Background Pandemic COVID-19 caused by the coronavirus SARS-CoV-2 has a high incidence of patients with severe acute respiratory syndrome (SARS). Many of these patients require admission to an intensive care unit (ICU) for invasive artificial ventilation and are at significant risk of developing a secondary, ventilator-associated pneumonia (VAP). Objectives To study the incidence of VAP, as well as differences in secondary infections, and bacterial lung microbiome composition of ventilated COVID-19 and non-COVID-19 patients. Methods In this prospective observational study, we compared the incidence of VAP and secondary infections using a combination of a TaqMan multi-pathogen array and microbial culture. In addition, we determined the lung microbime composition using 16S RNA analyisis. The study involved eighteen COVID-19 and seven non-COVID-19 patients receiving invasive ventilation in three ICUs located in a single University teaching hospital between April 13th 2020 and May 7th 2020. Results We observed a higher percentage of confirmed VAP in COVID-19 patients. However, there was no statistical difference in the detected organisms or pulmonary microbiome when compared to non-COVID-19 patients. Conclusion COVID-19 makes people more susceptible to developing VAP, partly but not entirely due to the increased duration of ventilation. The pulmonary dysbiosis caused by COVID-19, and the array of secondary infections observed are similar to that seen in critically ill patients ventilated for other reasons.
Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children in low- and middle-income countries. However, these bacteria are often identified in both patients and healthy controls.
BackgroundEscherichia coli (ETEC) are one of the top causes of diarrhoea in children in low- and middle-income countries (LMICs). However, large-scale pathogen burden studies in children have identified ETEC in the guts of symptomatic patients and controls. The factors that influence this balance between carriage and disease are poorly understood, but it is postulated that the gut microbiome may play a role in either resistance or progression to disease. In this study, we investigated the microbiome profiles, using shotgun DNA sequencing, of children and adults from Bangladesh who were asymptomatically or symptomatically infected with ETEC. ResultsSymptomatic patients had significantly higher numbers of sequenced reads mapping to both E. coli and the two ETEC toxins (LT and ST), suggesting higher bacterial burden. They were also significantly more likely to be co-infected with enteroaggregative E. coli (EAEC) and had higher proportions of other Gammaproteobacteria, including Klebsiella, Salmonella, and Haemophilus. Colonisation with ETEC (symptomatic or asymptomatic) was also associated with increased prevalence of antimicrobial resistance (AMR) genes, most notably those of the b-lactamase class. Taxonomic profiles were distinctly different between all groups in both species richness (alpha diversity) and composition (beta diversity), although the direction of these changes was different in adults and children. As seen in previous studies, children with high E. coli burdens also had higher proportions of Streptococcus spp., while healthy children were more heavily colonised by several Bifidobacterium spp. ConclusionsOur study provides insight into the microbiome changes that occur upon infection with ETEC in an endemic setting, and provides rationale for future studies investigating how the microbiome may protect or predispose individuals to symptomatic infections with gastrointestinal pathogens.
Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.
Background and Aims Cardiovascular (CV) disease remains the leading cause of death in peritoneal dialysis (PD) patients and traditional CV risk factors are unable to fully account for this high incidence. The aim of our study was to establish the incidence of CV events such as acute myocardial infarction (AMI) in the PD population and assess possible risk factors for its occurrence. Method We retrospectively studied patients on PD in our unit with a minimum 3-years dialysis vintage, between January 1st 2015 and April 30th 2022. Patients with previous CV disease were excluded. Demographic and clinical data were collected, such as traditional CV risk factors, AMI, peripheral artery disease, cerebrovascular events, as well as dialysis efficiency, hydration status obtained by Body Composition Monitor (Fresenius Medical Care) and PD-related infections before AMI or end of follow-up. Univariate analysis was performed and logistic regression was applied to access predictors of AMI. Results Of the 43 patients recruited, 53.5% were male, with a mean age of 56.4 ± 11.8 years. About 98% of patients were hypertensive, 21% were diabetic, 19% were obese, and 54% had dyslipidemia. Five (11.6%) patients had a CV event while on PD, 4 suffered AMI and 1 patient had an ischemic stroke. Patients’ characteristics are presented in Table 1. In the follow-up, peripheral arterial disease (p = 0.037), hyperphosphatemia (p = 0.035) and the cumulative number of peritonitis (p = 0.018) were associated with the occurrence of AMI. In our population we found a higher frequency of peritonitis in the year prior to the AMI (p = 0.024). In logistic regression, the cumulative number of peritonitis was a predictor of AMI (OR 4.918, CI 95%:1.093-22.132). In the mean follow-up time of 4.7 ± 1.4 years, the overall mortality was 21,7%, with CV disease accounting for 60% of the observed deaths. AMI and peritonitis were associated with higher mortality in PD patients (p = 0.016 and p = 0.009, respectively). Conclusion PD-related peritonitis was a predictor of AMI in these population. The risk is higher in the year following a peritonitis episode. This may be due to a chronic inflammatory state that persists after successful treatment of peritonitis which may predispose to enhanced CV risk. Similar to previous studies, we found that cumulative episodes of peritonitis were associated with increased mortality in PD population.
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