1,256
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity

, , , , , , , , , , , , , , , , , , , , , , , , & show all
Article: 2223340 | Received 28 Feb 2023, Accepted 05 Jun 2023, Published online: 12 Jun 2023

References

  • Choudhury S, Medina-Lara A, Smith R. Antimicrobial resistance and the COVID-19 pandemic. Bull World Health Organ. 2022;100(5):295–20. doi:10.2471/blt.21.287752.
  • Bassetti M, Mularoni A, Giacobbe DR, Castaldo N, Vena A. New antibiotics for hospital-acquired pneumonia and ventilator-associated pneumonia. Semin Respir Crit Care Med. 2022;43(2):280–294. doi:10.1055/s-0041-1740605.
  • Feng J, Li B, Jiang X, Yang Y, Wells GF, Zhang T, Li X. Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. Environ Microbio. 2018;20(1):355–368. doi:10.1111/1462-2920.14009.
  • Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes. 2022;14(1):2055944. doi:10.1080/19490976.2022.2055944.
  • Donà D, Di Chiara C, Sharland M. Multi-drug-resistant infections in the COVID-19 era: a framework for considering the potential impact. J Hosp Infect. 2020;106(1):198–199. doi:10.1016/j.jhin.2020.05.020.
  • Rezasoltani S, Yadegar A, Hatami B, Asadzadeh Aghdaei H, Zali MR. Antimicrobial resistance as a hidden menace lurking behind the COVID-19 outbreak: the global impacts of too much hygiene on AMR. Front Microbiol. 2020;11:590683. doi:10.3389/fmicb.2020.590683.
  • Monnet DL, Harbarth S. Will coronavirus disease (COVID-19) have an impact on antimicrobial resistance? Euro Surveill. 2020;25(45). doi:10.2807/1560-7917.Es.2020.25.45.2001886.
  • Cantón R, Gijón D, Ruiz-Garbajosa P. Antimicrobial resistance in ICUs: an update in the light of the COVID-19 pandemic. Curr Opin Crit Care. 2020;26(5):433–441. doi:10.1097/mcc.0000000000000755.
  • Kang Y, Chen S, Chen Y, Tian L, Wu Q, Zheng M, Li Z. Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure. Int J Hyg Environ Health. 2022;240:113882. doi:10.1016/j.ijheh.2021.113882.
  • Su Q, Liu Q, Zhang L, Xu Z, Liu C, Lu W, Ching JY, Li A, Mak JWY, Lui GCY, et al. Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients. Gut Microbes. 2022;14(1):2128603. doi:10.1080/19490976.2022.2128603.
  • Merenstein C, Bushman FD, Collman RG. Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance. Microbiome. 2022;10(1):165. doi:10.1186/s40168-022-01342-8.
  • Shen Y, Yu F, Zhang D, Zou Q, Xie M, Chen X, Yuan L, Lou B, Xie G, Wang R, et al. Dynamic alterations in the respiratory tract microbiota of patients with covid-19 and its association with microbiota in the gut. Adv Sci. 2022;9(27):e2200956. doi:10.1002/advs.202200956.
  • Broman N, Rantasärkkä K, Feuth T, Valtonen M, Waris M, Hohenthal U, Rintala E, Karlsson A, Marttila H, Peltola V, et al. IL-6 and other biomarkers as predictors of severity in COVID-19. Ann Med. 2021;53(1):410–412. doi:10.1080/07853890.2020.1840621.
  • Mittal R, Chourasia N, Bharti V, Singh S, Sarkar P, Agrawal A, Ghosh A, Pal R, Kanwar J, Kotnis A, et al. Blood-based biomarkers for diagnosis, prognosis, and severity prediction of COVID-19: opportunities and challenges. Fam Med Prim Care Rev. 2022;11(8):4330–4341. doi:10.4103/jfmpc.jfmpc_2283_21.
  • Kesmez Can F, Özkurt Z, Öztürk N, Sezen S. Effect of IL-6, IL-8/CXCL8, IP-10/CXCL 10 levels on the severity in COVID-19 infection. Int J Clin Pract. 2021;75(12):e14970. doi:10.1111/ijcp.14970.
  • Philips CA, Ahamed R, Abduljaleel JKP, Rajesh S, Augustine P. Identification and analysis of Gut Microbiota and functional metabolism in decompensated cirrhosis with infection. J Clin Transl Hepatol. 2023;11(1):15–25. doi:10.14218/jcth.2021.00428.
  • Luyt CE, Sahnoun T, Gautier M, Vidal P, Burrel S, Pineton de Chambrun M, Chommeloux J, Desnos C, Arzoine J, Nieszkowska A, et al. Ventilator-associated pneumonia in patients with SARS-CoV-2-associated acute respiratory distress syndrome requiring ECMO: a retrospective cohort study. Ann Intensive Care. 2020;10(1):158. doi:10.1186/s13613-020-00775-4.
  • Segrelles-Calvo G, de S Araújo GR, Llopis-Pastor E, Carrillo J, Hernández-Hernández M, Rey L, Melean NR, Escribano I, Antón E, Zamarro C, et al. Candida spp. co-infection in COVID-19 patients with severe pneumonia: prevalence study and associated risk factors. Respir Med. 2021;188:106619. doi:10.1016/j.rmed.2021.106619.
  • Zhou T, Wu J, Zeng Y, Li J, Yan J, Meng W, Han H, Feng F, He J, Zhao S, et al. SARS-CoV-2 triggered oxidative stress and abnormal energy metabolism in gut microbiota. MedComm. 2022;3(1):e112. doi:10.1002/mco2.112.
  • Shoieb SM, El-Ghiaty MA, El-Kadi AOS. Targeting arachidonic acid–related metabolites in COVID-19 patients: potential use of drug-loaded nanoparticles. Emerg Mater. 2021;4(1):265–277. doi:10.1007/s42247-020-00136-8.
  • Qiao M, Ying GG, Singer AC, Zhu YG. Review of antibiotic resistance in China and its environment. Environ Int. 2018;110:160–172. doi:10.1016/j.envint.2017.10.016.
  • Guffey AA, Loll PJ. Regulation of resistance in vancomycin-resistant enterococci: the VanRS two-component system. Microorganisms. 2021;9(10):2026. doi:10.3390/microorganisms9102026.
  • Mahmoudi H. Bacterial co-infections and antibiotic resistance in patients with COVID-19. GMS Hyg Infect Control.2020; 15. Doc35. doi:10.3205/dgkh000370.
  • Li XZ, Barré N, Poole K. Influence of the MexA-MexB-oprM multidrug efflux system on expression of the MexC-MexD-oprJ and MexE-MexF-oprN multidrug efflux systems in Pseudomonas aeruginosa. J Antimicrob Chemother. 2020;46(6):885–893. doi:10.1093/jac/46.6.885.
  • Markovic SS, Jovanovic M, Gajovic N, Jurisevic M, Arsenijevic N, Jovanovic M, Jovanovic M, Mijailovic Z, Lukic S, Zornic N, et al. IL 33 correlates with COVID-19 severity, radiographic and clinical finding. Front Med. 2021;8:749569. doi:10.3389/fmed.2021.749569.
  • Dickson RP, Erb-Downward JR, Falkowski NR, Hunter EM, Ashley SL, Huffnagle GB. The lung microbiota of healthy mice are highly variable, cluster by environment, and reflect variation in baseline lung innate immunity. Am J Respir Crit Care Med. 2018;198(4):497–508. doi:10.1164/rccm.201711-2180OC.
  • Segal LN, Clemente JC, Tsay J-CJ, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, et al. Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. Nat Microbiol. 2016;1:16031. doi:10.1038/nmicrobiol.2016.31.
  • Dhar D, Mohanty A. Gut microbiota and Covid-19- possible link and implications. Virus Res. 2020;285:198018. doi:10.1016/j.virusres.2020.198018.
  • Azkur AK, Akdis M, Azkur D, Sokolowska M, Veen W, Brüggen M-C, O’Mahony L, Gao Y, Nadeau K, Akdis CA, et al. Immune response to SARS-CoV-2 and mechanisms of immunopathological changes in COVID-19. Allergy. 2020;75(7):1564–1581. doi:10.1111/all.14364.
  • Hoenigl M, Seidel D, Sprute R, Cunha C, Oliverio M, Goldman GH, Ibrahim AS, Carvalho A. COVID-19-associated fungal infections. Nat Microbiol. 2022;7(8):1127–1140. doi:10.1038/s41564-022-01172-2.
  • Ren Z, Wang H, Cui G, Lu H, Wang L, Luo H, Chen X, Ren H, Sun R, Liu W, et al. Alterations in the human oral and gut microbiomes and lipidomics in COVID-19. Gut. 2021;70(7):1253–1265. doi:10.1136/gutjnl-2020-323826.
  • Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev. 2018;31(4). doi:10.1128/cmr.00088-17.
  • Ghanizadeh A, Najafizade M, Rashki S, Marzhoseyni Z, Motallebi M, Tsai F-M. Genetic diversity, antimicrobial resistance pattern, and biofilm formation in Klebsiella pneumoniae isolated from patients with coronavirus disease 2019 (COVID-19) and ventilator-associated pneumonia. Biomed Res Int. 2021;2021:1–11. doi:10.1155/2021/2347872.
  • Dell’annunziata F, Dell’aversana C, Doti N, Donadio G, Dal Piaz F, Izzo V, De Filippis A, Galdiero M, Altucci L, Boccia G, et al. Outer membrane vesicles derived from Klebsiella pneumoniae are a driving force for horizontal gene transfer. Int J Mol Sci. 2021;22(16):8732. doi:10.3390/ijms22168732.
  • Tian M, Liu W, Li X, Zhao P, Shereen MA, Zhu C, Huang S, Liu S, Yu X, Yue M, et al. HIF-1α promotes SARS-CoV-2 infection and aggravates inflammatory responses to COVID-19. Signal Transduct Target Ther. 2021;6(1):308. doi:10.1038/s41392-021-00726-w.
  • Köstenberger M, Hasibeder W, Dankl D, Germann R, Hörmann C, Joannidis M, Markstaller K, Müller-Muttonen S-O, Neuwersch-Sommeregger S, Schaden E, et al. SARS-CoV-2: recommendations for treatment in intensive care medicine. Wien Klin Wochenschr. 2020;132(21–22):664–670. doi:10.1007/s00508-020-01734-6.
  • Andrews S. FastQC a quality control tool for high throughput sequence data. 2014.
  • Patel RK, Jain M, Liu Z. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLos One. 2012;7(2):e30619. doi:10.1371/journal.pone.0030619.
  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562–578. doi:10.1038/nprot.2012.016.
  • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–2120. doi:10.1093/bioinformatics/btu170.
  • Rotmistrovsky K, Agarwala R. Bmtagger: best match tagger for removing human reads from metagenomics datasets.
  • Truong DT, Franzosa EA, Tickle TL, Scholz M, Weingart G, Pasolli E, Tett A, Huttenhower C, Segata N. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015;12(10):902–903. doi:10.1038/nmeth.3589.
  • Yin X, Jiang X-T, Chai B, Li L, Yang Y, Cole JR, Tiedje JM, Zhang T. Args-OAP v2.0 with an expanded SARG database and hidden Markov models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics. 2018;34(13):2263–2270. doi:10.1093/bioinformatics/bty053.
  • Yang Y, Jiang X, Chai B, Ma L, Li B, Zhang A, Cole JR, Tiedje JM, Zhang T. Args-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. Bioinformatics. 2016;32(15):2346–2351. doi:10.1093/bioinformatics/btw136.
  • Oksanen J, Kindt R, Legendre P, O’Hara B, Wagner H. The VEGAN package: community ecology package. 2008.
  • Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431–432. doi:10.1093/bioinformatics/btq675.
  • RColorBrewer S, Liaw MA. Package ‘randomForest’. Berkeley (CA):University of California,Berkeley; 2018.