Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan

Klebsiella pneumoniae is recognized as one of the most important healthcare-associated pathogens worldwide due to its tendency to develop antibiotic resistance and cause fatal outcomes. Bacterial identification methods such as culture and biochemical tests are routinely used with limited accuracy in many low- and middle income countries including Sudan. The aim of this study was to test the accuracy of identification of K. pneumoniae in Khartoum, Sudan. Two hundred and fifty K. pneumoniae isolates were collected and subjected to identification by conventional phenotypical methods, biochemical using API 20E, and genotypically by amplification of 16S-23S rDNA and sequencing of rpoB, gapA, and pgi. Only 139 (55.6%) of the isolates were confirmed as K. pneumoniae genotypically by PCR and 44.4% were identified as non-K. pneumoniae. The results demonstrate that the identification panels used by the hospitals were inaccurately identifying K. pneumonia and led to over estimation of the prevalence of this organism. The current identification methods used in Khartoum hospitals are highly inaccurate, and therefore we recommend the use of a comprehensive biochemical panel or molecular methods, when possible, for accurate identification of K. pneumoniae.