Distribution of Multidrug Resistance Bacterial Strains in Lower Respiratory Tract Infections and Comparison of Molecular/Conventional Methods used in diagnosis

Öz

Lower respiratory tract infections (LRTIs) are frequently associated with multidrug-resistant (MDR) bacterial pathogens. This study aimed to investigate the distribution of antimicrobial resistance among bacteria isolated from patients diagnosed with LRTIs and to evaluate the diagnostic performance of a multiplex molecular assay. This was a retrospective, single-center observational study conducted between January 2021 and March 2023. Respiratory specimens were processed using standard microbiological methods. Bacterial identification was performed using MALDI-TOF MS, and antimicrobial susceptibility results were interpreted according to EUCAST guidelines. A total of 3,366 lower respiratory tract specimens were analyzed. The most frequently isolated pathogens were Acinetobacter spp., Klebsiella spp., and Pseudomonas spp., with carbapenem resistance rates of 92%, 74%, and 68%, respectively. In a subgroup of 57 specimens analyzed simultaneously by conventional culture and multiplex real-time PCR, the multiplex PCR assay demonstrated positive predictive values (PPV) of 70–100%, negative predictive values (NPV) of 73.33–100%, and diagnostic accuracy ranging from 75.44% to 100% for bacterial detection. For carbapenem resistance detection, the assay showed a PPV of 100%, an NPV of 73.33%, and an accuracy of 78.95%. These findings highlight the high burden of antimicrobial resistance in LRTIs. The combined use of molecular and conventional methods may improve diagnostic accuracy and support targeted antimicrobial therapy.

Anahtar Kelimeler

• Lower respiratory tract infections
• multidrug-resistant bacteria
• molecular diagnostics
• carbapenem resistance

Alt Solunum Yolu Enfeksiyon Etkeni Çoğul İlaç Dirençli Bakterilerin Dağılımı ve Tanıda Kullanılan Moleküler/ Konvansiyonel Yöntemlerin Karşılaştırılması

Öz

Alt solunum yolu enfeksiyonları (ASYE), sıklıkla çoklu ilaca dirençli (MDR) bakteriyel patojenlerle ilişkilidir. Bu çalışmanın amacı, ASYE tanısı alan hastalardan izole edilen bakterilerde antimikrobiyal direnç dağılımını araştırmak ve çoklu hedefli bir moleküler testin tanısal performansını değerlendirmektir. Bu çalışma, Ocak 2021–Mart 2023 tarihleri arasında yürütülmüş tek merkezli, retrospektif bir gözlemsel araştırmadır. Solunum örnekleri standart mikrobiyolojik yöntemlerle işlenmiştir. Bakteriyel tanımlama MALDI-TOF MS yöntemiyle yapılmış, antimikrobiyal duyarlılık sonuçları EUCAST kılavuzlarına göre değerlendirilmiştir. Toplam 3.366 alt solunum yolu örneği analiz edilmiştir. En sık izole edilen patojenler sırasıyla Acinetobacter spp., Klebsiella spp. ve Pseudomonas spp. olup, karbapenem direnç oranları sırasıyla %92, %74 ve %68 olarak saptanmıştır. Hem konvansiyonel kültür hem de multipleks gerçek zamanlı PCR ile eş zamanlı analiz edilen 57 örnekten oluşan alt grupta, multipleks PCR testinin bakteri tespitindeki pozitif prediktif değeri (PPV) %70–100, negatif prediktif değeri (NPV) %73,33–100 ve tanısal doğruluğu %75,44–100 arasında bulunmuştur. Karbapenem direncinin saptanmasında ise PPV %100, NPV %73,33 ve doğruluk %78,95 olarak belirlenmiştir. Bu bulgular, ASYE’lerde yüksek antimikrobiyal direnç yükünü ortaya koymaktadır. Moleküler ve konvansiyonel yöntemlerin birlikte kullanımı, tanısal doğruluğu artırarak hedefe yönelik antimikrobiyal tedaviyi destekleyebilir.

Anahtar Kelimeler

• Alt solunum yolu enfeksiyonları
• çoklu ilaca dirençli bakteriler
• moleküler tanı
• karbapenem direnci

Kaynakça

1. 1. Lanks CW, Musani AI, Hsia DW. Community-acquired Pneumonia and Hospital-acquired Pneumonia. Med Clin North Am. 2019;103(3):487-501.
2. 2. Safiri S, Mahmoodpoor A, Kolahi A-A, Nejadghaderi SA, Sullman MJ, Mansournia MA, et al. Global burden of lower respiratory infections during the last three decades. Frontiers in Public Health. 2023;10:1028525.
3. 3. Tian J-Y, Hao X-Y, Cao F-Y, Liu J-J, Li Y-X, Guo Y-X, et al. Preoperative frailty assessment predicts postoperative mortality, delirium and pneumonia in elderly lung cancer patients: a retrospective cohort study. Annals of Surgical Oncology. 2023;30(12):7442-51.
4. 4. Li S, Shang L, Yuan L, Li W, Kang H, Zhao W, et al. Construction and Validation of a Predictive Model for the Risk of Ventilator‐Associated Pneumonia in Elderly ICU Patients. Canadian Respiratory Journal. 2023;2023(1):7665184.
5. 5. Wu M, Li Z, Zheng W, Zhuang J, Wu S, Zhou Q, et al. Association between anticholinergic medication uses and the risk of pneumonia in elderly adults: a meta-analysis and systematic review. Annals of Medicine. 2023;55(1):2209736.
6. 6. Metlay JP, Waterer GW, Long AC, Anzueto A, Brozek J, Crothers K, et al. Diagnosis and Treatment of Adults with Community-acquired Pneumonia. An Official Clinical Practice Guideline of the American Thoracic Society and Infectious Diseases Society of America. American Journal of Respiratory and Critical Care Medicine. 2019;200(7):e45-e67.
7. 7. Centers for Disease C, Prevention/National Healthcare Safety N. Pneumonia (Ventilator-associated [VAP] and non-ventilator-associated Pneumonia [PNEU]) Event.
8. 8. Cillóniz C, Dominedò C, Torres A. Multidrug Resistant Gram-Negative Bacteria in Community-Acquired Pneumonia. Crit Care. 2019;23(1):79.

9. 9. Carroll KC, Adams LtL. Lower Respiratory Tract Infections. Microbiology Spectrum. 2016;4(4):10.1128/microbiolspec.dmih2-0029-2016.
10. 10. Kuloglu TO, Unuvar GK, Cevahir F, Kilic AU, Alp E. Risk factors and mortality rates of carbapenem-resistant Gram-negative bacterial infections in intensive care units. Journal of Intensive Medicine. 2024.
11. 11. Craven DE, Hjalmarson KI. Ventilator-Associated Tracheobronchitis and Pneumonia: Thinking Outside the Box. Clinical Infectious Diseases. 2010;51(Supplement_1):S59-S66.
12. 12. Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcare-associated pneumonia. Am J Respir Crit Care Med. 2005;171(4):388-416.
13. 13. Hersh AL, Shapiro DJ, Pavia AT, Shah SS. Antibiotic prescribing in ambulatory pediatrics in the United States. Pediatrics. 2011;128(6):1053-61.
14. 14. Torres A, Niederman MS, Chastre J, Ewig S, Fernandez-Vandellos P, Hanberger H, et al. International ERS/ESICM/ESCMID/ALAT guidelines for the management of hospital-acquired pneumonia and ventilator-associated pneumonia: Guidelines for the management of hospital-acquired pneumonia (HAP)/ventilator-associated pneumonia (VAP) of the European Respiratory Society (ERS), European Society of Intensive Care Medicine (ESICM), European Society of Clinical Microbiology and Infectious Diseases (ESCMID) and Asociación Latinoamericana del Tórax (ALAT). European Respiratory Journal. 2017;50(3).
15. 15. Lee CC, Lee CH, Yang CY, Hsieh CC, Tang HJ, Ko WC. Beneficial effects of early empirical administration of appropriate antimicrobials on survival and defervescence in adults with community-onset bacteremia. Crit Care. 2019;23(1):363.
16. 16. Buchan BW, Windham S, Balada-Llasat JM, Leber A, Harrington A, Relich R, et al. Practical Comparison of the BioFire FilmArray Pneumonia Panel to Routine Diagnostic Methods and Potential Impact on Antimicrobial Stewardship in Adult Hospitalized Patients with Lower Respiratory Tract Infections. J Clin Microbiol. 2020;58(7).
17. 17. Lee SH, Ruan SY, Pan SC, Lee TF, Chien JY, Hsueh PR. Performance of a multiplex PCR pneumonia panel for the identification of respiratory pathogens and the main determinants of resistance from the lower respiratory tract specimens of adult patients in intensive care units. J Microbiol Immunol Infect. 2019;52(6):920-8.
18. 18. Murray PR, Rosenthal KS, Pfaller MA. Medical Microbiology. 9 ed. Philadelphia: Elsevier; 2020.
19. 19. Rattani S, Farooqi J, Jabeen G, Chandio S, Kash Q, Khan A, et al. Evaluation of semi-quantitative compared to quantitative cultures of tracheal aspirates for the yield of culturable respiratory pathogens - a cross-sectional study. BMC Pulm Med. 2020;20(1):284.
20. 20. Garcia LS. Clinical Microbiology Procedures Handbook. 4 ed. Washington, DC: ASM Press; 2016.
21. 21.https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_14.0_Breakpoint_Tables.pdf [press release]. 2024.
22. 22. Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clinical Microbiology and Infection. 2012;18(3):268-81.
23. 23. Basak S, Singh P, Rajurkar M. Multidrug Resistant and Extensively Drug Resistant Bacteria: A Study. J Pathog. 2016;2016:4065603.
24. 24. Murphy CN, Fowler R, Balada-Llasat JM, Carroll A, Stone H, Akerele O, et al. Multicenter Evaluation of the BioFire FilmArray Pneumonia/Pneumonia Plus Panel for Detection and Quantification of Agents of Lower Respiratory Tract Infection. J Clin Microbiol. 2020;58(7).
25. 25. Lee SH, Ruan S-Y, Pan S-C, Lee T-F, Chien J-Y, Hsueh P-R. Performance of a multiplex PCR pneumonia panel for the identification of respiratory pathogens and the main determinants of resistance from the lower respiratory tract specimens of adult patients in intensive care units. Journal of Microbiology, Immunology and Infection. 2019;52(6):920-8.
26. 26. Altman DG, Bland JM. Diagnostic tests 1: sensitivity and specificity. BMJ. 1994;308:1552-.
27. 27. Zilberberg MD, Nathanson BH, Puzniak LA, Shorr AF. Descriptive epidemiology and outcomes of nonventilated hospital-acquired, ventilated hospital-acquired, and ventilator-associated bacterial pneumonia in the United States, 2012–2019. Critical care medicine. 2022;50(3):460-8.
28. 28. Martin-Loeches I, Reyes LF, Nseir S, Ranzani O, Povoa P, Diaz E, et al. European Network for ICU-Related Respiratory Infections (ENIRRIs): a multinational, prospective, cohort study of nosocomial LRTI. Intensive care medicine. 2023;49(10):1212-22.
29. 29. Hidron AI, Edwards JR, Patel J, Horan TC, Sievert DM, Pollock DA, et al. Antimicrobial-Resistant Pathogens Associated With Healthcare-Associated Infections: Annual Summary of Data Reported to the National Healthcare Safety Network at the Centers for Disease Control and Prevention, 2006–2007. Infection Control & Hospital Epidemiology. 2008;29(11):996-1011.
30. 30. Mert D, Demirkıran BÇ, İskender G, Avşar Z, Timuroğlu A, Binay S, et al. Six-year evaluation of device-associated nosocomial infections in intensive care units. The Journal of Infection in Developing Countries. 2024;18(06):937-42.
31. 31. Niu H, Shen X, Liang H, Wu G, Cai S, Shen Q, et al. Risk factors for progression to bacteremia among patients with nosocomial carbapenem-resistant Acinetobacter baumannii pneumonia in the Intensive Care Unit. Eur J Clin Microbiol Infect Dis. 2023;42(11):1337-46.
32. 32. Qiu J, Zhu P, Wagh K, singh N, Dong S. Phenotypic and Molecular Characterization of Hypervirulent and Multidrug-Resistant Acinetobacter baumannii Isolated from ICU Respiratory Infections. Canadian Journal of Infectious Diseases and Medical Microbiology. 2024;2024(1):9670708.
33. 33. Diao H, Lu G, Zhang Y, Wang Z, Liu X, Ma Q, et al. Risk factors for multidrug-resistant and extensively drug-resistant Acinetobacter baumannii infection of patients admitted in ICU: a systematic review and meta-analysis. Journal of Hospital Infection. 2024.
34. 34. Report ARSiE, Control, World Health Organization. Regional Office for E. Antimicrobial resistance surveillance in Europe 2022 – 2020 data. Copenhagen: World Health Organization. Regional Office for Europe; 2022 2022.
35. 35. Antimicrobial resistance surveillance in Europe 2023 - 2021 data 2023.
36. 36. Guclu AU, Kocak AA, Ok MA, Tutluoglu B, Basustaoglu AC, Group RS. Antibacterial resistance in lower respiratory tract bacterial pathogens: a multicenter analysis from Turkey. The Journal of Infection in Developing Countries. 2021;15(02):254-62.
37. 37. Bilen NM, Sahbudak Bal Z, Güner Özenen G, Yildirim Arslan S, Ozek G, Ozdemir Karadas N, et al. Risk Factors for Infection and Mortality Associated With Stenotrophomonas maltophilia Bloodstream Infections in Children; Comparison With Pseudomonas aeruginosa Bloodstream Infections. The Pediatric Infectious Disease Journal. 2023;42(5):374-80.
38. 38. Furuichi M, Ito K, Miyairi I. Characteristics of Stenotrophomonas maltophilia bacteremia in children. Pediatrics International. 2016;58(2):113-8.
39. 39. Tokatly Latzer I, Paret G, Rubinstein M, Keller N, Barkai G, Pessach IM. Management of Stenotrophomonas maltophilia Infections in Critically Ill Children. The Pediatric Infectious Disease Journal. 2018;37(10):981-6.
40. 40. Edin A, Eilers H, Allard A. Evaluation of the Biofire Filmarray Pneumonia panel plus for lower respiratory tract infections. Infectious Diseases. 2020;52(7):479-88.
41. 41. Faron M, Mahmutoglu D, Huang A, Balada-Llasat J, Relich R, Humphries R, et al., editors. Clinical evaluation of a semi-quantitative multiplex molecular assay for the identification of bacteria, viruses and fungi in lower respiratory specimens. Clinical Virology Symposium; 2017.
42. 42. Ginocchio CC, Garcia-Mondragon C, Mauerhofer B, Rindlisbacher C. Multinational evaluation of the BioFire® FilmArray® Pneumonia plus Panel as compared to standard of care testing. European Journal of Clinical Microbiology & Infectious Diseases. 2021;40:1609-22.
43. 43. Yoo IY, Huh K, Shim HJ, Yun SA, Chung YN, Kang OK, 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. International Journal of Infectious Diseases. 2020;95:326-31.
44. 44. Foschi C, Zignoli A, Gaibani P, Vocale C, Rossini G, Lafratta S, et al. Respiratory bacterial co-infections in intensive care unit-hospitalized COVID-19 patients: Conventional culture vs BioFire FilmArray pneumonia Plus panel. J Microbiol Methods. 2021;186:106259.
45. 45. Tellapragada C, Giske CG. The Unyvero Hospital-Acquired pneumonia panel for diagnosis of secondary bacterial pneumonia in COVID-19 patients. Eur J Clin Microbiol Infect Dis. 2021;40(12):2479-85.