key: cord-0813314-h8k0vjbd authors: Massey, R. title: Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia. date: 2020-09-22 journal: nan DOI: 10.1101/2020.09.17.20190033 sha: 5e12aaa1b1c410f34d16a17e75ba87b2016e07ac doc_id: 813314 cord_uid: h8k0vjbd The COVID-19 pandemic has brought with it the largest ever cohort of patients requiring mechanical ventilation. Here we describe such a patient who developed a recurring ventilator-associated pneumonia caused by a strain of Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis recovered whole genomes of the bacterium directly from samples, revealing the AMR genotype. While immunological analysis of longitudinally-collected blood samples revealed escalating levels of T-cell activation targeting both bacteria and virus, with evidence of bystander-activation, a feature which may have contributed to the continuing inflammation and prolonged requirement for ventilation. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The three x-rays taken during the patient's time in the ICU are presented, as is a later follow-up x-ray taken in an out-patient (OP) clinic three weeks after discharge. The time during which the antibiotics piperacillin and tazobactam (pip/taz) and meropenem were administered to the patient to treat the VAP are indicated in blue. The points at which endotracheal tube aspirates (ETT) were collected and the subsequent analysis of these also are indicated and described. . CC-BY-NC 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. . https://doi.org/10.1101/2020.09.17.20190033 doi: medRxiv preprint world-wide clone frequently associated with AMR epidemics 6 . While the S. haemolyticus 92 isolate corresponded to ST10 (albeit with a new allele for the SH1431 locus 5 ) and carried the 93 methicillin resistance conferring SCCmec element 7 . Coagulase negative staphylococci such 94 as S. haemolyticus are not recognised as lung pathogens and therefore typically ignored in a 95 diagnostic laboratory as probable contaminants from ETT samples. That we generated a 96 whole genome for this from this sample with no enrichment suggests it was present in a 97 significant abundance, although the clinical relevance of this remains to be determined. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. . https://doi.org/10.1101/2020.09.17.20190033 doi: medRxiv preprint 6 ETT-3 generated a whole genome for P. aeruginosa, again corresponding to ST253, that 104 aligned with >99% identify to the genome from ETT-1. There were however two noteworthy 105 SNPs in this later sample that explain the increased AMR of this isolate. The mexR gene 106 encodes a repressor of the MexAB antibiotic efflux pump, and we found a SNP in mexR that is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted September 22, 2020. . https://doi.org/10.1101/2020.09.17.20190033 doi: medRxiv preprint Clinical course and risk factors for mortality of adult inpatients 273 with COVID-19 in Wuhan, China: a retrospective cohort study Bacterial co-infection and secondary infection in 275 patients with COVID-19: a living rapid review and meta-analysis Management of post-acute 278 covid-19 in primary care Patient outcomes 280 after hospitalisation with COVID-19 and implications for follow-up; results from a 281 prospective UK cohort Open-access bacterial population genomics: BIGSdb 283 software, the PubMLST.org website and their applications Global emergence of the widespread 286 Pseudomonas aeruginosa ST235 clone Staphylococcus haemolyticus as an Important 288 Hospital Pathogen and Carrier of Methicillin Resistance Genes Molecular mechanisms of 291 antibiotic resistance Mutations affecting DNA-binding activity of the 293 MexR repressor of mexR-mexA-mexB-oprM operon expression Interplay of efflux system, ampC, and oprD 296 expression in carbapenem resistance of Pseudomonas aeruginosa clinical isolates Contribution of herpesvirus specific CD8 T cells 299 to anti-viral T cell response in humans Virus-specific T lymphocytes home to the skin 301 during natural dengue infection The activation of bystander CD8 + T cells and their roles in viral 303 infection The role of virus-305 specific CD8(+) cells in liver damage and viral control during persistent hepatitis B virus 306 infection Broad and strong memory CD4 + and CD8 + T cells 308 induced by SARS-CoV-2 in UK convalescent COVID-19 patients Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals The WHO Rapid Evidence Appraisal for COVID-19 Therapies (REACT) Working Group Association Between Administration of Systemic Corticosteroids and Mortality Among Rapid Method for Coextraction of 319 DNA and RNA from Natural Environments for Analysis of Ribosomal DNA-and rRNA-320 Selective progressive response of soil microbial community to wild oat roots Assembly of long, error-prone reads using 325 repeat graphs Fast and accurate de novo genome 327 assembly from long uncorrected reads Improved metagenomic analysis with Kraken 2 Mauve: multiple alignment of conserved 331 genomic sequence with rearrangements BLAST Ring Image Generator 333 (BRIG): simple prokaryote genome comparisons Chronic Infection by Mucoid Pseudomonas 335 aeruginosa Associated with Dysregulation in T-Cell Immunity to Outer Membrane Porin 336 F We would like to thank Kapil Gupta and Imre Berger for kindly providing us the Spike protein, Natalie Di Bartolo and Ashley Toye for kindly providing us the N protein, both used for the SARS-CoV-2 serology work. We would also like to thank Keith Jolley and the Bristol University 262 . CC-BY-NC 4.0 International license It is made available under a perpetuity.is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted September 22, 2020. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted September 22, 2020. . https://doi.org/10.1101/2020.09.17.20190033 doi: medRxiv preprint It is made available under a perpetuity.is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprintThe copyright holder for this this version posted September 22, 2020. . https://doi.org/10.1101/2020.09.17.20190033 doi: medRxiv preprint