Research Article
Secondary Bacterial Agents and Antibiotic Resistance Profiles in Respiratory Tract Specimens of Patients with COVID-19 Pneumonia
Abstract
Objective: To assess secondary bacterial pneumonia agents and antibiotic resistance rates in patients with COVID-19 pneumonia and to compare findings with the pre-pandemic period.
Materials and Methods: Bacteria grown in endotracheal aspirate fluid and bronchoalveolar fluid samples of patients diagnosed with COVID-19 between January 2020 and December 2020, and antibiotic resistance rates were retrospectively compared with samples of the year before the pandemic. Isolates were identified at the species level with an automated system (VITEK 2, bioMérieux, France), and antimicrobial susceptibility was determined according to EUCAST criteria.
Results: A total of 900 culture results were examined in 2019. Acinetobacter baumannii was detected in 36%, Klebsiella pneumoniae in 23%, Pseudomonas aeruginosa in 14%, and Staphylococcus aureus in 8%. In 2020, 660 culture results were examined, and the same bacteria were detected in 43%, 23%, 16%, and 5%, respectively. K. pneumoniae's resistance to third-generation cephalosporins, and A. baumannii's resistance to gentamycin and tobramycin, were found to have increased significantly during the pandemic period.
Conclusions: The growth of multidrug-resistant Gram-negative bacteria was frequently detected in respiratory secretions obtained during the COVID-19 pandemic. Regional bacterial agents and antibiotic resistance profiles should be clarified, and empirical therapy should be selected accordingly in COVID-19.
Supporting Institution
YOK
Project Number
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Thanks
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References
- 1. Liu HH, Yaron D, Piraino AS, Kapelusznik L. Bacterial and fungal growth in sputum cultures from 165 COVID-19 pneumonia patients requiring intubation: evidence for antimicrobial resistance development and analysis of risk factors. Ann Clin Microbiol Antimicrob. 2021;20(1):1-13. doi:10.1186/s12941-021-00472-5
- 2. Khurana S, Singh P, Shara N, et al. Profile of co-infections & secondary infections in COVID-19 patients at a dedicated COVID-19 facility of a tertiary care Indian hospital: Implication on antimicrobial resistance. Indian J Med Microbiol. 2021;39(2):147-153. doi:10.1016/j.ijmmb.2020.10.014
- 3. Zhang H, Zhang Y, Wu J, et al. Risks and features of secondary infections in severe and critical ill COVID-19 patients. Emerg Microbes Infect. 2020;9(1):1958-1964. doi:10.1080/22221751.2020.1812437
- 4. Ceballos ME, Nuñez C, Uribe J, et al. Corticosteroids use and risk of respiratory coinfections in mechanically ventilated patients with COVID-19. Research Square 2021. doi:10.21203/rs.3.rs-966047/v1
- 5. Soltani S, Zakeri A, Zandi M, et al. The role of bacterial and fungal human respiratory microbiota in COVID-19 patients. BioMed Research International 2021. doi:10.1155/2021/6670798
- 6. Bengoechea JA, Bamford CG. SARS-CoV-2, bacterial co-infections, and AMR: the deadly trio in COVID-19? EMBO Mol Med. 2020;12(7):e12560. doi:10.15252/emmm.202012560
- 7. Rollas K, Ersan G, Zincircioğlu C, et al. Septic shock in patients admitted to intensive care unit with COVID-19 pneumonia. Eurasian J Pulmonol. 2021;23(2):95-100. doi:10.4103/ejop.ejop_101_20
- 8. Guo M, Gao M, Gao J, et al. Identifying risk factors for secondary infection post-SARS-CoV-2 infection in patients with severe and critical COVID-19. Frontiers in Immunology 2021;3601. doi:10.3389/fimmu.2021.715023
- 9. Mutlu TA, Bozok T. COVID-19 Hastalarının alt solunum yolu örneklerinden izole edilen bakteriyel etkenlerin identifikasyonu ve antibakteriyel direnç paternlerinin incelenmesi. Türk Mikrobiyol Cemiy Derg. 2022;52(1):48-55. doi:10.54453/TMCD.2022.98105
- 10. Rollas K, Şenoğlu N. Management of Covid-19 patients in intensive care unit. The Journal of Tepecik Education and Research Hospital. 2020;30:142-55. doi:10.5222/terh.2020.77044
- 11. Elabbadi A, Turpin M, Gerotziafas GT. Bacterial coinfection in critically ill COVID-19 patients with severe pneumonia. Infection 2021; 49(3): 559-562. doi:10.1007/s15010-020-01553-x
- 12. Işık SA, Şaylan B, Yenilmez E. Ağır Covid-19’da bakteriyel pnömoni riski artıyor mu? Mersin Univ Saglık Bilim Derg. 2021;14(2):291-297. doi:10.26559/mersinsbd.900945
- 13. Senok A, Alfaresi M, Khansaheb H, et al. Coinfections in patients hospitalized with COVID-19: a descriptive study from the United Arab Emirates. Infect Drug Resist. 2021;14:2289-2296. doi:10.2147/IDR.S314029
- 14. Li J, Wang J, Yang Y, et al. Etiology and antimicrobial resistance of secondary bacterial infections in patients hospitalized with COVID-19 in Wuhan, China: a retrospective analysis. Antimicrobial Resistance & Infection Control. 2020;9(1):1-7. doi:10.1186/s13756-020-00819-1
- 15. Morris DE, Cleary DW, Clarke SC. Secondary bacterial infections associated with influenza pandemics. Front. Microbiol. 2017;8:1041. doi:10.3389/fmicb.2017.01041
- 16. Lansbury L, Lim B, Baskaran V, Lim W. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect. 2020;81(2):266-275. doi:10.1016/j.jinf.2020.05.046
- 17. Langford BJ, So M, Raybardhan S, et al. Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis. Clin Microbiol Infect. 2020;26(12):1622-1629. doi:10.1016/j.cmi.2020.07.016
- 18. Caméléna F, Moy AC, Dudoignon E, et al. Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19. Diagn Microbiol Infect Dis. 2021;99(1):115183. doi:10.1016/j.diagmicrobio.2020.115183
- 19. Yoo IY, Huh K, Shim HJ, et al. Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens. Int J Infect Dis. 2020;95:326-331. doi:10.1016/j.ijid.2020.03.024
- 20. Timbrook TT, Hueth KD, Ginocchio CC. Identification of bacterial co-detections in COVID-19 critically ill patients by BioFire® FilmArray® pneumonia panel: a systematic review and meta-analysis. Diagn Microbiol Infect Dis. 2021;101(3):115476. doi:10.1016/j.diagmicrobio.2021.115476
- 21. Zhu X, Ge Y, Wu T, et al. Co-infection with respiratory pathogens among COVID-2019 cases. Virus Res. 2020;285:198005. doi:10.1016/j.virusres.2020.198005
- 22. Grasselli G, Cattaneo E, Florio G. Secondary infections in critically ill patients with COVID-19. Critical Care. 2021;25(1):1-6. doi:10.1186/s13054-021-03672-9
- 23. Rawson TM, Moore LS, Zhu N, et al. Bacterial and fungal coinfection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis 2020;71(9):2459-2468. doi:10.1093/cid/ciaa530
- 24. Aydemir O, Aydemir Y, Şahin EO, Şahin F, Koroglu M, Erdem AF. Secondary bacterial infection in patients with coronavirus disease-2019 associated pneumonia. Revista da Associação Médica Brasileira. 2022;68:142-146. doi:10.1590/1806-9282.20210745
COVID-19 Pnömonili Hastaların Solunum Yolu Örneklerinde Sekonder Bakteriyel Ajanlar ve Antibiyotik Direnç Profilleri
Abstract
Amaç: COVID-19 pnömonisi olan hastalardaki sekonder bakteriyel pnömoni etkenleri ve antibiyotik direnç oranlarının değerlendirilmesi ve sonuçların pandemi öncesi dönemle karşılaştırılmasıdır.
Materyal ve Metot: Ocak 2020-Aralık 2020 arasında COVID-19 tanısı konan hastaların endotrakeal aspirat sıvı ve bronkoalveolar sıvı örneklerinde üreyen bakteriler ve antibiyotik direnç oranları, pandemiden önceki yıl gelen hasta örnekleriyle retrospektif olarak karşılaştırılmıştır. Kültürde üremesi olan örnekler, otomatize sistemle (VITEK 2, bioMérieux, France) tür düzeyinde tanımlanmış ve antimikrobiyal duyarlılıkları EUCAST kriterlerine göre değerlendirilmiştir.
Bulgular: 2019 da mikrobiyolojik kültürlerinde üreme saptanan 900 hasta örneği incelendi. Acinetobacter baumannii %36, Klebsiella pneumoniae %23, Pseudomonas aeruginosa %14, Staphylococcus aureus ise %8 oranında saptandı. 2020 de ise 660 hasta örneği incelendi ve sırasıyla aynı bakteriler %43, %23, %16 ve %5 oranında saptandı. K. pneumoniae'nin 3. kuşak sefalosporin direncinde ve A. baumannii'nin gentamisin ve tobramisin direncinde pandemi öncesine göre anlamlı bir artış görüldü.
Sonuç: COVID-19 pandemisinde solunum sekresyonlarında çoğunlukla çok ilaca dirençli Gram negatif bakterilerin ürediği görüldü. COVID-19 hastalığı olanlarda, bölgesel bakteriyel etkenler ve antibiyotik direnç profilleri bilinip, uygun ampirik tedavi seçilmelidir.
Project Number
-
References
- 1. Liu HH, Yaron D, Piraino AS, Kapelusznik L. Bacterial and fungal growth in sputum cultures from 165 COVID-19 pneumonia patients requiring intubation: evidence for antimicrobial resistance development and analysis of risk factors. Ann Clin Microbiol Antimicrob. 2021;20(1):1-13. doi:10.1186/s12941-021-00472-5
- 2. Khurana S, Singh P, Shara N, et al. Profile of co-infections & secondary infections in COVID-19 patients at a dedicated COVID-19 facility of a tertiary care Indian hospital: Implication on antimicrobial resistance. Indian J Med Microbiol. 2021;39(2):147-153. doi:10.1016/j.ijmmb.2020.10.014
- 3. Zhang H, Zhang Y, Wu J, et al. Risks and features of secondary infections in severe and critical ill COVID-19 patients. Emerg Microbes Infect. 2020;9(1):1958-1964. doi:10.1080/22221751.2020.1812437
- 4. Ceballos ME, Nuñez C, Uribe J, et al. Corticosteroids use and risk of respiratory coinfections in mechanically ventilated patients with COVID-19. Research Square 2021. doi:10.21203/rs.3.rs-966047/v1
- 5. Soltani S, Zakeri A, Zandi M, et al. The role of bacterial and fungal human respiratory microbiota in COVID-19 patients. BioMed Research International 2021. doi:10.1155/2021/6670798
- 6. Bengoechea JA, Bamford CG. SARS-CoV-2, bacterial co-infections, and AMR: the deadly trio in COVID-19? EMBO Mol Med. 2020;12(7):e12560. doi:10.15252/emmm.202012560
- 7. Rollas K, Ersan G, Zincircioğlu C, et al. Septic shock in patients admitted to intensive care unit with COVID-19 pneumonia. Eurasian J Pulmonol. 2021;23(2):95-100. doi:10.4103/ejop.ejop_101_20
- 8. Guo M, Gao M, Gao J, et al. Identifying risk factors for secondary infection post-SARS-CoV-2 infection in patients with severe and critical COVID-19. Frontiers in Immunology 2021;3601. doi:10.3389/fimmu.2021.715023
- 9. Mutlu TA, Bozok T. COVID-19 Hastalarının alt solunum yolu örneklerinden izole edilen bakteriyel etkenlerin identifikasyonu ve antibakteriyel direnç paternlerinin incelenmesi. Türk Mikrobiyol Cemiy Derg. 2022;52(1):48-55. doi:10.54453/TMCD.2022.98105
- 10. Rollas K, Şenoğlu N. Management of Covid-19 patients in intensive care unit. The Journal of Tepecik Education and Research Hospital. 2020;30:142-55. doi:10.5222/terh.2020.77044
- 11. Elabbadi A, Turpin M, Gerotziafas GT. Bacterial coinfection in critically ill COVID-19 patients with severe pneumonia. Infection 2021; 49(3): 559-562. doi:10.1007/s15010-020-01553-x
- 12. Işık SA, Şaylan B, Yenilmez E. Ağır Covid-19’da bakteriyel pnömoni riski artıyor mu? Mersin Univ Saglık Bilim Derg. 2021;14(2):291-297. doi:10.26559/mersinsbd.900945
- 13. Senok A, Alfaresi M, Khansaheb H, et al. Coinfections in patients hospitalized with COVID-19: a descriptive study from the United Arab Emirates. Infect Drug Resist. 2021;14:2289-2296. doi:10.2147/IDR.S314029
- 14. Li J, Wang J, Yang Y, et al. Etiology and antimicrobial resistance of secondary bacterial infections in patients hospitalized with COVID-19 in Wuhan, China: a retrospective analysis. Antimicrobial Resistance & Infection Control. 2020;9(1):1-7. doi:10.1186/s13756-020-00819-1
- 15. Morris DE, Cleary DW, Clarke SC. Secondary bacterial infections associated with influenza pandemics. Front. Microbiol. 2017;8:1041. doi:10.3389/fmicb.2017.01041
- 16. Lansbury L, Lim B, Baskaran V, Lim W. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect. 2020;81(2):266-275. doi:10.1016/j.jinf.2020.05.046
- 17. Langford BJ, So M, Raybardhan S, et al. Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis. Clin Microbiol Infect. 2020;26(12):1622-1629. doi:10.1016/j.cmi.2020.07.016
- 18. Caméléna F, Moy AC, Dudoignon E, et al. Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19. Diagn Microbiol Infect Dis. 2021;99(1):115183. doi:10.1016/j.diagmicrobio.2020.115183
- 19. Yoo IY, Huh K, Shim HJ, et al. Evaluation of the BioFire FilmArray Pneumonia Panel for rapid detection of respiratory bacterial pathogens and antibiotic resistance genes in sputum and endotracheal aspirate specimens. Int J Infect Dis. 2020;95:326-331. doi:10.1016/j.ijid.2020.03.024
- 20. Timbrook TT, Hueth KD, Ginocchio CC. Identification of bacterial co-detections in COVID-19 critically ill patients by BioFire® FilmArray® pneumonia panel: a systematic review and meta-analysis. Diagn Microbiol Infect Dis. 2021;101(3):115476. doi:10.1016/j.diagmicrobio.2021.115476
- 21. Zhu X, Ge Y, Wu T, et al. Co-infection with respiratory pathogens among COVID-2019 cases. Virus Res. 2020;285:198005. doi:10.1016/j.virusres.2020.198005
- 22. Grasselli G, Cattaneo E, Florio G. Secondary infections in critically ill patients with COVID-19. Critical Care. 2021;25(1):1-6. doi:10.1186/s13054-021-03672-9
- 23. Rawson TM, Moore LS, Zhu N, et al. Bacterial and fungal coinfection in individuals with coronavirus: a rapid review to support COVID-19 antimicrobial prescribing. Clin Infect Dis 2020;71(9):2459-2468. doi:10.1093/cid/ciaa530
- 24. Aydemir O, Aydemir Y, Şahin EO, Şahin F, Koroglu M, Erdem AF. Secondary bacterial infection in patients with coronavirus disease-2019 associated pneumonia. Revista da Associação Médica Brasileira. 2022;68:142-146. doi:10.1590/1806-9282.20210745
There are 24 citations in total.
Details
| Primary Language | English |
|---|---|
| Subjects | Health Care Administration |
| Journal Section | Research article |
| Authors | |
| Project Number | - |
| Early Pub Date | March 2, 2023 |
| Publication Date | March 5, 2023 |
| Submission Date | March 28, 2022 |
| Acceptance Date | January 25, 2023 |
| Published in Issue | Year 2023 Volume: 8 Issue: 1 |
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