Non-sequencing based molecular bacterial typing as an affordable tool for outbreak investigation in low-income countries

Document Type : Original Article


1 Microbiology department, Medical Research Institute, Alexandria University, Egypt

2 Microbiology and Immunology Department, Faculty of Pharmacy, Pharos University in Alexandria, Egypt.


Background: Multidrug-resistant bacteria represent a potential threat to patients in healthcare facilities, with higher abundance and more profound consequences in the developing world. Controlling the spread of these bacteria requires timely identification of clonally related isolates that are cross transmitted from one patient to another within healthcare facilities. The relatively high cost of sequencing-based typing methods hinders their routine use in low-income countries. This highlights the need for an alternative easily applicable molecular typing method that can be routinely used in laboratories with basic equipment and low financial resources, for epidemiologic investigation of outbreaks. Aim and methods: This study aimed to evaluate molecular typing of 30 multidrug-resistant (MDR) Klebsiella pneumoniae (K. pneumoniae) isolates, that were isolated in a previous hospital outbreak and were of previously identified clonal relatedness, by 2 non-sequencing-based typing methods: Plasmid Profile Analysis and Random Amplified Polymorphic DNA (RAPD).The obtained banding patterns were converted into binary data and phylogenetically analyzed by DARwin 6.0.21 software. Results: There was a statistically significant fair agreement between the 2 methods in grouping of the isolates into distinct clusters (Kappa=.23, p < /em>=.025). Both methods proved to be of high typeability of near 100% and discriminatory power of more than 0.9. Both methods fulfilled the performance and convenience criteria evaluated. Conclusion: Any of the two methods may be applicable for routine investigation of outbreaks by MDR bacteria in the developing world, when more precise molecular typing methods are not applicable for shortage of resources.


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