Abstract
Objective: Co-infection of SARS CoV-2 with other respiratory pathogens worsens the course of the disease. For the successful treatment of COVID-19, antimicrobial therapy is applied. Inappropriate antimicrobial use causes an increase in resistant pathogens, the emergence of new resistance patterns, and infections that are difficult to treat and have high mortality. Co-infections in our own center were analyzed to contribute to the determination of empirical antimicrobial treatment strategies to achieve beter therapeutic results in COVID-19 patients.
Methods: Nasopharyngeal swab samples were tested for COVID-19 virus using the RT-PCR test method, and respiratory tract samples (sputum, bronchoalveolar lavage, tracheal aspirate) were tested for routine bacterial/fungal cultures. Vitek 2 Compact (Biomerieux, France) device was used for the identification and antibiotic susceptibility of the isolates.
Results: Among patients who tested positive for COVID-19, 15/1093 cases (1.4%) showed bacterial and/or fungal coinfection. These were 10 gram-negative bacteria (55.6%), 2 gram-positive bacteria (11.1%), 6 yeasts (33.3%), respectively: Aeromonas hydrophila/caviae (n 2), Burkholderia cepacia (n=2), It was defined as Pseudomonas aeruginosa (n = 2), Acinetobacter baumannii (n=2), Achromobacter xylosoxidans (n=1), Serratia marcescens (n=1) and Staphylococcus aureus (n = 2). Candida albicans (n=2), Candida glabrata (n=2) and Candida kefyr (n=2) were also identified as fungal pathogens grown in respiratory tract samples. Burkholderia cepaciave, Pseudomonas aeruginosa, Acinetobacter baumannii isolates were found to be Multidrug Resistant. Carbapenem resistance was not found in any isolates except for two Acinetobacter baumannii species. The highest resistance was found against gentamicin (83.3%) and ciprofloxacin (83.3%). At lower rates; resistance to trimethoprim/sulfamethoxazole (66.7%), piperacillin/tazobactam (66.7%) and amikacin (40%) was detected. No resistance to colistin was observed in any of the bacteria. Gram positive bacteria were found susceptible to vancomycin, linezolid and tigecycline. Methicillin resistance was detected in both Staphylococcus aureus.
Conclusion: In our study, we examined bacterial/fungal co-infections in patients diagnosed with COVID-19 and simultaneously cultured respiratory tract samples. Despite the low frequency of coinfection, the isolated microorganisms had a high antimicrobial resistance pattern. According to these results, each center should implement a serious antimicrobial management program to preventin creasing antimicrobial resistance rates. Compliance with infection control methods and avoidance of inappropriate use of broad-spectrum antimicrobials; It will prevent the increase of resistant pathogens, the emergence of new resistance patterns, infections that are difficult to treat and have high mortality, and new epidemics. The prevalence and profile of bacterial/fungal co-infections in patients with COVID-19 in our country are not yet well understood. We think that our study will be beneficial in guiding the optimal antimicrobial use in patients with COVID-19.
Keywords
References
- 1. Bhimraj A, Morgan RL, Shumaker AH, et al. Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients With Coronavirus Disease 2019 (COVID-19). Clin Infect Dis 2020;ciaa478. doi: 10.1093/cid/ciaa478.
- 2. 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 Infect Dis 2020;20:1-7.
- 3. Mirzaei R, Goodarzi P, Asadi M, Soltani A, et al. Bacterial co-infections with SARS-CoV-2. IUBMB Life 2020;72:2097-111.
- 4. Dyar OJ, Huttner B, Schouten J, Pulcini C. What is antimicrobial stewardship? Clin Microbiol Infect 2017;23:793-8.
- 5. Wu CP, Adhi F, Highland K. Recognition and management of respiratory coinfection and secondary bacterial pneumonia in patients with COVID-19. Cleve Clin J Med 2020;87:659-63.
- 6. Zhou P, Liu Z, Chen Y, Xiao Y, Huang X, Fan XG. Bacterial and fungal infections in COVID-19 patients: A matter of concern. Infect Control Hosp Epidemiol 2020;41:1124-5.
- 7. Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 2020;382:727-33.
- 8. Sopirala MM. Predisposition of COVID-19 patients to secondary infections. Curr Opin Infect Dis 2021;34:357-64.
- 9. Nori P, Cowman K, Chen V, et al. Bacterial and fungal coinfections in COVID-19 patients hospitalized during the New York City pandemic surge. Infect Control Hosp Epidemiol 2021;42:84-8.
- 10. Rawson TM, Moore LSP, 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;71:2459-68.
- 11. Chong WH, Saha BK, Ananthakrishnan R, Chopra A. State of the art review of secondary pulmonary infections in patients with COVID-19 pneumonia. Infection 2021;49:591-605.
- 12. Lansbury L, Lim B, Baskaran V, Lim WS. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect 2020;81:266-75.
- 13. Fu Y, Yang Q, Xu M, et al. Secondary Bacterial Infections in Critical Ill Patients With Coronavirus Disease 2019. Open Forum Infect Dis 2020;7:ofaa220. doi: 10.1093/ofid/ofaa220.
- 14. Hughes S, Troise O, Donaldson H, Mughal N, Moore LSP. Bacterial and fungal coinfection among hospitalized patients with COVID-19: a retrospective cohort study in a UK secondary-care setting. Clin Microbiol Infect 2020;26:1395-9.
- 15. Wang L, Amin AK, Khanna P, et al. An observational cohort study of bacterial co-infection and implications for empirical antibiotic therapy in patients presenting with COVID-19 to hospitals in North West London. J Antimicrob Chemother 2021;76:796-803.
- 16. Ramadan HKA, Mahmoud MA, Aburahma MZ, et al. Predictors of severity and co-infection resistance profile in COVID-19 patients: First report from upper Egypt. Infect Drug Resist 2020;13:3409-22.
- 17. Dizbay M, Tunccan OG, Sezer BE, Aktas F, Arman D. Nosocomial Burkholderia cepacia infections in a Turkish university hospital: a five-year surveillance. J Infect Dev Ctries 2009;3:273-7.
- 18. Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 2020;395:507-13.
- 19. Leitão JH, Sousa SA, Ferreira AS, Ramos CG, Silva IN, Moreira LM. Pathogenicity, virulence factors, and strategies to fight against Burkholderia cepacia complex pathogens and related species. Appl Microbiol Biotechnol 2010;87:31-40.
- 20. Clancy CJ, Nguyen H. Coronavirus Disease 2019, Superinfections, and Antimicrobial Development: What Can We Expect? Clin Infect Dis 2020;71:2736-43.
- 21. WHO. Clinical management of COVID-19: interim guidance, 27 May 2020. World Health Organization. 2020.
- 22. Hoque MN, Akter S, Mishu ID, et al. Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis. Microb Pathog 2021;156:104941.
- 23. Chedid M, Waked R, Haddad E, Chetata N, Saliba G, Choucair J. Antibiotics in treatment of COVID-19 complications: a review of frequency, indications, and efficacy. J Infect Public Health 2021;14:570-6.
- 24. Mete B, Zerdali EY, Aygun G, ve ark. Change in species distribution and antifungal susceptibility of candidemias in an intensive care unit of a university hospital (10-year experience). Eur J Clin Microbiol Infect Dis 2021;40:325-33.
- 25. Baddley JW, Thompson GR, Chen SCA, et al. Coronavirus Disease 2019-Associated Invasive Fungal Infection. Open Forum Infect Dis 2021;8:1-11.
- 26. Lai CC, Yu WL. COVID-19 associated with pulmonary aspergillosis: A literature review. J Microbiol Immunol Infect 2021;54:46-53.
- 27. Shweihat Y, Perry J, Shah D. Isolated Candida infection of the lung. Respir Med Case Rep 2015;16:18-9.
- 28. Samonis G, Galanakis E, Ntaoukakis M, et al. Effects of carbapenems and their combination with amikacin on murine gut colonisation by Candida albicans. Mycoses 2013;56:105-9.
Abstract
Giriş: SARS CoV-2’nin, diğer solunum yolu patojenleri ile koenfeksiyonu, hastalığın seyrini kötüleştirir. COVID-19'un başarılı tedavisi için, antimikrobiyal tedavi uygulanmaktadır. Uygunsuz antimikrobiyal kullanımı, dirençli patojenlerin artmasına, yeni direnç paternlerinin ortaya çıkmasına, tedavisi güç, mortalitesi yüksek enfeksiyonlara neden olur. COVID-19 hastalarında daha iyi terapötik sonuçlar elde etmek için ampirik antimikrobiyal tedavi stratejilerinin belirlenmesine katkı sağlamak amacıyla kendi merkezimizdeki koenfeksiyonlar analiz edildi.
Yöntem: Nazofaringeal sürüntü örnekleri RT-PZR test yöntemi kullanılarak COVID-19 virüsü yönünden, solunum yolu örnekleri (balgam, bronkoalveolar lavaj, trakeal aspirat) de rutin bakteri/mantar kültürleri yönünden test edildi. İzolatların tanımlanması ve antibiyotik duyarlılığı için Vitek 2 Compact (Biomerieux, Fransa) cihazı kullanıldı.
Bulgular: COVID-19 testi pozitif olan hastalar arasında 15/1093 vakada (%1.4) bakteriyel ve/veya fungal koenfeksiyon görüldü. Bunlar 10 gram-negatif bakteri (%55.6), 2 gram-pozitif bakteri (%11.1), 6 maya mantarı (%33.3) olarak, sırası ile: Aeromonas hydrophila/caviae (n=2), Burkholderia cepacia (n=2), Pseudomonas aeruginosa (n=2), Acinetobacter baumannii (n=2), Achromobacter xylosoxidans (n=1), Serratia marcescens (n=1) ve Staphylococcus aureus (n=2) olarak tanımlandı. Candida albicans (n=2), Candida glabrata (n=2) ve Candida kefyr (n=2) de solunum yolu örneklerinde üreyen fungal patojenler olarak tanımlandı. Burkholderia cepacia, Pseudomonas aeruginosa, Acinetobacter baumannii izolatları Çok ilaca dirençli olarak bulundu. İki Acinetobacter baumannii türü hariç hiçbir izolatta karbapenem direncine rastalanmadı. En yüksek direnç gentamisin (%83.3) ve siprofloksasine (%83.3) karşı bulundu. Daha düşük oranlarda olmak üzere; trimetoprim/sulfametoxazole (%66.7), piperasillin/tazobactam (%66.7) ve amikasin’e (%40) direç tespit edildi. Bakterilerin hiçbirinde kolistine direnç görülmedi. Gram pozitif bakteriler vankomisin, linezolid ve tigesikline duyarlı olarak bulundu. Her iki Staphylococcus aureus’ta metisilin direnci tespit edildi.
Sonuç: Çalışmamızda COVID-19 tanısı almış ve eş zamanlı solunum yolu örnekleri kültürü yapılan hastalardaki bakteriyel/fungal koenfeksiyonları inceledik. Düşük koenfeksiyon sıklığına rağmen izole edilen mikroorganizmalar yüksek antimikrobiyal direnç paternine sahipti. Bu sonuçlara göre, artan antimikrobiyal direnç oranlarının önüne geçmek için her merkez ciddi bir antimikrobiyal yönetim programı uygulamalıdır. Enfeksiyon kontrolü yöntemlerine uyulması ve geniş spektrumlu antimikrobiyallerin uygunsuz kullanılmasından kaçınılması; dirençli patojenlerin artmasına, yeni direnç paternlerinin ortaya çıkmasına, tedavisi güç, mortalitesi yüksek enfeksiyonlara ve yeni salgınlara engel olacaktır. Ülkemizde COVID-19’lu hastalarda bakteriyel/fungal koenfeksiyonlarının prevalansı ve profili henüz çok iyi anlaşılmamıştır. Çalışmamızın, COVID-19 hastalarında optimal antimikrobiyal kullanımını yönlendirmekte fayda sağlayacağını düşünmekteyiz
Keywords
References
- 1. Bhimraj A, Morgan RL, Shumaker AH, et al. Infectious Diseases Society of America Guidelines on the Treatment and Management of Patients With Coronavirus Disease 2019 (COVID-19). Clin Infect Dis 2020;ciaa478. doi: 10.1093/cid/ciaa478.
- 2. 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 Infect Dis 2020;20:1-7.
- 3. Mirzaei R, Goodarzi P, Asadi M, Soltani A, et al. Bacterial co-infections with SARS-CoV-2. IUBMB Life 2020;72:2097-111.
- 4. Dyar OJ, Huttner B, Schouten J, Pulcini C. What is antimicrobial stewardship? Clin Microbiol Infect 2017;23:793-8.
- 5. Wu CP, Adhi F, Highland K. Recognition and management of respiratory coinfection and secondary bacterial pneumonia in patients with COVID-19. Cleve Clin J Med 2020;87:659-63.
- 6. Zhou P, Liu Z, Chen Y, Xiao Y, Huang X, Fan XG. Bacterial and fungal infections in COVID-19 patients: A matter of concern. Infect Control Hosp Epidemiol 2020;41:1124-5.
- 7. Zhu N, Zhang D, Wang W, et al. A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med 2020;382:727-33.
- 8. Sopirala MM. Predisposition of COVID-19 patients to secondary infections. Curr Opin Infect Dis 2021;34:357-64.
- 9. Nori P, Cowman K, Chen V, et al. Bacterial and fungal coinfections in COVID-19 patients hospitalized during the New York City pandemic surge. Infect Control Hosp Epidemiol 2021;42:84-8.
- 10. Rawson TM, Moore LSP, 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;71:2459-68.
- 11. Chong WH, Saha BK, Ananthakrishnan R, Chopra A. State of the art review of secondary pulmonary infections in patients with COVID-19 pneumonia. Infection 2021;49:591-605.
- 12. Lansbury L, Lim B, Baskaran V, Lim WS. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect 2020;81:266-75.
- 13. Fu Y, Yang Q, Xu M, et al. Secondary Bacterial Infections in Critical Ill Patients With Coronavirus Disease 2019. Open Forum Infect Dis 2020;7:ofaa220. doi: 10.1093/ofid/ofaa220.
- 14. Hughes S, Troise O, Donaldson H, Mughal N, Moore LSP. Bacterial and fungal coinfection among hospitalized patients with COVID-19: a retrospective cohort study in a UK secondary-care setting. Clin Microbiol Infect 2020;26:1395-9.
- 15. Wang L, Amin AK, Khanna P, et al. An observational cohort study of bacterial co-infection and implications for empirical antibiotic therapy in patients presenting with COVID-19 to hospitals in North West London. J Antimicrob Chemother 2021;76:796-803.
- 16. Ramadan HKA, Mahmoud MA, Aburahma MZ, et al. Predictors of severity and co-infection resistance profile in COVID-19 patients: First report from upper Egypt. Infect Drug Resist 2020;13:3409-22.
- 17. Dizbay M, Tunccan OG, Sezer BE, Aktas F, Arman D. Nosocomial Burkholderia cepacia infections in a Turkish university hospital: a five-year surveillance. J Infect Dev Ctries 2009;3:273-7.
- 18. Chen N, Zhou M, Dong X, et al. Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet 2020;395:507-13.
- 19. Leitão JH, Sousa SA, Ferreira AS, Ramos CG, Silva IN, Moreira LM. Pathogenicity, virulence factors, and strategies to fight against Burkholderia cepacia complex pathogens and related species. Appl Microbiol Biotechnol 2010;87:31-40.
- 20. Clancy CJ, Nguyen H. Coronavirus Disease 2019, Superinfections, and Antimicrobial Development: What Can We Expect? Clin Infect Dis 2020;71:2736-43.
- 21. WHO. Clinical management of COVID-19: interim guidance, 27 May 2020. World Health Organization. 2020.
- 22. Hoque MN, Akter S, Mishu ID, et al. Microbial co-infections in COVID-19: Associated microbiota and underlying mechanisms of pathogenesis. Microb Pathog 2021;156:104941.
- 23. Chedid M, Waked R, Haddad E, Chetata N, Saliba G, Choucair J. Antibiotics in treatment of COVID-19 complications: a review of frequency, indications, and efficacy. J Infect Public Health 2021;14:570-6.
- 24. Mete B, Zerdali EY, Aygun G, ve ark. Change in species distribution and antifungal susceptibility of candidemias in an intensive care unit of a university hospital (10-year experience). Eur J Clin Microbiol Infect Dis 2021;40:325-33.
- 25. Baddley JW, Thompson GR, Chen SCA, et al. Coronavirus Disease 2019-Associated Invasive Fungal Infection. Open Forum Infect Dis 2021;8:1-11.
- 26. Lai CC, Yu WL. COVID-19 associated with pulmonary aspergillosis: A literature review. J Microbiol Immunol Infect 2021;54:46-53.
- 27. Shweihat Y, Perry J, Shah D. Isolated Candida infection of the lung. Respir Med Case Rep 2015;16:18-9.
- 28. Samonis G, Galanakis E, Ntaoukakis M, et al. Effects of carbapenems and their combination with amikacin on murine gut colonisation by Candida albicans. Mycoses 2013;56:105-9.
Details
| Primary Language | Turkish |
|---|---|
| Subjects | Health Care Administration |
| Journal Section | Research Articles |
| Authors | |
| Early Pub Date | July 28, 2023 |
| Publication Date | July 28, 2023 |
| Published in Issue | Year 2023 Volume: 4 Issue: 2 |
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