Microbial aetiology of community acquired pneumonia at a tertiary institution in Johannesburg, South Africa

Abstract

A research report submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in partial fulfillment of the requirements for the degree of Master of Medicine in the branch of Clinical Microbiology and Infectious Diseases. Johannesburg, 2013Introduction To determine the spectrum of aetiological agents in adult Community Acquired Pneumonia (CAP) admitted to an academic hospital in Johannesburg using a novel transport medium (PrimeStore™ MTM), in addition to traditional specimen processing. PrimeStore™ MTM preserves released nucleic acids, including labile RNA. Materials and Methods Forty-eight adult patients with radiologically confirmed CAP were prospectively studied over three months. Microbiological investigation included culture from blood and sputum, with pulmonary tuberculosis being excluded by sputum microscopy and culture. Nasopharyngeal swabs (PrimeStore™ MTM) were analysed using two commercial multiplex PCR assays for the detection of 6 major bacteria and 12 major respiratory viruses. The BinaxNOW Legionella urinary antigen test was also used. Results A probable microbial aetiology of CAP was established for 62.5% (30 of the 48 patients) when the PCR platform was added to the conventional methods with the use of the PrimeStore™ MTM swabs. In contrast, the definite bacterial aetiology was 16.7% (8 of 48 patients) when conventional culture methods were used; none had more than one bacterial species identified. Five patients had no aetiological pathogens determined. The urine Legionella pneumophila antigen was negative in all patients. Of the eight patients (16.7%) with a definite bacterial aetiology; Streptococcus pneumoniae was isolated from blood cultures of all eight patients