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Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection

Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection
Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection

Neisseria lactamica is a harmless coloniser of the infant respiratory tract, and has a mutually-excluding relationship with the pathogen Neisseria meningitidis. Here we report controlled human infection with genomically-defined N. lactamica and subsequent bacterial microevolution during 26 weeks of colonisation. We find that most mutations that occur during nasopharyngeal carriage are transient indels within repetitive tracts of putative phase-variable loci associated with host-microbe interactions (pgl and lgt) and iron acquisition (fetA promotor and hpuA). Recurrent polymorphisms occurred in genes associated with energy metabolism (nuoN, rssA) and the CRISPR-associated cas1. A gene encoding a large hypothetical protein was often mutated in 27% of the subjects. In volunteers who were naturally co-colonised with meningococci, recombination altered allelic identity in N. lactamica to resemble meningococcal alleles, including loci associated with metabolism, outer membrane proteins and immune response activators. Our results suggest that phase variable genes are often mutated during carriage-associated microevolution.

Pandey, Anish
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Cleary, David W.
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Laver, Jay R.
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Gorringe, Andrew
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Deasy, Alice M.
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Dale, Adam P.
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Morris, Paul D.
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Didelot, Xavier
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Maiden, Martin C.J.
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Read, Robert C.
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Pandey, Anish
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Cleary, David W.
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Laver, Jay R.
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Gorringe, Andrew
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Deasy, Alice M.
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Dale, Adam P.
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Morris, Paul D.
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Didelot, Xavier
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Maiden, Martin C.J.
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Read, Robert C.
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Pandey, Anish, Cleary, David W., Laver, Jay R., Gorringe, Andrew, Deasy, Alice M., Dale, Adam P., Morris, Paul D., Didelot, Xavier, Maiden, Martin C.J. and Read, Robert C. (2018) Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection. Nature Communications, 9 (1), [4753]. (doi:10.1038/s41467-018-07235-5).

Record type: Article

Abstract

Neisseria lactamica is a harmless coloniser of the infant respiratory tract, and has a mutually-excluding relationship with the pathogen Neisseria meningitidis. Here we report controlled human infection with genomically-defined N. lactamica and subsequent bacterial microevolution during 26 weeks of colonisation. We find that most mutations that occur during nasopharyngeal carriage are transient indels within repetitive tracts of putative phase-variable loci associated with host-microbe interactions (pgl and lgt) and iron acquisition (fetA promotor and hpuA). Recurrent polymorphisms occurred in genes associated with energy metabolism (nuoN, rssA) and the CRISPR-associated cas1. A gene encoding a large hypothetical protein was often mutated in 27% of the subjects. In volunteers who were naturally co-colonised with meningococci, recombination altered allelic identity in N. lactamica to resemble meningococcal alleles, including loci associated with metabolism, outer membrane proteins and immune response activators. Our results suggest that phase variable genes are often mutated during carriage-associated microevolution.

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Accepted/In Press date: 17 October 2018
e-pub ahead of print date: 12 November 2018
Published date: 12 November 2018

Identifiers

Local EPrints ID: 426506
URI: http://eprints.soton.ac.uk/id/eprint/426506
PURE UUID: 38a8831d-5f73-4a57-abf9-f6a2c8ac6064
ORCID for David W. Cleary: ORCID iD orcid.org/0000-0003-4533-0700
ORCID for Jay R. Laver: ORCID iD orcid.org/0000-0003-3314-5989
ORCID for Adam P. Dale: ORCID iD orcid.org/0000-0001-8163-7481
ORCID for Robert C. Read: ORCID iD orcid.org/0000-0002-4297-6728

Catalogue record

Date deposited: 29 Nov 2018 17:30
Last modified: 26 Nov 2021 03:11

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Contributors

Author: Anish Pandey
Author: David W. Cleary ORCID iD
Author: Jay R. Laver ORCID iD
Author: Andrew Gorringe
Author: Alice M. Deasy
Author: Adam P. Dale ORCID iD
Author: Paul D. Morris
Author: Xavier Didelot
Author: Martin C.J. Maiden
Author: Robert C. Read ORCID iD

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