Over 80 patients have been infected with the enterobacterium Klebsiella at Maasstad hospital, Rotterdam in the Netherlands due to the outbreak of a multiple antibiotic-resistant bacterium named Klebsiella pneumoniae Oxa-48.
The hospital has estimated that over 2000 people were at risk of being infected.
The Dutch National Institute for Public Health and the Environment (RIVM) was asked to assist the hospital in containing the outbreak.
An international team started to develop a rapid molecular (DNA) screening test to detect the superbug, to identify the already infected people and prevent firther infections.
As a first task the whole genome sequencing of the outbreak strain was carried out.
Then sequence data laid the ground for the development of a specific molecular test. That is a true first real-time ‘genomics for diagnostics’ application − said the scentific team leader.
The team compared the genome of the outbreak strain to other publicly available Klebsiella genomes and identified 36 candidate signature sequences that could be used to develop an outbreak strain-specific PCR test.
By comparing these candidate signature sequences against the publically available data for over two-hundred additional Klebsiella genomes from an ongoing worldwide population study, two regions that remain entirely specific for the Dutch hospital outbreak strain were identified.
PCR assays targeting these two unique sequences together with the antibiotic resistance genes were then evaluated and field-tested to develop a multiplex molecular screening test.
The protocol for the new test and test kits have been made available to all Dutch hospitals.
This is a good example of how rapid next generation sequencing can help controlling outbreaks and how joint forces from different countries and continents can achieve quick results to prevent further infections.
http://www.rivm.nl/en/persberichten/klebsiellatest.jsp