Abstract
The Burkholderia cepacia complex (Bcc) is a closely related group of bacteria, composed of at least 20 different species, the accurate identification of which is essential in the context of infectious diseases. In industry, they can contaminate non-food products, including home and personal care products and cosmetics. The Bcc are problematic contaminants due to their ubiquitous presence and intrinsic antimicrobial resistance, which enables them to occasionally overcome preservation systems in non-sterile products. Burkholderia lata and Burkholderia contaminans are amongst the Bcc bacteria encountered most frequently as industrial contaminants, but their identification is not straightforward. Both species were historically established as a part of a group known collectively as taxon K, based upon analysis of the recA gene and multilocus sequence typing (MLST). Here, we deploy a straightforward genomics-based workflow for accurate Bcc classification using average nucleotide identity (ANI) and core-gene analysis. The workflow was used to examine a panel of 23 Burkholderia taxon K industrial strains, which, based on MLST, comprised 13 B. lata, 4 B. contaminans and 6 unclassified Bcc strains. Our genomic identification showed that the B. contaminans strains retained their classification, whilst the remaining strains were reclassified as Burkholderia aenigmatica sp. nov. Incorrect taxonomic identification of industrial contaminants is a problematic issue. Application and testing of our genomic workflow allowed the correct classification of 23 Bcc industrial strains, and also indicated that B. aenigmatica sp. nov. may have greater importance than B. lata as a contaminant species. Our study illustrates how the non-food manufacturing industry can harness whole-genome sequencing to better understand antimicrobial-resistant bacteria affecting their products.
Highlights
The Burkholderia cepacia complex (Bcc) is a group of closely related Gram-n egative bacteria with a continuously evolving taxonomy, and currently comprises 20 named species [1, 2]
average nucleotide identity (ANI) analysis confirms that the industrial isolates historically identified as B. lata or Bcc novel taxon K belong to B. aenigmatica sp. nov
Of the 23 industrial isolates subjected to genomic analysis, ANI-based species-level identification (Fig. 1) was only concordant with the genomes previously classified as B. contaminans by multilocus sequence typing (MLST) (Fig. 2a)
Summary
The Burkholderia cepacia complex (Bcc) is a group of closely related Gram-n egative bacteria with a continuously evolving taxonomy, and currently comprises 20 named species [1, 2]. They have a diverse range of importance, including causing infection in people with cystic fibrosis (CF) [3] and plant pathogenesis [4], and, in relation to biotechnology, having roles in bioremediation and biological control [5] and being problematic industrial contaminants [6, 7]. Despite the widespread application of these molecular marker sequencing techniques, multiple novel species groups exist within the Bcc [1, 12]
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