encoding the AcrAB efflux pump that confers resistance to a broad spectrum of antibiotics. Colistin and quinolone resistance can be attributed to mutation in and/or and GyrA/GyrB, respectively. The sp. nov. genome contained copies of type IV secretion system (T4SS)-type integrative and conjugative elements (ICEs); integrative mobilizable elements (IME); and Tn-type and IS, IS, IS, and IS families, suggesting an important role in the development and dissemination of antibiotic resistance. The isolate presented a range of virulence-associated genes related to biofilm formation, adhesion, and invasion that can be relevant for its pathogenicity. Our findings provide a wealth of data to hinder the transmission of MDR and highlight the need for monitoring and identifying new bacterial species in hospital environments. species is considered an opportunistic human pathogen that can cause multiple types of invasive and severe infections in patients with underlying pathologies. Treatment of these pathogens has become a major challenge because many isolates are resistant to most antibiotics used in clinical practice. Furthermore, there are no consistent therapeutic results demonstrating the efficacy of antibacterial agents. Although considered a rare pathogen, recent studies have provided evidence of the emergence of in clinical settings. Hence, we identified a novel pathogenic bacterium, sp. nov., that presented a multidrug resistance (MDR) profile and carried diverse genes related to drug resistance, virulence, and mobile genetic elements. Such data can serve as a baseline for understanding the genomic diversity, adaptation, evolution, and pathogenicity of MDR
Topics: Infant, Newborn; Humans; RNA, Ribosomal, 16S; Brazil; Anti-Bacterial Agents; Colistin; DNA
PubMed: 37067439
DOI: 10.1128/spectrum.04415-22