Phenotypic and Molecular characterization of Community- acquired Bacterial Pneumonia in Khartoum State

Abstract

Typical respiratory pathogens Streptococcus pneumoniae (S. pneumoniae), Klebsiella pneumoniae (K. pneumoniae), and Haemophilus influenzae (H. influenzae) are now recognized as a significant cause of acute respiratory tract infections. These pathogens account for more than two third of all cases of community-acquired pneumonia (CAP). The organisms also occur as co-pathogens in mixed infections with mortality rate as high as 25 %. This study was essentially designed to investigate CAP among Sudanese patients acquiring infection from community in Khartoum State. Classical microbiological techniques as well as molecular technique were used achieve the objectives of the study. A total of 360 Sudanese patients (218 males and 142 females) suspected to have CAP and attended outpatient units at different hospitals in Khartoum State were enrolled in this study. These hospitals were AL-Shaab Teaching Hospital, Khartoum North Teaching Hospital, Abu Anja Teaching Hospital and Omdurman Teaching Hospital. The patients were grouped according to their ages as follows (year); 13 to 30, 31 to 60 and 61 to 90. Sputum specimens were collected from each patient and transported to the laboratory under the standard conditions following the Guideline of National Committee for Clinical Laboratories Standards. All specimens were inoculated on an agar media and incubated overnight to isolate the causative agents. DNA was extracted from each sputum specimen by Jena bioscience kit, Germany, and then stored in -20°C until used. A set of specific primers were used to detect the pathogens using PCR machine. Gene sequence was done for PCR product of S. pneumoniae to confirm the results. The results showed 122(33.8%) of the specimens were positive for bacterial growth. The rest 238(66.2%) demonstrated no bacterial growth. Out of the investigated specimens (n=360), CAP agents were identified as follows; 64(17.8%) S. pneumoniae, 39(10.8%) K. pneumoniae and 19(5.3%) H. influenzae. Moreover, PCR results showed 157(43.6%) of the investigated specimens were positive, while 203(56.4%) were negative. The detected agents were S. pneumoniae 81(22.5%), K. pneumoniae 43(11.9%) and H. influenzae 33(9.2%). CAP agents were more prevalent in males 97(26.9%) than females 60 (16.6%), but this result was statistically insignificant. On the other hand, CAP agents were more prevalent in age group 31-60 years. This result was statistically significant only with K. pneumoniae (P= 0.041). The result of the gene sequences showed that the average query cover between 74% to 100% and the identity between 92% to 100%. The study concluded that the prevalence of CAP in Khartoum State is relatively high. S. pneumoniae is ranking the top of the causative agents. PCR is very useful in detection of CAP agents. SHV resistance genes were detected only in K. pneumoniae. Further studies are recommended for detection of the other bacterial species in sputum samples coupled with viral agent using PCR, especially for bacterial PCR-negative samples