Infectious Diseases

Microbial Identification and Typing Databases

Hosted at the Centre for Infections, Colindale, London

The HPA is a major provider of microbial identification and typing data for micro-organisms causing disease in humans. A number of micro-organism-specific databases, developed through European or world-wide collaborations, are now available to allow colleagues, collaborators and the scientific community to compare (and to contribute) their microbial data. It is intended that this will provide a resource for the scientists within the Public Health Microbiology community, in order to enhance our understanding of the molecular epidemiology of these organisms. Please note that use of the databases is according to the HPA terms and conditions.

Access to some of the databases below does not require a password and is therefore open to all. However, some of the databases, or components of the databases, are available only to specific collaborative groups (i.e. are password protected). Please address any queries regarding access to the databases to bioinformatics@hpa.org.uk.

Hepatitis B Virus sequence database

The International Repository for Hepatitis B Virus Strain Data

The aim of this initiative is to develop a web-accessible, quality-based, molecular, clinical and epidemiological database for hepatitis B infection as a tool for the research community and for those involved in hepatitis B case management. This new web database development is funded by the UK Department of Health and is curated and hosted by the Health Protection Agency.

Access the database here

 

EWGLI

The EWGLI SBT database for the typing of Legionella pneumophila

The HPA is pleased to host the EWGLI SBT database for the typing of Legionella pneumophila.

A Sequence-Based Typing (SBT) approach has been developed and evaluated for implementation in the investigation of outbreaks of legionellosis caused by Legionella pneumophila [ Ratzow et al. (2007), Gaia et al. (2005) ].

To access the database and suite of tools click here

 

mip gene

The mip gene sequence database for identification of Legionella species

The HPA is pleased to host the mip gene database for Legionella.
This sequence-based classification scheme was first described by Dr. Rod Ratcliff, Infectious Disease Laboratories, Institute of Medical and Veterinary Science, Adelaide, Australia. Following amplification and sequencing this database will allow you to compare mip DNA sequence data obtained from your Legionella isolate with sequences in the database. The database will return details of reference sequences from Legionella species giving the closest matches.

 

Salm-Gene

"Strengthening international Salmonella surveillance through strain typing and differentiation (SalmGene)"

SalmGene is a project funded by the European Commission (DG-RESEARCH) aiming to strengthen international Salmonella surveillance through molecular strain typing and differentiation. As part of the project, two online databases have been established:

 

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The ARPAC Acinetobacter baumannii Typing Database

The HPA is pleased to host the databases for the EU ARPAC Concerted Action ('Antibiotic Resistance Prevention and Control'). ARPAC aims to set-up an electronic data exchange network that will allow rapid local detection and epidemiological tracing of specific clones of antibiotic-resistant pathogens that cause problems in hospitals throughout the EU. Currently, pilot databases based on standardised pulsed-field gel electrophoresis techniques are available for Acinetobacter baumannii and MRSA.

 

The ARPAC Pseudomonas aeruginosa Typing Database

This database will allow you to compare PFGE profiles obtained in your laboratory using the ARPAC PFGE protocol for Pseudomonas aeruginosa [ Pseudomonas aeruginosa PFGE protocol (PDF, 132 KB)

] against the profiles of previously identified P. aeruginosa clones. Currently, profiles can only be compared by submitting the molecular sizes (or relative mobility) of bands. The database will return details of the nearest matches. Please login in as "arpac_guest2". You do not require a password to access the public databases. ARPAC participants should use their logins to obtain full access to the databases.

 

HARMONY

The HARMONY IUMS Global MRSA Database

H armonisation of A ntibiotic R esistant measurement, M ethods of typing O rganisms and ways of using these and other tools to increase the effectiveness of N osocomial infection control.
HARMONY was originally a European Union DG-XII-funded Fourth Framework Concerted Action. Its deliverables are now being used in several other projects in the EU. A major deliverable has now become this MRSA database. This is the pilot site which Centres will help develop for external access to query MRSA strains.

 

The UK National Database for Norwalk-like viruses (NLVs):

This database contains polymerase gene and capsid gene sequences from NLVs (also known as small round structured viruses) from outbreaks of gastroenteritis occurring in England and Wales between 1998-2003.

 

The WHO Measles Molecular Typing Database

The WHO European Center for Measles surveillance and the WHO Measles strain bank are within the Enteric, Respiratory and Neurological Virus Laboratory at the HPA Centre for Infections, London. The Measles Molecular Typing Database is available online.


 

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