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The pathogenic bacterium Clostridioides difficile is a worldwide health burden with increasing morbidity, mortality and antibiotic resistances. Therefore, extensive research efforts are made to unravel its virulence and dissemination. One crucial aspect for C. difficile is its mobilome, which for instance allows the spread of antibiotic resistance genes (ARG) or influence strain virulence. As a nosocomial pathogen, the majority of strains analyzed originated from clinical environments and infected individuals. Nevertheless, C. difficile can also be present in human intestines without disease development or occur in diverse environmental habitats such as puddle water and soil, from which several strains could already be isolated. We therefore performed comprehensive genome comparisons of closely related clinical and non-clinical strains to identify the effects of the clinical background. Analyses included the prediction of virulence factors, ARGs, mobile genetic elements (MGEs), and detailed examinations of the pan genome. Clinical-related trends were thereby observed. While no significant differences were identified in fundamental C. difficile virulence factors, the clinical strains carried more ARGs and MGEs, and possessed a larger accessory genome. Detailed inspection of accessory genes revealed higher abundance of genes with unknown function, transcription-associated, or recombination-related activity. Accessory genes of these functions were already highlighted in other studies in association with higher strain virulence. This specific trend might allow the strains to react more efficiently on changing environmental conditions in the human host such as emerging stress factors, and potentially increase strain survival, colonization, and strain virulence. These findings indicated an adaptation of the strains to the clinical environment. Further, implementation of the analysis results in pairwise genome comparisons revealed that the majority of these accessory genes were encoded on predicted MGEs, shedding further light on the mobile genome of C. difficile. We therefore encourage the inclusion of non-clinical strains in comparative analyses.
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PURPOSE: Even though workflow analysis in the operating room has come a long way, current systems are still limited to research. In the quest for a robust, universal setup, hardly any attention has been given to the dimension of audio despite its numerous advantages, such as low costs, location, and sight independence, or little required processing power. METHODOLOGY: We present an approach for audio-based event detection that solely relies on two microphones capturing the sound in the operating room. Therefore, a new data set was created with over 63 h of audio recorded and annotated at the University Hospital rechts der Isar. Sound files were labeled, preprocessed, augmented, and subsequently converted to log-mel-spectrograms that served as a visual input for an event classification using pretrained convolutional neural networks. RESULTS: Comparing multiple architectures, we were able to show that even lightweight models, such as MobileNet, can already provide promising results. Data augmentation additionally improved the classification of 11 defined classes, including inter alia different types of coagulation, operating table movements as well as an idle class. With the newly created audio data set, an overall accuracy of 90%, a precision of 91% and a F1-score of 91% were achieved, demonstrating the feasibility of an audio-based event recognition in the operating room. CONCLUSION: With this first proof of concept, we demonstrated that audio events can serve as a meaningful source of information that goes beyond spoken language and can easily be integrated into future workflow recognition pipelines using computational inexpensive architectures.
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Apnoeic oxygenation has experienced a resurgence in interest in critical care and perioperative medicine. However, its effect on cerebral oxygenation and factors influencing it, have not yet been investigated in detail. By using near-infrared spectroscopy, we intended to provide further evidence for the safety of apnoeic oxygenation and to increase our understanding of the association between cerebral perfusion, haemodynamic, respiratory and demographic factors. In this secondary analysis of a prospective randomized controlled noninferiority trial, we recruited 125 patients, who underwent surgery under general anaesthesia with neuromuscular blockade. Arterial blood samples were taken every 2 min for a total of 15 min under apnoeic oxygenation with 100% oxygen. Near-infrared spectroscopy and cardiac output were continuously measured. Statistical analysis was performed using uni- and multivariable statistics. Ninety-one complete data sets were analysed. In six patients the SpO2 fell below 92% (predefined study termination criterion). The significant average increase of cerebral oxygenation was 0.5%/min and 2.1 mmHg/min for the arterial pressure of carbon dioxide (paCO2). The median cardiac output increased significantly from 5.0 l/min (IQR 4.5-6.0) to 6.5 l/min (IQR 5.7-7.5). The most significant effect on cerebral oxygenation was exhibited by the variable paCO2 and non-specific patient factors, followed by cardiac output and paO2. Apnoeic oxygenation proves to have a high safety profile while significantly increasing cerebral oxygenation, paCO2 and cardiac output. In reverse, NIRS might act as a reliable clinical surrogate of paCO2 and cardiac output during stable arterial oxygenation.
Subject(s)
Carbon Dioxide , Respiration, Artificial , Humans , Cardiac Output , Oxygen , Prospective StudiesABSTRACT
The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.
Subject(s)
Diptera , Gammaproteobacteria , Animals , Humans , Gammaproteobacteria/genetics , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Diptera/microbiology , Genomics , LarvaABSTRACT
OBJECTIVES: Previous studies applying Sepsis-3 criteria to children were based on retrospective analyses of PICU cohorts. We aimed to compare organ dysfunction criteria in children with blood culture-proven sepsis, including emergency department, PICU, and ward patients, and to assess relevance of organ dysfunctions for mortality prediction. DESIGN: We have carried out a nonprespecified, secondary analysis of a prospective dataset collected from September 2011 to December 2015. SETTING: Emergency departments, wards, and PICUs in 10 tertiary children's hospitals in Switzerland. PATIENTS: Children younger than 17 years old with blood culture-proven sepsis. We excluded preterm infants and term infants younger than 7 days old. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: We compared the 2005 International Pediatric Sepsis Consensus Conference (IPSCC), Pediatric Logistic Organ Dysfunction-2 (PELOD-2), pediatric Sequential Organ Failure Assessment (pSOFA), and Pediatric Organ Dysfunction Information Update Mandate (PODIUM) scores, measured at blood culture sampling, to predict 30-day mortality. We analyzed 877 sepsis episodes in 807 children, with a 30-day mortality of 4.3%. Percentage with organ dysfunction ranged from 32.7% (IPSCC) to 55.3% (pSOFA). In adjusted analyses, the accuracy for identification of 30-day mortality was area under the curve (AUC) 0.87 (95% CI, 0.82-0.92) for IPSCC, 0.83 (0.76-0.89) for PELOD-2, 0.85 (0.78-0.92) for pSOFA, and 0.85 (0.78-0.91) for PODIUM. When restricting scores to neurologic, respiratory, and cardiovascular dysfunction, the adjusted AUC was 0.89 (0.84-0.94) for IPSCC, 0.85 (0.79-0.91) for PELOD-2, 0.87 (0.81-0.93) for pSOFA, and 0.88 (0.83-0.93) for PODIUM. CONCLUSIONS: IPSCC, PELOD-2, pSOFA, and PODIUM performed similarly to predict 30-day mortality. Simplified scores restricted to neurologic, respiratory, and cardiovascular dysfunction yielded comparable performance.
Subject(s)
Multiple Organ Failure , Sepsis , Infant , Child , Humans , Adolescent , Cohort Studies , Multiple Organ Failure/diagnosis , Multiple Organ Failure/etiology , Retrospective Studies , Prospective Studies , Blood Culture , Intensive Care Units, Pediatric , Organ Dysfunction Scores , Sepsis/diagnosis , Tertiary Care CentersABSTRACT
BACKGROUND: Rapid-sequence tracheotomy and scalpel-bougie tracheotomy are two published approaches for establishing emergency front-of-neck access in infants. It is unknown whether there is a difference in performance times and success rates between the two approaches. AIMS: The aim of this cross-over randomized control trial study was to investigate whether the two approaches were equivalent for establishing tracheal access in rabbit cadavers. The underlying hypothesis was that the time to achieve the tracheal access is the same with both techniques. METHODS: Between May and September 2022, thirty physicians (pediatric anesthesiologists and intensivists) were randomized to perform front-of-neck access using one and then the other technique: rapid-sequence tracheotomy and scalpel-bougie tracheotomy. After watching training videos, each technique was practiced four times followed by a final tracheotomy during which study measurements were obtained. Based on existing data, an equivalence margin was set at ∆ = ±10 s for the duration of the procedure. The primary outcome was defined as the duration until tracheal tube placement was achieved successfully. Secondary outcomes included success rate, structural injuries, and subjective participant self-evaluation. RESULTS: The median duration of the scalpel-bougie tracheotomy was 48 s (95% CI: 37-57), while the duration of the rapid-sequence tracheotomy was 59 s (95% CI: 49-66, p = .07). The difference in the median duration between the two approaches was 11 s (95% CI: -4.9 to 29). The overall success rate was 93.3% (95% CI: 83.8%-98.2%). The scalpel-bougie tracheotomy resulted in significantly fewer damaged tracheal rings and was preferred among participants. CONCLUSIONS: The scalpel-bougie tracheotomy was slightly faster than the rapid-sequence tracheotomy and favored by participants, with fewer tracheal injuries. Therefore, we propose the scalpel-bougie tracheostomy as a rescue approach favoring the similarity to the adult approach for small children. The use of a comparable equipment kit for both children and adults facilitates standardization, performance, and logistics. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT05499273.
Subject(s)
Airway Management , Tracheostomy , Animals , Humans , Infant , Rabbits , Airway Management/methods , Intubation, Intratracheal/methods , Neck , Tracheostomy/methods , Tracheotomy/methods , Cross-Over StudiesABSTRACT
The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.
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Gastrointestinal Microbiome , Microbiota , Humans , Male , Gastrointestinal Microbiome/genetics , Metagenome , Phylogeny , Prevotella , FemaleABSTRACT
The focus of this study was to investigate the sensitivity of different drug formulations to differences in process parameters based on previously developed scale-up strategies. Three different formulations were used for scale-up experiments from a QbCon® 1 with a screw diameter of 16 mm and a throughput of 2 kg/h to a QbCon® 25 line with a screw diameter of 25 mm and a throughput of 25 kg/h. Two of those formulations were similar in their composition of excipients but had a different API added to the blend to investigate the effect of solubility of the API during twin-screw wet granulation, while the third formulation was based on a controlled release formulation with different excipients and a high fraction of HPMC. The L/S-ratio had to be set specifically for each formulation as depending on the binder and the overall composition the blends varied significantly in their response to water addition and their overall granulation behavior. Before milling there were large differences in granule size distributions based on scale (Earth Mover's Distance 140-1100 µm, higher values indicating low similarity) for all formulations. However, no major differences in granule properties (e.g. Earth Mover's Distance for GSDs: 23-88 µm) or tablet tensile strength (> 1.8 MPa at a compaction pressure of 200 MPa for all formulations with a coefficient of variation < 0.1, indicating high robustness for all formulations) were observed after milling, which allowed for a successful scale-up independent of the selected formulations.
Subject(s)
Excipients , Technology, Pharmaceutical , Particle Size , Solubility , Tablets , Drug CompoundingABSTRACT
The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis 16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsia comprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsia diversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming.
Subject(s)
Fish Diseases , Piscirickettsia , Piscirickettsiaceae Infections , Animals , Humans , Piscirickettsia/genetics , Piscirickettsiaceae Infections/veterinary , Piscirickettsiaceae Infections/microbiology , RNA, Ribosomal, 16S/genetics , Fishes , Fish Diseases/microbiologyABSTRACT
16S rRNA sequence types associated with the candidate family env.OPS 17 have been reported from various environments, but no representatives have been characterized and validly named. Bacteria of env.OPS 17 are affiliated with the order Sphingobacteriales and were first detected more than two decades ago in the vicinity of a thermal spring in Yellowstone National Park. Strain Swamp196T, isolated from the soil surrounding a swamp in Northern Germany, is the first characterized representative of candidate family env.OPS 17. Cells of strain Swamp196T are rod-shaped, non-motile, non-spore-forming, non-capsulated and stain Gram-negative. Colonies are small and orange-coloured. The strain is mesophilic and grows under aerobic or microaerophilic conditions. It grows chemo-organotrophically over a narrow range of pH and exclusively on proteinaceous substrates. The major cellular fatty acids are iso-C15â:â0, iso-C15â:â1 ω10c, C18â:â1 ω9c and C16â:â1 ω7c and the major polar lipids are two unidentified aminophospholipids, one unidentified aminolipid and one unidentified lipid. The predominant respiratory quinone is MK-7. The DNA G+C content of genomic DNA is 35.5 mol%. Strain Swamp196T is related to Pedobacter cryophilus AR-3-17T, Arcticibacter pallidicorallinus Hh36T and Pedobacter daechungensis Dae 13T with 16S rRNA gene sequence similarity of 84.1, 83.8 and 83.5â%, respectively. Based on our phenotypic, genomic and phylogenetic analysis, we propose the novel species Aurantibacillus circumpalustris sp. nov (type strain Swamp196T=DSM 105849T=CECT 30420T) of the novel genus Aurantibacillus gen. nov. and the novel family Aurantibacillaceae fam. nov.
Subject(s)
Fatty Acids , Ubiquinone , Fatty Acids/chemistry , Phylogeny , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Sequence Analysis, DNA , Base Composition , Bacterial Typing Techniques , Ubiquinone/chemistry , Phospholipids/chemistryABSTRACT
Background: Obese patients frequently develop pulmonary atelectasis upon general anesthesia. The risk is increased during laparoscopic surgery. This prospective, observational single-center study evaluated atelectasis dynamics using Electric Impedance Tomography (EIT) in patients undergoing laparoscopic bariatric surgery. Methods: We included adult patients with ASA physical status I-IV and a BMI of ≥40. Exclusion criteria were known severe pulmonary hypertension, home oxygen therapy, heart failure, and recent pulmonary infections. The primary outcome was the proportion of poorly ventilated lung regions (low tidal variation areas) and the global inhomogeneity (GI) index assessed by EIT before discharge from the Post Anesthesia Care Unit compared to these same measures prior to initiation of anesthesia. Results: The median (IQR) proportion of low tidal variation areas at the different analysis points were T1 10.8% [3.6-15.1%] and T5 10.3% [2.6-18.9%], and the mean difference was -0.7% (95% CI: -5.8% -4.5%), i.e., lower than the predefined non-inferiority margin of 5% (p = 0.022). There were no changes at the four additional time points compared to T1 or postoperative pulmonary complications during the 14 days following the procedure. Conclusion: We found that obese patients undergoing laparoscopic bariatric surgery do not leave the Post Anesthesia Care Unit with increased low tidal variation areas compared to the preoperative period.
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Background: International Classification of Diseases 10th edition (ICD-10) is widely used to describe the burden of disease. Aim: To describe how well ICD-10 coding captures sepsis in children admitted to the hospital with blood culture-proven bacterial or fungal infection and systemic inflammatory response syndrome. Methods: Secondary analysis of a population-based, multicenter, prospective cohort study on children with blood culture-proven sepsis of nine tertiary pediatric hospitals in Switzerland. We compared the agreement of validated study data on sepsis criteria with ICD-10 coding abstraction obtained at the participating hospitals. Results: We analyzed 998 hospital admissions of children with blood culture-proven sepsis. The sensitivity of ICD-10 coding abstraction was 60% (95%-CI 57-63) for sepsis; 35% (95%-CI 31-39) for sepsis with organ dysfunction, using an explicit abstraction strategy; and 65% (95%-CI 61-69) using an implicit abstraction strategy. For septic shock, the sensitivity of ICD-10 coding abstraction was 43% (95%-CI 37-50). Agreement of ICD-10 coding abstraction with validated study data varied by the underlying infection type and disease severity (p < 0.05). The estimated national incidence of sepsis, inferred from ICD-10 coding abstraction, was 12.5 per 100,000 children (95%-CI 11.7-13.5) and 21.0 per 100,000 children (95%-CI 19.8-22.2) using validated study data. Conclusions: In this population-based study, we found a poor representation of sepsis and sepsis with organ dysfunction by ICD-10 coding abstraction in children with blood culture-proven sepsis when compared against a prospective validated research dataset. Sepsis estimates in children based on ICD-10 coding may thus severely underestimate the true prevalence of the disease. Supplementary Information: The online version contains supplementary material available at 10.1007/s44253-023-00006-1.
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The aim of this study was to compare different scale-up strategies in twin-screw wet granulation and investigate the impact of the selected strategy on granule and tablet properties for a defined formulation. For the scale-up, a granulation process was transferred from a QbCon® 1 with a screw diameter of 16 mm to a QbCon® 25 line with a screw diameter of 25 mm. Three different scale-up strategies were introduced based on differences in process parameters and their resulting effects on various aspects. such as the powder feed number as a surrogate for the barrel fill level or the circumferential speed. Both are highly dependent on screw diameter and screw speed (SS), while the barrel fill level also depends on the overall throughput. Granules produced on the larger scale were significantly larger due to the larger gap size in the granulator, however, these differences were eliminated after milling. Despite major differences in powder feed number, circumferential speed, overall throughput and SS, product properties for both tablets and granules were strikingly similar after milling on both scales and with all applied strategies. For the selected formulation the effect of varying liquid to solid ratio at the same scale was much higher than the differences between scale-up strategies. The results of this study are promising for future process scale-up from lab scale to production scale in twin-screw wet granulation, as they are indicating towards a robust granulation process leading to similar tablet properties afterwards.
Subject(s)
Bone Screws , Technology, Pharmaceutical , Powders , Particle Size , Temperature , Tablets , Drug Compounding/methods , Technology, Pharmaceutical/methodsABSTRACT
In recent years, Arcobacter butzleri has gained clinical significance as an emerging diarrheagenic pathogen associated with poultry and water reservoirs. The full clinical significance of Arcobacter remains rather speculative due to variable virulence and antibiotic susceptibility of individual strains. The aims of the present study were (i) to identify antibiotic resistance genes (ARGs) in the genome sequences of two multidrug-resistant A. butzleri isolates, (ii) to use multilocus-sequence typing (MLST) to generate a guiding phylogeny of A. butzleri isolates collected in Kumasi, Ghana, (iii) to examine the distribution of ARGs in the test cohort, and (iv) to assess the strain's virulence and possible antibiotic treatment options for arcobacteriosis based on the genome sequences and the ARG distribution. A total of 48 A. butzleri isolates obtained from poultry were included in the analysis. These isolates were genotyped by MLST and the antibiotic susceptibilities of isolates to ampicillin, ciprofloxacin, tetracycline, gentamicin, and erythromycin were tested by disk diffusion. Whole genome sequence data of two multidrug-resistant (MDR) A. butzleri isolates were obtained by a combination of single-molecule real-time (SMRT) and Illumina sequencing technology. A total of 14 ARGs were identified in the two generated genome sequences. For all 48 isolates, the frequency of these 14 ARGs was investigated by PCR or amplicon sequencing. With 44 different sequence types found among 48 isolates, strains were phylogenetically heterogeneous. Four of 48 isolates showed an ARG constellation indicating a multidrug-resistant phenotype. The virulence genes in the two A. butzleri genomes showed that the species might be characterized by a somewhat lower virulence as Campylobacter species. The phenotypic susceptibility data combined with the distribution of the particular ARGs especially oxa-464 and the T81I point mutation of the quinolone resistance determining region (QRDR) in a significant percentage of isolates indicated that macrolides and tetracycline can be recommended for calculated antibiotic treatment of arcobacteriosis in Ghana, but not ampicillin and quinolones.
Subject(s)
Arcobacter , Gram-Negative Bacterial Infections , Animals , Poultry , Arcobacter/genetics , Multilocus Sequence Typing , Ghana , Anti-Bacterial Agents/pharmacology , Tetracycline/pharmacologyABSTRACT
OBJECTIVE: Acute and hard-to-heal wounds are a significant burden to both a patient's quality of life and resources in healthcare systems. Here, we evaluate the outcomes of a non-comparative case series study in which Ringer's solution-preactivated polyacrylate dressings were used to treat acute and hard-to-heal wounds (the presence of Ringer's solution provides a wound dressing that allows, upon application, the immediate hydration of the underlying wound tissue). METHOD: Patients with acute and hard-to-heal wounds were enrolled into an open-labelled, non-comparative observational study. Patients were treated with Ringer's solution-preactivated polyacrylate dressings to enable wound debridement and wound cleansing for up to 12 weeks. RESULTS: A total of 303 patients were enrolled in the study and 278 were included in the analysis. Wound size decreased, from a median of 3.6cm2 (interquartile range (IQR): 1.2-9.3] at baseline to a median of 2.6cm2 (IQR: 1.1-7.8] at 84 days. Relative wound area reduction (WAR) was 43.1% at 84 days and estimated probability of achievement of a WAR of ≥40% and ≥60% was 68.7% and 53.4%, respectively. Median time to achieve a WAR of ≥40% and ≥60% was 54 days and 75 days, respectively. The median percentage of wound area covered by fibrin had decreased from 50.0% to 10% and granulation tissue had increased from 25% to 50% after 84 days. In addition, periwound skin condition, local signs of infection and pain all showed improvement. The majority of the wounds were assessed as 'healed' or 'better' at the conclusion of the evaluation period. CONCLUSION: Based on the findings of this study, the use of Ringer's solution-preactivated polyacrylate dressings in daily practice has the potential to improve clinical outcomes, including healing, in patients with acute and hard-to-heal wounds.
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Quality of Life , Humans , Ringer's SolutionABSTRACT
The NeuMoDx96 platform is a fully automated real-time PCR (RT-PCR) system. To provide continued testing quality with the introduction of new assays, the primary aim of this study was to evaluate the analytical and clinical performance of the NeuMoDx platform for the detection and quantification of CMV and EBV DNA in EDTA plasma. As no conversion from log10 international units per milliliter to copies per milliliter was provided, the secondary aim was to calculate and establish a conversion factor for the output of results in copies per milliliter for CMV and EBV. Archived ETDA plasma samples (cytomegalovirus [CMV], n = 290; Ebstein-Barr virus [EBV], n = 254) were used to evaluate the analytical performance of the NeuMoDx96 platform against the routine real-time quantitative PCR (qPCR) assays. Additionally, the first WHO international standards (WHO-IS) for CMV (n = 70) and EBV (n = 72) were used for the calculation of the intra- and interassay variation. WHO-IS qualitative agreement between the assays was 100%. Intra-assay variability was low for both CMV assays (coefficient of variation [CV], phosphate-buffered saline [PBS], 3 log10 IU/mL NeuMoDx, 3.67%; Abbott RealTime, CMV, 3.35%) and NeuMoDx EBV assay (CV, PBS, 3 log10 IU/mL, 3.05%) but high for the Altona EBV assay (CV, PBS, 3 log10 IU/mL, 26.13%). The overall qualitative concordance in clinical samples was 96.8% (270/279) for CMV and 96.7% (237/245) for EBV. The mean difference between the assays was -0.2 log10 IU/mL (CMV) and -0.18 log10 IU/mL (EBV). High qualitative concordance and a significant correlation of quantitative values for both assays make NeuMoDx CMV and EBV assays suitable for routine diagnostic testing. The new RT-PCR system and conversion formulas to report results in copies per milliliter are now applied in clinical routine testing. IMPORTANCE Clinical management of solid organ transplant (SOT) patients requires the careful monitoring of immunosuppression and viral infection or reactivation. qPCR is the gold standard for the detection and quantification of very small amounts of viral DNA and allows for an early assessment of viral load kinetics. The tested NeuMoDx 96 platform provides faster results than the previously used RT-PCR workflows for CMV (Abbott m2000 and RealTime CMV assay) and EBV (LightCycler 480 II, Roche high pure extraction, and Altona RealStar EBV assay) DNA detection. The implemented conversion formulas allow the continued reporting in clinically established copies per milliliter, important for long-term care of SOT patients.
Subject(s)
Cytomegalovirus Infections , Cytomegalovirus , Humans , Cytomegalovirus/genetics , Real-Time Polymerase Chain Reaction/methods , Herpesvirus 4, Human/genetics , Edetic Acid , DNA, Viral , Reverse Transcriptase Polymerase Chain Reaction , Cytomegalovirus Infections/diagnosis , Viral Load/methodsABSTRACT
Microbiome research needs comprehensive repositories of cultured bacteria from the intestine of mammalian hosts. We expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to 212 strains, all publicly available and taxonomically described. This includes strain-level diversity, small-sized bacteria, and previously undescribed taxa (one family, 10 genera, and 39 species). This collection enabled metagenome-educated prediction of synthetic communities (SYNs) that capture key functional differences between microbiomes, notably identifying communities associated with either resistance or susceptibility to DSS-induced colitis. Additionally, nine species were used to amend the Oligo-Mouse Microbiota (OMM)12 model, yielding the OMM19.1 model. The added strains compensated for phenotype differences between OMM12 and specific pathogen-free mice, including body composition and immune cells in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available for future studies. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates.
Subject(s)
Gastrointestinal Microbiome , Microbiota , Mice , Animals , Gastrointestinal Microbiome/genetics , Bacteria , Metagenome , Intestines , Disease Models, Animal , Mammals/geneticsABSTRACT
BACKGROUND: Previous studies concerning humidified, heated high-flow nasal oxygen delivered in spontaneously breathing patients postulated an increase in functional residual capacity as one of its physiological effects. It is unclear wheter this is also true for patients under general anesthesia. METHODOLOGY: The sincle-center noninferiority trial was registered at ClinicalTrials.gov (NCT NCT03478774). This secondary outcome analysis shows estimated differences in lung volume changes using electrical impedance tomography between different flow rates of 100% oxygen in apneic, anesthetized and paralyzed adults prior to intubation. One hundred and twenty five patients were randomized to five groups with different flow rates of 100% oxygen: i) minimal-flow: 0.25 l.min-1 via endotracheal tube; ii) low-flow: 2 l.min-1 + continuous jaw thrust; iii) medium-flow: 10 l.min-1 + continuous jaw thrust; iv) high-flow: 70l.min-1 + continuous jaw thrust; and v) control: 70 l.min-1 + continuous video-laryngoscopy. After standardized anesthesia induction with non-depolarizing neuromuscular blockade, the 15-minute apnea period and oxygen delivery was started according to the randomized flow rate. Continuous electrical impedance tomography measurements were performed during the 15-minute apnea period. Total change in lung impedance (an estimate of changes in lung volume) over the 15-minute apnea period and times to 25%, 50% and 75% of total impedance change were calculated. RESULTS: One hundred and twenty five patients completed the original study. Six patients did not complete the 15-minute apnea period. Due to maloperation, malfunction and artefacts additional 54 measurements had to be excluded, resulting in 65 patients included into this secondary outcome analysis. We found no differences between groups with respect to decrease in lung impedance or curve progression over the observation period. CONCLUSIONS: Different flow rates of humidified 100% oxygen during apnea result in comparable decreases in lung volumes. The demonstrated increase in functional residual capacity during spontaneous breathing with high-flow nasal oxygenation could not be replicated during apnea under general anesthesia with neuromuscular blockade.