Following the COVID-19 infection, the sternum dislocation and wound dehiscence resulted in an infection complicating the recovery of an immunosuppressed patient after bilateral lung transplantation. Anaerobic culture (96 h) of milky cloudy wound secretion resulted in the growth of pinpoint haemolytic colonies identified as Metamycoplasma hominis (formerly Mycoplasma hominis). The search for the endogenous source of the infection found the bacterium exclusively in the patient's sputum, making a possible link to donor lung M. hominis colonization. Unfortunately, the donor samples were no longer available. The wound infection was successfully treated with 17 days of clindamycin despite the continuous PCR detection of M. hominis in the sputum after the end of the treatment.
- MeSH
- antibakteriální látky terapeutické užití MeSH
- COVID-19 diagnóza MeSH
- hostitel s imunodeficiencí MeSH
- infekce chirurgické rány * mikrobiologie farmakoterapie diagnóza MeSH
- klindamycin terapeutické užití MeSH
- lidé středního věku MeSH
- lidé MeSH
- Mycoplasma hominis * genetika izolace a purifikace MeSH
- mykoplazmové infekce * mikrobiologie diagnóza farmakoterapie MeSH
- SARS-CoV-2 genetika izolace a purifikace MeSH
- sputum mikrobiologie MeSH
- transplantace plic * škodlivé účinky MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
BACKGROUND AND AIMS: Treatment with anti-tumour necrosis factor α antibodies [anti-TNF] changes the dysbiotic faecal bacteriome in Crohn's disease [CD]. However, it is not known whether these changes are due to decreasing mucosal inflammatory activity or whether similar bacteriome reactions might be observed in gut-healthy subjects. Therefore, we explored changes in the faecal bacteriome and metabolome upon anti-TNF administration [and therapeutic response] in children with CD and contrasted those to anti-TNF-treated children with juvenile idiopathic arthritis [JIA]. METHODS: Faecal samples collected longitudinally before and during anti-TNF therapy were analysed with regard to the bacteriome by massively parallel sequencing of the 16S rDNA [V4 region] and the faecal metabolome by 1H nuclear magnetic resonance imaging. The response to treatment by mucosal healing was assessed by the MINI index at 3 months after the treatment started. We also tested several representative gut bacterial strains for in vitro growth inhibition by infliximab. RESULTS: We analysed 530 stool samples from 121 children [CD 54, JIA 18, healthy 49]. Bacterial community composition changed on anti-TNF in CD: three members of the class Clostridia increased on anti-TNF, whereas the class Bacteroidia decreased. Among faecal metabolites, glucose and glycerol increased, whereas isoleucine and uracil decreased. Some of these changes differed by treatment response [mucosal healing] after anti-TNF. No significant changes in the bacteriome or metabolome were noted upon anti-TNF in JIA. Bacterial growth was not affected by infliximab in a disc diffusion test. CONCLUSIONS: Our findings suggest that gut mucosal healing is responsible for the bacteriome and metabolome changes observed in CD, rather than any general effect of anti-TNF.
- MeSH
- Bacteria MeSH
- Crohnova nemoc * patologie MeSH
- dítě MeSH
- infliximab farmakologie terapeutické užití MeSH
- inhibitory TNF farmakologie terapeutické užití MeSH
- lidé MeSH
- metabolom MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2 positively affect the fecal bacteriome in children with celiac disease autoimmunity after 6 months of supplementation. The aim of the present investigation was to study the effects of Lactiplantibacillus plantarum HEAL9 and Lacticaseibacillus paracasei 8700:2 on the single-cell parasitome, with a primary focus on Blastocystis. METHODS: Stool samples were collected from 78 Swedish children with celiac disease autoimmunity participating in a randomized, double-blind, placebo-controlled clinical trial to either receive a mixture of supplementation with L. plantarum HEAL9 and L. paracasei 8700:2 (n = 38) or placebo (n = 40). A total of 227 stool samples collected at baseline and after 3 and 6 months of intervention, respectively, were retrospectively analyzed for Blastocystis by quantitative real-time PCR and subtyped by massively parallel amplicon sequencing. Other single-cell parasites were detected by untargeted 18S rDNA amplicon sequencing and verified by real-time PCR. The relation between the parasites and the bacteriome community was characterized by using 16S rDNA profiling of the V3-V4 region. RESULTS: Three different single-cell protists were identified, of which the highest prevalence was found for Dientamoeba fragilis (23.1%, 18/78 children), followed by Blastocystis (15.4%, 12/78) and Entamoeba spp. (2.6%, 2/78). The quantity of the protists was stable over time and not affected by probiotic intervention (P = 0.14 for Blastocystis, P = 0.10 for D. fragilis). The positivity of the protists was associated with increased bacteriome diversity (measured by multiple indices, P < 0.03). Bacterial composition was influenced by the presence of the protists: positivity of Blastocystis was inversely associated with Akkermansia (at the levels of the genus as well as its family, order, class and phylum); P < 0.002), Faecalibacterium (P = 0.003) and Romboutsia (P = 0.029); positivity of D. fragilis was inversely associated with families Enterobacteriaceae (P = 0.016) and Coriobacteriaceae (P = 0.022) and genera Flavonifractor (P < 0.001), Faecalibacterium (P = 0.009), Lachnoclostridium (P = 0.029), Ruminococcus (P < 0.001) and Granulicatella (P = 0.018). CONCLUSIONS: The prevalence of single-cell protists is low in children with celiac disease autoimmunity. The colonization was stable regardless of the probiotic intervention and associated with increased diversity of the fecal bacteriome but inversely associated with some beneficial bacteria.
- MeSH
- autoimunita MeSH
- Bacteria MeSH
- Blastocystis * genetika MeSH
- celiakie * MeSH
- dítě MeSH
- dvojitá slepá metoda MeSH
- feces parazitologie MeSH
- Lacticaseibacillus MeSH
- Lactobacillus paracasei * MeSH
- lidé MeSH
- probiotika * terapeutické užití farmakologie MeSH
- retrospektivní studie MeSH
- ribozomální DNA MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- randomizované kontrolované studie MeSH
OBJECTIVES: Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) is a widely used method for bacterial species identification. Incomplete databases and mass spectral quality (MSQ) still represent major challenges. Important proxies for MSQ are the number of detected marker masses, reproducibility, and measurement precision. We aimed to assess MSQs across diagnostic laboratories and the potential of simple workflow adaptations to improve it. METHODS: For baseline MSQ assessment, 47 diverse bacterial strains, which are challenging to identify by MALDI-TOF MS, were routinely measured in 36 laboratories from 12 countries, and well-defined MSQ features were used. After an intervention consisting of detailed reported feedback and instructions on how to acquire MALDI-TOF mass spectra, measurements were repeated and MSQs were compared. RESULTS: At baseline, we observed heterogeneous MSQ between the devices, considering the median number of marker masses detected (range = [2-25]), reproducibility between technical replicates (range = [55%-86%]), and measurement error (range = [147 parts per million (ppm)-588 ppm]). As a general trend, the spectral quality was improved after the intervention for devices, which yielded low MSQs in the baseline assessment as follows: for four out of five devices with a high measurement error, the measurement precision was improved (p-values <0.001, paired Wilcoxon test); for six out of ten devices, which detected a low number of marker masses, the number of detected marker masses increased (p-values <0.001, paired Wilcoxon test). DISCUSSION: We have identified simple workflow adaptations, which, to some extent, improve MSQ of poorly performing devices and should be considered by laboratories yielding a low MSQ. Improving MALDI-TOF MSQ in routine diagnostics is essential for increasing the resolution of bacterial identification by MALDI-TOF MS, which is dependent on the reproducible detection of marker masses. The heterogeneity identified in this external quality assessment (EQA) requires further study.
INTRODUCTION: Several studies have demonstrated dysbiosis in irritable bowel syndrome (IBS). Therefore, faecal microbiota transplantation, whose effect and safety have been proven in Clostridioides difficile infections, may hold promise in other conditions, including IBS. Our study will examine the effectiveness of stool transfer with artificially increased microbial diversity in IBS treatment. METHODS AND ANALYSIS: A three-group, double-blind,randomised, cross-over, placebo-controlled study of two pairs of gut microbiota transfer will be conducted in 99 patients with diarrhoeal or mixed type of IBS. Patients aged 18-65 will be randomised into three equally sized groups: group A will first receive two enemas of study microbiota mixture (deep-frozen stored stool microbiota mixed from eight healthy donors); after 8 weeks, they will receive two enemas with placebo (autoclaved microbiota mixture), whereas group B will first receive placebo, then microbiota mixture. Finally, group C will receive placebos only. The IBS Severity Symptom Score (IBS-SSS) questionnaires will be collected at baseline and then at weeks 3, 5, 8, 11, 13, 32. Faecal bacteriome will be profiled before and regularly after interventions using 16S rDNA next-generation sequencing. Food records, dietary questionnaires, anthropometry, bioimpedance, biochemistry and haematology workup will be obtained at study visits during the follow-up period. The primary outcome is the change in the IBS-SSS between the baseline and 4 weeks after the intervention for each patient compared with placebo. Secondary outcomes are IBS-SSS at 2 weeks after the intervention and 32 weeks compared with placebo and changes in the number of loose stools, Bristol stool scale, abdominal pain and bloating, anthropometric parameters, psychological evaluation and the gut microbiome composition. ETHICS AND DISSEMINATION: The study was approved by the Ethics Committee of Thomayer University Hospital, Czechia (G-18-26); study results will be published in peer-reviewed journals and presented at international conferences and patient group meetings. TRIAL REGISTRATION NUMBER: NCT04899869.
- MeSH
- dysbióza terapie MeSH
- fekální transplantace metody MeSH
- klinické křížové studie MeSH
- lidé MeSH
- mikrobiota * MeSH
- průjem terapie MeSH
- randomizované kontrolované studie jako téma MeSH
- syndrom dráždivého tračníku * terapie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- protokol klinické studie MeSH
- MeSH
- Blastocystis * genetika MeSH
- Dientamoeba genetika MeSH
- feces MeSH
- lidé MeSH
- syndrom dráždivého tračníku * MeSH
- zmrazování MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- dopisy MeSH
3. vydání xiii, 637 stran : ilustrace, tabulky ; 24 cm
Vysokoškolská učebnice, která se zaměřuje na lékařskou mikrobiologii, zejména na diagnostiku.
- Konspekt
- Učební osnovy. Vyučovací předměty. Učebnice
- Mikrobiologie
- NLK Obory
- mikrobiologie, lékařská mikrobiologie
- NLK Publikační typ
- kolektivní monografie
- učebnice vysokých škol
Cíl: Test, založený na detekci antigenu SARS-CoV-2, je v souvislosti s potřebou screeningu větších skupin obyvatelstva často chápán jako alternativa k metodě PCR. Aby bylo možné posoudit vhodnost takového přístupu, hodnotili jsme senzitivitu dvou antigenních testů na skupině jedinců, zahrnujících jak pacienty s příznaky onemocnění covid-19, tak asymptomatické a zdravé osoby. Metody: Výtěry z nosohltanu jsme vyšetřili pomocí antigenního testu č. 1 (Panbio Covid-19 Ag Rapid Test, Abbott) a antigenního testu č. 2 (Standard F Covid-19 Ag FIA, SD Biosensor). Druhý výtěr z nosohltanu, doplněný o výtěr z orofaryngu od téže osoby jsme zkontrolovali metodou PCR (Allplex SARS-nCoV-2, Seegene). Celkem jsme během 4 dní v říjnu 2020 nasbírali vzorky od 591 jedinců, z nichž 290 mělo symptomy spojené s nemocí covid-19. Výsledky: Pozitivita metodou PCR byla zaznamenána ve 223 případech. Antigenní test č. 1 odhalil 148 pozitivních vzorků (senzitivita 0,664, 95% CI 0,599; 0,722), antigenní test č. 2 zachytil 141 pozitivit (senzitivita 0,623, 95% CI 0,558; 0,684). Senzitivita vyšetření se zvýšila u antigenního testu č. 1 na 0,738 (95 % CI 0,667; 0,799) a u antigenního testu č. 2 na 0,685 (95% CI 0,611, 0,750), pokud byli do analýzy zařazeni pouze symptomatičtí jedinci. Výrazný pokles v citlivosti na 12,9 % (95% CI 0,067; 0,234) jsme pozorovali u vzorků, jejichž prahový cyklus PCR se pohyboval nad hodnotou 30. Závěry: Nízká citlivost antigenních testů přináší významné riziko falešně negativních nálezů. Z tohoto důvodu doporučujeme v případě použití antigenního testu coby screeningového nástroje zavést testování v režimu opakování s dostatečně častou frekvencí. Testování zranitelných skupin obyvatelstva by mělo být doplňováno metodou PCR.
Objectives: Antigen tests have emerged as an alternative to SARS-CoV-2 diagnostic PCR, thought to be valuable especially for the screening of bigger communities. To check appropriateness of the antigen based testing, we determined sensitivity of two point-of-care antigen tests when applied to a cohort of COVID-19 symptomatic, COVID-19 asymptomatic and healthy persons. Methods: We examined nasopharyngeal swabs with antigen test 1 (Panbio Covid-19 Ag Rapid Test, Abbott) and antigen test 2 (Standard F Covid-19 Ag FIA, SD Biosensor). An additional nasopharyngeal and oropharyngeal swab of the same individual was checked with PCR (Allplex SARS-nCoV-2, Seegene). Within a 4-day period in October 2020, we collected specimens from 591 subjects. Of them, 290 had COVID-19 associated symptoms. Results: While PCR positivity was detected in 223 cases, antigen test 1 and antigen test 2 were found positive in 148 (sensitivity 0.664, 95%CI 0.599, 0.722) and 141 (sensitivity 0.623, 95%CI 0.558, 0.684) patients, respectively. When only symptomatic patients were analysed, sensitivity increased to 0.738 (95%CI 0.667, 0.799) for the antigen test 1 and to 0.685 (95%CI 0.611, 0.750) for the antigen test 2. The substantial drop in sensitivity to 12.9% (95%CI 0.067, 0.234) was observed for samples with the PCR threshold cycle above > 30. Conclusions: Low sensitivity of antigen tests leads to the considerable risk of false negativity. It is advisable to implement repeated testing with high enough frequency if the antigen test is used as a frontline screening tool, and to follow with PCR if it is applied to vulnerable populations.
2. vydání xii, 622 stran : ilustrace, tabulky ; 24 cm
Vysokoškolská učebnice, která se zaměřuje na lékařskou mikrobiologii.
- Konspekt
- Mikrobiologie
- Učební osnovy. Vyučovací předměty. Učebnice
- NLK Obory
- mikrobiologie, lékařská mikrobiologie
- NLK Publikační typ
- kolektivní monografie
- učebnice vysokých škol
In the microbiological diagnosis of bloodstream infections (BSI), blood culture (BC) is considered the gold standard test despite its limitations such as low sensitivity and slow turnaround time. A new FDA-cleared and CE-marked platform utilizing magnetic resonance to detect amplified DNA of the six most common and/or problematic BSI pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli; referred to as ESKAPEc) is available and may shorten the time to diagnosis and potentially improve antimicrobial utilization. Whole blood samples from hospitalized patients with clinical signs of sepsis were analyzed using the T2Bacteria Panel (T2Biosystems) and compared to simultaneously collected BC. Discrepant results were evaluated based on clinical infection criteria, combining supporting culture results and the opinion of treating physicians. A total of 55 samples from 53 patients were evaluated. The sensitivity and specificity of the T2Bacteria panel was 94% (16 out of 17 detections of T2Bacteria-targeted organisms) and 100%, respectively, with 36.4% (8 of 22) causes of BSI detected only by this method. The T2Bacteria Panel detected pathogens on average 55 hours faster than standard BC. In our study, 9 of 15 patients with positive T2Bacteria Panel results received early-targeted antibiotic therapy and/or modification of antimicrobial treatment based on T2Bacteria Panel findings. Given the high reliability, faster time to detection, and easy workflow, the technique qualifies as a point-of-care testing approach.
- MeSH
- Acinetobacter baumannii účinky léků genetika izolace a purifikace MeSH
- antibakteriální látky farmakologie MeSH
- antibiotická politika metody MeSH
- bakteriemie krev farmakoterapie mikrobiologie MeSH
- Enterococcus faecium účinky léků genetika izolace a purifikace MeSH
- Escherichia coli účinky léků genetika izolace a purifikace MeSH
- Klebsiella pneumoniae účinky léků genetika izolace a purifikace MeSH
- krev mikrobiologie MeSH
- kultivační vyšetření krve MeSH
- lidé MeSH
- prospektivní studie MeSH
- Pseudomonas aeruginosa účinky léků genetika izolace a purifikace MeSH
- Staphylococcus aureus účinky léků genetika izolace a purifikace MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
