meningotype

In silico typing of Neisseria meningitidis contigs

• Serotyping
• MLST
• Finetyping (porA, fetA, porB)
• Bexsero antigen sequence typing (BAST) (fHbp, NHBA, NadA, PorA)

Quick start

# install
$ pip install git+https://github.com/MDU-PHL/meningotype.git

# just serotype
$ meningotype NMA.fasta

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA    FetA    PorB    fHbp    NHBA    NadA    BAST
NMA.fasta  A          ctrA    -       -       -       -       -       -       -       -

# include all genotypes
$ meningotype --all NMA.fasta

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA       FetA    PorB            fHbp    NHBA    NadA    BAST
NMA.fasta  A          ctrA    4       7,13-1     F1-5    NEIS2020_28     5       29      0       639

# type lots of files at once
$ meningotype --all *.fna

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA       FetA    PorB            fHbp    NHBA    NadA    BAST
A.fna      A          ctrA    4       7,13-1     F1-5    NEIS2020_28     5       29      0       639
B.fna      B          ctrA    8       5-2,10-1   F3-6    NEIS2020_12     16      20      8       150
C.fna      C          ctrA    177     21,26-2    F1-5    NEIS2020_3      17      101     9       118
W.fna      W          ctrA    11      5,2        F1-1    NEIS2020_244    623     29      6       141
X.fna      X          ctrA    181     5-1,10-1   F4-23   NEIS2020_509    391     358     0       -
Y.fna      Y          ctrA    23      5-2,10-1   F4-1    NEIS2020_67     25      7       0       228

Installation

Dependencies

• Python 2.7.x
• BioPython
• isPcr v33
• NCBI BLAST+ >= 2.4
• mlst

The simplest way to install dependencies is to use the Brew (MacOS) or Linuxbrew (Linux) packaging system.

$ brew tap homebrew/science
$ brew tap tseemann/homebrew-bioinformatics-linux
$ brew install ispcr blast mlst

Installing

The easiest way of installing meningotype is using pip:

$ pip install --user git+https://github.com/MDU-PHL/meningotype.git

The --user option will install the package locally, rather than in the global python directory.

Thus, by default, this will install the package in $HOME/.local/, and the executable in $HOME/.local/bin/. To install the executable in a custom location (e.g., $HOME/bin), use the following:

$ pip install --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/meningotype.git

To upgrade to a newer version:

$ pip install --upgrade --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/meningotype.git

Testing

Once installed, you can run the following to ensure meningotype is successfully working:

$ meningotype.py --test

If everything works, you will see the following:

$ meningotype.py --test
Running meningotype.py on test examples ... 
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID	SEROGROUP	ctrA	MLST	PorA	FetA	PorB	fHbp	NHBA	NadA	BAST
meningotype/test/A.fna	A	ctrA	-	-	-	-	-	-	-	-
meningotype/test/B.fna	B	ctrA	-	-	-	-	-	-	-	-
meningotype/test/C.fna	C	ctrA	-	-	-	-	-	-	-	-
meningotype/test/W.fna	W	ctrA	-	-	-	-	-	-	-	-
meningotype/test/X.fna	X	ctrA	-	-	-	-	-	-	-	-
meningotype/test/Y.fna	Y	ctrA	-	-	-	-	-	-	-	-

or to check finetyping:

$ meningotype.py --test --finetype
Running meningotype.py on test examples ... 
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID	SEROGROUP	ctrA	MLST	PorA	        FetA	PorB	fHbp	NHBA	NadA	BAST
meningotype/test/A.fna	A	ctrA	-	7,13-1		F1-5	-	-	-	-	-
meningotype/test/B.fna	B	ctrA	-	5-2,10-1	F3-6	-	-	-	-	-
meningotype/test/C.fna	C	ctrA	-	21,26-2		F1-5	-	-	-	-	-
meningotype/test/W.fna	W	ctrA	-	5,2		F1-1	-	-	-	-	-
meningotype/test/X.fna	X	ctrA	-	5-1,10-1	F4-23	-	-	-	-	-
meningotype/test/Y.fna	Y	ctrA	-	5-2,10-1	F4-1	-	-	-	-	-

or to check finetyping and Bexsero antigen sequence typing:

$ meningotype.py --test --all
Running meningotype.py on test examples ... 
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID	SEROGROUP	ctrA	MLST	PorA		FetA	PorB		fHbp	NHBA	NadA	BAST
meningotype/test/A.fna	A	ctrA	4	7,13-1		F1-5	NEIS2020_28		5	29	0	639
meningotype/test/B.fna	B	ctrA	8	5-2,10-1	F3-6	NEIS2020_12		16	20	8	150
meningotype/test/C.fna	C	ctrA	177	21,26-2		F1-5	NEIS2020_3		17	101	9	118
meningotype/test/W.fna	W	ctrA	11	5,2		F1-1	NEIS2020_244	623	29	6	141
meningotype/test/X.fna	X	ctrA	181	5-1,10-1	F4-23	NEIS2020_509	391	358	0	-
meningotype/test/Y.fna	Y	ctrA	23	5-2,10-1	F4-1	NEIS2020_67		25	7	0	228

Usage

$ meningotype.py -h
usage: 
  meningotype.py [OPTIONS] <fasta1> <fasta2> <fasta3> ... <fastaN>

In silico typing for Neisseria meningitidis
Default: Serotyping, MLST and ctrA PCR

PCR Serotyping Ref: Mothershed et al, J Clin Microbiol 2004; 42(1): 320-328
PorA and FetA typing Ref: Jolley et al, FEMS Microbiol Rev 2007; 31: 89-96
Bexsero antigen sequence typing (BAST) Ref: Brehony et al, Vaccine 2016; 34(39): 4690-4697
See also http://www.neisseria.org/nm/typing/

positional arguments:
  FASTA       input FASTA files eg. fasta1, fasta2, fasta3 ... fastaN

optional arguments:
  -h, --help  show this help message and exit
  --finetype  perform porA and fetA fine typing (default=off)
  --porB      perform porB sequence typing (NEIS2020) (default=off)
  --bast      perform Bexsero antigen sequence typing (BAST) (default=off)
  --mlst      perform MLST (default=off)
  --all       perform MLST, porA, fetA, porB, BAST typing (default=off)
  --db DB     specify custom directory containing allele databases for porA/fetA typing
              directory must contain database files: "FetA_VR.fas", "PorA_VR1.fas", "PorA_VR2.fas"
              for Bexsero typing: "fHbp_peptide.fas", "NHBA_peptide.fas", "NadA_peptide.fas", "BASTalleles.txt"
  --printseq  save porA/fetA or BAST allele sequences to file (default=off)
  --updatedb  update allele database from <pubmlst.org>
  --test      run test example
  --version   show program's version number and exit

Examples

To perform in silico serotyping on FASTA files:

$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN>`

The serotypes are printed in tab-separated format to stdout. To save results to a tab-separated text file, redirect stdout:

$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN>  > results.txt

To perform in silico serotyping AND finetyping of the porA and fetA genes:

$ meningotype --finetype <fasta1> <fasta2> <fasta3> ... <fastaN>

To save finetyping sequences of the alleles to a file (eg. for uploading "new" sequences to http://pubmlst.org/neisseria/):

$ meningotype --finetype --printseq <fasta1> <fasta2> <fasta3> ... <fastaN>

These are placed into a folder called printseq in the current directory.

Updating the allele databases

To update the allele databases from http://pubmlst.org/neisseria/

$ meningotype.py --updatedb

A copy of the original database is saved to *.old just in case, but is overwritten with each subsequent --updatedb. Ensure you back up your old databases if you wish to keep them.

Citation

Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP, Seemann T.
meningotype: in silico typing for Neisseria meningitidis.
GitHub https://github.com/MDU-PHL/meningotype

Bugs

• Software - submit via the GitHub issues page.
• Database - contact the pubmlst curator

Software Licence

GPL3

Authors

• Jason Kwong (@kwongjc)
• Anders Gonçalves da Silva (@drandersg)
• Torsten Seemann (@torstenseemann)

References

• PubMLST Neisseria Database.
• Mothershed et al. J Clin Microbiol. 2004; 42(1):320-328.
• Jolley et al. FEMS Microbiol Rev. 2007; 31:89-96.
• Brehony et al. Vaccine. 2016; 34(39):4690-4697.
• Bambini et al. PLoS One. 2013; 8(5):e65043.