PCR amplification of potential bla TEM genes in ampr isolates The amplification of bla TEM alleles in individual bacterial isolates was performed in a reaction mixture containing 1× HotStartTaq DNA master mix Fer-1 in vivo (Qiagen), 0.2 μM of each primer, and 2 μl of the crude DNA solution in a final volume of 30 μl. Reactions were denatured at 95°C for 15 min and then subjected to 30 cycles of 94°C for 45 s, 61°C for 45 s, and 72°C for 1 min, with a final extension at 72°C for 10 min. For all bla TEM PCR analyses, the primers BlaF and BlaR (Table 6) were used to amplify a product of 828 bp (TEM-1

allele of E. coli) [15]. The following controls were used: five strains of E. coli carrying the bla alleles TEM-1, TEM-3, TEM-6, TEM-9, and TEM-10 as positive controls, and one strain carrying the SHV-2 allele as negative control. The specificity of the primers were confirmed by ‘in silico’ amplification and by aligning the primer binding region of approximately

100 sequence polymorphic bla TEM alleles [15]. Sequencing of 16S rRNA, bla TEM, and bla TEM flanking regions The identity of putative ampr positive isolates was determined by sequencing, with primers 16S-27F, 16S-1494R, and Bact 338 (Table 6), on a 3130 Genetic analyzer using the ABI BigDye Terminator chemistry. To PKC412 confirm the presence of and determine the location of bla TEM in the DNA extract from ampr isolates, sequencing of the immediate flanking regions of the bla TEM gene was performed using the sequencing primers

TemI3, TemI5a or TemI5b Selleckchem ARRY-162 (Table 6) as described in [15]. Acknowledgements This study was funded by the Norwegian Research Council and Roald ioxilan Amundsen Centre for Arctic Research (University of Tromsø, Norway). The sequencing laboratory at the Faculty of Medicine, University of Tromsø is acknowledged for their sequencing of the bacterial 16S rRNA genes. Control strains used for the bla TEM PCR analyses and the identification of E. coli by ID32 E were kindly provided by Prof. Arnfinn Sundsfjord, University Hospital of North Norway, Tromsø, Norway. References 1. Bjerrum L, Engberg RM, Leser TD, Jensen BB, Finster K, Pedersen K: Microbial community composition of the ileum and cecum of broiler chickens as revealed by molecular and culture-based techniques. Poult Sci 2006,85(7):1151–1164.PubMed 2. Brooks SPJ, McAllister M, Sandoz M, Kalmokoff ML: Culture-independent phylogenetic analysis of the faecal flora of the rat. Can J Microbiol 2003, 49:589–601.PubMedCrossRef 3. Koike S, Yoshitani S, Kobayashi Y, Tanaka K: Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria. FEMS Microbiol Lett 2003,229(1):23–30.PubMedCrossRef 4. Leser TD, Amenuvor JZ, Jensen TK, Lindecrona RH, Boye M, Moller K: Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited.