A genomic polymorphism located downstream of the gcvP gene of Escherichia coli that correlates with ecological niche

Current evolutionary theory proposes that niche‐adapted microbial populations might evolve through selection for favoured genotypes followed by clonal expansion (Maynard‐Smith, 1991). Possible correlations between genomic variation and ecological niche in Escherichia coli isolates derived from human and animal sources were investigated by randomly amplified polymorphic DNA (RAPD) analysis. A 1.6‐kb polymorphic marker was identified which was present in 60% of isolates from human clinical specimens but was present in less than 5% of isolates derived from ovine and bovine faeces. The marker maps to a region of the chromosome located immediately downstream from the gene encoding the glycine decarboxylase P‐protein (gcvP). DNA sequences from marker‐positive and marker‐negative isolates exhibit an abrupt loss of homology immediately downstream from the transcription termination point of the gene which extends for at least 130‐base pairs beyond the gcvP transcription terminator. Sequences spanning this region in marker‐negative isolates exhibit similarity to the cognate sequence from E. coli K‐12, while the corresponding region in marker‐positive isolates bears no similarity to any other published sequence. The utility of the marker for investigating the occurrence of human‐derived E. coli in the environment was studied in a rural stream. Although the stream carried a high background of animal‐derived E. coli, the marker could only be detected in isolates obtained downstream of the human faecal input. The polymorphism therefore shows promise for identification of human‐derived E. coli within environments containing isolates from multiple and diverse sources. The methods described here could be used to generate further markers suitable for investigating microbial population ecology.