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Nefrologia : Publicacion Oficial de La... 2016
Topics: Animals; Catheter-Related Infections; Dogs; Environmental Exposure; Female; Gram-Negative Bacterial Infections; Humans; Middle Aged; Paracoccus; Peritoneal Dialysis; Peritonitis; Soil Microbiology
PubMed: 27039709
DOI: 10.1016/j.nefro.2016.02.009 -
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 -
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 -
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 -
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 -
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 -
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 -
Journal of Clinical Microbiology Jul 2004Paracoccus yeei was isolated in pure culture from an aerobic blood culture and bulla fluid from a 67-year-old male. The biochemical identification scheme for this...
Paracoccus yeei was isolated in pure culture from an aerobic blood culture and bulla fluid from a 67-year-old male. The biochemical identification scheme for this recently described species is outlined. Because of its reaction pattern it is not unlikely that P. yeei is underdiagnosed.
Topics: Aged; Base Sequence; Gram-Negative Bacterial Infections; Humans; Male; Molecular Sequence Data; Paracoccus
PubMed: 15243119
DOI: 10.1128/JCM.42.7.3366-3368.2004 -
Microorganisms Oct 2020Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic...
Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., and ). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.
PubMed: 33023015
DOI: 10.3390/microorganisms8101522 -
Medicine May 2008The etiologic evaluation of uveitis is frequently unsuccessful when noninvasive methods are used. We conducted a prospective study to evaluate systematic screening for...
The etiologic evaluation of uveitis is frequently unsuccessful when noninvasive methods are used. We conducted a prospective study to evaluate systematic screening for pathogens of uveitis. All patients with uveitis referred to the participating tertiary ophthalmology departments from January 2001 to September 2007 underwent intraocular and serum specimen collection. The standardized protocol for laboratory investigations included universal polymerase chain reaction (PCR)-based detection of any bacteria and mycoses, specific PCR-based detection of fastidious (difficult-to-grow) bacteria and herpes viruses, and culture of vitreous fluid. Sera were tested for fastidious bacteria. Among the 1321 included patients (1520 specimens), infection was diagnosed in 147 (11.1%) patients: 78 (53%) were caused by fastidious bacteria that included spirochetes, Bartonella species, intracellular bacteria (Chlamydia species, Rickettsia species, Coxiella burnetii), and Tropheryma whipplei; 18 by herpes viruses; and 9 by fungi. Bartonella quintana, Coxiella burnetii, Paracoccus yeei, Aspergillus oryzae, and Cryptococcus albidus were found to be associated with uveitis for the first time, to our knowledge. We recommend applying a 1-step diagnostic procedure that incorporates intraocular, specific microbial PCR with serum analyses in tertiary centers to determine the etiology of uveitis.
Topics: Adult; Aged; Aged, 80 and over; Bacteria; Child, Preschool; Eye Infections, Bacterial; Female; Humans; Male; Middle Aged; Polymerase Chain Reaction; Serologic Tests; Tropheryma; Uveitis
PubMed: 18520326
DOI: 10.1097/MD.0b013e31817b0747