12 AJTCCM VOL. 30 NO. 1 2024
ORIGINAL RESEARCH: ARTICLES
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 conrmed 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 rst 2 days aer ICU admission/transfer, between days 3 and 6, and aer 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, aer 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 identied. Later, Acinetobacter baumannii
and carbapenem-resistant K. pneumoniae became the predominant micro-organisms, identied 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 identied by culture.
Conclusion. Our study conrms that colonisation of the respiratory tract occurs early in the course of ICU stay. Superinfections are
predominantly caused by multidrug-resistant Gram-negative bacteria.
Keywords. COVID-19, SARS-CoV-2, superinfection, colonisation, polymerase chain reaction, PCR.
Afr J Thoracic Crit Care Med 2024;30(1):e1293. https://doi.org/10.7196/AJTCCM.2024.v30i1.1293
Despite a decline in the number of COVID-19 cases, the pandemic
remains the most signicant healthcare crisis of the 21st century.[1]
Many researchers continue to investigate the role of bacterial infections
in COVID-19.[2,3] On the one hand, there is sufficient evidence
suggesting that coinfection as opposed to superinfection is infrequent.
It would therefore be advisable to restrict the routine use of antibiotics
e signicance of monitoring respiratory sample cultures and
polymerase chain reaction tests for detecting bacterial pathogens
in severely and critically ill patients with COVID-19
D Strelkova,1 MD; V Kuleshov,2 MD; E Burmistrova,2 MD; I Sychev,3 MD, PhD; Y Savochkina,4 Specialist Degree in Biophysics, PhD;
D Danilov,4 MSc; S Yatsyshina,5 Specialist Degree in Biochemistry, PhD; E Glushchenko,4 MSc; M Elkina,5 Specialist Degree in Biochemis-
try; N Ananicheva,2 MD; A Yasneva,1 medical student; S Topolyanskaya,1 MD, PhD; S Rachina,1 MD, PhD
1 I. M. Sechenov First Moscow State Medical University, Moscow, Russian Federation
2 City Clinical Hospital named aer S. S. Yudin, Moscow, Russian Federation
3 Russian Medical Academy of Continuous Professional Education, Moscow, Russian Federation
4 Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks of the Federal Medical and
Biological Agency, Moscow, Russian Federation
5 Central Research Institute of Epidemiology (CRIE) of the Federal Service for Surveillance on Consumer Rights Protection and Human
Wellbeing, Moscow, Russian Federation
Corresponding author: D Strelkova (dashastrelkova@gmail.com)
Study synopsis
What the study adds.is real-world study provides valuable insights into the signicance of microbiological monitoring of critically ill
COVID-19 patients. It conrms that bacterial colonisation of the respiratory tract occurs early in the course of ICU stay, with nosocomial
superinfections caused predominantly by multidrug-resistant Gram-negative pathogens. Polymerase chain reaction (PCR) testing can assist
in ruling out colonisation and in early detection of potential bacterial superinfections.
Implications of the ndings. Bacterial superinfections present a major challenge in critically ill COVID-19 patients, owing to their high
prevalence and mortality rates. eir early detection, determination of causative agents, and antibiotic susceptibility proling are therefore of
paramont importance. PCR testing of clinical specimens appears to be a valuable supplement to respiratory culture, enhancing the precision
of diagnosis of lower respiratory tract infections.
AJTCCM VOL. 30 NO. 1 2024 13
ORIGINAL RESEARCH: ARTICLES
for COVID-19 unless specic indications are present.[2,4] Superinfections,
on the other hand, develop in a substantial proportion of hospitalised
patients with severe disease, oen aecting the outcome. According
to a meta-analysis of 118 studies, the incidence of superinfection in
COVID-19 was 24%, and patients with superinfection had longer
hospital stays and an increased risk of death.[3] In a multicentre
study by He et al.,[5] it was found that the risk of death in hospitalised
patients with COVID-19 and bacterial superinfection increased by
8.2-fold (95% condence interval 4.5 - 15.1). In another study, Buehler
et al.[6] found that bacterial superinfections in patients with severe
or critical COVID-19 were linked to fewer days without mechanical
ventilation, despite a high rate of empirical antibiotic therapy. In
addition to the traditional predisposing factors, the risk of secondary
bacterial complications in COVID-19 patients may be increased as a
result of the widespread use of immunosuppressive therapy.[7]
Lower respiratory tract infections (LRTIs), including ventilator-
associated pneumonia, frequently occur in mechanically ventilated
patients.[8] Among intubated patients, the rate of superinfections can
be as high as 42 - 61%.[6,9-11] Regular testing of respiratory specimens
for the presence of potential bacterial pathogens may therefore be
considered so that antibacterial therapy can be prescribed timeously.
The diagnosis of superinfections in COVID-19 poses specific
challenges. New infiltrates on chest computed tomography (CT)
scans are oen poorly visible in patients with extensive lung disease,
and the presence of leucocytosis and neutrophilia may be linked to
the use of corticosteroids.[12] Moreover, the use of dexamethasone
and/or interleukin-6 antagonists can reduce the diagnostic value of
procalcitonin as a marker for bacterial superinfection, because they
may suppress its production.[13] Elevated procalcitonin and C-reactive
protein levels are also associated with a severe course and poor
prognosis in COVID-19, making it challenging to establish precise
threshold values for these biomarkers.[14,15]
The present study aimed to determine the time frame for
colonisation and identify the potential range of bacterial pathogens in
respiratory samples from patients with severe and critical COVID-19,
using routine culture and polymerase chain reaction (PCR) testing.
Methods
A prospective observational study was conducted in a multidisciplinary
hospital in Moscow between December 2021 and February 2022. e
study included patients aged ≥18 years with conrmed severe and
critical COVID-19, who were either admitted directly or transferred
to the ICU.
А respiratory sample (expectorated sputum or endotracheal
aspirate (ETA) for intubated patients or bronchoalveolar lavage (BAL)
when clinically indicated) was collected for Gram staining and culture
within the rst 2 days of ICU admission/transfer, between days 3 and
6, and aer 7 days of ICU stay.
Sputum quality was assessed according to standard criteria. To
isolate aerobic and facultative anaerobic micro-organisms, selective
and differential media were used in accordance with standard
methods and procedures. Micro-organisms were identied using a BD
Phoenix M50 automatic analyser (Becton Dickinson, USA). Antibiotic
susceptibility was evaluated according to national guidelines[16] closely
aligned with the European Committee on Antimicrobial Susceptibility
Testing (EUCAST) methodology and EUCAST clinical breakpoints
from 2021. e micro-organisms isolated were considered potentially
signicant if the sputum contained ≥105 colony-forming units (CFUs)/
mL (≥104 CFUs/mL for ETA and ≥103 CFUs/mL for BAL).
In a subset of patients, real-time PCR was performed concurrently
with culture to detect common bacterial pathogens and markers of
antibiotic resistance. DNA from Klebsiella pneumoniae, Acinetobacter
baumannii, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus
aureus and the MecA gene indicating S. aureus resistance to
methicillin was detected and quantied using the AmpliTest K.p./
A.b./P.a./ E.c. (research use only (RUO), Centre for Strategic Planning
and Management of Biomedical Health Risk of the Federal Medical
Biological Agency (CSP), Russia) and AmpliSens MRSA-screen-
titre-FRT (in vitro diagnostics (IVD), Central Research Institute
of Epidemiology (CRIE), Russia). Stenotrophomonas maltophilia
DNA was detected using the AmpliTest SM (RUO, CSP, Russia).
Identication of carbapenemase genes belonging to the NDM, OXA-
48-like and KPC groups was performed using AmpliSens MDR MBL-
FRT (IVD) and AmpliSens MDR KPC/OXA-48-FRT (IVD) reagent
kits (CRIE, Russia).
e initial sample was also tested for RNA/DNA of respiratory
viruses, including influenza viruses A and B, human respiratory
syncytial virus, human adenovirus, human metapneumovirus, human
coronaviruses (229E, HKUI, OC43, NL63), human parainuenza
viruses 1 - 4, human rhinovirus, human bocavirus, Mycoplasma
pneumoniae and Chlamydia pneumoniae, as well as Streptococcus
pneumoniae and Haemophilus influenzae DNA. These tests were
carried out using real-time PCR kits (AmpliSens Inuenza virus
A/B-FRT (IVD), AmpliSens ARVI-screen-FRT (IVD), AmpliSens
Mycoplasma pneumoniae/Chlamydophila pneumoniae-FRT (IVD)
and AmpliSens Pneumo-quantum-FRT (IVD) (CRIE, Russia)) to
reveal potential cases of co-infection. Real-time PCR was performed
using a CFX96 system (Bio-Rad, USA). RNA/DNA extraction from
the samples was done using the AmpliSens RIBO-prep reagent
kit, and reverse transcription was performed using the AmpliSens
REVERTA-L RT reagent kit (CRIE, Russia). A positive PCR result
was dened as a bacterial DNA load ≥104 genome equivalents per mL.
We documented clinical, demographic and laboratory data, chest
CT scan results, comorbidities, and pharmacological and non-
pharmacological treatments, as well as all documented cases of
nosocomial LRTI and outcomes.
The decision about the significance of the micro-organisms
identied and the presence of infection was made by two clinicians
based on the following criteria: the presence of symptoms indicating
secondary infection (such as increasing respiratory failure and
haemodynamic disorders, relapse of fever and the development of
purulent respiratory secretions); observed laboratory changes (severe
leucocytosis and increased procalcitonin level); and the emergence of
new lung inltrates that could be interpreted as indicators of bacterial
superinfection.
Descriptive statistics were performed using SPSS version 26.0
(IBM, USA). We used the Shapiro-Wilk test to check continuous data
for normality. Continuous data are shown as means with standard
deviations or medians with interquartile ranges (IQRs), while
categorical data are presented as frequencies and percentages. To
compare PCR with culture, we provided the number (and percentage)
of concordant positive results (indicating the same micro-organism
detected), concordant negative results and discordant results. e
study was approved by the Local Ethics Committee of City Clinical
14 AJTCCM VOL. 30 NO. 1 2024
ORIGINAL RESEARCH: ARTICLES
Hospital named aer S. S. Yudin (ethics approval letter no. 1, dated
11 January 2021).
Results
A total of 82 patients with an median (IQR) age of 74.5 (67.3 - 81.0)
years were enrolled in the study (Table 1). e median Charlson
comorbidity index was 4 (3 - 5), with arterial hypertension and
diabetes mellitus being the most common concomitant conditions.
Most of the patients (77%) required invasive mechanical ventilation.
Initially, during the first 2 days of ICU admission, respiratory
samples were obtained from 55 (67%) of the patients. e remaining
27 patients (33%) did not have a productive cough and were not
intubated. Initial culture of the respiratory samples identied a micro-
organism in only 15 patients (18%). e most frequently detected
potential bacterial pathogens were K. pneumoniae without acquired
antibiotic resistance, and methicillin-susceptible S. aureus (MSSA).
All samples tested with PCR were negative for M. pneumoniae and
Chlamydia pneumoniae DNA; however, 3 cases of S. pneumoniae and
1 case of H. inuenzae were detected. Additionally, 2 cases of co-
infection with human adenovirus were identied among the viruses.
Between days 3 and 6 of the ICU stay, 30 patients had positive
culture results. Using both culture and PCR, we identified K.
pneumoniae and A. baumannii as the most common micro-
organisms, with 27% of K. pneumoniae being carbapenem resistant.
Aer day 7 in the ICU, A. baumannii and K. pneumoniae continued
to be the most frequently isolated pathogens, and the proportion
Table 1. Characteristics of patients with severe/critical COVID-19 (N=82)
n (%)*
Demographic data
Age (years), median (IQR) 74.5 (67.3 - 81.0)
Women 56 (68.3)
Recent previous hospitalisation 10 (12.2)
Hospital stay before admission to ICU (days), median (IQR) 3.5 (2.0 - 5.0)
ICU stay (days), median (IQR) 8 (5.0 - 12.0)
COVID-19 severity
Chest CT stage
CT-2 2 (2.4)
CT-3 44 (53.7)
CT-4 36 (43.9)
Invasive mechanical ventilation 63 (76.8)
Main comorbidities
Arterial hypertension 77 (93.9)
Type 2 diabetes mellitus 26 (31.7)
Congestive heart failure 16 (19.5)
Stroke/TIA 11 (13.4)
Active cancer 9 (11.0)
Laboratory data†
Lymphopenia (lymphocytes <1.26 × 109/L) 53 (64.6)
Anemia (haemoglobin <12 g/dL in females and <13 g/dL in males) 36 (43.9)
rombocytopenia (platelets <180 × 109/L) 27 (32.9)
Leucopenia (leucocytes <4 × 109/L) 6 (7.3)
Serum CRP (mg/L), median (IQR) 56.4 (18.7 - 103.4)
Elevated procalcitonin (procalcitonin >0.5 ng/mL) 15 (18.3)
Treatment
Glucocorticosteroids 82 (100)
Monoclonal antibodies 56 (68.3)
Levilimab 52 (63.4)
Olokizumab 4 (4.9)
Tofacitinib 2 (2.4)
Outcomes
Death 62 (75.6)
Transfer to rehabilitation facility 4 (4.9)
Discharge 16 (19.5)
IQR = interquartile range; ICU = intensive care unit; CT = computed tomography; CT-2 = 25 - 50% of lung involvement on CT, CT-3 = 50 - 75% of lung involvement on CT, CT-4 = >75% of lung involvement
on CT;[17] TIA = transient ischaemic attack; CRP = C-reactive protein.
*Except where otherwise indicated.
†All thresholds determined according to the local laboratory reference range.
AJTCCM VOL. 30 NO. 1 2024 15
ORIGINAL RESEARCH: ARTICLES
of carbapenem-resistant K. pneumoniae had risen to 86%. All A.
baumannii isolates, regardless of the time period, were multidrug
resistant, including resistance to carbapenems. Additionally, we
identified genes from the following сarbapenemase groups in
samples from 10 patients: NDM + OXA-48 in 6/10 cases, OXA-48
in 3/10 cases, and KPC + NDM + OXA-48 in 1/10 cases. e MecA
gene was found in one sample containing S. aureus DNA, which
corresponded to the culture results. Details of the monitoring
process and pathogen ndings are shown in Fig. 1.
e median time to colonisation of respiratory samples by various
bacterial pathogens is presented in Table 2. Colonisation with any
pathogen occurred in 55 patients (67%). e median (IQR) time to
colonisation was 7 (5 - 11) days of hospital stay and 4 (2 - 6) days
of ICU stay. In 37 patients, A. baumannii, carbapenem-resistant K.
pneumoniae or both were detected.
Comparison of microbiological and PCR ndings showed a 74%
overlap of the results. PCR revealed additional micro-organisms in
17% of samples, which were not identied by culture (Fig. 2).
Clinical, laboratory and radiological data supported a diagnosis
of LRTI (nosocomial pneumonia or ventilator-associated
tracheobronchitis) in 49 patients (60%). Among the causative agents
of LRTI, A. baumannii and carbapenem-resistant K. pneumoniae
were the predominant pathogens, responsible for 69% of cases, when
considering mixed infections. A detailed description of the pathogens
identied is presented in Table 3.
During the observation period, 78 patients (95%) received a median
(IQR) of 3 (2 - 3.75) courses of antibiotics. e antibiotics administered
at dierent stages of hospital stay are detailed in Table 4. Ampicillin +
sulbactam and cefepime were the most frequently prescribed antibiotics
before transfer to the ICU. Cefepime + sulbactam and meropenem
10 20
12
8
4
2
2 2
1
1
82 patients
30 patients had positive culture 30 patients had positive culture
PCR (for viruses and typical
community-acquired bacterial pathogens)
performed in 36 patients
2 patients positive for human adenovirus,
3 for S. pneumoniae, 1 for Haemophilus inuenzae
PCR (for typical nosocomial bacterial pathogens)
performed in 34 patients
19 patients positive
K. pneumoniae
A. baumanii
S. maltophilia
S. aureus
E. coli
PCR (for typical nosocomial bacterial pathogens)
performed in 31 patients
23 patients positive
7
15
21
14
43
1
14
5
5 5
2
2 2 2
1 1 1
Klebsiella pneumoniae
Staphylococcus aureus
Acintobacter baumanii
Stenotrophomonas maltophilia
Serratia marcescens
Streptococcus pneumoniae
K. pneumoniae
A. baumanii
S. aureus
S. maltophilia
Escherichia coli
Burkholderia cepacia
Pseudomonas aeruginosa
A. baumanii
K. pneumoniae
S. maltophilia
S. aureus
P. aeruginosa
55 with respiratory sample
27 with unproductive cough
15 patients had positive culture
73 patients
63 with respiratory sample
2 with unproductive cough
8 with missed observation point
50 patients 40 with respiratory sample
10 with missed observation point
A. baumannii
K. pneumoniae
S. maltophilia
S. aureus
E. coli
Patients, n
Patients, nPatients, n
Patients, nPatients, n
Pathogens
Pathogens
Pathogens Pathogens
Pathogens
Day 0 - 2 Day 3 - 6 Day 7+
PCR Culture Samples
Fig. 1. Sample collection process and ndings in patients with severe/critical COVID-19. (PCR = polymerase chain reaction.)
16 AJTCCM VOL. 30 NO. 1 2024
ORIGINAL RESEARCH: ARTICLES
were used during the earlier ICU stay, whereas increases in the use of
polymyxin B and tigecycline were noted during the later ICU stay.
Discussion
In the present study, clinically signicant pathogens were detected
in 18% of patients during the early days of their ICU stay. Inability
to obtain sputum from some patients meant that it was not possible
to perform cultures on all patients. Subsequently, the proportion of
patients with positive ndings on microbiological examination of
respiratory specimens increased to 67%.
A systematic review found Acinetobacter spp., P. aeruginosa, E. coli,
K. pneumoniae, Enterococcus faecium and S. maltophilia to be the
Culture and PCR positive, but for dierent pathogens
Culture and PCR negative
Culture and PCR positive for the same pathogen
Culture and PCR positive for the same pathogen, and some other pathogens identied by PCR
Culture and PCR positive for the same pathogen, and some other pathogens identied by culture
Culture positive but PCR negative
PCR positive but culture negative
n=1; 1.1%
n=31; 35.2%
n=34; 38.6%
n=9; 10.2%
n=3; 3.4%
n=4; 4.5% n=6;
6.8%
Fig. 2. Comparison of respiratory culture and PCR ndings in patients with severe/critical COVID-19. (PCR = polymerase chain reaction.)
Table 2. Time to colonisation of respiratory specimens with various bacterial pathogens in patients with severe/critical COVID-19
(N=55)
Micro-organism Patients, n*
Hospital stay (days),
median (IQR)
ICU stay (days),
median (IQR)
Gram negative
Non-fermenting bacteria 43 10 (7 - 13) 6 (4 - 8.75)
Acinetobacter baumannii, carbapenem resistant 34 10 (8 - 14) 7 (5 - 9)
Enterobacterales 30 9 (7 - 11.25) 4.5 (2.75 - 7)
Klebsiella pneumoniae, carbapenem resistant 15 10 (7 - 17) 7 (6 - 12)
Enterobacterales, carbapenem susceptible 20 7 (5 - 10) 3 (1 - 5)
K. pneumoniae, no acquired antibiotic resistance 16 8 (5 - 10) 3 (1 - 4)
Gram positive
All Gram-positive bacteria 12 7 (5 - 10) 3 (1 - 5)
MSSA 11 7 (5 - 10) 3 (2 - 5)
IQR = interquartile range; ICU = intensive care unit; MSSA = methicillin-susceptible Staphylococcus aureus.
*Culture was performed in all patients and was negative in 27. Some patients were colonised with more than one pathogen.
Table 3. Spectrum of lower respiratory tract infection pathogens in patients with severe/critical COVID-19 (N=82)
Pathogen Patients, n*
Acinetobacter baumannii, carbapenem resistant 30
Klebsiella pneumoniae, carbapenem resistant 15
MSSA 6
Stenotrophomonas maltophilia 5
K. pneumoniae, no acquired antibiotic resistance 4
Pseudomonas aeruginosa 2
K. pneumoniae, third-generation cephalosporin resistant 1
Causative agent not identied 7
MSSA = methicillin-susceptible Staphylococcus aureus.
*Some patients were infected with more than one pathogen.
AJTCCM VOL. 30 NO. 1 2024 17
ORIGINAL RESEARCH: ARTICLES
most
common bacterial superinfections in COVID-19 patients.[3] e
prevalence of multidrug-resistant bacterial pathogens in critically ill
COVID-19 patients varies from 32% to 50%, with A. baumannii and
carbapenem-resistant K. pneumoniae being particularly concerning.[18]
In our study, K. pneumoniae, A. baumannii and S. aureus were
detected most frequently. Colonisation was noted to occur relatively
early, aer a median of 4 days in the ICU. Importantly, the resistance
proles of organisms identied early v. those identied later were
Table 4. Frequency of prescribing antibiotics to patients with severe/critical COVID-19 during dierent periods of hospitalisation (N=82)
Patients, n
Before admission to ICU, new antibiotic prescribed to 28/75 patients
Ampicillin + sulbactam 9
Cefepime 7
Cefepime + sulbactam 5
Meropenem 4
Moxioxacin 3
Cefoperazone + sulbactam 2
Imipenem + cilastatin 1
Levooxacin 1
Day 0 - 2 in ICU, new antibiotic prescribed to 35/82 patients
Cefepime + sulbactam 10
Meropenem 9
Ampicillin + sulbactam 5
Levooxacin 5
Cefoperazone + sulbactam 2
Cefotaxime + sulbactam 2
Fosfomycin 2
Cefepime 1
Imipenem + cilastatin 1
Moxioxacin 1
Day 3 - 6 in ICU, new antibiotic prescribed to n=53/73 patients
Meropenem 17
Imipenem + cilastatin 9
Cefepime + sulbactam 7
Polymyxin B 7
Tigecycline 7
Cefoperazone + sulbactam 5
Levooxacin 2
Moxioxacin 2
Fosfomycin 2
Ampicillin + sulbactam 1
Cefazolin 1
Amikacin 1
Linezolid 1
Aer day 7 in ICU, new antibiotic prescribed to n=33/50 patients
Tigecycline 18
Polymyxin B 11
Meropenem 11
Co-trimoxazole 4
Imipenem + cilastatin 3
Fosfomycin 3
Linezolid 2
Ampicillin + sulbactam 1
Cefazolin 1
Cefepime + sulbactam 1
Amikacin 1
ICU = intensive care unit.
18 AJTCCM VOL. 30 NO. 1 2024
ORIGINAL RESEARCH: ARTICLES
significantly different. During the first days of ICU admission, K.
pneumoniae without acquired antibiotic resistance and MSSA prevailed.
As the ICU stay progressed, A. baumannii and carbapenem-resistant
K. pneumoniae became the predominant isolates. ese same micro-
organisms were the most common causative agents of documented
respiratory superinfections, aecting more than half of the patients.
In general, the resistance prole of the pathogens identied in the
present study did not dier from the pattern observed prior to the
pandemic. is trend is conrmed by the results of other Russian and
international studies.[19-21] For instance, in a study by Maes et al.,[19]
no signicant dierences in bacterial pathogens were found between
patients with ventilator-associated pneumonia with and without
COVID-19. However, the COVID-19 group had a signicantly higher
risk of developing ventilator-associated pneumonia, as well as isolated
cases of invasive aspergillosis.
In our study, we employed both culture and PCR to identify
potentially signicant bacterial pathogens. Cohen et al.[22] used culture
as the gold standard, and PCR showed high negative predictive values
(99.6%) and moderate positive predictive values (~60%). Similar results
were reported by Paz et al.[23] Pickens et al.[24] performed PCR on BAL
specimens from intubated COVID-19 patients to determine whether
antibiotics were necessary, and showed that they could be avoided in
75% of cases. Our study demonstrated generally good concordance
between the results obtained by the two methods. Additionally, PCR
appeared to detect the DNA of micro-organisms that oen turned
out to be clinically signicant infectious agents somewhat earlier.
Owing to the rapidity with which results may be obtained, PCR may
oer a promising alternative to culture for identifying nosocomial
pathogens. Furthermore, the additional detection of key resistance
genes, especially the presence and type of carbapenemases among
Enterobacterales, can enable earlier initiation of adequate antibiotic
therapy in the presence of clinical signs of infection. Meanwhile,
despite the advantages of PCR, it should be recognised that micro-
organisms detected by this method may be colonisers and do not
necessarily represent the true causative agents of LRTI.
Another important concern in patients with severe COVID-19 is the
timing of administration of systemic antibiotics. On the one hand, as
mentioned earlier, diagnosing nosocomial infections presents certain
objective challenges. On the other hand, early antibiotic prescription
for patients without clinical and laboratory signs of bacterial infection
not only increases the risk of adverse drug reactions but can also foster
colonisation by multidrug-resistant micro-organisms, which was
found in our study. Consequently, at least one-third of COVID-19
patients received antibiotic therapy either before transfer to the ICU
or during the initial days of their ICU stay, when the likelihood of
superinfection was low. Although patterns of antibiotic use were
beyond of the scope of the study, it is noteworthy that a substantial
proportion of drugs fell within the Watch and Reserve groups
according to the World Health Organization AWaRe (Access, Watch,
Reserve) classication. is nding is consistent with the results
of another Russian study, where the proportion of Watch group
antibiotics administered to COVID-19 ICU patients reached as high
as 70.4% and non-compliance with local guidelines reached 27%.[25]
Our study has some limitations. Firstly, ~9% of all observation
points were missed, potentially resulting in failure to identify micro-
organisms in some patients. Secondly, PCR was performed in only
about half of the samples, reducing the value of comparing it with
microbial culture. irdly, this single-centre study had a relatively
small sample size, making it challenging to extrapolate the ndings
to the general population.
Conclusion
To the best of our knowledge, this is one of a few prospective studies
that encompass clinical, microbiological and PCR monitoring of
patients with severe and critical COVID-19. e study conrms the
high prevalence of bacterial colonisation in the respiratory tract, which
appears quite early during the ICU stay, along with superinfections
predominantly caused by multidrug-resistant Gram-negative bacterial
pathogens. PCR testing can be considered as a swi and reliable tool
to rule out colonisation and facilitate the early detection of potential
bacterial superinfection.
Declaration. None.
Acknowledgements. None.
Author contributions. DS: data collection, conception and design of the
study, analysis and interpretation of the data, writing, review, approval
of the manuscript for submission; VK: data collection, approval of the
manuscript for submission; EB: data collection, microbial culture,
approval of the manuscript for submission; IS: data collection, analysis and
interpretation of the data, microbial culture, approval of the manuscript for
submission; YS: PCR testing, writing, and approval of the manuscript for
submission; DD: PCR testing, approval of the manuscript for submission;
SY: PCR testing, writing and approval of the manuscript for submission;
EG: PCR testing, approval of the manuscript for submission; ME: PCR
testing, approval of the manuscript for submission; NA: data collection,
approval of the manuscript for submission; AY: data collection, writing,
approval of the manuscript for submission; ST: analysis and interpretation
of the data, writing, review, approval of the manuscript for submission; SR:
conception and design of the study, analysis and interpretation of the data,
writing, review, approval of the manuscript for submission.
Funding.None.
Conicts of interest.None.
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Submitted 20 July 2023. Accepted 8 January 2024. Published 4 April 2024
