Epidemiology and Infectious Diseases » The efficiency of molecular genetic methods for the diagnosis of infections caused by S. pneumoniae и H. influenzae

The efficiency of molecular genetic methods for the diagnosis of infections caused by S. pneumoniae и H. influenzae

DOI: https://dx.doi.org/10.18565/epidem.2023.13.2.56-62

Elkina M.A., Yatsyshina S.B., Tronza T.V., Ratchina S.A., Spichak T.V., Akimkin V.G.
1) Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection, and Human Well-Being, Moscow, Russia; 2) I.M. Sechenov First Moscow State Medical University (Sechenov University), Ministry of Health of Russia, Moscow, Russia

Objective. To develop and validate reagent kits for the quantitative determination of S. pneumoniae and H. influenzae DNA by real-time polymerase chain reaction (RT-PCR). To evaluate its efficiency versus that of other laboratory diagnostic methods.
Subjects and methods. The authors studied the isolates of S. pneumoniae (n = 181) and H. influenzae (n = 101) and the biological materials from patients with severe community-acquired pneumonia (CAP) in 60 adults and from those with moderate CAP in 66 children. They compared the results of RT-PCR, a bacteriological method, and a rapid test for S. pneumoniae antigen.
Results. In the structure of pathogens of severe CAP, there was a preponderance of S. pneumoniae (63%), H. influenzae were found in 32% of patients. S. pneumoniae was detected by RT-PCR 2-3 times more frequently than by other diagnostic methods. RT-PCR revealed H. influenzae DNA in the sputum of 19 patients; the culture was isolated only in 1 patient. The etiology of CAP in children was established in 91% of cases; of which, the viral etiology was found in 18%; S. pneumoniae was detected in 23%.
Conclusion. RT-PCR was shown to be highly effective in diagnosing infections caused by S. pneumoniae and H. influenzae. When CAP was diagnosed by RT-PCR, the material taken from the lower respiratory tract was more informative than that from the upper one.

Keywords: PT-PCR, H. influenzae, S. pneumoniae, community-acquired pneumonia

Read entire article

Literature

1. Пшеничная Н.Ю., Гопаца Г. В., Углева С.В., Сергевнин В.И., Кудрявцева Л.Г., Лазарьков П.В. Эпидемиологические аспекты респираторных инфекций верхних и нижних отделов дыхательных путей в период пандемии COVID-19. Эпидемиол. инфекц. болезни. Актуал. вопр. 2022; 12(4): 72–6. DOI: https://dx.doi.org/10.18565/epidem. 2022.12.4.72-6

Pshenichnaya N.Yu., Gopatsa G.V., Ugleva S.V., Sergevnin V.I., Kudryavtseva L.G., Lazarkov P.V. [Epidemiological aspects of upper and lower respiratory tract infections during the COVID-19]. Epidemiоlоgy and infectious diseases. Сurrent items 2022; 12(4): 72–6. (In Russ.). DOI: https://dx.doi. org/10.18565/epidem.2022.12.4.72-6

2. Torres A., Blasi F., Dartois N., Akova M. Which individuals are at increased risk of pneumococcal disease and why? Impact of COPD, asthma, smoking, diabetes, and/or chronic heart disease on community-acquired pneumonia and invasive pneumococcal disease. Thorax 2015; 70(10): 984–9. DOI: 10.1136/thoraxjnl-2015-206780

3. Rozenbaum M.H., Pechlivanoglou P., van der Werf T.S., Lo-Ten-Foe J.R., Postma M.J., Hak E. The role of Streptococcus pneumoniae in community-acquired pneumonia among adults in Europe: a meta-analysis. Eur. J. Clin. Microbiol. Infect. Dis. 2013; 32(3): 305–16. DOI: 10.1007/s10096-012-1778-4

4. Внебольничная пневмония у детей. Клинические рекомендации. М.: Оригинал-макет, 2015. 64 с. – ISBN 978-5-9906603-4-2.

. [Community-acquired pneumonia in children. Clinical recommendations]. Moscow: Original layout, 2015. 64 p. (In Russ.). ISBN 978-5-9906603-4-2.

5. Farajzadeh Sheikh A., Rahimi R., Meghdadi H., Alami A., Saki M. Multiplex polymerase chain reaction detection of Streptococcus pneumoniae and Haemophilus influenzae and their antibiotic resistance in patients with community-acquired pneumonia from southwest Iran. BMC Microbiol. 2021; 21(1): 343. DOI: 10.1186/s12866-021-02408-7

6. Fally M., Israelsen S., Anhøj J., Benfield T., Tarp B., Kolte L. et al. The increasing importance of Haemophilus influenzae in community-acquired pneumonia: results from a Danish cohort study. Infect. Dis. (London) 2021; 53(2): 122–30. DOI: 10.1080/23744235.2020.1846776

7. Yatsyshina S., Mayanskiy N., Shipulina O., Kulichenko T., Alyabieva N., Katosova L. et al. Detection of respiratory pathogens in pediatric acute otitis media by PCR and comparison of findings in the middle ear and nasopharynx. Diagn. Microbiol. Infect. Dis. 2016; 85(1): 125–30. DOI: 10.1016/j.diagmicrobio.2016.02.010

8. Vergison A. Microbiology of otitis media: a moving target. Vaccine. 2008; 26 (Suppl 7): G5–10. DOI: 10.1016/j.vaccine.2008.11.006

9. Королева И.С., Белошицкий Г.В., Королева М.А., Грицай М.И. Эпидемиологические аспекты пневмококкового менингита в Российской Федерации. Эпидемиол. инфекц. болезни. Актуал. вопр. 2020; 10(2): 6–10. DOI: https://dx.doi.org/10.18565/epidem.2020.10.2.6-10

Koroleva I.S., Beloshitsky G.V., Koroleva M.A., Gritsai M.I.[Epidemiological aspects of pneumococcal meningitis in the Russian Federation]. Epidemiоlоgy and infectious diseases. Сurrent items 2020; 10(2): 6–10. (In Russ.). DOI: https://dx.doi.org/10.18565/epidem.2020.10. 2.6-10

10. Oordt-Speets A.M., Bolijn R., van Hoorn R.C., Bhavsar A., Kyaw M.H. Global etiology of bacterial meningitis: A systematic review and meta-analysis. PLoS One 2018; 13(6): e0198772. DOI: 10.1371/journal.pone.0198772

11. Sanaei Dashti A., Abdinia B., Karimi A. Nasopharyngeal carrier rate of Streptococcus pneumoniae in children: serotype distribution and antimicrobial resistance. Arch. Iran Med. 2012; 15(8): 500–3. PMID: 22827788

12. Mukundan D., Ecevit Z., Patel M., Marrs C.F., Gilsdorf J.R. Pharyngeal colonization dynamics of Haemophilus influenzae and Haemophilus haemolyticus in healthy adult carriers. J. Clin. Microbiol. 2007; 45(10): 3207–17. DOI: 10.1128/JCM.00492-07

13. Zhu H., Wang A., Tong J., Yuan L, Gao W., Shi W. et al. Nasopharyngeal carriage and antimicrobial susceptibility of Haemophilus influenzae among children younger than 5 years of age in Beijing, China. BMC Microbiol. 2015; 15: 6. DOI: 10.1186/s12866-015-0350-7

14. Steens A., Knol M.J., Freudenburg-de Graaf W., de Melker H.E., van der Ende A. et al. Pathogen- and Type-Specific Changes in Invasive Bacterial Disease Epidemiology during the First Year of the COVID-19 Pandemic in The Netherlands. Microorganisms 2022; 10(5): 972. DOI: 10.3390/microorganisms10050972

15. Mitsi E., Reiné J., Urban B.C., Solórzano C., Nikolaou E., Hyder-Wright A.D. et al. Streptococcus pneumoniae colonization associates with impaired adaptive immune responses against SARS-CoV-2. J. Clin. Invest. 2022; 132(7): e157124. DOI: 10.1172/JCI157124

16. Danino D., Ben-Shimol S., van der Beek B.A., Givon-Lavi N., Avni Y.S. et al. Decline in Pneumococcal Disease in Young Children During the Coronavirus Disease 2019 (COVID-19) Pandemic in Israel Associated With Suppression of Seasonal Respiratory Viruses, Despite Persistent Pneumococcal Carriage: A Prospective Cohort Study. Clin. Infect. Dis. 2022; 75(1): e1154–64. DOI: 10.1093/cid/ciab1014

17. Cardozo D.M., Nascimento-Carvalho C.M., Souza F.R., Silva N.M. et al. Nasopharyngeal colonization and penicillin resistance among pneumococcal strains: a worldwide 2004 update. Braz. J. Infect. Dis. 2006; 10(4): 293–304. DOI: 10.1590/s1413-86702006000400015

18. Bruin J.P., Kostrzewa M., van der Ende A., Badoux P., Jansen R., Boers S.A. et al. Identification of Haemophilus influenzae and Haemophilus haemolyticus by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Eur. J. Clin. Microbiol. Infect. Dis. 2014; 33(2): 279–84. DOI: 10.1007/s10096-013-1958-x

19. Korppi M., Leinonen M., Ruuskanen O. Pneumococcal serology in children’s respiratory infections. Eur. J. Clin. Microbiol. Infect. Dis. 2008; 27(3): 167–75. DOI: 10.1007/s10096-007-0436-8

20. Лабораторная диагностика внебольничной пневмонии пневмококковой этиологии. Методические рекомендации МР 4.2.0114-16. Эпидемиология и вакцинопрофилактика 2016; 15(5): 85.

[Laboratory diagnostics of community-acquired pneumonia of pneumococcal etiology. Methodological recommendations MR 4.2.0114-16]. Epidemiology and Vaccine Prevention 2016; 15(5): 85. (In Russ.).

21. Idelevich E.A., Schlattmann A., Kostrzewa M., Becker K. Development of a novel MALDI-TOF MS-based bile solubility test for rapid discrimination of Streptococcus pneumoniae. Int. J. Med. Microbiol. 2020; 310(3): 151413. DOI: 10.1016/j.ijmm.2020.151413

22. Nix I.D., Idelevich E.A., Schlattmann A., Sparbier K., Kostrzewa M., Becker K. MALDI-TOF Mass Spectrometry-Based Optochin Susceptibility Testing for Differentiation of Streptococcus pneumoniae from other Streptococcus mitis Group Streptococci. Microorganisms 2021; 9(10): 2010. DOI: 10.3390/microorganisms9102010

23. Hinz R., Zautner A.E., Hagen R.M., Frickmann H. Difficult identification of Haemophilus influenzae, a typical cause of upper respiratory tract infections, in the microbiological diagnostic routine. Eur. J. Microbiol. Immunol. (Bp.) 2015; 5(1): 62–7. DOI: 10.1556/EUJMI-D-14-00033

24. Gadsby N.J., McHugh M.P.., Russell CD., Mark H., Conway M.A., Laurenson I.F. et al. Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections. Clin. Microbiol. Infect. 2015; 21(8): 788.e1-788.e13. DOI: 10.1016/j.cmi.2015.05.004

25. Abdeldaim G., Herrmann B., Mölling P., Holmberg H., Blomberg J., Olcén P. et al. Usefulness of real-time PCR for lytA, ply, and Spn9802 on plasma samples for the diagnosis of pneumococcal pneumonia. Clin. Microbiol. Infect. 2010; 16(8): 1135–41. DOI: 10.1111/j.1469-0691.2009.03069.x

26. Kais M., Spindler C., Kalin M., Ortqvist A., Giske C.G. Quantitative detection of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in lower respiratory tract samples by real-time PCR. Diagn. Microbiol. Infect. Dis. 2006; 55(3): 169–78. DOI: 10.1016/j.diagmicrobio.2006.01.007

27. Krenke K., Sadowy E., Podsiadły E., Hryniewicz W., Demkow U., Kulus M. Etiology of parapneumonic effusion and pleural empyema in children. The role of conventional and molecular microbiological tests. Respir. Med. 2016; 116: 28–33. DOI: 10.1016/j.rmed.2016.05.009

28. Захаренков И.А., Рачина С.А., Дехнич Н.Н., Козлов Р.С., Синопальников А.И., Иванчик Н.В. и др. Этиология тяжелой внебольничной пневмонии у взрослых: результаты первого российского многоцентрового исследования. Терапевтический архив 2020; 92(1): 36–42. DOI: 10.26442/00403660.2020.01.000491

Zakharenkov I.A., Ratchina S.A., Dekhnich N.N., Kozlov R.S., Sinopalnikov A.I., Ivanchik N.V. et al. [Etiology of severe community – acquired pneumonia in adults: results of the first Russian multicenter study]. Therapeutic Archive 2020; 92(1): 36–42. (In Russ.). DOI: 10.26442/00403660.2020.01.000491

29. Strålin K., Bäckman A., Holmberg H., Fredlund H., Olcén P. Design of a multiplex PCR for Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae and Chlamydophila pneumoniae to be used on sputum samples. APMIS 2005; 113(2): 99–111. DOI: 10.1111/j.1600-0463.2005.apm1130203.x

30. Luznik D., Kosnik M., Tomic V. Comparison of Seeplex PneumoBacter aCE detection assay and in-house multiplex PCR for the identification of Streptococcus pneumoniae. New Microbiol. 2015; 38(1): 51-8. PMID: 25742147

31. Rolo D., Simões A., Domenech A., Fenoll A., Liñares J., de Lencastre H. et al. Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain. PLoS One 2013; 8(2): e57047. DOI: 10.1371/journal.pone.0057047

32. de Gier C., Kirkham L.A., Nørskov-Lauritsen N. Complete Deletion of the Fucose Operon in Haemophilus influenzae Is Associated with a Cluster in Multilocus Sequence Analysis-Based Phylogenetic Group II Related to Haemophilus haemolyticus: Implications for Identification and Typing. J. Clin. Microbiol. 2015; 53(12): 3773–8. DOI: 10.1128/JCM.01969-15

33. Meyler K.L., Meehan M., Bennett D., Cunney R., Cafferkey M. Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples. Diagn. Microbiol. Infect. Dis. 2012; 74(4): 356–62. DOI: 10.1016/j.diagmicrobio.2012.08.018

34. Ladhani S., Slack M.P., Heath P.T., von Gottberg A., Chandra M., Ramsay M.E.; European Union Invasive Bacterial Infection Surveillance participants. Invasive Haemophilus influenzae Disease, Europe, 1996–2006. Emerg. Infect .Dis. 2010; 16(3): 455–63. DOI: 10.3201/eid1603.090290

35. Abdeldaim G.M., Strålin K., Kirsebom L.A, Olcén P., Blomberg J., Herrmann B. Detection of Haemophilus influenzae in respiratory secretions from pneumonia patients by quantitative real-time polymerase chain reaction. Diagn. Microbiol. Infect. Dis. 2009; 64(4): 366–73. DOI: 10.1016/j.diagmicrobio.2009.03.030

36. Binks M.J., Temple B.., Kirkham LA., Wiertsema S.P., Dunne E.M, Richmond P.C. et al. Molecular surveillance of true nontypeable Haemophilus influenzae: an evaluation of PCR screening assays. PLoS One. 2012; 7(3): e34083. DOI: 10.1371/journal.pone.0034083

37. Janson H., Melhus A., Hermansson A., Forsgren A. Protein D, the glycerophosphodiester phosphodiesterase from Haemophilus influenzae with affinity for human immunoglobulin D, influences virulence in a rat otitis model. Infect. Immun. 1994; 62(11): 4848–54. DOI: 10.1128/iai.62.11.4848-4854.1994

38. Johnson R.W., McGillivary G., Denoël P., Poolman J., Bakaletz L.O. Abrogation of nontypeable Haemophilus influenzae protein D function reduces phosphorylcholine decoration, adherence to airway epithelial cells, and fitness in a chinchilla model of otitis media. Vaccine 2011; 29(6): 1211–21. DOI: 10.1016/j.vaccine.2010.12.003

39. Price E.P., Sarovich D.S., Nosworthy E., Beissbarth J., Marsh R.L., Pickering J. et al. Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen. BMC Genomics 2015; 16(1): 641. DOI: 10.1186/s12864-015-1857-x

40. Hu F., Rishishwar L., Sivadas A., Mitchell G.J., Jordan I.K., Murphy T.F. et al. Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination. J. Clin. Microbiol. 2016; 54(12): 3010–7. DOI: 10.1128/JCM.01511-16

41. Strålin K., Herrmann B., Abdeldaim G., Olcén P., Holmberg H., Mölling P. Comparison of sputum and nasopharyngeal aspirate samples and of the PCR gene targets lytA and Spn9802 for quantitative PCR for rapid detection of pneumococcal pneumonia. J. Clin. Microbiol. 2014; 52(1): 83–9. DOI: 10.1128/JCM.01742-13

About the Autors

Maria A. Elkina, Junior Researcher, Laboratory for the Molecular Diagnosis and Epidemiology of Respiratory Tract Infections, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection, and Human Well-Being, Moscow, Russia; melkina@cmd.su; https://orcid.org/0000-0003-4769-6781
Svetlana B. Yatsyshina, Cand. Biol. Sci.; Head, Laboratory for the Molecular Diagnosis and Epidemiology of Respiratory Tract Infections, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection, and Human Well-Being, Moscow, Russia; svetlana.yatsyshina@pcr.ms; https://orcid.org/0000-0003-4737-941X
Tatiana V. Tronza, Head in the Area of Laboratory Studies, Laboratory for Clinical Microbiology and Human Microbial Ecology, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection, and Human Well-Being, Moscow, Russia; tronza@cmd.su; https://orcid.org/0000-0002-0606-0747
Svetlana A. Ratchina, MD; Head, Hospital Therapy Department Two, I.M. Sechenov First Moscow State Medical University (Sechenov University), Ministry of Health of Russia, Moscow, Russia; Svetlana.Ratchina@antibiotic.ru; https://orcid.org/0000-0002-3329-7846
Tatiana V. Spichak, MD; Professor, Department of Pediatrics and Public Health, Institute for Medical Personnel Training, National Medical Research Center of Children’s Health, Ministry of Health of Russia, Moscow, Russia; tv.spichak@mail.ru
Professor Vasily G. Akimkin, Academician of the Russian Academy of Sciences, MD, Director, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection, and Human Well-Being, Moscow, Russia; akimkin@pcr.ms; https://orcid.org/0000-0003-4228-9044

The efficiency of molecular genetic methods for the diagnosis of infections caused by S. pneumoniae и H. influenzae

Literature

About the Autors

Similar Articles