Improved Detection of Extended Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli in Input and Output Samples of German Biogas Plants by a Selective Pre-Enrichment Procedure
Fig 3
Differentiation of ESBL-producing E. coli isolates by molecular fingerprinting using BOX-PCR and detailed characterization of respective isolates.
Cluster analysis was performed in Gel Compare II (Applied Maths) with UPGMA clustering based on a similarity matric calculated using the Pearson correlation (1.0% optimization and 1.0% position tolerance). Characterization of the isolates included the determination of ST-types (MLST analysis), phylogenetic E. coli typing, ESBL-gene characterization. Growth on CHROMagar ESBL and STEC. CTX-M groups were assigned by sequencing CTX-M-type genes. E. coli phylogenetic groups were determined by multiplex PCR and a dichotomous decision tree. *: assigned in group A was but there was a yjaA gene present. C: CTX-M; T: TEM; +: positive;-: negative. BGA shows to which biogas plant isolates belong; I = input sample, O = output sample. Names of the strains include information of the origin of the isolates: pre-enrichment (ESBL before strain number) Bxx (Biogas plant shortcut)_12, 13 or 14 (year of cultivation/isolation: either 2012, 2013 or 2014)_input or output.