48 AJTCCM VOL. 31 NO. 2 2025
EDITORIAL
Lower respiratory tract infection is one of the most important
communicable causes of death worldwide.[1] In South Africa,
community-acquired pneumonia (CAP) ranks among the top
10 causes of death, surpassed only by tuberculosis as the leading
infective cause.[2] In a well-known study in patients with septic shock,
a frequent complication of CAP, it was found that each hour’s delay
in initiating appropriate antimicrobial therapy was associated with
a 7.6% decrease in survival.[3] It is therefore critically important for
antimicrobial treatment for severe CAP to be instituted timeously. For
this reason, antimicrobial therapy is oen prescribed before microbial
culture results are available. Empirical therapeutic options for CAP
target the most common aetiological pathogens, such as Streptococcus
pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae,
Staphylococcus aureus, Legionella species, Chlamydia pneumoniae
and Moraxella catarrhalis.[4] ere are, however, a growing number
of multidrug-resistant bacterial species that complicate decisions on
empirical therapy. Inappropriate broad-spectrum antibiotic use not
only results in increased mortality, but can also inadvertently contribute
to the development of antimicrobial resistance. Antimicrobial
stewardship principles dictate that every eort should be made to
de-escalate to a narrower-spectrum antimicrobial agent as soon as
a causative organism is identied and antimicrobial susceptibility
results are available. Traditional microbial culture methods, however,
require organisms to rst grow on culture medium in the laboratory
before antimicrobial susceptibility testing can be performed. is
process can take 48 - 72 hours, invariably resulting in either prolonged
inappropriate broad-spectrum antimicrobial agents being used before
de-escalation is possible, or prescribing empirical therapy to which the
causative organism is resistant.
Molecular techniques have the potential to signicantly reduce the
time to identify potential pathogenic organisms. Multiplex molecular
assays, such as the Biore FilmArray Pneumonia Panel, use nucleic
acid amplication techniques to detect genes of more than 20 dierent
organisms with a single test run. e positive and negative agreement
with conventional culture results are >96%.[5] ese techniques allow
for fast identication of potential pathogenic organisms, both bacteria
and viruses, as well as the presence of resistance genes within 2 hours.
[6] As part of antimicrobial stewardship practices, Buchan etal.[7] found
that the Biore FilmArray Pneumonia Panel result had the potential
for antibiotic adjustment in 70.7% of patients hospitalised with lower
respiratory tract infections.
Most of the studies on molecular techniques for pneumonia
were conducted in hospitalised or intensive care unit patients,
usually in higher-income settings. In the current issue of AJTCCM,
Worodria et al.[8] compared the diagnostic yield of the BioFire
FilmArray Pneumonia Panel with conventional culture techniques
in hospitalised patients with HIV in a low-income setting. ey
found that <25%of patients with CAP had a positive sputum culture,
whereas the FilmArray Pneumonia Panel could detect a possible
bacterial aetiology in 83.2% of patients. e FilmArray Pneumonia
Panel improved the diagnostic yield by 64.5%. A viral pathogen could
be detected in 49.5% of patients, with 44.9% of patients having both
bacterial and viral infections detectable by the polymerase chain
reaction (PCR) method. More than one pathogen was identied
with PCR in 56.0% of patients who had a positive sputum culture,
suggesting mixed infections. Antimicrobial resistance could be
detected in 58.8% of patients using sputum cultures, whereas PCR
could detect resistance genes in 79.3%.
e investigators rightly point out that the study did not assess the
clinical outcomes of the patients, and the impact of molecular testing
on important outcomes such as morbidity or mortality could therefore
not be evaluated. A well-known and important drawback of molecular
testing is the diculty in dierentiating between infection and mere
colonisation. Furthermore, the Biore FilmArray Pneumonia Panel
does not include testing for important opportunistic infections such
as Pneumocystis jirovecii or Mycobacterium tuberculosis. e attending
clinician should therefore specically request tests for these organisms.
e advantages of molecular techniques in terms of turnaround
time, increased diagnostic yield and detection of viruses as a cause
for CAP, as well as the detection of resistance genes, are clear. Why is
it then that molecular tests are not routinely performed in the current
era of increasing antimicrobial resistance, especially in low-income
settings? Cost associated with molecular tests may still be a signicant
barrier. It may also be that there is still concern regarding a lack of
understanding or interpretation of results, especially in patients with
mixed infections or limited symptoms in whom detected pathogens
may simply be colonisers. Interestingly, despite these potential barriers,
PCR-based methods are already well established in diagnosing
and managing pulmonary tuberculosis in low-income settings.
Conventional culture remains important for phenotypic susceptibility
testing and therefore still has a vital role. It is, however, high time for
molecular techniques to be incorporated in the diagnostic algorithms
for CAP to the benet of our patients.
S D Maasdorp, MB ChB, MMed (Int Med), FCP (SA), Cert Pulm-
onology (SA), PhD
Department of Internal Medicine, School of Medicine, Faculty of Health
Sciences, University of the Free State, Bloemfontein, South Africa
maasdorpsd1@gmail.com
B van der Westhuizen, MB ChB, MMed (Micro), FC Path (SA)
Micro, DTM&H
Department of Microbiology, School of Pathology, Faculty of Health
Sciences, University of the Free State, Bloemfontein, South Africa
1. World Health Organization. e top 10 causes of death. 7 August 2024. https://www.who.
int/news-room/fact-sheets/detail/the-top-10-causes-of-death (accessed 12 April 2025).
2. Statistics South Africa. Causes of death 2013. 4 December 2024. https://www.statssa.
gov.za/?page_id=737&id=3 (accessed 12 April 2025).
3. Kumar A, Roberts D, Wood KE, etal. Duration of hypotension before initiation
of eective antimicrobial therapy is the critical determinant of survival in human
septic shock. Crit Care Med 2006;34(6):1589-1596. https://doi.org/10.1097/01.
CCM.0000217961.75225.E9
Molecular techniques v. conventional culture: Should there really
be a debate?
AJTCCM VOL. 31 NO. 2 2025 49
EDITORIAL
4. Metlay JP, Waterer GW, Long AC, etal. Diagnosis and treatment of adults with
community-acquired pneumonia: An official clinical practice guideline of the
American oracic Society and Infectious Diseases Society of America. Am J Respir
Crit Care Med 2019;200(7):e45-e67. https://doi.org/10.1164/rccm.201908-1581ST
5. Buchan BW, Armand-Lefevre L, Anderson N. Molecular diagnosis of pneumonia
(including multiplex panels). Clin Chem 2021;68(1):59-68. https://doi.org/10.1093/
clinchem/hvab143
6. Ferrer J, Clari MÁ, Giménez E, etal. e Biore® Filmarray® Pneumonia Plus panel for
management of lower respiratory tract infection in mechanically-ventilated patients in
the COVID-19 era: A diagnostic and cost-benet evaluation. Diagn Microbiol Infect
Dis 2023;105(2):115847. https://doi.org/10.1016/j.diagmicrobio.2022.115847
7. Buchan BW, Windham S, Balada-Llasat JM, etal. 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):10.1128/jcm.00135-20. https://doi.
org/10.1128/JCM.00135-20
8. Worodria W, Andama A, Sanyu I, etal. Afr J oracic Crit Care Med 2025;31(2):e2415.
https://doi.org/10.7196/AJTCCM.2025.v31i2.2415
Afr J Thoracic Crit Care Med 2025;31(2):e3653. https://doi.org/10.7196/AJTCCM.2025.
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