Diarrhoea – not the worst symptom you could have, but it could be a sign of a bacterial infection. Shiga toxin-producing Escherichia coli (STEC) is known to cause watery or bloody diarrhoea with the potential to develop severe sequelae and even lead to death. For diagnosis of an STEC infection, PCR is used to detect the key virulence genes stx1/2, and bioinformatics analysis of isolate genomic sequences provide details on other genetic features which are essential for epidemiological surveillance. However, bioinformatics approaches cannot reliably detect the stx1/2 genes. Our research aims to (1) understand why bioinformatics approaches cannot reliably detect stx1/2 genes and (2) develop a bioinformatics method that can reliably detect stx1/2 genes. The genomic sequences of 47 patient faecal isolates that had been confirmed as STEC by PCR, were analysed using two bioinformatics tools for the detection of stx1/2 genes. Our results showed (1) 93.6% (44/47) concordance between the PCR and bioinformatics results for the detection of stx1/2 genes and 100% concordance between the output of the two bioinformatics tools. The discrepancies between the PCR and bioinformatics results are likely to be attributable to stx1/2 gene excision from the E. coli genome during laboratory cultivation. Decreasing the number of cultivation steps between PCR and isolate genome sequencing may prevent this excision and enable (2) the development of a reliable bioinformatics method for the detection of stx1/2 genes. This work highlights the importance of understanding all processes involved in isolate genome sequencing which is part of being a modern-day detective.