290
Views
2
CrossRef citations to date
0
Altmetric
Research Article

Diagnostic performance of an in-house multiplex PCR assay and the retrospective surveillance of bacterial respiratory pathogens at a teaching hospital, Kelantan, Malaysia

ORCID Icon, , , &

References

  • WHO. The top 10 causes of death. Geneva: World Health Organization; 2020. [updated 9 Dec 2020; cited 2020; cited 2021 Dec 2020; cited 2021 May 9 Dec 2020; cited 2021 May 11].
  • Department of Statistics Malaysia D. Statistics on Causes of Death, Malaysia, 2020 Putrajaya: Department of Statistics Malaysia Official Website; 2020 [cited 2021 Jul 22]. Available from 2021 Jul 22: https://www.dosm.gov.my/v1/index.php?r=column/cthemeByCat&cat=401&bul_id=QTU5T0dKQ1g4MHYxd3ZpMzhEMzdRdz09&menu_id=L0pheU43NWJwRWVSZklWdzQ4TlhUUT09#.
  • Das S, Dunbar S, Tang Y-W. Laboratory diagnosis of respiratory tract infections in children - the state of the art. Front Microbiol. 2018;9:2478. PubMed PMID: 30405553.
  • Nik Zuraina NMN, Goni MD, Amalina KN, et al. Thermostable heptaplex PCR assay for the detection of six respiratory bacterial pathogens. Diagnostics. 2021;11(5):753. PubMed PMID.
  • Buderer NM. Statistical methodology: i. Incorporating the prevalence of disease into the sample size calculation for sensitivity and specificity. Acad Emerg Med. 1996;3(9):895–900. PubMed PMID: 8870764.
  • Arifin WN, Sample size calculator (Version 2.0); 2017; Accessed on: 5 January 2017; https://wnarifin.github.io/ssc_excel.html
  • Yousif TK, Khaleq BA. Epidemiology of acute respiratory tract infections (ARI) among children under five years old attending Tikrit general teaching hospital. Middle Eastern J Fam Med. 2006;4(3):48–51.
  • Stralin K, Korsgaard J, Olcen P. Evaluation of a multiplex PCR for bacterial pathogens applied to bronchoalveolar lavage. Eur Respir J. 2006;28(3):568–575. PubMed PMID: 16737990.
  • Enk MJ, Oliveira E, Silva G, et al. Diagnostic accuracy and applicability of a PCR system for the detection of Schistosoma mansoni DNA in human urine samples from an endemic area. PLoS One. 2012;7(6):e38947. PubMed PMID: 22701733; PubMed Central PMCID: PMCPMC3372502.
  • Saravolatz LD, Manzor O, VanderVelde N, et al. Broad-range bacterial polymerase chain reaction for early detection of bacterial meningitis. Clin Infect Dis. 2003;36(1):40–45. PubMed PMID: 12491200.
  • Nomanpour B, Ghodousi A, Babaei T, et al. Single tube real time PCR for detection of Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae and Legionella pneumophila from clinical samples of CAP. Acta Microbiol Immunol Hung. 2012;59(2):171–184. PubMed PMID: 22750778.
  • Al-Marzooq F, Imad MA, How SH, et al. Development of multiplex real-time PCR for the rapid detection of five bacterial causes of community acquired pneumonia. Trop Biomed. 2011;28(3):545–556. PubMed PMID: 22433883.
  • Li X, Chen B, Zhang S, et al. Rapid detection of respiratory pathogens for community-acquired pneumonia by capillary electrophoresis-based multiplex PCR. SLAS Technol. 2019;24(1):105–116. PubMed PMID: 30048599.
  • Steensels D, Delforge M, Lagrou K, et al. Development of a customized TaqMan® array card for simultaneous detection of 32 respiratory pathogens. Adv Tech Clin Microbiol. 2017;2(1):1–8.
  • Garcia-Vazquez E, Marcos MA, Mensa J, et al. Assessment of the usefulness of sputum culture for diagnosis of community-acquired pneumonia using the PORT predictive scoring system. Arch Intern Med. 2004;164(16):1807–1811. PubMed PMID: 15364677.
  • Lee YJ, Shin S, Roh EY, et al. Acceptability of sputum specimens for diagnosing pulmonary tuberculosis. J Korean Med Sci. 2015;30(6):733–736. Epub 05/13. PubMed PMID: 26028925
  • Nair B, Stapp J, Stapp L, et al. Utility of gram staining for evaluation of the quality of cystic fibrosis sputum samples. J Clin Microbiol. 2002;40(8):2791–2794. PubMed PMID: 12149331; PubMed Central PMCID: PMCPMC120690.
  • Samuel LP, Balada-Llasat JM, Harrington A, et al. Multicenter assessment of gram stain error rates. J Clin Microbiol. 2016;54(6):1442–1447. PubMed PMID: 26888900; PubMed Central PMCID: PMCPMC4879281.
  • Lutfiyya MN, Henley E, Chang LF, et al. Diagnosis and treatment of community-acquired pneumonia. Am Fam Physician. 2006;73(3):442–450. PubMed PMID: 16477891.
  • Loens K, Van Heirstraeten L, Malhotra-Kumar S, et al. Optimal sampling sites and methods for detection of pathogens possibly causing community-acquired lower respiratory tract infections. J Clin Microbiol. 2009;47(1):21–31. PubMed PMID: 19020070; PubMed Central PMCID: PMCPMC2620840.
  • Orth H. Interpretation of microbiological reports: Sensible interpretation of microbiological reports can make a difference to patient management. United States: Accredation Council for Continuing Medical Education; 2008.
  • Fukuyama H, Yamashiro S, Kinjo K, et al. Validation of sputum Gram stain for treatment of community-acquired pneumonia and healthcare-associated pneumonia: a prospective observational study. BMC Infect Dis. 2014;14(1):534.
  • Alves MS, Dias RC, de Castro AC, et al. Identification of clinical isolates of indole-positive and indole-negative Klebsiella spp. J Clin Microbiol. 2006;44(10):3640–3646. PubMed PMID: 16928968; PubMed Central PMCID: PMCPMC1594763.
  • Sabat AJ, van Zanten E, Akkerboom V, et al. Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification - increased discrimination of closely related species. Sci Rep. 2017;7(1):3434.
  • Garza-Ramos U, Barrios-Camacho H, Moreno-Dominguez S, et al. Phenotypic and molecular characterization of Klebsiella spp. isolates causing community-acquired infections. New Microbes New Infect. 2018;23:17–27. PubMed PMID: 29692906; PubMed Central PMCID: PMCPMC5913063.
  • Hansen DS, Aucken HM, Abiola T, et al. Recommended test panel for differentiation of Klebsiella species on the basis of a trilateral interlaboratory evaluation of 18 biochemical tests. J Clin Microbiol. 2004;42(8):3665–3669. PubMed PMID: 15297514; PubMed Central PMCID: PMCPMC497635.
  • Berry GJ, Loeffelholz MJ, Williams-Bouyer N. An investigation into laboratory misidentification of a bloodstream Klebsiella variicola infection. J Clin Microbiol. 2015;53(8):2793–2794. PubMed PMID: 26063851; PubMed Central PMCID: PMCPMC4508421.
  • Fontana L, Bonura E, Lyski Z, et al. The brief case: Klebsiella variicola-Identifying the misidentified. J Clin Microbiol. 2019;57(1): PubMed PMID: 30602547; PubMed Central PMCID: PMCPMC6322460. DOI:10.1128/JCM.00826-18.
  • Long SW, Linson SE, Ojeda Saavedra M, et al. Whole-genome sequencing of human clinical Klebsiella pneumoniae isolates reveals misidentification and misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. mSphere. 2017;2(4). PubMed PMID: 28776045; PubMed Central PMCID: PMCPMC5541162. 10.1128/mSphereDirect.00290-17.
  • Wong K, Roberts MC, Owens L, et al. Selective media for the quantitation of bacteria in cystic fibrosis sputum. J Med Microbiol. 1984;17(2):113–119. PubMed PMID: 6423825.
  • Bhattacharya A. Role of sputum cultures in diagnosis of respiratory tract infections. Lung India. 2006;23(1):20–24.
  • Loh LC, Chin HK, Chong YY, et al. Klebsiella pneumoniae respiratory isolates from 2000 to 2004 in a Malaysian hospital: characteristics and relation to hospital antibiotics consumption. Singapore Med J. 2007;48(9):813–818. PubMed PMID: 17728961.
  • Liam CK, Lim KH, Wong CM. Community-acquired pneumonia in patients requiring hospitalization. Respirology. 2001;6(3):259–264. PubMed PMID: 11555386.
  • Morris DE, McNeil H, Hocknell RE, et al. Carriage of upper respiratory tract pathogens in rural communities of Sarawak, Malaysian Borneo. Pneumonia (Nathan). 2021;13(1):6. PubMed PMID: 33894778; PubMed Central PMCID: PMCPMC8070298.
  • Hooi LN, Looi I, Ng AJ. A study on community acquired pneumonia in adults requiring hospital admission in Penang. Med J Malaysia. 2001;56(3):275–284. PubMed PMID: 11732071.
  • Shorr AF, Zilberberg MD, Micek ST, et al. Viruses are prevalent in non-ventilated hospital-acquired pneumonia. Respir Med. 2017;122:76–80. PubMed PMID: 27993295; PubMed Central PMCID: PMCPMC7135153.
  • Jain S, Self WH, Wunderink RG, et al. Community-acquired pneumonia requiring hospitalization among U.S. adults. N Engl J Med. 2015;373(5):415–427. PubMed PMID: 26172429; PubMed Central PMCID: PMCPMC4728150.
  • Musher DM, Abers MS, Bartlett JG. Evolving understanding of the causes of pneumonia in adults, with special attention to the role of pneumococcus. Clin Infect Dis. 2017;65(10):1736–1744. PubMed PMID: 29028977; PubMed Central PMCID: PMCPMC7108120.
  • Mardian Y, Menur Naysilla A, Lokida D, et al. Approach to identifying causative pathogens of community-acquired pneumonia in children using culture, molecular, and serology tests. Front Pediatr. 2021;9:629318. PubMed PMID: 34123961; PubMed Central PMCID: PMCPMC8193353.
  • Murdoch DR. How best to determine causative pathogens of pneumonia. Pneumonia (Nathan). 2016;8(1):1. PubMed PMID: 28702281; PubMed Central PMCID: PMCPMC5469189.
  • Najafi S, Sandrock C. Hospitalized patients with acute pneumonia. Hosp Med Clin. 2017;6(4): 456–469. PubMed PMID: 32288999; PubMed Central PMCID: PMCPMC7104154.
  • Bhuiyan MU, Snelling TL, West R, et al. Role of viral and bacterial pathogens in causing pneumonia among Western Australian children: a case–control study protocol. BMJ Open. 2018;8(3):e020646. PubMed PMID: 29549211; PubMed Central PMCID: PMCPMC5857668.
  • Memish ZA, Assiri A, Turkestani A, et al. Mass gathering and globalization of respiratory pathogens during the 2013 Hajj. Clin Microbiol Infect. 2015;21(6):571 e1–8. PubMed PMID: 25700892.
  • Torres A, Lee N, Cilloniz C, et al. Laboratory diagnosis of pneumonia in the molecular age. Eur Respir J. 2016;48(6):105–116. PubMed PMID: 27811073.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.