Metagenomic, genomic and functional genomic approaches for the characterisation of antibiotic resistance

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McInnes, Ross Stuart ORCID: https://orcid.org/0000-0003-3223-6440 (2022). Metagenomic, genomic and functional genomic approaches for the characterisation of antibiotic resistance. University of Birmingham. Ph.D.

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Abstract

Antibiotic resistance is an emerging threat to global public health. To tackle antibiotic resistance, we must take a One Health approach in which we study antibiotic resistance in combined human, animal and environmental contexts. Here I studied antibiotic resistance at the environmental, clinical and molecular level using different genomics-based approaches. Bacterial culturing and metagenomics were used to uncover that a major reservoir of antibiotic resistance in Bangladesh was the urban surface water environment and that the discharge of untreated human waste into these water bodies was the possible source of antibiotic-resistant bacteria. Short and long-read whole genome shotgun sequencing were used to reveal the structure of a hospital vancomycin resistant Enterococcus faecium (VRE) outbreak and to examine the genetic background of vancomycin-variable E. faecium (VVE) isolates found in this environment. Long-read sequencing and RT-qPCR were also used to uncover that the VVE isolates could rapidly revert to a vancomycin-resistant phenotype by co-transcribing the vanHAX vancomycin resistance genes with one of the rRNA operons. Transcriptomics and transposon insertion sequencing were leveraged to identify genes important for the fitness of VRE strains in the presence of vancomycin at sub-inhibitory concentrations. Exposure to vancomycin led to wide-ranging alterations in the transcriptional program of E. faecium, particularly the downregulation of phosphotransferase system genes. A currently uncharacterised gene avrB, was identified by both RNA-seq and Tn-seq and shown to confer a growth advantage to E. faecium E745 in the presence of vancomycin at ½ minimum inhibitory concentration compared to a deletion mutant. This study demonstrated that important insights can be gained by taking a One Health approach when studying antibiotic resistance. These data suggest that increased sanitation in Bangladesh could prevent the high levels of antibiotic resistance in the urban environment. Increased sequencing of E. faecium in the clinical setting may be required in the future to prevent treatment failures caused by vancomycin-variable E. faecium strains. Novel targets were identified for the development of drugs that can be used in conjunction with vancomycin for the treatment of E. faecium infections.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):