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Clinical Laboratory Aug 2019Parotid cyst is a common problem in patients treated by surgeons. However, Paracoccus yeei was isolated from an aerobic blood culture in a patient with parotid cyst as...
BACKGROUND
Parotid cyst is a common problem in patients treated by surgeons. However, Paracoccus yeei was isolated from an aerobic blood culture in a patient with parotid cyst as an unusual etiologic opportunistic agent.
METHODS
Since old biochemical identification kits are not able to identify this species, MALDI-TOF MS correctly was recommended to identify this isolate. Its identity was confirmed by sequencing of the 16S rRNA gene.
RESULTS
The aligned sequences (16S rRNA gene) were used for a phylogenetic analysis (phylogenetic tree), which was produced using the BLAST pair-wise alignments. The sequence analysis determined that the best matches were with Paracoccus yeei.
CONCLUSIONS
Paracoccus yeei has been reported as a rare opportunistic human pathogen, we should actively com-municate to the clinic to improve the real positive rate.
Topics: Bacterial Typing Techniques; Cysts; DNA, Bacterial; Humans; Male; Middle Aged; Paracoccus; Parotid Diseases; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
PubMed: 31414739
DOI: 10.7754/Clin.Lab.2019.190125 -
Environmental Microbiology Reports Jun 2020Bacteria are known to communicate with each other through signalling molecules that regulate gene expression within the population. However, the way in which hydrophobic...
Bacteria are known to communicate with each other through signalling molecules that regulate gene expression within the population. However, the way in which hydrophobic signals are released and transmitted among bacterial population is not well understood. Recent studies show that membrane vesicles (MVs) are involved in delivering hydrophobic signals, such as in N-hexadecanoyl-l-homoserine lactone (C16-HSL) signalling in Paracoccus denitrificans Pd1222. In this study, we identified the AHLs produced in Paracoccus aminophilus JCM7686, Paracoccus aminovorans NBRC16711, Paracoccus thiocyanatus JCM20756, Paracoccus versutus JCM20754 and Paracoccus yeei ATCC BAA-599, and show that the main AHL produced in all the strains is C16-HSL. Our results show that these Paracoccus species also release MVs that carry C16-HSL, but at different proportions. Most of the strains carry C16-HSL in MVs, while in P. aminophilus JCM7686, very little C16-HSL was detected in MVs, but was found in other fractions of the supernatant. Given the utilization of a common signal, we showed that these Paracoccus species can share signals with P. denitrificans Pd1222, and examined the role of MVs in signalling. Our study provides new insights into the way in which bacteria communicate using hydrophobic signals.
Topics: Acyl-Butyrolactones; Biological Transport; Extracellular Vesicles; Microbial Interactions; Paracoccus; Paracoccus denitrificans; Quorum Sensing
PubMed: 32291967
DOI: 10.1111/1758-2229.12843 -
Enzyme and Microbial Technology Jan 2022In this publication an alternative approach to investigations of bacterial growth is proposed. Contrary to the conventional physical methods it is based on enzyme...
In this publication an alternative approach to investigations of bacterial growth is proposed. Contrary to the conventional physical methods it is based on enzyme activity detection. The procedure for real-time and on-line monitoring of microbial ureolytic activity (applied as a model experimental biosystem) in the flow analysis format is presented. The developed fully-mechanized bioanalytical flow system is composed of solenoid micropumps and microvalves actuated by Arduino microcontroller. The photometric detection based on Nessler reaction is performed using dedicated flow-through optoelectronic detector made of paired light emitting diodes. The developed bioanalytical system allows discrete assaying of microbial urease in the wide range of activity up to 5.4 U mL with detection limit below 0.44 U mL, a high sensitivity in the linear range of response (up to 200 mV U mL and relatively high throughput (9 detection per hour). The proposed differential procedure of measurements (i.e. a difference between peaks register for sample with and without external addition of urea is treated as an analytical signal) allows elimination of interfering effects from substrate and products of biocatalysed reaction as well as other components of medium used for microbial growth. The developed bioanalytical system was successfully applied for the control of growth of urease-positive bacteria strains (Proteus vulgaris, Klebsiella pneumoniae and Paracoccus yeei) including examination of effects from various microbial cultivation conditions like temperature, composition of culture medium and amount of substrate required for induction of bacterial enzymatic activity. The developed bioanalytical flow system can be applied for metabolic activity-based estimation of parameters of lag and log phases of microbial growth as well as for detection of decline phase.
Topics: Bacteria; Culture Media; Klebsiella pneumoniae; Urea; Urease
PubMed: 34670184
DOI: 10.1016/j.enzmictec.2021.109899 -
Journal of Biotechnology Aug 2020The CO fixation by autotrophic microbes has an important significance for improving carbon sequestration in composting. In this work, the succession of autotrophic...
The CO fixation by autotrophic microbes has an important significance for improving carbon sequestration in composting. In this work, the succession of autotrophic CO-fixing bacterial communities was investigated using quantitative PCR and high-throughput sequencing of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes (cbbL and cbbM). The results presented that the number of autotrophic CO-fixing bacteria was comparable to that in the soil, and most species have not been classified into known bacterial groups, only part of them was assigned into Proteobacteria and Actinobacteria. Phylogenetic analysis displayed that the dominant known cbbL-containing bacteria were Allochromatium vinosum, Rhodobacter sphaeroides, Nitrobacter winogradskyi, Paracoccus yeei and Porphyrobacter sp. CACIAM 03H1, while the dominant known cbbM-containing bacteria were Sulfuritalea hydrogenivorans, Pseudomonas resinovorans, Achromobacter xylosoxidans, Sphingopyxis macrogoltabida and Thermomonospora curvata. In addition, canonical correspondence analysis showed that the evolution of autotrophic CO-fixing bacterial communities was greatly affected by physico-chemical parameters such as temperature, C/N and pH.
Topics: Autotrophic Processes; Bacteria; Bacterial Proteins; Carbon Dioxide; Composting; High-Throughput Nucleotide Sequencing; Microbial Consortia; Ribulose-Bisphosphate Carboxylase
PubMed: 32553532
DOI: 10.1016/j.jbiotec.2020.06.010 -
Microorganisms Dec 2020Mobile phones (MPs) of healthcare workers (HCWs) may represent an important source of transmission of infectious agents. This longitudinal study documents the...
Mobile phones (MPs) of healthcare workers (HCWs) may represent an important source of transmission of infectious agents. This longitudinal study documents the contamination of these tools. Ten MPs handled by senior pediatricians were sampled once a week during 23 weeks in three pediatric wards of the University Hospital of Saint-Etienne, France. Cultures were performed for bacteria and multiplex PCR assays for a panel of respiratory and enteric viruses. A questionnaire on hygiene habits regarding phoning and care was filled-in by pediatricians before and after the study. From a total of 230 samples, 145 (63%) were contaminated by at least one pathogen. The MPs from emergency departments were the most impacted. Viruses were detected in 179 samples; bacteria were isolated in 59 samples. Contamination increased during the winter epidemic peak. A cross-contamination by between hands and MPs of different HCWs was demonstrated. The communication of the study results influenced the hygiene behaviors. This study highlights the contamination of MPs by pathogens that are resistant in the environment, and its sustainability along the winter season. The role of MPs as vectors of nosocomial infection needs to be better investigated.
PubMed: 33339327
DOI: 10.3390/microorganisms8122011 -
Membranes Oct 2022Biomembranes based on an organosilica sol-gel matrix were used to immobilize bacteria VKM B-3302 as part of a biochemical oxygen demand (BOD) biosensor....
Biomembranes based on an organosilica sol-gel matrix were used to immobilize bacteria VKM B-3302 as part of a biochemical oxygen demand (BOD) biosensor. Diethoxydimethylsilane (DEDMS) and tetraethoxysilane (TEOS) were used as precursors to create the matrix in a 1:1 volume ratio. The use of scanning electron microscopy (SEM) and the low-temperature nitrogen adsorption method (BET) showed that the sol-gel matrix forms a capsule around microorganisms that does not prevent the exchange of substrates and waste products of bacteria to the cells. The use of DEDMS as part of the matrix made it possible to increase the sensitivity coefficient of the biosensor for determining BOD by two orders of magnitude compared to a biosensor based on methyltriethoxysilane (MTES). Additionally, the long-term stability of the bioreceptor increased to 68 days. The use of such a matrix neutralized the effect of heavy metal ions on the microorganisms' catalytic activity in the biosensor. The developed biosensor was used to analyze water samples from water sources in the Tula region (Russia).
PubMed: 36295743
DOI: 10.3390/membranes12100983 -
Biofilm Dec 2022In patients with acute respiratory failure, mechanical ventilation through an endotracheal tube (ET) may be required to correct hypoxemia and hypercarbia. However,...
In patients with acute respiratory failure, mechanical ventilation through an endotracheal tube (ET) may be required to correct hypoxemia and hypercarbia. However, biofilm formation on these ETs is a risk factor for infections in intubated patients, as the ET can act as a reservoir of microorganisms that can cause infections in the lungs. As severely ill COVID-19 patients often need to be intubated, a better knowledge of the composition of ET biofilms in this population is important. In Spring 2020, during the first wave of the COVID-19 pandemic in Europe, 31 ETs were obtained from COVID-19 patients at Ghent University Hospital (Ghent, Belgium). Biofilms were collected from the ET and the biofilm composition was determined using culture-dependent (MALDI-TOF mass spectrometry and biochemical tests) and culture-independent (16S and ITS1 rRNA amplicon sequencing) approaches. In addition, antimicrobial resistance was assessed for isolates collected via the culture-dependent approach using disc diffusion for 11 antimicrobials commonly used to treat lower respiratory tract infections. The most common microorganisms identified by the culture-dependent approach were those typically found during lung infections and included both presumed commensal and potentially pathogenic microorganisms like , , and . More unusual organisms, such as , were also identified, but each only in a few patients. The culture-independent approach revealed a wide variety of microbes present in the ET biofilms and showed large variation in biofilm composition between patients. Some biofilms contained a diverse set of bacteria of which many are generally considered as non-pathogenic commensals, whereas others were dominated by a single or a few pathogens. Antimicrobial resistance was widespread in the isolates, e.g. 68% and 53% of all isolates tested were resistant against meropenem and gentamicin, respectively. Different isolates from the same species recovered from the same ET biofilm often showed differences in antibiotic susceptibility. Our data suggest that ET biofilms are a potential risk factor for secondary infections in intubated COVID-19 patients, as is the case in mechanically-ventilated non-COVID-19 patients.
PubMed: 35720435
DOI: 10.1016/j.bioflm.2022.100079 -
Frontiers in Physiology 2021New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However,...
Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream () Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization.
New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal and was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of associated with the presence of . The intestinal gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and ) and metal-reducing ( and ) bacteria. Other inflammatory markers (α) were up-regulated in PAP fish, positively correlating the intestinal gene with the inflammasome activator , whereas the systemic expression of and α was negatively correlated with the Bacilli class in PAP fish and positively correlated with in non-PAP fish. Overall changes in the expression pattern of , galectins (), and toll-like receptors () reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of - and -mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.
PubMed: 34675821
DOI: 10.3389/fphys.2021.748265 -
F1000Research 2021: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains...
: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized. We sought to conduct metagenomic sequencing on cases of ocular and periocular sarcoidosis, none of them with previously identified infectious causes. : Archival tissue specimens of 16 subjects with biopsies of ocular and periocular tissues that were positive for non-caseating granulomas were used as cases. Four archival tissue specimens that did not demonstrate non-caseating granulomas were also included as controls. Genomic DNA was extracted from tissue sections. DNA libraries were generated from the extracted genomic DNA and the libraries underwent next-generation sequencing. : We generated between 4.8 and 20.7 million reads for each of the 16 cases plus four control samples. For eight of the cases, we identified microbial pathogens that were present well above the background, with one potential pathogen identified for seven of the cases and two possible pathogens for one of the cases. Five of the eight cases were associated with bacteria ( and ), two cases with fungi ( ) and one case with a virus (Mupapillomavirus 1). Interestingly, four of the five bacterial species are also part of the human oral microbiome. : Using a metagenomic sequencing we identified possible infectious causes in half of the ocular and periocular sarcoidosis cases analyzed. Our findings support the proposition that sarcoidosis could be an etiologically heterogenous disease. Because these are previously banked samples, direct follow-up in the respective patients is impossible, but these results suggest that sequencing may be a valuable tool in better understanding the etiopathogenesis of sarcoidosis and in diagnosing and treating this disease.
Topics: Bacteria; High-Throughput Nucleotide Sequencing; Humans; Metagenome; Metagenomics; Microbiota; Sarcoidosis
PubMed: 36212901
DOI: 10.12688/f1000research.55090.1 -
Enfermedades Infecciosas Y... Nov 2020
Topics: Bacteremia; Humans; Liver Cirrhosis; Paracoccus
PubMed: 32127236
DOI: 10.1016/j.eimc.2020.01.013