Pathogen distribution and microbial resistance pattern in endotracheal aspirate samples of intensive care unit patients before and after the COVID-19 pandemic
Öz
Aims: The aim of this study is to evaluate the distribution of pathogen microorganisms and antimicrobial resistance rates isolated from endotracheal aspirate (ETA) samples of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) polymerase chain reaction (PCR) positive and negative patients followed and treated in the intensive care unit (ICU) of our hospital, and to examine the effect of the COVID-19 (coronavirus disease 2019) pandemic on this.
Methods: In this study, ETA samples sent to the microbiology laboratory from hospitalized patients in Tekirdağ Namık Kemal University Hospital general ICU-1 and general ICU-2 between March 11, 2018 and March 10, 2022 were retrospectively analyzed. During the COVID-19 pandemic, it was used to follow up patients with SARS-CoV-2 PCR positive in ICU-1 and SARS-CoV-2 PCR negative patients in ICU-2. The working period is divided into two parts as pre-pandemic (2018 - 2019) and post-pandemic (2020 - 2021). Bacterial identification and antibiotic susceptibility tests were performed using conventional methods and automated systems. Colistin sensitivity was studied by broth microdilution, and ceftazidime avibactam (CZA) sensitivity was studied by disk diffusion method. Statistical analysis was performed with the chi-square test, p<0.05 was considered significant.
Results: A total of 1669 ETA samples from 856 patients were sent to our laboratory over a four-years period, and culture positivity was detected in 63.6% of the samples. With the COVID-19 pandemic, it was found that the culture positivity increased significantly in ETA samples of patients hospitalized in ICU-1, and there were no significant difference in ICU-2. 836 isolates from 1061 specimens were included to the study. The three most commonly isolated pathogens were Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae, respectively. While P. aeruginosa was the most frequently isolated microorganism in both ICU-1 and ICU-2 in the pre-pandemic period, it was replaced by A. baumannii in both clinics with the pandemic, and the increase in the frequency of A. baumannii in ICU-1 was statistically significant. Antibiotic resistance rates were generally found to be higher in ICU-1 than in ICU-2, and even in ICU-2, resistance rates to some antimicrobials were found to be decreased. In A. baumannii, a statistically significant increase was observed in the resistance rates against all antibiotics, including colistin, in ICU-1, and a significant increase was found in resistance only against amikacin in ICU-2. In P. aeruginosa, a significant increase was found in the resistance rates against cephalosporins and carbapenems in ICU-1, ceftazidime, ciprofloxacin and colistin in ICU-2, and a significant decrease in resistance to amikacin in ICU-2. In K. pneumoniae, a significant increase was found in the resistance rates against amoxicillin-clavulanate (AMC), ceftriaxone, ertapenem, amikacin and colistin in ICU-1, ertapenem and amikacin in ICU-2, and a significant decrease in resistance to AMC and all cephalosporins in ICU-2. CZA susceptibility in K. pneumoniae isolates was examined in 2020 and 2021, and no resistance was found in either clinic.
Conclusion: In our study, it was determined that the culture positivity rate in ETA samples increased, the distribution of pathogen microorganisms and antimicrobial resistance rates changed with the COVID-19 pandemic. For this reason, it is important to follow up possible pathogen microorganisms and antimicrobial resistance rates during similar pandemic periods such as COVID-19.
Anahtar Kelimeler
antimicrobial resistance COVID-19 endotracheal aspirate pathogen microorganism
Proje Numarası
yok
Kaynakça
- Artik Y, Cosgun AB, Cesur NP, et al. Comparison of COVID‐19 laboratory diagnosis by commercial kits:Effectivity of RT‐PCR to the RT‐LAMP. J Med Virol. 2022;94(5):1998–2007.
- Budak F, Korkmaz S. An overall evaluation for the COVID-19 pandemic process: the case of Turkey. SAYOD. 2020;1:62-79.
- Ayoglu H. Intensive care approach in COVID-19 patients. Turk J Diab Obes. 2020;4(2):183-193.
- Langford BJ, So M, Raybardhan S, et al. Bacterial co-infection and secondary infection in patients with COVID-19:A living rapid review and metaanalysis. Clin Microbiol Infect. 2020;26(12):1622-1629.
- Huttner BD, Catho G, Pano-Pardo JR, Pulcini C, Schouten J. COVID-19:Don't neglect antimicrobial stewardship principles! Clin Microbiol Infect. 2020;26(7):808-810.
- Hamidi AA, Yılmaz S. Antibiotic consumption in the hospital during COVID-19 pandemic, distribution of bacterial agents and antimicrobial resistance: a single-center study. J Surg Med. 2021;5(2):124-127.
- Rawson TM, Moore LSP, Zhu N, et al. Bacterial and fungal co-infection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis. 2020;71(9):2459-2468.
- Centers for Disease Control and Prevention:Guideline for Prevention of Health–Care-Associated Pneumonia. MMWR. 2004;53:1-36.
- Solunum Sistemi Örneklerinin Laboratuvar İncelemesi Rehberi, sayfa 27-41. KLİMUD, 2. Baskı, 2022 / Ankara.
- European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters Version 9.0, http://www.eucast.org [erişim 01.10.2022].
- Thomsen K, Pedersen HP, Iversen S, et al. Extensive microbiological respiratory tract specimen characterization in critically ill COVID-19 patients. APMIS. 2021;129(7):431-437.
- Bahçe YG, Acer Ö, Özüdoğru O. 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. Microb Pathog. 2022;164:105409.
- Rafat Z, Ramandi A, Khaki PA, et al. Fungal and bacterial co-infections of the respiratory tract among patients with COVID-19 hospitalized in intensive care units. Gene Reports. 2022;27:101588-101593.
- Duran H, Ceken N, Atik TK. Bacteria Isolated from endotracheal aspirate samples and antibiotic resistance rates: 5-year retrospective analysis. J Med Sci. 2021;41(3):327-334.
- Ayvalık T, Cetin ES, Sirin MC, Arıdogan BC, Yagcı S. Antibiotic resistance rates of bacteria isolated from endotracheal aspirate samples of intensive care unit patients. SDÜ Tıp Fak Derg. 2022:29(3):398-404.
- Sharifipour E, Shams S, Esmkhani M, et al. Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU. BMC Infec Dis. 2020;20:646-653.
- Molina FJ, Botero LE, Isaza JP, et al. Diagnostic concordance between BioFire® FilmArray® pneumonia panel and culture in patients with COVID-19 pneumonia admitted to intensive care units: the experience of the third wave in eight hospitals in Colombia. Crit Care. 2022;26(1):130.
- Karatas M, Yasar-Duman M, Tunger A, Cilli F, Aydemir S, Ozenci V. Secondary bacterial infections and antimicrobial resistance in COVID-19: comparative evaluation of pre-pandemic and pandemic-era, a retrospective single center study. Ann Clin Microbiol Antimicrob. 2021;20(1):51-59.
- Nordmann P, Poirel L. Epidemiology and diagnostics of carbapenem resistance in Gram-negative bacteria. Clin Infec Dis. 2019;69(7):521-528.
- Sarikaya A, Mumcuoglu I, Baran I, Aksoy A, Dinc B. Comparision of colistin broth disc elution, rapid resapolymyxin NP and broth microdilution methods in determining colistin sensitivity in Acinetobacter, Pseudomonas and Enterobacterales species. Mikrobiyol Bul. 2022;56(3):404-415.
- Caycı YT, Seyfi Z, Vural DG, Bilgin K, Birinci A. Investigation of growth and antibiotic susceptibility in bacterial culture samples of patients diagnosed with COVID-19. Saglik Bil Deger. 2022;12(2):199-202.
- Rao CM, Rout P, Pattnaik AP, Singh N, Rajendran A, Patro S. The microbial profile and resistance pattern of pathogens isolated from long COVID pneumonia patients and their correlation to clinical outcome: our experience from a tertiary care hospital. Cureus. 2022;14(3):23644-23656.
- Havuz SG. Acinetobacter baumannii strains grown in endotracheal aspirate culture in Samsun Bafra State Hospital intensive care units and the effect of COVID-19 on Acinetobacter baumannii strains (2019-2020). Turk Hij Den Biyol Derg. 2022;79(2):229–242.
- Kocabas D, Ozbek N, Aydın NN, et al. Evaluation of colistin sensitivity in samples isolated from blood in intensive care units. KÜ Tıp Fak Derg. 2021;23(2):385-394.
- Gorgun S, Usanmaz M, Odabası H. A meta-analysis study on colistin resistance in Acinetobacter baumannii species in Turkey. WJARR. 2021;10(02):90–97.
- Aygar IS. In vitro evaluation of the increase in MIC value of colistin in the carbapenem resistant Klebsiella pneumoniae strains over the years. Turk Mikrobiyol Cemiy Derg. 2020;50(3):164-171.
- Yakut S. Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa ve Acinetobacter baumannii klinik izolatlarında kolistin direnci saptanmasında BD Phoenix yarı otomatize sistem ve sıvı mikrodilüsyon yöntemlerinin karşılaştırılması. Tıpta Uzmanlık Tezi, Diyarbakır 2019.
- Hosbul T, Aydogan CN, Kaya S, Bedir O, Ozcan H, Gumral R. In vitro activity of ceftazidime-avibactam and colistin against carbapenem-resistant Pseudomonas aeruginosa clinical isolates. J Ist Faculty Med. 2022;85(3):355-361.
- Oztaş S, Er DK, Dundar D. Antimicrobial resistance of various antimicrobial agents in carbapenem resistant and susceptible isolates of Klebsiella pneumoniae. KOU Sag Bil Derg. 2022;8(3):229-232.
- Knight GM, Glover RE, McQuaid CF, et al. Antimicrobial resistance and COVID-19: intersections and implications. eLife. 2021;10:64139-64166.
Öz
Destekleyen Kurum
yok
Proje Numarası
yok
Teşekkür
yok
Kaynakça
- Artik Y, Cosgun AB, Cesur NP, et al. Comparison of COVID‐19 laboratory diagnosis by commercial kits:Effectivity of RT‐PCR to the RT‐LAMP. J Med Virol. 2022;94(5):1998–2007.
- Budak F, Korkmaz S. An overall evaluation for the COVID-19 pandemic process: the case of Turkey. SAYOD. 2020;1:62-79.
- Ayoglu H. Intensive care approach in COVID-19 patients. Turk J Diab Obes. 2020;4(2):183-193.
- Langford BJ, So M, Raybardhan S, et al. Bacterial co-infection and secondary infection in patients with COVID-19:A living rapid review and metaanalysis. Clin Microbiol Infect. 2020;26(12):1622-1629.
- Huttner BD, Catho G, Pano-Pardo JR, Pulcini C, Schouten J. COVID-19:Don't neglect antimicrobial stewardship principles! Clin Microbiol Infect. 2020;26(7):808-810.
- Hamidi AA, Yılmaz S. Antibiotic consumption in the hospital during COVID-19 pandemic, distribution of bacterial agents and antimicrobial resistance: a single-center study. J Surg Med. 2021;5(2):124-127.
- Rawson TM, Moore LSP, Zhu N, et al. Bacterial and fungal co-infection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis. 2020;71(9):2459-2468.
- Centers for Disease Control and Prevention:Guideline for Prevention of Health–Care-Associated Pneumonia. MMWR. 2004;53:1-36.
- Solunum Sistemi Örneklerinin Laboratuvar İncelemesi Rehberi, sayfa 27-41. KLİMUD, 2. Baskı, 2022 / Ankara.
- European Committee on Antimicrobial Susceptibility Testing. Breakpoint tables for interpretation of MICs and zone diameters Version 9.0, http://www.eucast.org [erişim 01.10.2022].
- Thomsen K, Pedersen HP, Iversen S, et al. Extensive microbiological respiratory tract specimen characterization in critically ill COVID-19 patients. APMIS. 2021;129(7):431-437.
- Bahçe YG, Acer Ö, Özüdoğru O. 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. Microb Pathog. 2022;164:105409.
- Rafat Z, Ramandi A, Khaki PA, et al. Fungal and bacterial co-infections of the respiratory tract among patients with COVID-19 hospitalized in intensive care units. Gene Reports. 2022;27:101588-101593.
- Duran H, Ceken N, Atik TK. Bacteria Isolated from endotracheal aspirate samples and antibiotic resistance rates: 5-year retrospective analysis. J Med Sci. 2021;41(3):327-334.
- Ayvalık T, Cetin ES, Sirin MC, Arıdogan BC, Yagcı S. Antibiotic resistance rates of bacteria isolated from endotracheal aspirate samples of intensive care unit patients. SDÜ Tıp Fak Derg. 2022:29(3):398-404.
- Sharifipour E, Shams S, Esmkhani M, et al. Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU. BMC Infec Dis. 2020;20:646-653.
- Molina FJ, Botero LE, Isaza JP, et al. Diagnostic concordance between BioFire® FilmArray® pneumonia panel and culture in patients with COVID-19 pneumonia admitted to intensive care units: the experience of the third wave in eight hospitals in Colombia. Crit Care. 2022;26(1):130.
- Karatas M, Yasar-Duman M, Tunger A, Cilli F, Aydemir S, Ozenci V. Secondary bacterial infections and antimicrobial resistance in COVID-19: comparative evaluation of pre-pandemic and pandemic-era, a retrospective single center study. Ann Clin Microbiol Antimicrob. 2021;20(1):51-59.
- Nordmann P, Poirel L. Epidemiology and diagnostics of carbapenem resistance in Gram-negative bacteria. Clin Infec Dis. 2019;69(7):521-528.
- Sarikaya A, Mumcuoglu I, Baran I, Aksoy A, Dinc B. Comparision of colistin broth disc elution, rapid resapolymyxin NP and broth microdilution methods in determining colistin sensitivity in Acinetobacter, Pseudomonas and Enterobacterales species. Mikrobiyol Bul. 2022;56(3):404-415.
- Caycı YT, Seyfi Z, Vural DG, Bilgin K, Birinci A. Investigation of growth and antibiotic susceptibility in bacterial culture samples of patients diagnosed with COVID-19. Saglik Bil Deger. 2022;12(2):199-202.
- Rao CM, Rout P, Pattnaik AP, Singh N, Rajendran A, Patro S. The microbial profile and resistance pattern of pathogens isolated from long COVID pneumonia patients and their correlation to clinical outcome: our experience from a tertiary care hospital. Cureus. 2022;14(3):23644-23656.
- Havuz SG. Acinetobacter baumannii strains grown in endotracheal aspirate culture in Samsun Bafra State Hospital intensive care units and the effect of COVID-19 on Acinetobacter baumannii strains (2019-2020). Turk Hij Den Biyol Derg. 2022;79(2):229–242.
- Kocabas D, Ozbek N, Aydın NN, et al. Evaluation of colistin sensitivity in samples isolated from blood in intensive care units. KÜ Tıp Fak Derg. 2021;23(2):385-394.
- Gorgun S, Usanmaz M, Odabası H. A meta-analysis study on colistin resistance in Acinetobacter baumannii species in Turkey. WJARR. 2021;10(02):90–97.
- Aygar IS. In vitro evaluation of the increase in MIC value of colistin in the carbapenem resistant Klebsiella pneumoniae strains over the years. Turk Mikrobiyol Cemiy Derg. 2020;50(3):164-171.
- Yakut S. Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa ve Acinetobacter baumannii klinik izolatlarında kolistin direnci saptanmasında BD Phoenix yarı otomatize sistem ve sıvı mikrodilüsyon yöntemlerinin karşılaştırılması. Tıpta Uzmanlık Tezi, Diyarbakır 2019.
- Hosbul T, Aydogan CN, Kaya S, Bedir O, Ozcan H, Gumral R. In vitro activity of ceftazidime-avibactam and colistin against carbapenem-resistant Pseudomonas aeruginosa clinical isolates. J Ist Faculty Med. 2022;85(3):355-361.
- Oztaş S, Er DK, Dundar D. Antimicrobial resistance of various antimicrobial agents in carbapenem resistant and susceptible isolates of Klebsiella pneumoniae. KOU Sag Bil Derg. 2022;8(3):229-232.
- Knight GM, Glover RE, McQuaid CF, et al. Antimicrobial resistance and COVID-19: intersections and implications. eLife. 2021;10:64139-64166.
Ayrıntılar
| Birincil Dil | İngilizce |
|---|---|
| Konular | Sağlık Kurumları Yönetimi |
| Bölüm | Orijinal Makale |
| Yazarlar | |
| Proje Numarası | yok |
| Erken Görünüm Tarihi | 28 Ekim 2023 |
| Yayımlanma Tarihi | 29 Ekim 2023 |
| Yayımlandığı Sayı | Yıl 2023 Cilt: 6 Sayı: 6 |
Üniversitelerarası Kurul (ÜAK) Eşdeğerliği: Ulakbim TR Dizin'de olan dergilerde yayımlanan makale [10 PUAN] ve 1a, b, c hariç uluslararası indekslerde (1d) olan dergilerde yayımlanan makale [5 PUAN]
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Not: Dergimiz WOS indeksli değildir ve bu nedenle Q olarak sınıflandırılmamıştır.
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