Application of nanopore sequencing for accurate identification of bacterial colonies

Abstract

Culture based detection remains to be one of the most reliable and acceptable techniques to detect extremely low quantity pathogens present in a sample. The process typically involves inoculating the sample on an agar plate to allow growth of the microorganisms to form colonies, followed by the identification of the individual colonies, commonly by DNA sequencing of a PCR-amplified targeted gene. Sanger method is often the default choice of sequencing as it offers affordable and accurate results for a single species. However, the technique could pose limitations in certain situations such as identification of multi-species microbial colonies. In this work, we compared the performance of Sanger sequencing with MinION nanopore sequencing in identifying bacterial colonies derived from bioaerosol samples. We conducted Sanger and nanopore sequencing of full-length 16S rRNA genes from seven bacterial colonies derived from bioaerosol samples and compared the outcome by alignment against NCBI 16S reference database. We found that for five out of seven colonies both techniques indicated the presence of the same bacterial genus. For one of the remaining colonies, a noisy Sanger electropherogram failed to generate a meaningful sequence, but nanopore sequencing identified it to be a mix of two bacterial genera Alkalihalobacillus and Kocuria. For the other remaining colony, the Sanger sequencing suggested Micrococcus with a clean electropherogram, however, the nanopore sequencing suggested the presence of an additional genus Paraburkholderia. Further corroborating these findings with mock multispecies colonies from pure bacterial DNA samples, we confirm that nanopore sequencing is comparable to the Sanger method in identifying colonies with single bacterial species but is the superior method in classifying individual bacterial components with their relative abundances in multispecies colonies. Our results suggest that nanopore sequencing could be advantageous over Sanger sequencing for colony identification in culture-based analysis of environmental samples such as bioaerosol where direct inoculation of the sample to culture plate might lead to formation of multispecies colonies.