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 .

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii From Khartoum State, Sudan

“…Routine identification in clinical microbiology laboratories in Sudan relies primarily on phenotypic methods in combination with simple biochemical methods, which are not always reliable for accurate bacterial species identification, and 29 isolates (40%) were excluded in the study due to misidentification. Similar findings were reported in a study in Sudan on Klebsiella pneumoniae where 40% of isolates were misidentified (Osman et al, 2020). These data highlight an urgent need to improve diagnostic facilities across LMICs such as Sudan, in order to obtain accurate information of the local burden of infections and resistance, and to select optimal treatment options.…”

Microbiological and Molecular Study of K1, K2 Genes among Klebsiella pneumoniae isolated from Urine Specimens in Duhok city, Iraq

“…However, the difference in prevalence with other studies could be due to the number of samples taken and the study's time period. Molecular biology approaches, according to (Osman et al, 2020), could be used as critical diagnostic tools in microbiology laboratories.…”

“…was gave successful amplification of specific 16S rRNA region with 130 bp (Figure1) as well as capsular K1 and K2 serotypes have been identified using particular primers for it. The 16S ribosomal RNA gene is a highly proper and adaptable technique for identifying microbes to the species level, even when the species in question is normally hard to detect by biochemical procedures, to prevent being misidentified (Osman et al, 2020).…”

Detection of mobile genetic elements in multidrug-resistant Klebsiella pneumoniae isolated from different infection sites in Hamadan, west of Iran

“…One hundred twenty-six clinical isolates of K. pneumoniae were isolated from patients admitted to the hospitals from August 2019 to January 2021 in Hamadan, west of Iran. After colony morphology and gram staining, the biochemical tests including indole, citrate, urease, and Kligler iron agar (KIA) tests are employed and API method were applied [ 18 ].…”