RESPIRATORY PATHOGENS PANEL PCR

1) Nasopharyngeal swabs and throat swabs.

Use flocked swab and send dry in sterile container or swab sheath. Laryngeal swabs will be rejected.

2) Bronchoalveolar lavage (BAL), endotracheal aspirates and sputum samples.

​For detection of 22 common agents of respiratory infections, i.e. adenovirus, metapneumovirus, coronavirus 229E, NL63, HKU1 and OC43, parainfluenza virus types 1,2, 3 and 4, influenza virus types A (subtypes seasonal H1N1, H3N2, and H1N1 pdm-2009)  and B, respiratory syncytial virus, SARS-CoV-2, rhinovirus/enterovirus, Bordetella parapertussis, Bordetella pertussis, Chlamydophila (formerly Chlamydia) pneumoniae and Mycoplasmoides (formerly Mycoplasma) pneumoniae from respiratory sample.

Outside of these indications, clinicians are encouraged to consult Infectious Diseases physicians before ordering for this test. 

​1) Refrigerate sample until transfer to laboratory. Do not freeze. Send sample at 2 - 8°C (with an ice-pack).

2) Sample must reach laboratory within 24 hours after collection.

BioFire® FilmArray® Respiratory 2.1 plus (RP2.1plus) (BioMerieux)

​1-3 days

​Mondays to Saturdays (except public holidays) 

​

Performance Characteristics:

Analytical Sensitivity (Manufacturer's claim):

Viruses

3000 IU/mL for Adenovirus (Species C, Serotype 2 - 100% confidence level)

330 copies/mL for Influenza A H1-2009 (100% confidence level)

21 copies/mL for Influenza A H3 (100% confidence level)

34 copies/mL for Influenza B (100% confidence level)

9 copies/mL for Respiratory Syncytial Virus (100% confidence level)

160 copies/mL for SARS-CoV-2 (100% confidence level)

Bacteria

41 CFU/mL for Bordetella parapertussis (IS1001 - 95% confidence level)

1000 CFU/mL for Bordetella pertussis (ptxP - 100% confidence level)

130 copies/mL for Chlamydia pneumoniae (100% confidence level)

460 copies/mL for Mycoplasma pneumoniae (100% confidence level)

Analytical Specificity (Manufacturer's claim):

No cross reactivity with Acinetobacter calcoaceticus, Bordetella avium, Bordetella bronchiseptica, Bordetella hinzii, Bordetella holmesii, Legionella bozemanii, Legionella dumoffii, Legionella feeleii, Legionella longbeacheae, Legionella micdadei, Legionella pneumophila, Chlamydia trachomatis, Corynebacterium diphtheriae, Enterobacter aerogenes, Escherichia coli, Haemophilus influenzae, Klebsiella oxytoca, Klebsiella pneumoniae, Lactobacillus acidophilus, Lactobacillus plantarum, Moraxella catarrhalis, Mycoplasma genitatlium, Mycoplasma hominis, Mycoplasma orale, Mycobacterium tuberculosis, Neisseria elongata, Neisseria gonorrhoeae, Neisseria meningitidis, Proteus mirabilis, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Staphylococcus epidermis, Stenotrophomonas maltophilia, Streptococcus pneumoniae, Streptococcus agalactiae, Streptococcus pyogenes, Streptococcus salivarius, Ureaplasma urealyticum, BAT SARS-like Coronavirus (recombinant), BAT SARS-like Coronavirus HKU5 (recombinant), Severe Acute Respiratory Syndrome Coronavirus (SARS), Bocavirus, Cytomegalovirus (CMV), Epstein-Barr Virus (EBV), Herpes Simplex Virus 1, Herpes Simplex Virus 2, Human Herpes Virus 6, Human Parechovirus, Influenza C, Measles Virus, Mumps, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus and Aspergillus flavus.

Assay limitations:

1. The Influenza A H1-2009 assay may react with H1 hemagglutinin gene sequences from viruses of swine origin. This assay will report either Influenza A H1 or Influenza A H1-2009, depending on the strain and concentration in the sample. Swine origin Hsw1N1 (A/New Jersey/8/1976 ; ATCC VR-897) was detected as either Influenza A H1 or Influenza A H1-2009 at a concentration of 8.9E+06 CEID 50/mL.

2. Performance characteristics for Influenza A were established when influenza A H1-2009 (H1N1pdm09), A H1, and A H3 were the predominant Influenza A viruses in circulation. Performance of detecting influenza A may vary if other influenza A strains are circulating or a novel influenza A virus emerges.

3. The influenza A subtyping assays target the influenza A hemagglutinin (H) gene only. The assay does not detect or differentiate the influenza A neuraminidase (N) subtypes.

4. The assay may not be able to distinguish between existing viral strains and new variants as they emerge. For example, the assay can detect Influenza A H3N2v (first recognized in August, 2011), but will not be able to distinguish this variant from Influenza A H3N2 seasonal.

5. At a sufficiently high concentration (e.g. >4.5E+07 CFU/mL of Bordetella pertussis), cross reactivity may occur between Bordetella spp. and the Human Rhinovirus/Enterovirus assays. The following results may be seen:

• B.pertussis present: reported as "Bordetella pertussis (ptxP) Detected AND "Human Rhinovirus/Enterovirus Detected"
• B.parapertussis present: reported as "Bordetella parapertussis (IS1001) Detected AND "Human Rhinovirus/Enterovirus Detected"
• B.bronchiseptica (non-IS1001-carrying strains) present: reported (falsely) as only "Human Rhinovirus/Enterovirus Detected"

6. Due to the genetic similarity between Human Rhinovirus and Enterovirus, the assay cannot reliably differentiate them– i.e. will all be reported as 'Rhinovirus/enterovirus'. A "Rhinovirus/Enterovirus" Detected result should be followed-up using an alternate method (e.g.  enterovirus PCR available in SGH Molecular Laboratory if differentiation between the viruses is required.

7. Does not differentiate between RSV A and RSV B – i.e. will all be reported as RSV.

8. Does not target Human Bocavirus.

9. We have found the assay to be less sensitive for the bacterial analytes compared to our current "Pneumonia Multiplex PCR" test and does NOT cover Legionella pneumophila. As such, our Pneumonia Multiplex PCR (which tests for Bordetella parapertussis, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasmoides pneumoniae and Legionella pneumophila) will remain available for separate order, if clinically indicated.

10. Currently does not give cycle threshold (CT) values for SARS-CoV-2.

11. Primers for both SARS-CoV-2 assays share substantial homology with the Bat coronavirus RaTG13 (accession: MN996532) and cross-reactivity with this closely-related viral sequence is predicted. In addition, the SARS-CoV-2 assay may cross-react with Pangolin coronavirus (accession: MT084071) and two other bat SARS-like coronavirus sequences (accession MG772933 and MG772934). It is unlikely that these viruses would be found in a human clinical nasopharyngeal swab; but if present, the cross-reactive product(s) produced by the assay will be detected as Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

12. Some strains of B. bronchiseptica (rarely isolated from humans) do carry IS1001 insertion sequences identical to those carried by most strains of B. parapertussis. These sequences will be amplified by the IS1001 assay and reported by the assay as Bordetella parapertussis (IS1001).