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International Journal of Systematic and... Apr 2020A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23, was isolated from surface-sterilized leaf tissue of an oil palm grown in...
A Gram-stain-negative, aerobic, rod-shaped, leaf-associated bacterium, designated JS23, was isolated from surface-sterilized leaf tissue of an oil palm grown in Singapore and was investigated by polyphasic taxonomy. Phylogenetic analyses based on 16S rRNA gene sequences and 180 conserved genes in the genome of several members of revealed that strain JS23 formed a distinct evolutionary lineage independent of other taxa within the family . The predominant ubiquinone was Q-8. The primary polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified aminophospholipid. The major fatty acids were C, summed feature 3 (C 7 /C 6) and summed feature 8 (C 7 /C 6). The size of the genome is 5.36 Mbp with a DNA G+C content of 66.2 mol%. Genomic relatedness measurements such as average nucleotide identity, genome-to-genome distance and digital DNA-DNA hybridization clearly distinguished strain JS23 from the closely related genera , , , , , , and . Furthermore, average amino acid identity values and the percentages of conserved proteins, 56.0-68.4 and 28.2-45.5, respectively, were well below threshold values for genus delineation and supported the assignment of JS23 to a novel genus. On the basis of the phylogenetic, biochemical, chemotaxonomic and phylogenomic evidence, strain JS23 is proposed to represent a novel species of a new genus within the family , for which the name gen. nov., sp. nov., is proposed with the type strain of JS23 (= DSM 27307=KACC 17592).
Topics: Arecaceae; Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Plant Leaves; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Singapore; Ubiquinone
PubMed: 32202992
DOI: 10.1099/ijsem.0.004084 -
Microorganisms Feb 2020As an environmental pollutant, tetracycline (TC) can persist in the soil for years and damage the ecosystem. So far, many methods have been developed to handle the TC...
As an environmental pollutant, tetracycline (TC) can persist in the soil for years and damage the ecosystem. So far, many methods have been developed to handle the TC contamination. Microbial remediation, which involves the use of microbes to biodegrade the pollutant, is considered cost-efficient and more suitable for practical application in soil. This study isolated several strains from TC-contaminated soil and constructed a TC-degrading bacterial consortium containing sp. XY-1 and sp. XY-2, which exhibited better growth and improved TC degradation efficiency compared with single strain (81.72% TC was biodegraded within 12 days in Lysogeny broth (LB) medium). Subsequently, lab-scale soil remediation was conducted to evaluate its effectiveness in different soils and the environmental effects it brought. Results indicated that the most efficient TC degradation was recorded at 30 °C and in soil sample Y which had relatively low initial TC concentration (around 35 mg/kg): TC concentration decreased by 43.72% within 65 days. Soil properties were affected, for instance, at 30 °C, the pH value of soil sample Y increased to near neutral, and soil moisture content (SMC) of both soils declined. Analysis of bacterial communities at the phylum level showed that , , , and were the four dominant phyla, and the relative abundance of significantly increased in both soils after bioremediation. Further analysis of bacterial communities at the genus level revealed that sp. XY-1 successfully proliferated in soil, while sp. XY-2 was undetectable. Moreover, bacteria associated with nitrogen cycling, biodegradation of organic pollutants, soil biochemical reactions, and plant growth were affected, causing the decline in soil bacterial diversity. Variations in the relative abundance of tetracycline resistance genes (TRGs) and mobile gene elements (MGEs) were investigated, the results obtained indicated that , , , , and had higher relative abundance in original soils, and the relative abundance of most TRGs and MGEs declined after the microbial remediation. Network analysis indicated that may dominate the transfer of TRGs, and , , , , , and were possible hosts of TRGs or MGEs. This study comprehensively evaluated the effectiveness and the ecological effects of the TC-degrading bacterial consortium in soil environment.
PubMed: 32093355
DOI: 10.3390/microorganisms8020292 -
Microbiology Resource Announcements Jan 2020strain TF-18 was isolated from the roots of rice seedlings on selective medium containing four classes of antibiotics for isolation of Using Pacific Biosciences...
strain TF-18 was isolated from the roots of rice seedlings on selective medium containing four classes of antibiotics for isolation of Using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology, we report here a complete genome of 5,499,432 bases, a GC content of 64.8%, and 4,849 coding sequences.
PubMed: 31896624
DOI: 10.1128/MRA.01008-19 -
Journal of Cystic Fibrosis : Official... May 2020A structured survey of the cystic fibrosis pathogens Achromobacter, Pandoraea and Ralstonia species from thirteen sentinel hospitals throughout England was undertaken by...
A structured survey of the cystic fibrosis pathogens Achromobacter, Pandoraea and Ralstonia species from thirteen sentinel hospitals throughout England was undertaken by Public Health England. One isolate per patient of these genera collected from CF patients during the seven-month survey period in 2015 was requested from participating hospitals. Species-level identification was performed using nrdA/gyrB sequence cluster analysis, and genotyping by pulsed-field gel electrophoresis. In total, 176 isolates were included in the survey; 138 Achromobacter spp. (78.4%), 29 Pandoraea spp. (16.5%) and 9 Ralstonia spp. (5.1%). Novel Achromobacter and Pandoraea clusters were identified. High levels of antimicrobial resistance were found, particularly among Pandoraea isolates. Genotyping analysis revealed considerable diversity, however one geographically-widespread cluster of A. xylosoxidans isolates from six hospitals was found, in addition to two other clusters, both comprising isolates from two hospitals, either derived from the same region (A. xylosoxidans), or from hospitals within the same city (P. apista).
Topics: Achromobacter denitrificans; Adult; Anti-Bacterial Agents; Burkholderiaceae; Child; Cross Infection; Cystic Fibrosis; Drug Resistance, Microbial; England; Epidemiological Monitoring; Female; Gram-Negative Bacterial Infections; Humans; Male; Microbial Sensitivity Tests; Multilocus Sequence Typing; Ralstonia; Respiratory Tract Infections
PubMed: 31862307
DOI: 10.1016/j.jcf.2019.11.005 -
Frontiers in Microbiology 2019Comparative analysis of partial , , and gene sequences of 84 reference strains and field isolates revealed several clusters that included no taxonomic reference...
Comparative analysis of partial , , and gene sequences of 84 reference strains and field isolates revealed several clusters that included no taxonomic reference strains. The , , and phylogenetic trees were used to select 27 strains for whole-genome sequence analysis and for a comparative genomics study that also included 41 publicly available genome sequences. The phylogenomic analyses included a Genome BLAST Distance Phylogeny approach to calculate pairwise digital DNA-DNA hybridization values and their confidence intervals, average nucleotide identity analyses using the OrthoANIu algorithm, and a whole-genome phylogeny reconstruction based on 107 single-copy core genes using bcgTree. These analyses, along with subsequent chemotaxonomic and traditional phenotypic analyses, revealed the presence of 17 novel species among the strains analyzed, and allowed the identification of several unclassified strains reported in the literature. The genus has an open pan genome that includes many orthogroups in the 'Xenobiotics biodegradation and metabolism' KEGG pathway, which likely explains the enrichment of these species in polluted soils and participation in the biodegradation of complex organic substances. We propose to formally classify the 17 novel species as sp. nov. (type strain LMG 31117 = CCUG 73385), sp. nov. (type strain LMG 31108 = CCUG 73386), sp. nov. (type strain LMG 31011 = CCUG 73384), sp. nov. (type strain LMG 20603 = ATCC BAA-110), sp. nov. (type strain LMG 20602 = ATCC BAA-109), sp. nov. (type strain LMG 31118 = CCUG 73387), sp. nov. (type strain LMG 31106 = CCUG 39680), sp. nov. (type strain LMG 31010 = CCUG 73378), sp. nov. (type strain LMG 31110 = CCUG 73383), sp. nov. (type strain LMG 31012 = CCUG 73380), sp. nov. (type strain LMG 31112 = CCUG 73379), sp. nov. (type strain LMG 31009 = CCUG 73377), sp. nov. (type strain LMG 31116 = CCUG 73389), sp. nov. (type strain LMG 31109 = CCUG 73390), sp. nov. (type strain LMG 31114 = CCUG 73388), sp. nov. (type strain LMG 31014 = CCUG 73382), and sp. nov. (type strain LMG 31013 = CCUG 73381).
PubMed: 31781066
DOI: 10.3389/fmicb.2019.02556 -
Future Microbiology Nov 2019Genetic characterization of strains recovered from cystic fibrosis patients. The whole-genome sequence of 12 strains was determined using Illumina technology. The...
Genetic characterization of strains recovered from cystic fibrosis patients. The whole-genome sequence of 12 strains was determined using Illumina technology. The position of the strains within the genus was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. The results show that some strains previously identified as , , and belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. The taxonomy of the genus needs to be revised.
Topics: Bacterial Typing Techniques; Burkholderiaceae; Cystic Fibrosis; DNA, Ribosomal; Genome, Bacterial; Gram-Negative Bacterial Infections; Humans; Multilocus Sequence Typing; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Whole Genome Sequencing; beta-Lactamases
PubMed: 31762328
DOI: 10.2217/fmb-2019-0038 -
Current Eye Research May 2020: This study aimed to evaluate the microbial contamination level and its influencing factors of rigid gas permeable (RGP) trial lenses and lens cases in China.: A total...
: This study aimed to evaluate the microbial contamination level and its influencing factors of rigid gas permeable (RGP) trial lenses and lens cases in China.: A total of 107 RGP trial lenses and lens cases were collected from 7 main hospitals or optometric centers in China. Three sites including the lenses, case interiors and case screw tops were sampled for bacterial and fungal culture and identification. The contamination rates of these three sites and their relationship with lens care regimes were further analyzed.: The overall contamination rate was 73.8% for either lenses or cases, and 43.0% of lenses, 57.0% of case interiors and 65.4% of case screw tops respectively. The most frequently isolated microorganisms were spp., spp., spp., and spp. from all three sites. The contamination rate was positively related to the lens use frequency. Compared with dry-stored lenses, the contamination rate was significantly higher in wet-stored group ( < .001*). Inadequate disinfection and improper lens and case care regimes were also associated with higher contamination rates.: Our study reported that the RGP trial lenses and cases used for fittings had a considerably high contamination rate. The safe use of RGP trial lenses and education of optometrists on the regular maintenance of trial lenses should be emphasized.
Topics: Adult; Bacteria; Bacteriological Techniques; China; Contact Lens Solutions; Contact Lenses; Equipment Contamination; Equipment and Supplies; Female; Fungi; Humans; Male; Pyrrolidines; Young Adult
PubMed: 31697186
DOI: 10.1080/02713683.2019.1687726 -
Infection and Drug Resistance 2019(), an emerging pathogen, is able to trigger a pronounced pro-inflammatory response that results in lung dysfunction in cystic fibrosis (CF) patients. All previous...
(), an emerging pathogen, is able to trigger a pronounced pro-inflammatory response that results in lung dysfunction in cystic fibrosis (CF) patients. All previous isolates have been obtained from the respiratory samples of CF patients, with no reported cases of bacteremia. For the first time, we report isolates recovered twice from the blood cultures of a patient with liver cancer who had undergone allogeneic liver transplantation. These isolates were successfully identified by combining mass spectrometry and molecular techniques based on 16S rRNA sequencing methods. At the onset of the bacteremia, the patient's peripheral T, B and NK cell counts were 181.68/μL, 59.57/μL and 70.66/μL, respectively. The serum procalcitonin level, C-reactive protein level and peripheral neutrophil granulocyte percentage were 0.56 ng/mL, 61.00 mg/L and 96.8%, respectively. We found these isolates to be susceptible to ciprofloxacin and piperacillin/tazobactam and to be intermediate to amikacin. Previous studies have found isolates to be resistant. All of the data combined showed that compromised immune function from allogeneic liver transplantation plus immunosuppressive therapy contributes to the occurrence of bacteremia. Furthermore, the isolates demonstrated characteristic resistance profiles.
PubMed: 31695454
DOI: 10.2147/IDR.S227643 -
BMC Infectious Diseases Oct 2019Pandoraea species is a newly described genus, which is multidrug resistant and difficult to identify. Clinical isolates are mostly cultured from cystic fibrosis (CF)... (Review)
Review
BACKGROUND
Pandoraea species is a newly described genus, which is multidrug resistant and difficult to identify. Clinical isolates are mostly cultured from cystic fibrosis (CF) patients. CF is a rare disease in China, which makes Pandoraea a total stranger to Chinese physicians. Pandoraea genus is reported as an emerging pathogen in CF patients in most cases. However, there are few pieces of evidence that confirm Pandoraea can be more virulent in non-CF patients. The pathogenicity of Pandoraea genus is poorly understood, as well as its treatment. The incidence of Pandoraea induced infection in non-CF patients may be underestimated and it's important to identify and understand these organisms.
CASE PRESENTATION
We report a 44-years-old man who suffered from pneumonia and died eventually. Before his condition deteriorated, a Gram-negative bacilli was cultured from his sputum and identified as Pandoraea Apista by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS).
CONCLUSION
Pandoraea spp. is an emerging opportunistic pathogen. The incidences of Pandoraea related infection in non-CF patients may be underestimated due to the difficulty of identification. All strains of Pandoraea show multi-drug resistance and highly variable susceptibility. To better treatment, species-level identification and antibiotic susceptibility test are necessary.
Topics: Adult; Burkholderiaceae; China; Cystic Fibrosis; Gram-Negative Bacterial Infections; Humans; Intracranial Hemorrhage, Traumatic; Male; Pneumonia, Bacterial; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Sputum
PubMed: 31640582
DOI: 10.1186/s12879-019-4420-6 -
Proceedings of the National Academy of... Nov 2019Despite the omnipresence of specific host-symbiont associations with acquisition of the microbial symbiont from the environment, little is known about how the...
Despite the omnipresence of specific host-symbiont associations with acquisition of the microbial symbiont from the environment, little is known about how the specificity of the interaction evolved and is maintained. The bean bug acquires a specific bacterial symbiont of the genus from environmental soil and harbors it in midgut crypts. The genus consists of over 100 species, showing ecologically diverse lifestyles, and including serious human pathogens, plant pathogens, and nodule-forming plant mutualists, as well as insect mutualists. Through infection tests of 34 species and 18 taxonomically diverse bacterial species, we demonstrate here that nonsymbiotic and even its outgroup could stably colonize the gut symbiotic organ and provide beneficial effects to the bean bug when inoculated on aposymbiotic hosts. However, coinoculation revealed that the native symbiont always outcompeted the nonnative bacteria inside the gut symbiotic organ, explaining the predominance of the native symbiont in natural bean bug populations. Hence, the abilities for colonization and cooperation, usually thought of as specific traits of mutualists, are not unique to the native symbiont but, to the contrary, competitiveness inside the gut is a derived trait of the native symbiont lineage only and was thus critical in the evolution of the insect gut symbiont.
Topics: Animals; Burkholderia; Heteroptera; Host-Pathogen Interactions; Intestines; Models, Biological; Symbiosis
PubMed: 31636183
DOI: 10.1073/pnas.1912397116