Genomics reveals the novel species placement of industrial contaminant isolates incorrectly identified as Burkholderia lata

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.

Induction of Resistance of Antagonistic Bacterium Burkholderia contaminans to Postharvest Botrytis cinerea in Rosa vinifera

“…At present, there are many kinds of grape storage and preservation technologies studied at home and abroad, mainly divided into physical and chemical methods. Although various technical principles focus on different aspects, they all achieve the purpose of preservation by controlling the process of fruit senescence, controlling the growth and reproduction of pathogenic microorganisms, and controlling internal water loss [ 6 ]. At present, the commonly used fresh-keeping methods include SO 2 and H 2 O 2 fumigation storage, low-temperature storage, controlled atmosphere storage, and radiation storage.…”

Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products – a retrospective, real-time analysis

“…The workflow presented shows that cultivation-independent, automated DNA extraction can be applied directly to HPC products and provides a promising alternative to cultivation-based methodologies for contamination surveillance within preserved industrial products. It can also overcome issues seen in growth-based approaches, which can take up to 7 days for microorganism recovery [41] and are potentially inaccurate depending on the methodology used for identification [19]. Moreover, the use of genomic methodologies such as ANIm and popANI reliably enables detection of down to 10 3 CFU/ml and identification with species or consensus MAG-level accuracy, respectively.…”

“…Sample processing was performed during: (i) the week of contamination (week 1), and (ii) repeated 2 weeks post-contamination (week 3); this was used to detect whether the contamination signatures were stable or increased over time. All culture and product DNA extractions were then sequenced on a NovaSeq 6000, using 150 bp paired-end sequencing by a commercial sequencing provider (Novogene, Cambridge, UK) as described previously [19].…”

“…Metagenomic approaches also have the benefit of generating genomic DNA sequence data which can provide accurate taxonomic identification of microbial contaminants, a gap which needs to be addressed in the international product recall databases which report spoilage incidents [7]. Genomic-level taxonomy is also vital for the accurate resolution of Burkholderia cepacia complex contaminants which belong to novel species groups such as Burkholderia aenigmatica , for which techniques such as 16S ribosomal RNA (rRNA) gene sequencing provide insufficient resolution for accurate identification [19]. With extensive DNA databases in place, genomic identification also enables strain-level identification of bacterial contaminants [19].…”

“…Genomic-level taxonomy is also vital for the accurate resolution of Burkholderia cepacia complex contaminants which belong to novel species groups such as Burkholderia aenigmatica , for which techniques such as 16S ribosomal RNA (rRNA) gene sequencing provide insufficient resolution for accurate identification [19]. With extensive DNA databases in place, genomic identification also enables strain-level identification of bacterial contaminants [19].…”