Dr Amy Katherine Cain

Postdoctoral Fellow


This person is a member of Sanger Institute Alumni.

Amy is a scientific researcher at the Wellcome Trust Sanger Institute, Cambridge, aiming to tackle the terrifying problem of antibiotic resistance that is occuring world-wide. For this purpose, she studies the movement and spread of antibiotic resistance genes around bacterial populations, particularly those infections that are acquired in hospitals. Amy has a background in detailed molecular biology of mobile genetic elements, particularly in the pathogen that causes typhoid, Salmonella. Now she focuses on exploiting genomics and large-scale mutagenesis, using a method called Transposon Directed Insertion Sequencing (TraDIS), to understand what genes are important in antibiotic resistance across a range of dangerous bugs.


PhD at the University of Sydney; Supervior: Prof Ruth Hall; Co-Supervisor: Prof Tom Ferenci

Mobile Genetic Elements Driving the Evolution of IncHI plasmids Conferring Resistance to Antibiotics and Heavy Metals from Salmonella enterica; 2007-2011

BSc (Molecular Biology and Genetics; Advanced) Graduated with Class I Honours at the University of Sydney, Major in Biochemistry; 2003 to 2005

Honours Supervisor: Prof Ruth Hall; Thesis Title: Frequency and Mechanisms for Loss of Mobilizable Genetic Elements Conferring Antibiotic Resistance in Gram Negative Bacteria; 2006

Research Experience

Postdoctoral Researcher, Wellcome Trust Sanger Institute, Under the supervision of Prof. Julian Parkhill; June 2012 – current.

Project – Using Transposon Directed Insertion-site Sequencing (TraDIS), to search nosocomial pathogen genomes for antibiotic resistance (AMR) modifiers. I developed methods to construct large random mutant libraries and in collaboration with team programmers, a bioinformatic analysis pipeline for large sets of Illumina sequencing data. I also utilise SNP and RNAseq analysis of AMR.

Postdoctoral Researcher, Macquarie University, Sydney, Under the supervision of Professor Ian Paulsen; 2011- 2012 – Using next generation 454 sequencing of marine environments, to reveal communities structures of Synechococcus species. Reverse transcriptomics to examine gene expression in environmental strains of Pseudomonas in stress conditions.

Laboratory Technician, Cancer Council NSW, Blood Biobank, Centre of Immunology, St Vincent’s Hospital, Sydney; 2010- 2011 – Processing, achieving and stock taking large amounts of blood samples for a number of nationwide epidemiological cancer surveys.

Work Experience in a Public Health Laboratory; Under the supervision of Prof. John Wain and Dr. Satheesh Nair 2009 – A short 3-month research project undertaken at the Health Protection Agency (now Public Health England), in Collindale, London, UK, examining historical plasmids.


My publications

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