In silico typing of Neisseria meningitidis contigs
- Serotyping
- MLST
- Finetyping (porA, fetA, porB)
- Bexsero antigen sequence typing (BAST) (fHbp, NHBA, NadA, PorA)
- MenDeVAR (Meningococcal Deduced Vaccine Antigen Reactivity) Index
# install
$ pip install git+https://github.com/MDU-PHL/meningotype.git
# just serotype
$ meningotype *.fna
SAMPLE_ID SEROGROUP ctrA
NMA.fasta A ctrA
# type lots of files at once and include all typing results
$ meningotype --all *.fna
SAMPLE_ID SEROGROUP ctrA MLST PorA FetA PorB fHbp NHBA NadA BAST Bexsero MenDeVAR Trumenba MenDeVAR
A.fna A ctrA 4 7,13-1 F1-5 NEIS2020_28 5 29 0 639 insufficient data insufficient data
B.fna B ctrA 8 5-2,10-1 F3-6 NEIS2020_12 16 20 8 150 exact match cross-reactive
C.fna C ctrA 177 21,26-2 F1-5 NEIS2020_3 17 101 9 118 insufficient data insufficient data
W.fna W ctrA 11 5,2 F1-1 NEIS2020_244 623 29 6 141 cross-reactive insufficient data
X.fna X ctrA 181 5-1,10-1 F4-23 NEIS2020_509 391 358 0 3042 insufficient data insufficient data
Y.fna Y ctrA 23 5-2,10-1 F4-1 NEIS2020_67 25 7 0 228 insufficient data cross-reactive
The easiest way of installing meningotype is using conda, which will install all required dependencies:
$ conda create -n meningotype -c bioconda meningotype
Once installed, you can run the following to ensure meningotype is successfully working:
$ meningotype --version
meningotype v0.9.0
$ meningotype --checkdeps
Checking dependencies:
isPcr ....... Found "/home/user/bin/isPcr" ....... [OK]
blastn ....... Found "/home/user/bin/blastn" ....... [OK]
blastx ....... Found "/home/user/bin/blastx" ....... [OK]
mlst ....... Found "/home/user/bin/mlst" ....... [OK]
$ meningotype --test
If everything works, you will see the following:
$ meningotype --test
Running meningotype on test examples ...
$ meningotype A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID SEROGROUP ctrA
A.fna A ctrA
B.fna B ctrA
C.fna C ctrA
W.fna W ctrA
X.fna X ctrA
Y.fna Y ctrA
or to check finetyping:
$ meningotype --test --finetype
Running meningotype on test examples ...
$ meningotype A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID SEROGROUP ctrA PorA FetA
A.fna A ctrA 7,13-1 F1-5
B.fna B ctrA 5-2,10-1 F3-6
C.fna C ctrA 21,26-2 F1-5
W.fna W ctrA 5,2 F1-1
X.fna X ctrA 5-1,10-1 F4-23
Y.fna Y ctrA 5-2,10-1 F4-1
or to check finetyping and Bexsero antigen sequence typing and MenDeVAR Vaccine Antigen Reactivity Index:
$ meningotype --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 Bexsero MenDeVAR Trumenba MenDeVAR
A.fna A ctrA 4 7,13-1 F1-5 NEIS2020_28 5 29 0 639 insufficient data insufficient data
B.fna B ctrA 8 5-2,10-1 F3-6 NEIS2020_12 16 20 8 150 exact match cross-reactive
C.fna C ctrA 177 21,26-2 F1-5 NEIS2020_3 17 101 9 118 insufficient data insufficient data
W.fna W ctrA 11 5,2 F1-1 NEIS2020_244 623 29 6 141 cross-reactive insufficient data
X.fna X ctrA 181 5-1,10-1 F4-23 NEIS2020_509 391 358 0 3042 insufficient data insufficient data
Y.fna Y ctrA 23 5-2,10-1 F4-1 NEIS2020_67 25 7 0 228 insufficient data cross-reactive
$ meningotype -h
usage:
meningotype [OPTIONS] <fasta1> <fasta2> <fasta3> ... <fastaN>
In silico typing for Neisseria meningitidis
Default: Serotyping 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
MenDeVAR Vaccine Reactivity Index Ref: Rodrigues et al. J Clin Microbiol. 2020; 59(1):e02161-20
See also https://pubmlst.org/organisms/neisseria-spp
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 and MenDeVAR index (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 DIR specify directory to save extracted porA/fetA/porB or BAST allele sequences (default=off)
--cpus CPUS number of cpus to use in BLAST search (default=1)
--updatedb update allele database from <pubmlst.org>
--test run test example
--checkdeps check dependencies are installed and exit
--version show program's version number and exit
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.tsv
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.
To perform in silico serotyping AND finetyping AND Bexsero antigen sequence typing AND determine the MenDeVAR Vaccine Antigen Reactivity Index
$ meningotype --all --printseq <fasta1> <fasta2> <fasta3> ... <fastaN>
The MenDeVAR index assigns each record one of four categories:
- Green / Exact match: isolate contains one or more exact sequence match(es) to antigenic variants found in the vaccine
- Amber / Cross-reactive: isolate contains one or more antigenic variant deemed cross-reactive to vaccine variants through experimental studies.
- Red / No match: all the isolate's antigenic variants have been deemed not cross-reactive to vaccine variants through experimental studies.
- Grey / Insufficient data: isolate contains antigens for which there is insufficient data available or which are yet to be tested in experimental studies.
To update the allele databases from https://pubmlst.org/organisms/neisseria-spp/
$ meningotype --updatedb
A copy of the original database is saved to *.old,
but is overwritten with each subsequent --updatedb.
Ensure you back up your old databases if you wish to keep them.
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
- Software - submit via the GitHub issues page.
- Database - contact the PubMLST curator
- Jason Kwong (@kwongjc)
- Andreas Stroehlein (@stroehleina)
- Anders Gonçalves da Silva (@drandersg)
- Torsten Seemann (@torstenseemann)