Case study:

Screening candidate strains for live biotherapeutics development

The customer: CHAIN Biotechnology Ltd

CHAIN Biotechnology Ltd is an innovative UK-based company that was founded in 2014. They develop oral live biotherapeutic products (LBP’s) and offer a solution for delivering oral immunotherapies to the large intestine. Their programme focuses on oral vaccines for infectious disease and cancer.

CHAIN’s LBP’s are based on living Clostridium bacteria that have been engineered to deliver specific therapeutic functionality. Their Clostridium Assisted Drug Delivery Platform (CADD^TM) overcomes two key challenges associated with oral drug delivery to the gut:

firstly, the strain of bacteria used forms spores, which are resistant to stomach acid and digestive enzymes;
secondly, because the spores only germinate in the lower parts of the gut, the drug specifically targets the full length of the colon.

This is something that CHAIN highlights is difficult to achieve with oral drug delivery.

The requirement: Screening of candidate strains

As CHAIN’s therapeutic products are based on the use of live bacteria, safety was a crucial consideration in the evaluation of the candidate Clostridium strains. For example, it is important to ensure that the strains used are not themselves pathogenic, or resistant to antibiotics. Characterisation and documentation of risks inherent to the strains were flagged up as a key part of the assessment.

Antimicrobial sensitivity is one of the most important aspects of this risk analysis, as there needs to be sufficient options for controlling the growth and persistence of the live therapeutic.
CHAIN also needed to confirm that the strains selected do not harbour any genes that encode for toxins, virulence factors or antimicrobial resistance that could spread to other strains or species within the gut. Antimicrobial resistance is a serious threat to the effective prevention and treatment of infection and can spread by horizontal gene transfer between species. Virulence factors such as exotoxins are also known to spread in this way, and can turn harmless bacteria into dangerous pathogens. The human gut is reported to be one of the most favourable ecological niches for horizontal gene transfer, so screening for these elements was an important task.

The company also wanted to be able to use the whole gene sequence to identify genetic fingerprints within the strains and identify targets for strain engineering.

The Solution: A combination of MIC testing and whole genome screening

CHAIN Biotechnology asked NCIMB to undertake antimicrobial susceptibility testing, whole genome sequencing and bioinformatics analysis of two candidate Clostridium strains.

We carried out minimum inhibitory concentration (MIC) testing of the two strains to assess their susceptibility to antimicrobials. MIC testing establishes the lowest concentration of antimicrobial at which a strain cannot produce visible growth, and it allows the strains to be categorised as sensitive, intermediate or resistant to antimicrobials of interest.
We delivered a full genome sequence assembly and genome annotation of both strains. This allowed the customer to identify the genetic elements of interest to them with respect to engineering their innovative live biotherapeutic products.
We screened the sequence data for antimicrobial resistance and virulence factor genes, prophage insertions and plasmids.
- Using the latest antimicrobial resistance gene
  databases, we were able to correlate the genome
  data with the MIC results.
- Plasmids are transmissible between different species of bacteria and are a key element in horizontal gene transfer and the spread of antimicrobial resistance, so identifying them is essential.
- Prophage insertions are bacteriophage genetic material incorporated into the bacterial genome and are associated with the adaptation of pathogens to new hosts.

The Outcome: No known antimicrobial resistance genes or virulence factors were identified

Following this very thorough assessment of the two candidate strains, no known antimicrobial resistance genes or virulence factors were identified in the genomes of either of the strains. Prophage insertions were shown to be consistent with other Clostridia of the same type and only well characterised native plasmids were identified, indicating that the strains did not present a risk in terms of horizontal gene transfer with respect to antimicrobial resistance and virulence factors.