key: cord-0689769-hi26l1ua
authors: Bahçe, Yasemin Genç; Acer, Ömer; Özüdoğru, Osman
title: Evaluation of bacterial agents isolated from endotracheal aspirate cultures of Covid-19 general intensive care patients and their antibiotic resistance profiles compared to pre-pandemic conditions
date: 2022-01-15
journal: Microb Pathog
DOI: 10.1016/j.micpath.2022.105409
sha: 124a366867fd4755a01bbfedb3f006387fadbab9
doc_id: 689769
cord_uid: hi26l1ua

BACKGROUND: Early reports have shown that critically ill patients infected with SARS-CoV-2 have a high prevalence of nosocomial pneumonia, particularly ventilator-associated pneumonia (VAP). METHOD: In the present study, we determined the bacterial agents isolated in endotracheal aspirate (ETA) cultures of Covid-19 general intensive care patients and evaluated the antibiotic resistance profiles of common bacterial agents compared to the pre-pandemic period. RESULTS: While a total of 119 significant growths with polymicrobial growths were detected in the ETA cultures of 73 (7.5%) of 971 patients hospitalized in the intensive care unit before the pandemic, 87 significant growths were detected in the ETA cultures of 67 (11.1%) of 602 patients hospitalized in the Covid-19 intensive care unit (ICU) after the pandemic. While 61 (83.6%) of patients in the ICU died before the pandemic, 63 (94.0%) of patients in the Covid-19 ICU died after the pandemic. In terms of age, gender, and mortality, there was no significant difference between the two ICUs (p > 0.05). Before the pandemic, the mean length of stay in the ICU was 33.59 ± 32.89 days, and after the pandemic, it was 13.49 ± 8.03 days. This was a statistically significant difference (p < 0.05). Acinetobacter baumannii (28.5%), Klebsiella pneumoniae (22.6%), Pseudomonas aeruginosa (15.9%), Staphylococcus aureus (6.7%), Escherichia coli (7.5%), Candida spp. (5.0%) were the most prevalent causal bacteria discovered in pre-pandemic ICU ETA samples, whereas A. baumannii (54.0%), K. pneumoniae (10.3%), P. aeruginosa (6.8%), E. faecium (8%), and Candida spp.(13.7%) were the most common causative microorganisms detected in Covid-19 ICU ETA samples. Except for tigecycline, antibiotic resistance rates in A. baumannii strains increased following the pandemic. Only tobramycin showed a significant difference in the increase of resistance among these antibiotics (p = 0.037). The rate of tigecycline resistance, on the other hand, was 17.6% before the pandemic and 2.2% afterward (p < 0.05). After the pandemic, increased resistance of K. pneumoniae strains to colistin, meropenem, ertapenem, amoxicillin-clavulanic acid, piperacillin-tazobactam, ciprofloxacin, tigecycline, and cefepime antibiotics was observed. However, these increases were not statistically significant. Except for imipenem, antibiotic resistance rates in P. aeruginosa strains increased following the pandemic. The resistance rise of the antibiotics ceftazidime and levofloxacin was shown to be significantly different (p < 0.05). CONCLUSION: As a result, the Covid-19 pandemic requires intensive care follow-ups at an earlier age and with a more mortal course. Although the length of stay in the intensive care unit has been shortened, it is observed that this situation is observed due to early mortality. In P. aeruginosa strains, a significant difference was detected in the resistance increase of the ceftazidime and levofloxacin (p < 0.05) and with the exception of tigecycline, antibiotic resistance rates in A. baumannii strains increased following the pandemic. Only tobramycin showed a significant difference in the increase of resistance among these antibiotics (p = 0.037). Secondary infections in patients create more difficult treatment processes due to both Covid-19 and increasing antibiotic resistance today.

Coronavirus disease 2019 (Covid- 19) was first identified in December 2019 in Wuhan, China, and has spread all over the world. It is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Covid-19 is a respiratory illness with flu-like symptoms, manifesting as dry cough, fever, severe headache, and fatigue [1] . Viral agents causing respiratory tract infections predispose to secondary bacterial infections due to their effects on the immune system [2, 3] . Through a variety of mechanisms, viral infections have been shown to enhance bacterial colonization of the airway. Changes in mucus secretion, cell death, hyperplasia, decreased mucosal clearance, decreased oxygen exchange, and impaired surfactant secretion are among the negative effects [4, 5] . Depending on the virus, the type of bacteria, and the intensity of the host immune response against a bacterium or virus, each of these effects are caused by a variety of molecular mechanisms. Secondary or bacterial coinfections with other viruses can greatly increase the mortality rate in patients with viral infections, according to laboratory, clinical, and epidemiological investigations [6, 7] . In the 2009 H1N1 influenza pandemic, 4-33% of hospitalized patients were complicated by bacterial pneumonia [8] . Up to 30% of patients were diagnosed with secondary bacterial infections during the first SARS-CoV outbreak in 2003, and coinfection was positively associated with disease severity [9] . Bacterial coinfections are also prevalent in 2% to 65% of cases during normal flu seasons and have been linked to morbidity and mortality [10] .

Early reports have shown that critically ill patients infected with SARS-CoV-2 have a high prevalence of nosocomial pneumonia, particularly ventilator-associated pneumonia (VAP) [11] . Multiple broad-spectrum antibacterial agents were utilized during the Covid-19 outbreak, and the great majority of patients hospitalized with Covid-19 were given empirical antimicrobial therapy before secondary bacterial infections were confirmed [11, 12] .

Guidelines, on the other hand, advocate the use of culture-based approaches to limit overdiagnosis and facilitate appropriate antimicrobial therapy in VAP [13] . Therefore, determining the causative microorganisms and their antibiotic susceptibility in these units is important to both guide empirical treatment and to reduce mortality and morbidity [14] .

In this study; It was aimed to determine the bacterial agents isolated in ETA cultures of Covid-19 general intensive care patients and to evaluate the antibiotic resistance profiles of common bacterial agents compared to the pre-pandemic period. ETA samples taken into a Luken tube were evaluated in the microbiology laboratory. An equal amount of sterile saline was added to the samples and mixed. 0.01 mL of this mixture was inoculated on 5% sheep blood agar, Eosin-Methylene blue (EMB) agar, and chocolate agar media. The preparation was prepared from the samples for microscopic evaluation and stained by the gram method. The quality of the sample, the predominant microorganisms, and leukocytes were investigated.

The samples were incubated in an incubator at 37 °C for 24-48 hours. Growing bacteria were evaluated quantitatively and growths of 10 5 CFU/mL and above were considered significant [15, 16] . When the same agent was grown in more than one ETA culture of the same patient, only the first isolated strain was evaluated. Identification of bacteria and their antibiotic susceptibility were determined by the VITEK 2 (bioMerieux, France) automated identification system. The results were evaluated according to the "European Committee for Antimicrobial Susceptibility Tests "(EUCAST) standard.

Statistical analysis of the data was carried out with the Statistical Package for Social Science for Windows (SPSS) 26 program and it was studied with a confidence level of 95%. A value of p < J o u r n a l P r e -p r o o f 0.05 was considered statistically significant. In the study; a Chi-square test was applied to compare the antibiotic resistance profiles of common bacterial agents in ETA cultures of Covid-19 intensive care patients compared to the pre-pandemic period. The length of stay did not show a normal distribution, so the Mann-Whitney test was used. Chi-square test for mortality was used in relation to gender, and independent groups t-test was used in relation to age (showing normal distribution).

ETA cultures of 73 (7.5%) of 971 patients hospitalized in the ICU before the pandemic had a total of 119 significant growths, together with polymicrobial growths. 49 (67.1%) of the patients considered as causative were male, 24 (32.9%) were female; the mean age of men was found as 69.45±17.78, and the mean age of women was 76.38±16.30. After the pandemic, there were 87 significant growths in the ETA cultures of 67 (11.1%) of 602 patients hospitalized in the Covid-19 ICU. Of the patients considered as causative, 42 (62.7%) were male, 25 (37.3%) were female; the mean age of men was found as 70.31±11.76, and the mean age of women was found as 72.08±11.49. While 61 (83.6%) of the patients in the ICU died before the pandemic, 63 (94.0%) of the patients in the Covid-19 ICU died after the pandemic. There was no significant difference between the two ICUs in terms of age, gender, and mortality (p>0.05) ( Table 1 ). The mean length of stay in the ICU was found as 33.59±32.89 before the pandemic, and 13.49±8.03 in the post-pandemic ICU. This difference was statistically significant (p<0.05).

The most common causative microorganisms detected in pre-pandemic ICU ETA samples were before the pandemic and decreased to 2.2% after the pandemic. This difference was statistically significant (p<0.05). When the antibiotic resistance rates of K. pneumoniae strains were compared, an increase in resistance was observed in gentamicin, colistin, meropenem, ertapenem, amoxicillin-clavulanic acid, piperacillin tazobactam, ciprofloxacin, tigecycline, and cefepime antibiotics after the pandemic. However, these increases were not statistically

significant. An increase in antibiotic resistance rates was detected in P. aeruginosa strains after the pandemic, except for imipenem. A significant difference was found in the resistance increase of the studied antibiotics ceftazidime and levofloxacin (p<0.05).

The pandemic of SARS-CoV-2 infection in early 2020 hit most countries in the world seriously, in Acinetobacter strains was determined as 100%, and the rates of resistance to netilmicin and colistin were determined as 48.5% and 0%, respectively [23] . Similarly, in our study, carbapenem resistance in A. baumannii isolates was found to be 100%, colistin resistance was 0%, netilmicin resistance was found to be 30% before the pandemic and 44% after the pandemic. Colistin has become almost the only option for A. baumannii strains, which are the most common agents in ETA cultures in ICUs in our hospital. In our study, although more intensive care unit admissions were observed in the pre-pandemic period, A. baumannii infection was found much more frequently in patients followed up during the pandemic period.

In different studies on resistance, an increase in resistance rates in Gram-negative bacilli has been demonstrated [32, 33] . In our study, resistance increase occurred in almost all antibiotics we examined over the years in K. pneumoniae and P. aeruginosa isolates, which are the most J o u r n a l P r e -p r o o f common pathogens seen in ETA cultures after A. baumannii in both intensive care units. The increase in resistance in K. pneumoniae strains was not found statistically significant (p>0.05).

In P. aeruginosa strains, a significant difference was found in the resistance increase of the studied antibiotics ceftazidime and levofloxacin (p<0.05). The reason for this increase in resistance may be the increased need for antibiotics in Covid-19 patients or the increased use of unnecessary empirical antibiotics. Given the potential misuse of empirical broad-spectrum antibiotics in severe Covid-19 patients, the focus should be on the careful use of antibiotics based on culture results to reduce the development of resistance [34].

In conclusion, as seen in our study, the Covid-19 pandemic requires intensive care follow-ups at an earlier age and with a more mortal course. Although the length of stay in the intensive care unit has been shortened, it is observed that this situation is observed due to early mortality.

In P. aeruginosa strains, a significant difference was detected in the resistance increase of the ceftazidime and levofloxacin (p<0.05). With the exception of tigecycline, antibiotic resistance rates in A. baumannii strains increased following the pandemic. Only tobramycin showed a significant difference in the increase of resistance among these antibiotics (p=0.037). 

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European Centre for Disease Prevention and Control Stockholm; 2017. 1. In the present study, we determined the bacterial agents isolated in endotracheal aspirate (ETA) cultures of Covid-19 general intensive care patients and evaluated the antibiotic resistance profiles of common

Although the length of stay in the intensive care unit has been shortened, it is observed that this situation is observed due to early mortality

aeruginosa strains, a significant difference was detected in the resistance increase of the ceftazidime and levofloxacin (p<0.05) and with the exception of tigecycline

A. baumannii strains increased following the pandemic. Only tobramycin showed a significant difference in the increase of resistance among these antibiotics

Secondary infections in patients create more difficult treatment processes due to both Covid-19 and increasing antibiotic resistance today

J o u r n a l P r e -p r o o f J o u r n a l P r e -p r o o f J o u r n a l P r e -p r o o f J o u r n a l P r e -p r o o f

☒ The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.☐The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:J o u r n a l P r e -p r o o f