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Sci Rep. 2017 Jul 3;7(1):4536. doi: 10.1038/s41598-017-04707-4.

Failure of phylogeny inferred from multilocus sequence typing to represent bacterial phylogeny.

Tsang AKL1, Lee HH1, Yiu SM2, Lau SKP3,4,5,6,7, Woo PCY8,9,10,11,12.

Author information

1
Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong.
2
Department of Computer Science, The University of Hong Kong, Pok Fu Lam, Hong Kong.
3
Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong. skplau@hku.hk.
4
State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong. skplau@hku.hk.
5
Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong. skplau@hku.hk.
6
Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong. skplau@hku.hk.
7
Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong. skplau@hku.hk.
8
Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong. pcywoo@hku.hk.
9
State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong. pcywoo@hku.hk.
10
Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong. pcywoo@hku.hk.
11
Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong. pcywoo@hku.hk.
12
Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pok Fu Lam, Hong Kong. pcywoo@hku.hk.

Abstract

Although multilocus sequence typing (MLST) is highly discriminatory and useful for outbreak investigations and epidemiological surveillance, it has always been controversial whether clustering and phylogeny inferred from the MLST gene loci can represent the real phylogeny of bacterial strains. In this study, we compare the phylogenetic trees constructed using three approaches, (1) concatenated blocks of homologous sequence shared between the bacterial genomes, (2) genome single-nucleotide polymorphisms (SNP) profile and (3) concatenated nucleotide sequences of gene loci in the corresponding MLST schemes, for 10 bacterial species with >30 complete genome sequences available. Major differences in strain clustering at more than one position were observed between the phylogeny inferred using genome/SNP data and MLST for all 10 bacterial species. Shimodaira-Hasegawa test revealed significant difference between the topologies of the genome and MLST trees for nine of the 10 bacterial species, and significant difference between the topologies of the SNP and MLST trees were present for all 10 bacterial species. Matching Clusters and R-F Clusters metrics showed that the distances between the genome/SNP and MLST trees were larger than those between the SNP and genome trees. Phylogeny inferred from MLST failed to represent genome phylogeny with the same bacterial species.

PMID:
28674428
PMCID:
PMC5495804
DOI:
10.1038/s41598-017-04707-4
[Indexed for MEDLINE]
Free PMC Article

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