Plasmids were extracted from overnight samples using QIAprep Spin Mini Prep kit (Qiagen, Sussex, UK) according to the manufacturer’s instructions and sent for Sanger sequencing (Source BioSciences, Dublin, Ireland). Bioinformatic analysis Following Sanger sequencing, sequence

reads were analysed using the NCBI protein database (BlastX; (http://​blast.​ncbi.​nlm.​nih.​gov/​)). In the event where multiple hits occurred, the BLAST hit which displayed greatest homology is reported. Results and discussion A PCR-based approach highlights the presence of β-lactamase gene homologues in the gut microbiota The results of the β-lactamase-specific PCRs demonstrated the presence and diversity of class 2 β-lactamase genes in the gut microbiota of healthy adults (Table 2[32]). Of the β-lactam primers used, the primers designed find more to amplify bla TEM genes yielded the greatest number of unique sequence hits (42% of selected TOPO sub-clones gave a unique hit). The majority of these AG-881 nmr genes exhibited a high percentage identity with genes from various members of the Proteobacteria including E. coli, Klebsiella, Salmonella, Serratia, Vibrio parahaemolyticus and Escherichia vulneris. The resistance of PRIMA-1MET cell line strains of Salmonella and Serratia to β-lactams via bla TEM genes has been noted [33–35] and such strains have been associated with nosocomial infections [36]. In contrast, there have been relatively

few studies of bla TEM genes in Vibrio parahaemolyticus and Escherichia vulneris[37, 38]. The identification of genes homologous to those from Enterobacteriaceae is not surprising given the prevalence of resistance genes among

members of this family [12]. It was notable that the bla TEM primers also amplified genes that resembled bla TEM genes from some more unusual sources, including two genes from Baf-A1 clinical trial uncultured bacteria and from a Sar 86 cluster (a divergent lineage of γ-Proteobacteria) bacteria. This approach can thus provide an insight into possible novel/unusual sources of resistance genes, including those that culture-based approaches would fail to detect. Such results also highlight that had initial screening for resistant isolates been completed prior to PCR amplification of the resistance genes, such unusual sources of resistance genes may have been overlooked. Additionally, genes encoding ESBLs, including bla TEM-116, bla TEM-195 and bla TEM-96 amongst others, were also identified, with their closest homologues being members of the Proteobacteria (Table 2). Table 2 Homologues of β-lactamase genes detected in the human gut microbiota via PCR techniques Accession # Gene description Closest homologue E value % identity Bla TEM         ADE18890.1 β-lactamase TEM-1 S. enterica subsp. enterica 5e-154 99 AAS46844.1 β-lactamase TEM-1 S. marcescens 2e-156 100 AEN02824.1 β-lactamase TEM-1 K. pneumoniae 3e-111 99 AEN02817.