Understanding the role of the Gut microbiome

Supervisors: Professor Joseph Standing, Dr Mona Bajaj-Elliott, Professor Francois Balloux, Dr Lucy van Dorp

Understanding the role of the Gut microbiome as a reservoir for increasing antibiotic resistance in a clinical setting

Background:
The advent of modern medical practices e.g., prolonged immunosuppression and antibiotic therapies have inadvertently led to perturbation of microbial communities that live on animal/human mucosal surfaces¹. These surfaces including the skin, gastrointestinal (GI), urinary and respiratory tract². In addition to causing perturbations in microbial-microbial, microbial-host homeostasis, prolonged prophylaxis is also responsible for the emergence of antimicrobial resistance^3,4 (AMR), a major global health concern facing mankind today. Exposure to clinical levels of antibiotics usage has accelerated spread of antibiotic resistance genes (ARGs) culminating in increased risk of infection by newly emerging resistant strains. Preventing transmission by these pathogens in health and social care settings is problematic. The GI microbiome serves as an important reservoir for transmission and spread of ARGs. There is an emerging unmet clinical need to:

(a) Better understand how antibiotic exposure impacts on the abundance and expression of ARGs.
(b) Better understand how antibiotic usage impacts on the developing microbiota of the young.
(c) Urgent need to understand the above in-patient cohorts’ where substantial antibiotic usage is integral to their treatment regime, e.g., as in paediatric stem cell transplantation.

Aims/Objectives:
1.  Perform longitudinal gut microbial metagenomic analyses on patients undergoing allogeneic or autologous haematopoietic stem cell transplantation (HSCT) and compare ‘pre-versus post-transplant’ patient samples to identify mechanism(s) that promote (a) the emergence and transfer of AMR genes in the GI reservoir under selective ‘antibiotic’ pressure.
2.  Antibiotic usage ex-vivo: The hollow-fibre model system optimised in the Standing lab offers an opportunity to investigate antibiotic-mediated impact on genotype and phenotype of daughter cells. In addition, it offers an opportunity to explore transfer of AMR genes amongst bacterial communities within the paediatric gastrointestinal reservoir.

Methods:
We have longitudinal (5-10 samples/patient collected up to 3 months post-transplantation) samples stored from >30 patients ready for analysis. Methodologies will involve shotgun metagenomic sequencing and analysis of the gut microbiota and antibiotic resistant clinical isolates. In particular, bioinformatic and computational approaches will be used to resolve and quantify the taxa and ARG carriage of gut microbiota of patients pre- and post-transplant. All patients undergoing chemotherapy/conditioning prior to transplant are routinely given ciprofloxacin, and most receive other broad-spectrum antibiotics that are likely to cross into the gut including piperacillin/tazobactam and meropenem. To test the impact of prescribing practice, gut microbiota will be exposed to clinically appropriate antibiotic concentrations in an ex-vivo hollow-fibre model. A combined metagenomic and experimental approach offers new opportunities to investigate the antibiotic-mediated impact on genotype and phenotype changes in gut microbiota, which may include transfer of AMR genes amongst co-cultured bacterial communities within the paediatric gastrointestinal reservoir.

References:
1.  Shaw L et al., 2019 ISME J 10.1038_s41396-019-0392-1.
2. Shono Y et al., 2016.Sci Transl Med. 8:339.
3.  Taur Y et al., 2018 Sci Transl Med.10: 460.
4.  Magruder M et al., 2020 https://doi.org/10.1038/s41467-019-13467-w.