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Frontiers in Microbiology 2019The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called acyl-homoserine lactones (AHLs), which are synthesized by an...
The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called acyl-homoserine lactones (AHLs), which are synthesized by an enzyme AHL synthase (LuxI) and detected by a transcriptional regulator (LuxR) that are usually located in close proximity. However, many recent studies have also evidenced the presence of LuxR solos that are LuxR-related proteins in Proteobacteria that are devoid of a cognate LuxI AHL synthase. species are opportunistic pathogens frequently isolated from sputum specimens of cystic fibrosis (CF) patients. We have previously shown that strains possess QS activity. In this study, we examined the presence of QS activity in all type strains of species and acquired their complete genome sequences for holistic bioinformatics analyses of QS-related genes. Only four out of nine type strains (, , and ) showed QS activity, and C8-HSL was the only AHL detected. A total of 10 canonical s with adjacent s were predicted by bioinformatics from the complete genomes of aforementioned species and publicly available genomes. No orphan was identified in any of the genomes. However, genes for two LuxR solos (LuxR2 and LuxR3 solos) were identified in all genomes (except two draft genomes with one LuxR solo gene), and was the only species that harbored no QS-related activity and genes. Except the canonical LuxR genes, LuxIs and LuxR solos of species were distantly related to the other well-characterized QS genes based on phylogenetic clustering. LuxR2 and LuxR3 solos might represent two novel evolutionary branches of LuxR system as they were found exclusively only in the genus. As a few solos were located in close proximity with prophage sequence regions in the genomes, we thus postulated that these solos could be transmitted into genus by transduction process mediated by bacteriophage. The bioinformatics approach developed in this study forms the basis for further characterization of closely related species. Overall, our findings improve the current understanding of QS in species, which is a potential pharmacological target in battling infections in CF patients.
PubMed: 31447806
DOI: 10.3389/fmicb.2019.01758 -
Cureus Nov 2021Among patients infected with respiratory viruses, primary coinfection or secondary bacterial pneumonia is common in the severely ill. are multi-drug resistant...
Among patients infected with respiratory viruses, primary coinfection or secondary bacterial pneumonia is common in the severely ill. are multi-drug resistant gram-negative bacilli that have been newly classified in the past 20 years. We present the first reported case of co-infection with SARS-CoV-2 infection. A critically ill gentleman with COVID-19 in acute respiratory distress syndrome (ARDS) requiring mechanical ventilation developed ventilator-associated bacterial pneumonia (VAP). Initial sputum cultures grew species, with subsequent cultures growing , as well. The patient failed to improve despite several antibiotic regimens including meropenem. Send-out reference laboratory testing of the species showed susceptibility to amikacin, ciprofloxacin, levofloxacin, imipenem, and minocycline, but resistance to aztreonam, cefepime, ceftazidime, and meropenem. The patient had deteriorated to multi-organ failure by the time minocycline was initiated, and his family had transitioned him into hospice care. Carbapenems are vital agents in the treatment of VAP. species are often resistant to meropenem but often retain in-vitro sensitivity to imipenem-cilastin. Although mainly isolated from respiratory specimens of patients with cystic fibrosis, cases of infection in non-cystic fibrosis patients have been increasingly recognized. The presentation of this case aims to increase awareness of the high drug resistance of this rising species and reduce delays in treatment, especially in COVID-19 coinfection.
PubMed: 34912637
DOI: 10.7759/cureus.19498 -
Microbiology Spectrum May 2024Lovebugs appeared in large numbers across a wide area in Seoul, South Korea, in June 2023. The sudden appearance of exotic insects not only discomforts people but also...
Lovebugs appeared in large numbers across a wide area in Seoul, South Korea, in June 2023. The sudden appearance of exotic insects not only discomforts people but also fosters anxiety, as their potential for pathogen transmission would be unknown. In this study, targeted next-generation sequencing (NGS) of the 16S rRNA gene V4 region was performed using iSeq 100 to screen for bacteria in lovebugs. Forty-one lovebugs (20 females and 21 males) collected in Seoul, Korea, were identified as based on mitochondrial cytochrome oxidase subunit 1 sequencing data using PCR. We analyzed the microbiome of the lovebugs and detected 453 species of bacteria. Among all bacteria screened based on NGS, was detected in all samples with an average relative abundance of 80.40%, followed by and . Diversity (alpha and beta) between females and males did not differ; however, only showed a higher relative abundance in females. Sequencing analysis of using a gene-specific primer by PCR showed that it had higher sequence similarity to the symbiont of arthropods than to the spotted fever group rickettsiae. Eleven samples in which was detected by iSeq 100 were confirmed by PCR and exhibited 100% sequence identity to strain DSM 23570. Consequently, the likelihood of pathogen transmission to humans is low. The applied method may play a crucial role in swiftly identifying bacterial species in the event of future outbreaks of exotic insects that may be harmful to humans.IMPORTANCELovebugs have recently emerged in large numbers in Seoul, causing major concern regarding potential health risks. By performing the next-generation sequencing of the 16S rRNA gene V4 region, we comprehensively examined the microbiome of these insects. We identified the presence of numerous bacteria, including and . Reassuringly, subsequent tests confirmed that these detected bacteria were not pathogenic. The present study addresses health concerns related to lovebugs and shows the accuracy and efficiency of our detection technique. Such methods prove invaluable for rapidly identifying bacterial species during potential outbreaks of unfamiliar insects, thereby ensuring public safety.
PubMed: 38809007
DOI: 10.1128/spectrum.03809-23 -
Journal of Environmental Management Oct 2020Aerobic granular sludge (AGS) is a type of biofilm with good sedimentation and density, high biomass, high organic load tolerance and toxicity resistance....
Aerobic granular sludge (AGS) is a type of biofilm with good sedimentation and density, high biomass, high organic load tolerance and toxicity resistance. Oxytetracycline (OTC) is an antibiotic widely used in livestock and aquaculture, and its low absorption and high residue bring many risks and harms to the ecological environment. In this study, an OTC-degrading strain TJ3 was isolated from AGS and identified as Pandoraea sp. The biodegradation characteristics of OTC by strain TJ3 under different environmental conditions were also investigated. The results showed that the optimal initial pH value and temperature for the culture strain were 6.0 and 30 °C, respectively. At an inoculation dose of 6% (v/v), the removal rate of OTC by strain TJ3 was remarkable (59.4%). Furthermore, when the sodium acetate was present as an additional substrate, the biomass and the OTC removal rate of strain TJ3 were improved. The biodegradability of strain TJ3 to OTC was proved by LC-QTOF/MS, and two possible biotransformation products, i.e. m/z 416 and 219, were identified. In the bioaugmentation experiments of AGS by strain TJ3, the average OTC removal rate was 92.89% after the stable operation of bioreactor. The chemical oxygen demand (COD), ammonium nitrogen (NH-N) and total phosphorus (TP) were efficiently removed. The microbial community structure had significantly changed at the genus level, and the relative abundance of Zoogloea, Pandoraea, Cloacibacterium and Desulfovibrio increased evidently. These results implied that the OTC removal performance and the structural stability of AGS were improved. In this study, Pandoraea sp. TJ3 was applied to removal OTC for the first time, and results showed that Pandoraea sp. TJ3 may be a new auxiliary bacterial resource for the biodegradation of OTC and a potential candidate in the treatment of antibiotic wastewater.
Topics: Aerobiosis; Bacteria; Biological Oxygen Demand Analysis; Bioreactors; Nitrogen; Oxytetracycline; Sewage; Waste Disposal, Fluid
PubMed: 32738758
DOI: 10.1016/j.jenvman.2020.111115 -
Infection and Drug Resistance 2022() infection is of great concern as these gram-negative bacillus species are multidrug-resistant and usually isolated from the patients' respiratory tract suffering...
() infection is of great concern as these gram-negative bacillus species are multidrug-resistant and usually isolated from the patients' respiratory tract suffering from cystic fibrosis (CF). A few cases of infection have also been reported in non-CF patients due to its rare pathogenic nature with unclear and overlapping clinical, biochemical, and microbiological characteristics with other species. Here, we report an unusual case of a 46-year-old non-CF female, who presented with multiple pelvic fractures, acute traumatic brain injury, multiple rib fractures, and multiple burns (18% of the total body surface area, II°) by the collapse of a brick kiln, suffered from sepsis due to wound infection. Pandoraea species were isolated both from her blood and wound secretion. Antibiotic susceptibility testing indicated susceptibility to imipenem, tetracyclines, sulfamethoxazole, and ampicillin/sulbactam but resistance to meropenem, quinolones, aminoglycosides, and other beta-lactams. 16S ribosomal RNA (rRNA) PCR assays and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) were used to confirm the bacteria as . After effective anti-infection of intravenous antibiotics (imipenem 1.0 Q8H with tigecycline 50 mg Q12H for 14 days), wound care, and other comprehensive treatment for two months, the patient improved and was discharged from the hospital eventually. After reviewing the literature, we observed that the susceptibility results of Pandoraea species were often multidrug-resistant and had a unique pattern of being resistant to meropenem but sensitive to imipenem. Biofilm formation, carbapenemase production, and unique gene procession differed from the environmental isolates could help explain its resistance. This case report highlights the potential virulence of as a pathogen in patients with no underlying disease. Although they are often multi-resistant, imipenem can be a preferred treatment for Pandoraea species in the earliest identification steps.
PubMed: 36483145
DOI: 10.2147/IDR.S388520 -
MBio Aug 2021The closest relative of human pathogen , the trypanosomatid , harbors a bacterial endosymbiont " Pandoraea novymonadis." Based on genomic data, we performed a detailed...
The closest relative of human pathogen , the trypanosomatid , harbors a bacterial endosymbiont " Pandoraea novymonadis." Based on genomic data, we performed a detailed characterization of the metabolic interactions of both partners. While in many respects the metabolism of resembles that of other Leishmaniinae, the endosymbiont provides the trypanosomatid with heme, essential amino acids, purines, some coenzymes, and vitamins. In return, shares with the bacterium several nonessential amino acids and phospholipids. Moreover, it complements its carbohydrate metabolism and urea cycle with enzymes missing from the " Pandoraea novymonadis" genome. The removal of the endosymbiont from results in a significant reduction of the overall translation rate, reduced expression of genes involved in lipid metabolism and mitochondrial respiratory activity, and downregulation of several aminoacyl-tRNA synthetases, enzymes involved in the synthesis of some amino acids, as well as proteins associated with autophagy. At the same time, the genes responsible for protection against reactive oxygen species and DNA repair become significantly upregulated in the aposymbiotic strain of this trypanosomatid. By knocking out a component of its flagellum, we turned into a new model trypanosomatid that is amenable to genetic manipulation using both conventional and CRISPR-Cas9-mediated approaches. is a parasitic flagellate of the family Trypanosomatidae representing the closest insect-restricted relative of the human pathogen . It bears symbiotic bacteria in its cytoplasm, the relationship with which has been established relatively recently and independently from other known endosymbioses in protists. Here, using the genome analysis and comparison of transcriptomic profiles of with and without the endosymbionts, we describe a uniquely complex cooperation between both partners on the biochemical level. We demonstrate that the removal of bacteria leads to a decelerated growth of , substantial suppression of many metabolic pathways, and increased oxidative stress. Our success with the genetic transformation of this flagellate makes it a new model trypanosomatid species that can be used for the dissection of mechanisms underlying the symbiotic relationships between protists and bacteria.
Topics: Bacteria; Genome, Bacterial; Genomics; Phylogeny; Symbiosis; Trypanosoma
PubMed: 34399629
DOI: 10.1128/mBio.01606-21 -
Microbiology Resource Announcements Apr 2024is a pathogenic bacterium naturally resistant to various antimicrobials, including colistin. Here, we report the whole-genome sequence of , which exhibits high-level...
is a pathogenic bacterium naturally resistant to various antimicrobials, including colistin. Here, we report the whole-genome sequence of , which exhibits high-level multidrug resistance, isolated from a hospitalized patient in Japan.
PubMed: 38470265
DOI: 10.1128/mra.01166-23 -
Journal of Clinical Microbiology Jan 2023A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to... (Review)
Review
A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the or acceptance on Validation Lists published by the . Of particular significance among valid and effectively published taxa within the past 2 years were novel spp., coagulase-positive staphylococci, spp., and members of family . Noteworthy taxonomic revisions include those within the and genera, family (including unifications of subspecies designations to species level taxa), spp., and former members of spp. and spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.
Topics: Humans; Staphylococcus; Bacillus
PubMed: 36533910
DOI: 10.1128/jcm.00282-22 -
Canadian Journal of Microbiology Mar 2022In the Tohoku region of Japan, 72% of the land comprises mountain forest zones. During winter, severe climatic conditions include heavy snowfall. In such an environment,...
In the Tohoku region of Japan, 72% of the land comprises mountain forest zones. During winter, severe climatic conditions include heavy snowfall. In such an environment, which is considered high in biodiversity, we assumed that aerobic bacteria would be diverse and would possess the ability to degrade polychlorinated biphenyls (PCBs). In this study, 78 environmental samples were collected from the Tohoku region and 56 aerobic PCB-degrading bacterial strains were isolated. They belonged to the genera , , , , , , , , and . Previously reported aerobic PCB-degrading bacterial strains isolated in Japan belonged to the same genera, except that the genera and were not identified in the present study. In particular, the isolated strains YAZ2 and YU14-111 had high PCB-degrading abilities. Analysis of the sequences of the YAZ2 and YU14-111 strains showed that the gene structures of the operon, which encode enzymes associated with PCB degradation, were the same as those of the sp. KKS102 strain. Moreover, 2,3-biphenyl dioxygenase activity was responsible for the degradation characteristics of all the isolated strains. Overall, this study suggests that aerobic PCB-degrading bacteria are not specifically endemic to the Tohoku region but distributed across Japan.
Topics: Bacteria, Aerobic; Biodegradation, Environmental; Japan; Polychlorinated Biphenyls; Rhodococcus
PubMed: 35020498
DOI: 10.1139/cjm-2021-0056 -
Journal of Applied Microbiology Apr 2023Pandoraea pnomenusa MCB032 completely degrades chlorobenzene, whose metabolic pathway is encoded by cbs and clc gene clusters. The putative regulatory factors ClcR and...
AIMS
Pandoraea pnomenusa MCB032 completely degrades chlorobenzene, whose metabolic pathway is encoded by cbs and clc gene clusters. The putative regulatory factors ClcR and CbsR are predicted to regulate the cbs and clc gene clusters. This research aims to understand the function of ClcR and CbsR.
METHODS AND RESULTS
RT-PCR analyses demonstrated that the cbsFAaAbAcAdB operon that encodes catabolic pathways for the degradation of chlorobenzene to chlorocatechol is located on an operon. Moreover, the clcABCDE operon is involved in the 3-chlorocatechol pathway. Gene knockout and transcriptional analysis showed that the transcription of the cbsFAaAbAcAdB operon is positively regulated by CbsR, whereas the clcABCDE operon is activated by ClcR. Primer extension analysis was used to locate the transcription start sites of the cbsFAaAbAcAdB and cbsR operons. Electrophoretic mobility shift assay analyses showed that CbsR is bound to the sites in the promoter regions of cbsFAaAbAcAdB and cbsR operons.
CONCLUSION
The XylR/NtrC-type regulator CbsR positively regulates the transcription of the cbsFAaAbAcAdB operon encoding the upstream pathway of chlorobenzene catabolism, while the LysR-type regulator ClcR activates the clcABCDE operon encoding the downstream pathway.
Topics: Transcription Factors; Promoter Regions, Genetic; Base Sequence; Chlorobenzenes; Operon; Gene Expression Regulation, Bacterial; Bacterial Proteins
PubMed: 36965871
DOI: 10.1093/jambio/lxad064