Identification of potential pathogens of pneumonia in sputum samples from adult patients at the University Teaching Hospital in Lusaka

Abstract

Introduction: Pneumonia is a leading cause of morbidity and a significant cause of mortality worldwide. Although information is available on pneumonia in children in Zambia, the incidence in adults in many parts of Africa including Zambia is unknown. Knowledge of the local aetiological agents of pneumonia is critical for making rational decisions about treatment as differences in aetiology may result in poor response to therapy chosen to cover pathogens common in studies done in high income countries. Objective: The objective of this study was to identify aetiological agents of pneumonia in adult patients and determine their antibiotic susceptibility patterns at the University Teaching Hospital in Lusaka. Materials and Methods: This was a cross-sectional study carried out from March 2014 to August 2014. A total of 312 sputum samples from adults suspected of pneumonia were cultured and of which 146 samples were also analysed by PCR. Antibiotic susceptibility testing was done on bacterial isolates according to Clinical Laboratory Standards International guidelines. Results: Of the 312 samples cultured, 56.1% (175/312) yielded probable pathogens with the most common being Moraxella catarrhalis 20.8% (47/226), Pseudomonas aeruginosa 19.9% (45/226), and Klebsiella pneumoniae 14.2% (32/226). Almost all (10/11) K. pneumoniae isolates were multidrug resistant (7 of 9 drugs) and were ESBL positive. About 71% of the 146 samples tested using PCR yielded human cytomegalovirus 24.3% (44/181), K. pneumoniae 17.7% (32/181), H. influenzae non-type b 16.0% (29/181), S. pneumoniae and S. aureus 9.4% (17/181) each. Other agents, which included Rhinovirus (5.5%, 10/181), M. catarrhalis (4.4%, 8/181), Pneumocystis jirovecii (3.9%, 7/181), Respiratory Syncytial Virus (RSV) A/B (3.9%, 7/181), Adenovirus (1.7%, 3/181), Human bocavirus (1.1%, 2/181), Human metapneumoviruses A/B (1.1%, 2/181), Parainfluenzae type 1 (1.1%, 2/181), Parainfluenzae type 2 (1.1%, 2/181), Parainfluenzae type 4 (1.1%, 2/181), Salmonella species (0.6%, 1/181), Mycoplasma pneumoniae (0.6%, 1/181), Influenza virus type B (0.6%, 1/181), Human coronavirus 63 (0.6%, 1/181), and Parainfluenzae type 2 (0.6%, 1/181) were also detected. Multiple agents were detected in 42% of samples analysed by PCR. About 29.5% (13/44) of these specimens harboured K. pneumoniae and H. influenzae non-type B. The culture and PCR methods detected 30.1% and 69% community acquired agents, respectively. Conclusion: The study showed a wide variety of potential pathogens that included bacteria, viruses and fungi. PCR detected more organisms than the culture method, which included viruses and fungal agents. Some of the samples yielded multiple organisms which would makes it difficult to determine the causative agent of pneumonia in a patient. Most of the bacterial agents isolated displayed the multidrug resistant phenotype. These data shows the importance of employing better diagnostic methods, such as molecular tools, for identifying potential pathogens associated with pneumonia. The high drug resistance patterns observed with bacterial isolates presents physicians with very limited treatment options for the affected patients, which may require resorting to more expensive drugs. This calls for an urgent review of treatment practices at the University Teaching Hospital to avoid complications in the patients