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

Abstract

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 identified using conventional phenotypic methods, biochemically 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 overestimation 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 .

Keywords: Identification methods; Klebsiella pneumoniae; Sudan.

Fig. 1.

PCR amplification of the 16S−23S rDNA ITS of K. pneumoniae . Strain K1 was used as a positive control for all runs. K. pneumoniae isolates (K2, K3, K7 and K9) produced a band at 260 bp with the Pf/Pr2 primer pair, in addition to a 130 bp band with the Pf/Pr1 primer pair. Non- K. pneumoniae isolates (K4, K5 and K6) only produced a 260 bp band with primer pair Pf/Pr2 and failed to produce a band with Pf/Pr1, whereas K8 did not produce a band with Pf/Pr2, but did with Pf/Pr1. L, 100 bp ladder.

Fig. 2.

Samples from which K. pneumoniae was isolates. The blue bars indicate the number of isolates identified by the 16S−23S rDNA ITS, whereas the orange bars indicate the number of misidentified organisms.