Essay for Algorithm to Diagnose Infective COPD Exacerbation

The exacerbation of chronic obstructive pulmonary disease (COPD) is triggered by allergen, air pollution, extreme activities and smoking. Common signs and symptoms include increased breathlessness than routine, increased frequency of cough or developing a new cough or change in the colour of sputum, etc. The homozygosity for the Z allele of the alpha 1-antitrypsin gene is the only genetic risk factor for COPD prone to COPD exacerbation (Sandford, Weir and Pare’ 1997). Lareau, Moseson and Slatore (2018) claimed that respiratory infection is the most common cause of COPD exacerbation and presents pleuritic chest pain, consolidation/ diffuse shadowing in chest X-ray and fever. Further microbial laboratory investigations are essential for patients with infective COPD exacerbation to treat the cause.

Various clinical samples such as sputum, throat swab, nasal aspirates, bronchial aspirate lavage (BAL), blood and urine are used for microbiological investigations. Saxena et al. (2016) claimed that sputum samples are still used as the first-line investigations in exacerbation of COPD because it is easy to collect and non-invasive. However, Sethi (2004) argued that sputum samples can be contaminated by saliva leading to the limitation of the specificity of culture results. Usually, rapid diagnostic tests are run as primary tests to detect microorganisms causing the infective COPD exacerbation.

Natalie (2017) explained that polymerase chain reactions (PCR) is now widely used with various specimens including blood, urine, sputum, nasal discharges and other body fluids. It detects viruses, fungi and bacteria by amplifying even small amounts of genetic materials containing DNA and RNA.

Streptococcus pyogenes

(

S. pyogenes

) can be easily detected by PCR in most of the clinical samples. It can also detect atypical bacteria which cannot be cultured and gram-stained using standard methods (Shimizu et al. 2015). It is also fast, easy to use with excellent sensitivity, specificity and only a small amount of sample is required to run the test. The disadvantage is limited capacity for multiplexing and it cannot be run to detect unknown species. Jung et al. (2018) recommended to use PCR together with serology tests as PCR shows lower sensitivity than serology. Spellerberg and Brandt (2016) also mentioned that

S. pyogenes

can be rapidly distinguished within a few minutes by using PYR (Pyrrolindonyl Aminopeptidase) test which is a rapid colorimetric method by using paper strips that contain dried chromogenic substrates. The automated identification system such as matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) can even distinguish different strains according to the molecular signatures such as rRNA. It is used to detect

S. pyogenes

in sputum sample as primary testing because it is rapid, easy with high throughput characteristics and without the requirement of bacterial cultivation even though identification of several

Streptococci

species is still limited.

Natalie (2017) claimed that traditional methods such as culture using selective or differential medium, microscopy, gram-staining and biochemical tests are still used as the gold standard for confirmation. For example,

S. pyogenes

can be confirmed by culturing the throat swab or sputum on a sheep blood agar (differential medium) with optimal incubation at 35C to 37C in the presence of 5% CO

₂

or under anaerobic conditions and the typical colonies are observed after 24 hours of incubation (Spellerberg and Brandt 2016).

S. pyogenes

are gram positive cocci and beta hemolytic. They are identified in the sheep blood agar by the presence of a clear zone surrounding the colony because they produce exotoxins called hemolysins that destroy the blood cells. The cultures are sensitive, low-priced and reliable but they are usually mixed with diverse pathogens including normal flora resulting in difficulty to find out the specific organism of the cause. Moreover, it is time consuming, labour intensive and some culture take at least 1-3 days for growth or some organisms may not even grow on the artificial media (Natalie 2017).

Another rapid diagnostic test called immunochromatography (ICT) can be used for urine, blood and respiratory samples. Mercante and Winchell (2015) said that it can detect

Legionella pneumophila

and

Streptococcus pneumoniae

in the urine sample by using a card- or strip-based format like a pregnancy test kit and it takes only 10-15 minutes. It works by detecting the presence of antigens of specific microorganisms. It can also detect immunoglobulin M (IgM) in

Chlamydia pneumonia

e respiratory infections and requires only 10l of blood from the fingertip (Miyashita et al. 2008).

Aspergillus fumigatus

causes invasive pulmonary aspergillosis, a life threatening respiratory disease, and patients with COPD are at high risk (Alonso 2012). Even though PCR and ELISA are rapid and accurate primary diagnostic tests, Bauters and Nelis (2000) claimed that isolation of the organism on an agar plate such as Sabouraud dextrose agar with microscopic identification of the growth is still used as a daily routine test. However, it may take several days up to 5 days and other mold species can also present the similar morphological characteristics of

Aspergillus

species leading to false-negative results. Therefore, the organism can be confirmed by a new secondary culture method that combines membrane filtration and microcolony formation on a selective medium at 45C to detect the particular enzyme activity. The advantages are improvement in the sensitivity, specificity and rapidity of the routine culture and the organism can be detected within 14 hours. It is also simple and cost-effective (Bauters and Nelis 2000).

In COPD exacerbation caused by

Influenza


A

and

B

the primary tests such as PCR or ELISA are done by using sputum, throat swab or nasal aspirates. Enzyme linked immunoassay (ELISA) is used to detect influenza viral antigen within 30 minutes near patient or as a point-of-care test (WHO 2005). If the positive predictive value is high, the result can be accepted. If the result presents low negative predictive result, retesting is done by Immunofluorescent antibody test (IFA), culture or real time-PCR. The limitation of ELISA is reduced specificity and sensitivity due to difficulty in generating selective antibodies and large amounts of antigens for quantification are required (Natalie 2017). Traditional tube cell culture has still served as the gold standard for viral infection and it can isolate various viruses and the isolate can be used for serotyping and antiviral susceptibility testing. However, the incubation period is usually 5 to 10 days for some viruses and 2 to 6 tubes are used per culture, so purchasing different types of cell culture tubes is required (Leland and Ginocchio 2007). Therefore, centrifugation-enhanced shell vial assay has been used recently as a rapid culture method for detection of respiratory and other viruses. The viral infection of the cell is enhanced by centrifuging the vials after adding specimen. It has short turnaround time for detection which takes 24-48 hours and can isolate viruses that replicate poorly or not at all in tube cell cultures but it is time consuming and labour intensive to inoculate vials.

Overall, the development of new rapid diagnostic techniques has taken over the microbiology laboratory but traditional methods are still the standard for identification and antimicrobial susceptibility testing (Laupland and Valiquette 2013). Therefore, the traditional and rapid tests still should be used together if necessary to ensure the accurate result for the patients by weighing the advantages and disadvantages of each test.

References

• Alonso, M., Escribano, P., Guinea, J., Recio, S., Simon, A., Peláez, Bouza, E and Viedma, D.G., 2012. Rapid Detection and Identification of Aspergillus from Lower Respiratory Tract Specimens by Use of a Combined Probe-High-Resolution Melting Analysis.
  
  Journal of Clinical Microbiology
  
  [online]. (25 July), 1-26. DOI:10.1128/JCM.00176-12 [Accessed 10 January 2019].
• Bauters, T. G. M. and Nelis, H. J., 2000. Rapid and Sensitive Plate Method for Detection of Aspergillus fumigatus.
  
  Journal of Clinical Microbiology
  
  [online]. 38 (10) (October), 3796-3799. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC87478/ [Accessed 10 January 2019].
• Jung, C. Y., Choe, Y. H., Lee, S. Y., Kim, W. J., Lee, J. D., Ra, S. W., Choi, E. G., Lee, J. S., Park, M. J. and Na, J. O. 2018. Use of serology and polymerase chain reaction to detect atypical respiratory pathogens during acute exacerbation of chronic obstructive pulmonary disease.
  
  The Korean Journal of Internal Medicine
  
  [online]. 33 (5) (25 June), 941-951. DOI: 10.3904/kjim.2017.279 [Accessed 22 December 2018].
• Lareau, S., Moseson, E. and Slatore, C. G., 2018. Exacerbation of COPD.
  
  American Thoracic Society
  
  [online]. 198, 21-22. Available at:
  
  https://www.thoracic.org/patients/patient-resources/resources/copd-exacerbation-ecopd.pdf
  
  [Accessed 22 December 2018].
• Laupland, K. B. and Valiquette, L., 2013. The changing culture of the microbiology laboratory.
  
  Canadian Journal of Infectious Diseases and Medical Microbiology
  
  [online]. 24 (3), 125-128. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852448/ [Accessed 19 January 2019].
• Leland, D. S. and Ginocchio, C. C., 2007. Role of Cell Culture for Virus Detection in the Age of Technology.
  
  Clinical Microbiology Reviews
  
  [online]. 20 (1) (January), 49-78. DOI: 10.1128/CMR.00002-06 [Accessed 19 January 2019].
• Mercante, J. W. and Winchell, J. M., 2015. Current and Emerging Legionella Diagnostics for Laboratory and Outbreak Investigations.
  
  Clinical Microbiology Reviews
  
  [online]. 28 (1) (January), 95-39. DOI: 10.1128/CMR.00029-14 [Accessed 30 December 2018].
• Miyashita, N., Ouchi, K., Kishi, F., Tabuchi, M., Tsumura, N., Bannai, H., Iwata, S., Tanaka, T. and Oka, M. 2008. Rapid and Simple Diagnosis of
  
  Chlamydophila pneumoniae
  
  by an Immunochromatographic Test for Detection of Immunoglobulin M antibodies.
  
  Clinical and Vaccine Immunology
  
  [online]. 15 (7) (14 May), 1128-1131. DOI: 10.1128/CVI.00085-08 [Accessed 2 January 2019].

• Natalie, 2017. Will molecular techniques replace traditional cell-based assays in microbiological diagnostics?
  
  Biametrics
  
  [online, blog], 1 May. Available at: http://biametrics.com/microbiological-diagnostics-will-molecular-tests-replace-conventional-methods/ [Accessed 30 December 2018].
• Sandford, A. J., Weir, T. D. and Pare’ PD, 1997. Genetic risk factors for chronic obstructive pulmonary disease.
  
  European Respiratory Journal
  
  [online]. 10 (6) (June), 1380-91. Available at:
  
  https://www.ncbi.nlm.nih.gov/pubmed/9192947
  
  [Accessed 10 January 2019].
• Saxena, S., Ramnani, V. K., Nema, S., Tripathi, K., Dave, L. and Srivastava, N. 2016. Bacteriological Profile in Acute Exacerbation of Chronic Obstructive Lung Disease (AECOPD).
  
  Annals of International medical and dental Research
  
  [online]. 2 (5) (June), 1-6. DOI: 10.21276/aimdr.2016.2.5.MB1 [Accessed 22 December 2018].
• Sethi, S., 2004. Bacteria in Exacerbations of Chronic Obstructive Pulmonary Disease Phenomenon or Epiphenomenon?
  
  American Thoracic Society
  
  [online]. 1(2) (1 Arpil), 109-114. DOI: 10.1513/pats.2306029 [Accessed 21 December 2018].
• Shimizu, K., Yoshii, Y., Morozumi, M., Chiba, N., Ubukata, K., Uruga, H., Hanada, S., Saito, N., Kadota, T., Ito, S., Wakui, H., Takasaka, N., Minagawa, S., Kojima, J., Hara, H., Numata, T., Kawaishi, M., Saito, K., Araya, J., Kaneko, Y., Nakayama, K., Kishi, K. and Kuwano, K., 2015. Pathogens in COPD exacerbations identified by comprehensive real-time PCR plus older methods.
  
  International Journal of Chronic Obstructive Pulmonary Disease
  
  [online]. 10 (23 September), 2009-2016. DOI: 10.2147/COPD.S82752 [Accessed 22 December 2018].
• Spellerberg, B. and Brandt, C., 2016. Laboratory Diagnosis of Streptococcus pyogenes (group A streptococci).
  
  Streptococcus pyogenes: Basic Biology to Clinical Manifestations
  
  [online]. Available at:
  
  https://www.ncbi.nlm.nih.gov/books/NBK343617/
  
  [Accessed 28 December 2018].
• WHO, 2005. WHO recommendations on the use of rapid testing for influenza diagnosis. Available at:
  
  https://www.who.int/influenza/resources/documents/RapidTestInfluenza_WebVersion.pdf
  
  [Accessed 23 December 2018].