Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia
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Abstract
Here, we describe the case of a COVID-19 patient who developed recurring ventilator-associated pneumonia caused by Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis revealed the AMR genotype, while immunological analysis revealed massive and escalating levels of T-cell activation. These were both SARS-CoV-2 and P. aeruginosa specific, and bystander activated, which may have contributed to this patient’s persistent symptoms and radiological changes.
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SciScore for 10.1101/2020.09.17.20190033: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Blood/serum samples from pre-pandemic healthy controls and asymptomatic healthy controls were obtained under the Bristol Biobank (NHS Research Ethics Committee approval ref 14/WA/1253). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources SNP differences between the P. aeruginosa contigs for ETT-1 and ETT-3 was determined using Mauve24. P . aeruginosasuggested: NoneSoftware and Algorithms Sentences Resources Sequencing was performed on a PromethION R9.4.1 flow cell (FLO-PRO002) and run for 48 hours using live basecalling, … SciScore for 10.1101/2020.09.17.20190033: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: Blood/serum samples from pre-pandemic healthy controls and asymptomatic healthy controls were obtained under the Bristol Biobank (NHS Research Ethics Committee approval ref 14/WA/1253). Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources SNP differences between the P. aeruginosa contigs for ETT-1 and ETT-3 was determined using Mauve24. P . aeruginosasuggested: NoneSoftware and Algorithms Sentences Resources Sequencing was performed on a PromethION R9.4.1 flow cell (FLO-PRO002) and run for 48 hours using live basecalling, files were outputted in Fast5 and Fastq format. PromethIONsuggested: (PromethION, RRID:SCR_017987)Contigs were assigned to a taxon by Kraken 223. Krakensuggested: (Kraken, RRID:SCR_005484)Cells were acquired on a BD Fortessa X20 and data analyzed using FlowJo software v10.7. FlowJosuggested: (FlowJo, RRID:SCR_008520)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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