Chanda, R

Opperman, C J

English

South African Medical Journal (SAMJ)

CORRESPONDENCE437       June 2020, Vol. 110, No. 6Assessment of sputum cultures for the diagnosis of lower-respiratory tract infections in the outpatient settingTo the Editor: The clinical relevance of lower-respiratory tract (LRT) specimens remains debatable. While a positive blood or pleural fluid culture provides a definitive cause, an organism cultured from a respiratory specimen is not definitive proof of an aetiological agent. Many bacterial species are normal flora or colonisers of the respiratory tract; therefore, routine use of sputum cultures, except for suspected Mycobacterium tuberculosis (TB), is not endorsed. Notably, the South African (SA) guideline for the management of community-acquired pneumonia (CAP) in adults and the American Thoracic Society/Infectious Diseases Society of America do not recommend the submission of a sputum sample in outpatients.[1,2] The objective of this study was: (i) to determine the yield of positive cultures from sputum collected in the outpatient setting in the Cape Town metropole; and (ii) to establish the prevalence of recognised pathogens and corresponding antibiograms. In our laboratory survey, sputum cultures were analysed retrospectively over 1 year from samples collected in the outpatient setting and submitted to the National Health Laboratory Service (NHLS), Groote Schuur Hospital (GSH), during 2018 (Fig.1). Patients with underlying lung disease caused by cystic fibrosis, and patients from respiratory clinics, were excluded. A pathogen was identified in only 174 of 2 262 (7.7%) sputum cultures, while 2 088 cultures were reported as mixed growth or normal respiratory flora. Fifty-two percent (n=92/174) of specimens with a pathogen organism yielded Haemophilus influenzae, 12% (n=26/174) Moraxella catarrhalis and 9% (n=12/174) Streptococcus pneumoniae. These bacteria represent the common causes of CAP in adults and children between 2 months and 5 years of age in SA.[1,3] From the 174 cultures, only 5% (n=9) were from child ren ≤5 years old. Ninety-nine percent (n=90/91) of H. influenzae were susceptible to co-amoxiclav, 97% (n=87/91) to amoxicillin and 100% to ceftriaxone, while 48% (n=44/91) were resistant to co- trimoxazole. Only 2 of 16 S. pneumoniae isolates were not suscep-tible to penicillin.Numerous factors contribute to the low yield of pathogens cultured from sputum samples in the outpatient setting. These include patients with a low positive predictive value, given their symptoms and signs, and the likelihood of a viral infection, poor-quality samples collected with saliva and delayed transport from the healthcare facility to the laboratory, resulting in overgrowth of respiratory flora.[4,5] Non-significant cultures do not only affect patient management, but also increase the need for additional laboratory staff and healthcare workers to process and collect samples. This situation also ultimately has financial implications. The laboratory survey had the following limitations. It did not include clinical epidemiology, such as patient comorbidities, presence of structural lung diseases (e.g. acute exacerbations in chronic bronchitis), co-infection with TB or molecular diagnostics. We also did not investigate the diagnostic value of sputum-quality assessment. Data were obtained from community healthcare centres serviced by the NHLS at GSH. Furthermore, the retrospective nature of this study relied on the integrity of data extracted from the laboratory information system.In conclusion, the diagnostic yield of sputum samples collected in the outpatient setting remains very low, with only 7.7% of cultures in this laboratory survey growing a recognised bacterial pathogen. The interpretation of sputum cultures continues to be a challenge for microbiology laboratories and the value of obtaining LRT samples is questionable. Acknowledgements. We thank Prof. A Brink, head of the Division of Medical Microbiology, National Health Laboratory Service, University of Cape Town, for his input and review of this report. Author contributions. Both authors contributed equally in preparing the report.Funding. None.Conflicts of interest. None.Raphael Chanda, Christoffel J OppermanDivision of Medical Microbiology, National Health Laboratory Service, Groote Schuur Hospital and University of Cape Town, South Africastefanopperman1@gmail.com1. Boyles TH, Brink A, Calligaro GL, et al. South African guideline for the management of community-acquired pneumonia in adults. J Thorac Dis 2017;9(6):1469-1502. https://doi.org/10.21037/jtd.2017.05.312. Metlay JP, Waterer GW, Long AC, et al. Diagnosis and treatment of adults with community-acquired pneumonia. An Official Clinical Practice Guideline of the American Thoracic Society and Infectious Diseases Society of America. Am J Respir Crit Care Med 2019;200(7):45-67. https://doi.org/10.1164/rccm.201908-1581ST3. Zar HJ, Jeena P, Argent A, et al. Diagnosis and management of community-acquired pneumonia in childhood – South African Thoracic Society guidelines. S Afr Med J 2005;95(12):975-990. https://doi.org/10.7196/SAMJ.19404. Budayanti NS, Suryawan K, Iswari IS, Sukrama DM. The quality of sputum specimens as a predictor of isolated bacteria from patients with lower respiratory tract infections at a tertiary referral hospital, Denpasar, Bali-Indonesia. Front Med (Lausanne) 2019;6:64. https://doi.org/10.3389/fmed.2019.000645. Tessema B, Beer J, Emmrich F, Sack U, Rodloff AC. Rate of recovery of Mycobacterium tuberculosis from frozen acid-fast-bacillus smear-positive sputum samples subjected to long-term storage in Northwest Ethiopia. J Clin Microbiol 2011;49(7):2557-2561. https://doi.org/10.1128/JCM.00059-11S Afr Med J 2020;110(6):437. https://doi.org/10.7196/SAMJ.2020.v110i6.14786This open-access article is distributed under Creative Commons licence CC-BY-NC 4.0.1  SAMJ, April 2020. Assessment of sputum cultures for the diagnosis of lower respiratory tract infections in the outpatient setting                            050100150200250Jan-18Feb-18Mar-18Apr-18May-18Jun-18Jul-18Aug-18Sep-18Oct-18Nov-18Dec-18Sample numberMixed growth/ Respiratory flora Pathogen cultured250200150100500Sample, n2018JanuaryFebruaryMarchAprilMayJune JulyAugustSeptemberOctoberNovemberDecemberMixed growth/respiratory ora    Pathogen culturedFig. 1. Sputum cultures from suspected community-acquired pneumonia outpatients in 2018, submitted to the National Health Laboratory Service, Groote Schuur Hospital, South Africa. (Respiratory flora = normal nasopharynx-colonising flora; mixed growth = no predominance of Gram-negative or Gram-positive bacteria among normal respiratory flora.) 

Assessment of sputum cultures for the diagnosis of lower-respiratory tract infections in the outpatient setting

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Assessment of sputum cultures for the diagnosis of lower-respiratory tract infections in the outpatient setting

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South African Medical Journal (SAMJ)