The significance of monitoring respiratory sample cultures and polymerase chain reaction tests for detecting bacterial pathogens in severely and critically ill patients with COVID-19

Main Article Content

D Strelkova
V Kuleshov
E Burmistrova
I Sychev
Y Savochkina
D Danilov
S Yatsyshina
E Glushchenko
M Elkina
N Ananicheva
A Yasneva
S Topolyanskaya
S Rachina

Abstract





Background. Bacterial superinfection is one of the most common and potentially lethal complications in severely and critically ill patients with COVID-19.


Objectives. To determine the colonisation time frame and the spectrum of potential bacterial pathogens in respiratory samples from patients with severe and critical COVID-19, using routine culture and polymerase chain reaction (PCR) tests.


Methods. A prospective observational study was conducted on patients aged ≥18 years with confirmed severe and critical COVID-19 who were admitted to or transferred to the intensive care unit (ICU). Respiratory samples were collected for microbial culture and PCR testing within the first 2 days after ICU admission/transfer, between days 3 and 6, and after 7 days of ICU stay.


Results. A total of 82 patients, with a median (interquartile range) age of 74.5 (67.3 - 81.0) years and a median Charlson comorbidity index of 4 (3 - 5), were enrolled in the study. Colonisation with any pathogen was observed in 67% of patients, after a median of 4 (2 - 6) days in the ICU. On days 0 - 2 of the ICU stay, micro-organisms were detected in 18% of patients, with Klebsiella pneumoniae (without acquired antibiotic resistance) and methicillin-susceptible Staphylococcus aureus being most frequently identified. Later, Acinetobacter baumannii and carbapenem-resistant K. pneumoniae became the predominant micro-organisms, identified in nearly half of the patients. In 74% of the samples, the results of microbial culture and PCR tests were identical. In 17%, PCR revealed bacterial pathogens not identified by culture.


Conclusion. Our study confirms that colonisation of the respiratory tract occurs early in the course of ICU stay. Superinfections are predominantly caused by multidrug-resistant Gram-negative bacteria.





Downloads

Download data is not yet available.

Article Details

How to Cite
1.
Strelkova D, Kuleshov V, Burmistrova E, Sychev I, Savochkina Y, Danilov D, et al. The significance of monitoring respiratory sample cultures and polymerase chain reaction tests for detecting bacterial pathogens in severely and critically ill patients with COVID-19. Afr J Thoracic Crit Care Med [Internet]. 2024 Apr. 4 [cited 2024 Dec. 1];30(1):e1293. Available from: https://samajournals.co.za/index.php/ajtccm/article/view/1293
Section
Original Research: Articles

How to Cite

1.
Strelkova D, Kuleshov V, Burmistrova E, Sychev I, Savochkina Y, Danilov D, et al. The significance of monitoring respiratory sample cultures and polymerase chain reaction tests for detecting bacterial pathogens in severely and critically ill patients with COVID-19. Afr J Thoracic Crit Care Med [Internet]. 2024 Apr. 4 [cited 2024 Dec. 1];30(1):e1293. Available from: https://samajournals.co.za/index.php/ajtccm/article/view/1293

References

Blumenthal D, Fowler EJ, Abrams M, Collins SR. Covid-19 – implications for the health care system. N Engl J Med 2020;383(15):1483-1488. https://doi.org/10.1056/ NEJMsb2021088

LangfordBJ,SoM,RaybardhanS,etal.Bacterialco-infectionandsecondaryinfection in patients with COVID-19: A living rapid review and meta-analysis. Clin Microbiol Infect 2020;26(12):1622-1629. https://doi.org/10.1016/j.cmi.2020.07.016

Musuuza JS, Watson L, Parmasad V, Putman-Buehler N, Christensen L, Safdar N. Prevalence and outcomes of co-infection and superinfection with SARS- CoV-2 and other pathogens: A systematic review and meta-analysis. PLoS ONE 2021;16(5):e0251179. https://doi.org/10.1371/journal.pone.0251170

Lansbury L, Lim B, Baskaran V, et al. Co-infections in people with COVID-19: A systematic review and meta-analysis. J Infect 2020;81(2):266-275. https://doi. org/10.1016/j.jinf.2020.05.046

He S, Liu W, Jiang M, et al. Clinical characteristics of COVID-19 patients with clinically diagnosed bacterial co-infection: A multi-center study. PLoS ONE 2021;16(4):e0249668. https://doi.org/10.1371/journal.pone.0249668

Buehler PK, Zinkernagel AS, Hofmaenner DA, et al. Bacterial pulmonary superinfections are associated with longer duration of ventilation in critically ill COVID-19 patients. Cell Rep Med 2021;2(4):100229. https://doi.org/10.1016/j. xcrm.2021.100229

Somers EC, Eschenauer GA, Troost JP, et al. Tocilizumab for treatment of mechanically ventilated patients with COVID-19. Clin Infect Dis 2021;73(2):E445-E454. https:// doi.org/10.1093/cid/ciaa954

Grasselli G, Scaravilli V, Mangioni D, et al. Hospital-acquired infections in critically ill patients with COVID-19. Chest 2021;160(2):454-465. https://doi.org/10.1016/j. chest.2021.04.002

Ohki R, Fukui Y, Morishita N, Iwata K. Increase of blood culture contamination during COVID-19 pandemic: A retrospective descriptive study. Am J Infect Control 2021;49(11):1359-1361. https://doi.org/10.1016/j.ajic.2021.08.025

Søvik S, Barratt-Due A, Kåsine T, et al. Corticosteroids and superinfections in COVID-19 patients on invasive mechanical ventilation. J Infect 2022;85(1):57-63. https://doi.org/10.1016/j.jinf.2022.05.015

Blonz G, Kouatchet A, Chudeau N, et al. Epidemiology and microbiology of ventilator- associated pneumonia in COVID-19 patients: A multicenter retrospective study in 188 patients in an un-inundated French region. Crit Care 2021;25(1):72. https://doi. org/10.1186/S13054-021-03493-w

RonchettiS,RicciE,MiglioratiG,GentiliM,RiccardiC.Howglucocorticoidsaffectthe neutrophil life. Int J Mol Sci 2018;19(12):4090. https://doi.org/10.3390/ijms19124090

Kooistra EJ, van Berkel M, van Kempen NF, et al. Dexamethasone and tocilizumab treatment considerably reduces the value of C-reactive protein and procalcitonin to detect secondary bacterial infections in COVID-19 patients. Crit Care 2021;25(1):281. https://doi.org/10.1186/s13054-021-03717-z

Tong-Minh K, van der Does Y, Engelen S, et al. High procalcitonin levels associated with increased intensive care unit admission and mortality in patients with a COVID-19 infection in the emergency department. BMC Infect Dis 2022;22(1):165. https://doi. org/10.1186/s12879-022-07144-5

DolciA,RobbianoC,AloisioE,etal.Searchingforaroleofprocalcitonindetermination in COVID-19: A study on a selected cohort of hospitalised patients. Clin Chem Lab Med 2020;59(2):433-440. https://doi.org/10.1515/cclm-2020-1361

IACMAC.Recommendationsforthedeterminationofthesensitivityofmicroorganisms to antimicrobial drugs (2021), version 2021-01. https://www.antibiotic.ru/minzdrav/ category/clinical-recommendations/ (accessed 10 May 2023).

MinistryofHealthcare,RussianFederation.TemporaryguidelinesonCOVID-19prophylaxis, diagnostics and management, version 17 (14 December 2022). https://static-0.minzdrav. gov.ru/system/attachments/attaches/000/061/252/original/%D0%92%D0%9C%D0%A0_ COVID-19_V17.pdf (accessed 22 September 2023).

Pasero D, Cossu AP, Terragni P. Multi-drug resistance bacterial infections in critically ill patients admitted with COVID-19. Microorganisms 2021;9(8):1773. https://doi. org/10.3390/microorganisms9081773

Maes M, Higginson E, Pereira-Dias J, et al. Ventilator-associated pneumonia in critically ill patients with COVID-19. Crit Care 2021;25(1):25. https://doi.org/10.1186/ S13054-021-03460-5

ScottH,ZahraA,FernandesR,FriesBC,ThodeHC,SingerAJ.Bacterialinfectionsand death among patients with Covid-19 versus non Covid-19 patients with pneumonia. Am J Emerg Med 2022;51:1-5. https://doi.org/10.1016/j.ajem.2021.09.040

Romashov OM, Ni OG, Bykov AO, Kruglov AN, Procenko DN, Tyurin IN. Antimicrobial resistance and antimicrobial therapy modification during COVID-19 pandemic in large tertiary hospital. Clin Microb Antimicrob Chemother 2021;23(3):293-303. https://doi.org/10.36488/cmac.2021.3.293-303

Cohen R, Babushkin F, Finn T, et al. High rates of bacterial pulmonary co- infections and superinfections identified by multiplex PCR among critically ill COVID-19 patients. Microorganisms 2021;9(12):2483. https://doi.org/10.3390/ microorganisms9122483

Paz V, D’Agostino ML, Garibaldi F, Orellana R, Paniagua M, Santillán A. Multiplex PCR in the empirical antibiotic treatment of patients with SARS-CoV-2 and bacterial respiratory superinfection. Infect Prev Pract 2022;4(3):100227. https://doi. org/10.1016/J.infpip.2022.100227

PickensCO,GaoCA,CutticaMJ,etal.Bacterialsuperinfectionpneumoniainpatients mechanically ventilated for COVID-19 pneumonia. Am J Respir Crit Care Med 2021;204(8):921-932. https://doi.org/10.1164/rccm.202106-1354OC

Avdeev S, Rachina S, Belkova Y, et al. Antimicrobial prescribing patterns in patients with COVID-19 in Russian multi-field hospitals in 2021: Results of the Global-PPS Project. Trop Med Infect Dis 2022;7(5):75. https://doi.org/10.3390/ tropicalmed7050075