Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The aim of this work was to use the FT-IR microspectroscopy technique, a union of a FT-IR spectrometer with a microscope, to discriminate fecal Escherichia coli strains from cows, chickens and humans and to compare the efficiency of this method with the genomic fingerprinting method, BOX-PCR. The obtained BOX-PCR profiles were able to correctly discriminate 93.75% of the chicken strains, 80% of the cow strains and 65% of the human strains. An efficient PLS-DA model was developed, using orthogonal signal correction and the second derivate of the FT-IR spectra. This model allowed the correct discrimination, according to the animal source, of all the E. coil strains analyzed. The bands in the FT-IR spectra that were responsible for the strains discrimination were in the region between 2816 and 3026 cm(-1) wavenumber, described as fatty acids. It was demonstrated that FT-IR microspectroscopy can be a suitable tool for fecal E. coil discrimination, because it is fast, easy to carry out and presents a flexible discrimination power. (C) 2011 Elsevier B.V. All rights reserved.9911519Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAPESP [FAPESP 2007/55312-6, FAPESP 2006/07309-3, 07/57025-4]CNPq [CNPq 502198/2008-7]