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Health

Environmental metagenomics in urban environments and development of forensic inference

MetaSUB was set up in 2015 and King’s Forensics and the Environmental Research Group, now at Imperial, have been collecting touch samples from ticket machines and platform surfaces in all London Underground Stations, and air samples from selected stations since 2017 on an annual basis in order to describe city area species specificities, including antibiotic resistance patterns, and to capture ‘molecular echoes’ of environmental events and to develop a forensic capacity for geospatial metagenomic data.

We have a separate and ongoing collection of air and surface samples from the Victoria Line since 2017 to enable comparative and seasonal comparisons. On or close to 21st June three touched surfaces are sampled in every London underground station (ticket machine /subway entrance / platform seating) as part of a global collection and with analysis funded through Weill Cornell research funds. Since 2020 the collection in London has been limited to the Victoria line. While this data has provided a valuable dataset of variability between cities, our aim is to be able to use this information to make forensic inference. Microbes are, however, ubiquitous and knowledge of background material within the analytical environment is essential prior to making any forensic inference (location or habit) about a collected sample and our current research is about defining the ‘kitome’ and the ‘reagentome’ to enable removal of the laboratory background. As an extension to the MetaSub project we are also collecting duplicate air and surface samples from the Victoria Line to enable seasonal and London-wide comparisons in the future.

Our partners in the Norwegian Defence Research Establishment have been instrumental in developing the method for air microbe collection and colleagues at the Defence Science and Technology Laboratory are working on appropriate collection devices.

PhD Students

Jennie Latham

PhD Student

Kari Boeifot

 

PhD Student

Aims

  • To understand and characterise the background microbiome and determine global and local microbial similarities and differences in urban environments.
  • To develop a forensic capacity for geospatial metagenomic data

Methods

Shotgun metagenomic sequencing

Summary of Findings

A global atlas of almost 5000 samples across 60 cities has been published. Thirty-one non-human commensals were found in 97% of global samples. Some cities have distinct taxonomic signatures driven by climatic and geographical differences, but also reflect urban life-styles. Widespread and variable anti-microbial resistance was observed across the cities. Many thousands of newly discovered microbes were characterised as part of the study. The collection highlights potential public health and forensic applications for future development.

Conferences

2021

  • Population Health Sciences Seminar Series, King’s College London ‘Forensic Metagenomics’

2020

  • Qiagen Young Investigators in Forensics Summer Series ‘Fantastic Beasts and where to find them: a metagenomic map of London’.

2019

  • Population Health Sciences Seminar Series, King’s College London ‘Forensic Metagenomics’
  • International Symposium on Human Identification (ISHI), Palm Springs, California ‘Fantastic Beasts and where to find them: a metagenomic map of London’.
  • International Society for Forensic Genetics (ISFG), Prague, Czech Republic ‘Kitome: the Kryptonite of Forensic Metagenomics’
  • International Society for Forensic Genetics (ISFG), Prague, Czech Republic ‘Creating a Metagenomic “DNA Map” of the London Underground Transit system’
  • MetaSUB annual meeting, Istanbul, Turkey ‘Metagenomics for Intelligence – a forensic perspective’
  • Analytical and Environmental Sciences (AEFS) PhD symposium, King’s College London ‘A metagenomic “DNA Map” of the London Underground Transit System’.
  • Verogen user meeting at the Spurenworkshop, Jena, Germany ‘Forensic Metagenomics – exploring the “Kitome”

2018

  • DNA Evidence to Investigative Insights (DEII), Barcelona, Spain ‘Investigative Intelligence: a metagenomics approach’.
  • European Academy of Forensic Sciences, Lyon, France ‘Kitome – the kryptonite of trace level metagenomics analysis’.
  • King’s Forensics Symposium, King’s College London ‘Forensic Metagenomics: Simultaneous detection of diverse microbial taxa using massively parallel sequencing’

Conferences

2021

  • Population Health Sciences Seminar Series, King’s College London ‘Forensic Metagenomics’

2020

  • Qiagen Young Investigators in Forensics Summer Series ‘Fantastic Beasts and where to find them: a metagenomic map of London’.

2019

  • Population Health Sciences Seminar Series, King’s College London ‘Forensic Metagenomics’
  • International Symposium on Human Identification (ISHI), Palm Springs, California ‘Fantastic Beasts and where to find them: a metagenomic map of London’.
  • International Society for Forensic Genetics (ISFG), Prague, Czech Republic ‘Kitome: the Kryptonite of Forensic Metagenomics’
  • International Society for Forensic Genetics (ISFG), Prague, Czech Republic ‘Creating a Metagenomic “DNA Map” of the London Underground Transit system’
  • MetaSUB annual meeting, Istanbul, Turkey ‘Metagenomics for Intelligence – a forensic perspective’
  • Analytical and Environmental Sciences (AEFS) PhD symposium, King’s College London ‘A metagenomic “DNA Map” of the London Underground Transit System’.
  • Verogen user meeting at the Spurenworkshop, Jena, Germany ‘Forensic Metagenomics – exploring the “Kitome”

2018

  • DNA Evidence to Investigative Insights (DEII), Barcelona, Spain ‘Investigative Intelligence: a metagenomics approach’.
  • European Academy of Forensic Sciences, Lyon, France ‘Kitome – the kryptonite of trace level metagenomics analysis’.
  • King’s Forensics Symposium, King’s College London ‘Forensic Metagenomics: Simultaneous detection of diverse microbial taxa using massively parallel sequencing’

Our Partners

metasub 1

MetaSUB

Imperial College London

Imperial College London

Jagiellonian University logo

The Jagiellonian University

Weill Cornell Medicine logo

Weill Cornell Medicine

Norwegian Defence Research Establishment logo

Norwegian Defence Research Establishment

DSTL logo

Defence Science and Technology Laboratory

Keywords

FORENSICSMETAGENOMICS