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<p>Abstract</p> <p>Background</p> <p>Brucellosis, a zoonosis caused by the genus <it>Brucella</it>, has been eradicated in Northern Europe, Australia, the USA and Canada, but remains endemic in most areas of the world. The strain and biovar typing of <it>Brucella </it>field samples isolated in outbreaks is useful for tracing back source of infection and may be crucial for discriminating naturally occurring outbreaks versus bioterrorist events, being <it>Brucella </it>a potential biological warfare agent. In the last years MLVA-16 has been described for <it>Brucella </it>spp. genotyping. The MLVA band profiles may be resolved by different techniques i.e. the manual agarose gels, the capillary electrophoresis sequencing systems or the microfluidic Lab-on-Chip electrophoresis. In this paper we described a high throughput system of MLVA-16 typing for <it>Brucella </it>spp. by using of the microfluidics technology.</p> <p>Results</p> <p>The Caliper LabChip 90 equipment was evaluated for MLVA-16 typing of sixty-three <it>Brucella </it>samples. Furthermore, in order to validate the system, DNA samples previously resolved by sequencing system and Agilent technology, were <it>de novo </it>genotyped. The comparison of the MLVA typing data obtained by the Caliper equipment and those previously obtained by the other analysis methods showed a good correlation. However the outputs were not accurate as the Caliper DNA fragment sizes showed discrepancies compared with real data and a conversion table from observed to expected data was created.</p> <p>Conclusion</p> <p>In this paper we described the MLVA-16 using a rapid, sophisticated microfluidics technology for detection of amplification product sizes. The comparison of the MLVA typing data produced by Caliper LabChip 90 system with the data obtained by different techniques showed a general concordance of the results. Furthermore this platform represents a significant improvement in terms of handling, data acquiring, computational efficiency and rapidity, allowing to perform the strain genotyping in a time equal to one sixth respect to other microfluidics systems as e.g. the Agilent 2100 bioanalyzer.</p> <p>Finally, this platform can be considered a valid alternative to standard genotyping techniques, particularly useful dealing with a large number of samples in short time. These data confirmed that this technology represents a significative advancement in high-throughput accurate <it>Brucella </it>genotyping.</p>