Population structure and genetic diversity of Vibrio parahaemolyticus from a coastal area of China based on a multi-locus sequence typing (MLST) scheme

ABSTRACT Vibrio parahaemolyticus is an important human pathogen whose transmission is associated with the consumption of contaminated seafood. There is a growing public health concern due to the emergence of a pandemic strain causing severe outbreaks worldwide. Many questions remain unanswered regarding the evolution and population structure of V. parahaemolyticus. In this work, we describe a multilocus sequence typing (MLST) scheme for V. parahaemolyticus based on the internal fragment sequences of seven housekeeping genes. This MLST scheme was applied to 100 V. parahaemolyticus strains isolated from geographically diverse clinical (n = 37) and environmental (n = 63) sources. The sequences obtained from this work were deposited and are available in a public database (http://pubmlst.org/vparahaemolyticus ). Sixty-two unique sequence types were identified, and most (50) were represented by a single isolate, suggesting a high level of genetic diversity. Three major clonal complexes were identified by eBURST analysis. Separate clonal complexes were observed for V. parahaemolyticus isolates originating from the Pacific and Gulf coasts of the United States, while a third clonal complex consisted of strains belonging to the pandemic clonal complex with worldwide distribution. The data reported in this study indicate that V. parahaemolyticus is genetically diverse with a semiclonal population structure and an epidemic structure similar to that of Vibrio cholerae. Genetic diversity in V. parahaemolyticus appears to be driven primarily by frequent recombination rather than mutation, with recombination ratios estimated at 2.5:1 and 8.8:1 by allele and site, respectively. Application of this MLST scheme to more V. parahaemolyticus strains and by different laboratories will facilitate production of a global picture of the epidemiology and evolution of this pathogen.

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Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence typing

PLoS ONE ◽

10.1371/journal.pone.0243688 ◽

2021 ◽

Vol 16 (3) ◽

pp. e0243688

Author(s):

Rebeca Huebner ◽

Robert Mugabi ◽

Gabriella Hetesy ◽

Lawrence Fox ◽

Sarne De Vliegher ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Multilocus Sequence Typing ◽

Bovine Mastitis ◽

The United States ◽

Genetic Lineage ◽

Single Nucleotide Variants ◽

Discrimination Power ◽

Core Group ◽

Mlst Scheme

Staphylococcus chromogenes is a common skin commensal in cattle and has been identified as a frequent cause of bovine mastitis and intramammary infections. We have developed a seven locus Multilocus Sequence Typing (MLST) scheme for typing S. chromogenes. Sequence-based typing systems, such as MLST, have application in studies of genetic diversity, population structure, and epidemiology, including studies of strain variation as a factor in pathogenicity or host adaptation. The S. chromogenes scheme was tested on 120 isolates collected from three geographic locations, Vermont and Washington State in the United States and Belgium. A total of 46 sequence types (STs) were identified with most of the STs being location specific. The utility of the typing scheme is indicated by a discrimination power of 95.6% for all isolates and greater than 90% for isolates from each of the three locations. Phylogenetic analysis placed 39 of the 46 STs into single core group consistent with a common genetic lineage; the STs in this group differ by less than 0.5% at the nucleotide sequence level. Most of the diversification in this lineage group can be attributed to mutation; recombination plays a limited role. This lineage group includes two clusters of single nucleotide variants in starburst configurations indicative of recent clonal expansion; nearly 50% of the isolates sampled in this study are in these two clusters. The remaining seven STs were set apart from the core group by having alleles with highly variable sequences at one or more loci. Recombination had a higher impact than mutation in the diversification of these outlier STs. Alleles with hypervariable sequences were detected at five of the seven loci used in the MLST scheme; the average sequence distances between the hypervariable alleles and the common core alleles ranged from 12 to 34 nucleotides. The extent of these sequence differences suggests the hypervariable alleles may be remnants of an ancestral genotype.

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Multi-locus sequence typing of Mycoplasma bovis to assess its genetic diversity from 2009-2018 in Ningxia Hui Autonomous Region, China

10.21203/rs.3.rs-23294/v1 ◽

2020 ◽

Author(s):

Yanan Guo ◽

Haifeng Luo ◽

Shuqiang Guo ◽

Yuanyuan Lei ◽

Yong Li ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Scientific Basis ◽

Multi Locus Sequence Typing ◽

Mycoplasma Bovis ◽

Autonomous Region ◽

Mlst Analysis ◽

Ningxia Hui Autonomous Region ◽

And Control ◽

First Time

Abstract Background: Mycoplasma bovis (M. bovis) is a highly contagious cattle pathogen spreading worldwide and especially in Ningxia province in China. Methods: For investing epidemiology and population structure, we isolated 65 strains of M. bovis from infectious cattle with pneumonia or mastitis or arthritis. Multi-locus sequence typing (MLST) analysis were used to compare these 65 strains isolated from 2009 to 2018. The molecular epidemiology and population structure of M. bovis of these strains were further compared to PG45 strain and HB0801 reported for the first time in China and others strains isolated from different province of China through MLST analysis. Seven gene sequences of 65 strains in Ningxia and the strains of different STs in China and PG45 reference strains were concatenated to constructe a phylogenetic tree. Results: Totally two types of ST, ST10 and ST134, were identified in Ningxia. 37 Ningxia strains were classified to ST10 and 28 Ningxia strains were classified to ST134. ST134 strain was a new ST and first found in 2009 and was only widely distributed in Ningxia at present. The M. bovis of ST10 was widely spread in many provinces in China and was widespread in Ningxia since 2010. It is speculated that the prevalence of M. bovis ST10 in Ningxia began in 2010. Conclusion: This study is the first report on the genetic diversity of M. bovis from 2009 to 2018 in Ningxia Hui Autonomous Region and provides the epidemiological information, thus is meaningful for providing a scientific basis for the prevention and control of M.bovis in Ningxia, China.

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