Multilocus Sequence Typing of Aggregatibacter actinomycetemcomitans Competently Depicts the Population Structure of the Species

Housekeeping Genes ◽

Aggregatibacter Actinomycetemcomitans ◽

Content Type ◽

Typing Scheme ◽

We developed a multilocus sequence typing scheme (MLST) for Aggregatibacter actinomycetemcomitans based on seven housekeeping genes, adk , atpG , frdB , mdh , pgi , recA , and zwf . A total of 188 strains of seven serotypes were separated into 57 sequence types.

High Genetic Diversity among Strains of the Unindustrialized Lactic Acid Bacterium Carnobacterium maltaromaticum in Dairy Products as Revealed by Multilocus Sequence Typing

10.1128/aem.00681-14 ◽

2014 ◽

Vol 80 (13) ◽

pp. 3920-3929 ◽

Cited By ~ 12

Author(s):

Abdur Rahman ◽

Catherine Cailliez-Grimal ◽

Cyril Bontemps ◽

Sophie Payot ◽

Stéphane Chaillou ◽

...

Keyword(s):

Population Structure ◽

Lactic Acid ◽

Dairy Products ◽

High Genetic Diversity ◽

Content Type ◽

Opportunistic Bacteria ◽

Sequence Types ◽

Discriminatory Index ◽

High Diversity

ABSTRACTDairy products are colonized with three main classes of lactic acid bacteria (LAB): opportunistic bacteria, traditional starters, and industrial starters. Most of the population structure studies were previously performed with LAB species belonging to these three classes and give interesting knowledge about the population structure of LAB at the stage where they are already industrialized. However, these studies give little information about the population structure of LAB prior their use as an industrial starter.Carnobacterium maltaromaticumis a LAB colonizing diverse environments, including dairy products. Since this bacterium was discovered relatively recently, it is not yet commercialized as an industrial starter, which makesC. maltaromaticuman interesting model for the study of unindustrialized LAB population structure in dairy products. A multilocus sequence typing scheme based on an analysis of fragments of the genesdapE,ddlA,glpQ,ilvE,pyc,pyrE, andleuSwas applied to a collection of 47 strains, including 28 strains isolated from dairy products. The scheme allowed detecting 36 sequence types with a discriminatory index of 0.98. The whole population was clustered in four deeply branched lineages, in which the dairy strains were spread. Moreover, the dairy strains could exhibit a high diversity within these lineages, leading to an overall dairy population with a diversity level as high as that of the nondairy population. These results are in agreement with the hypothesis according to which the industrialization of LAB leads to a diversity reduction in dairy products.

Multilocus Sequence Typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic Lactic Acid Bacterium Causing Spoilage of Packaged Perishable Foods

10.1128/aem.04013-14 ◽

2015 ◽

Vol 81 (7) ◽

pp. 2474-2480 ◽

Cited By ~ 9

Author(s):

Riitta Rahkila ◽

Per Johansson ◽

Elina Säde ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Population Structure ◽

Lactic Acid ◽

Lactic Acid Bacterium ◽

Genetic Material ◽

Housekeeping Genes ◽

Content Type ◽

Mlst Scheme ◽

Global Comparison ◽

Leuconostoc Gelidum

ABSTRACTLeuconostoc gelidumsubsp.gasicomitatumis a psychrotrophic lactic acid bacterium (LAB) that causes spoilage of a variety of modified-atmosphere-packaged (MAP) cold-stored food products. During the past 10 years, this spoilage organism has been increasingly reported in MAP meat and vegetable products in northern Europe. In the present study, the population structure within 252L. gelidumsubsp.gasicomitatumstrains was determined based on a novel multilocus sequence-typing (MLST) scheme employing seven housekeeping genes. These strains had been isolated from meat and vegetable sources over a time span of 15 years, and all 68 previously detected pulsed-field gel electrophoresis (PFGE) genotypes were represented. A total of 46 sequence types (STs) were identified, with a majority of the strains (>60%) belonging to three major STs, which were grouped into three clonal complexes (CCs) and 17 singletons by Global Optimal eBURST (goeBURST). The results by Bayesian analysis of population structure (BAPS) mostly correlated with the grouping by goeBURST. Admixture analysis by BAPS indicated a very low level of exchange of genetic material between the subpopulations. Niche specificity was observed within the subpopulations: CC1 and BAPS cluster 1 consisted mostly of strains from a variety of MAP meats, whereas vegetable strains grouped together with strains from MAP poultry within CC2 and BAPS cluster 2. The MLST scheme presented in this study provides a shareable and continuously growing sequence database enabling global comparison of strains associated with spoilage cases. This will further advance our understanding of the microbial ecology of this industrially important LAB.

Multilocus Sequence Typing Scheme for Bacteria of the Bacillus cereus Group

10.1128/aem.70.1.191-201.2004 ◽

2004 ◽

Vol 70 (1) ◽

pp. 191-201 ◽

Cited By ~ 200

Author(s):

Erlendur Helgason ◽

Nicolas J. Tourasse ◽

Roger Meisal ◽

Dominique A. Caugant ◽

Anne-Brit Kolstø

Keyword(s):

Population Structure ◽

Bacillus Cereus ◽

Sequence Data ◽

Housekeeping Genes ◽

Industrial Applications ◽

Enzyme Electrophoresis ◽

Mlst Scheme ◽

High Level ◽

ABSTRACT In this study we developed a multilocus sequence typing (MLST) scheme for bacteria of the Bacillus cereus group. This group, which includes the species B. cereus, B. thuringiensis, B. weihenstephanensis, and B. anthracis, is known to be genetically very diverse. It is also very important because it comprises pathogenic organisms as well as bacteria with industrial applications. The MLST system was established by using 77 strains having various origins, including humans, animals, food, and soil. A total of 67 of these strains had been analyzed previously by multilocus enzyme electrophoresis, and they were selected to represent the genetic diversity of this group of bacteria. Primers were designed for conserved regions of housekeeping genes, and 330- to 504-bp internal fragments of seven such genes, adk, ccpA, ftsA, glpT, pyrE, recF, and sucC, were sequenced for all strains. The number of alleles at individual loci ranged from 25 to 40, and a total of 53 allelic profiles or sequence types (STs) were distinguished. Analysis of the sequence data showed that the population structure of the B. cereus group is weakly clonal. In particular, all five B. anthracis isolates analyzed had the same ST. The MLST scheme which we developed has a high level of resolution and should be an excellent tool for studying the population structure and epidemiology of the B. cereus group.

A Multilocus Sequence Typing Scheme Implies Population Structure and Reveals Several Putative Novel Achromobacter Species

Journal of Clinical Microbiology ◽

10.1128/jcm.00814-12 ◽

2012 ◽

Vol 50 (9) ◽

pp. 3010-3015 ◽

Cited By ~ 66

Author(s):

T. Spilker ◽

P. Vandamme ◽

J. J. LiPuma

Keyword(s):

Population Structure ◽

Typing Scheme

Population Genetics and Characterization ofCampylobacter jejuniIsolates from Western Jackdaws and Game Birds in Finland

10.1128/aem.02365-18 ◽

2018 ◽

Vol 85 (4) ◽

Cited By ~ 3

Author(s):

Sara Kovanen ◽

Mirko Rossi ◽

Mari Pohja-Mykrä ◽

Timo Nieminen ◽

Mirja Raunio-Saarnisto ◽

...

Keyword(s):

Host Specificity ◽

Campylobacter Jejuni ◽

Wild Birds ◽

Whole Genome ◽

Mallard Duck ◽

Content Type ◽

Game Birds ◽

Hygienic Measures ◽

ABSTRACTPoultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterizedCampylobacter jejunifrom western jackdaws (n= 91, 43%), mallard ducks (n= 82, 76%), and pheasants (n= 9, 9%). Most of the western jackdaw and mallard duckC. jejuniisolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdawC. jejuniisolates, e.g., a novelcdtABCgene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention.IMPORTANCEThe roles of environmental reservoirs, including wild birds, in the molecular epidemiology ofCampylobacter jejunihave not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they hadC. jejunigenomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships ofC. jejuniisolates.

Nonencapsulated or nontypeableHaemophilus influenzaeare more likely than their encapsulated or serotypeable counterparts to have mutations in their fucose operon

Canadian Journal of Microbiology ◽

10.1139/w11-017 ◽

2011 ◽

Vol 57 (12) ◽

pp. 982-986 ◽

Cited By ~ 14

Author(s):

Michelle L. Shuel ◽

Kathleen E. Karlowsky ◽

Dennis K.S. Law ◽

Raymond S.W. Tsang

Keyword(s):

Nucleotide Sequence ◽

Haemophilus Influenzae ◽

Dna Sequencing ◽

Population Biology ◽

Housekeeping Genes ◽

Sequence Variations ◽

Sequence Types ◽

Complete Deletion

Population biology of Haemophilus influenzae can be studied by multilocus sequence typing (MLST), and isolates are assigned sequence types (STs) based on nucleotide sequence variations in seven housekeeping genes, including fucK. However, the ST cannot be assigned if one of the housekeeping genes is absent or cannot be detected by the current protocol. Occasionally, strains of H. influenzae have been reported to lack the fucK gene. In this study, we examined the prevalence of this mutation among our collection of H. influenzae isolates. Of the 704 isolates studied, including 282 encapsulated and 422 nonencapsulated isolates, nine were not typeable by MLST owing to failure to detect the fucK gene. All nine fucK-negative isolates were nonencapsulated and belonged to various biotypes. DNA sequencing of the fucose operon region confirmed complete deletion of genes in the operon in seven of the nine isolates, while in the remaining two isolates, some of the genes were found intact or in parts. The significance of these findings is discussed.

The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins

10.1128/aem.00249-15 ◽

2015 ◽

Vol 81 (14) ◽

pp. 4774-4781

Author(s):

Min Zhang ◽

Xiaomin Hang ◽

Jing Tan ◽

Hong Yang

Keyword(s):

Twin Pair ◽

Bifidobacterium Longum ◽

Host Genotype ◽

Content Type ◽

Living Together ◽

Adult Twins ◽

The Impact ◽

Mz Twins ◽

ABSTRACTTo investigate the influences of host genotype and environment onBifidobacterium longumsubsp.longuminhabiting human intestines at the strain level, six pairs of twins, divided into two groups (children and adults), were recruited. Each group consisted of two monozygotic (MZ) twin pairs and one dizygotic (DZ) twin pair. Child twins had been living together from birth, while adult twins had been living separately for 5 to 10 years. A total of 345B. longumsubsp.longumisolates obtained from 60 fecal samples from these twins were analyzed by multilocus sequence typing (MLST), and 35 sequence types (STs) were finally acquired. Comparison of strains within and between the twin pairs showed that no strains with identical STs were observed between unrelated individuals or within adult DZ twin pairs. Eight STs were found to be monophyletic, existing within MZ twins and child DZ twins. The similarity of strain types within child cotwins was significantly higher than that within adult cotwins, which indicated that environment was one of the important determinants inB. longumsubsp.longumstrain types inhabiting human intestines. However, although these differences between MZ and DZ twins were observed, it is still difficult to reach an exact conclusion about the impact of host genotype. This is mainly because of the limited number of subjects tested in the present study and the lack of strain types tracing in the same twin pairs from birth until adulthood.

Population Structure and Antimicrobial Resistance of Canine UropathogenicEscherichia coli

Journal of Clinical Microbiology ◽

10.1128/jcm.00788-18 ◽

2018 ◽

Vol 56 (9) ◽

Cited By ~ 12

Author(s):

Tessa E. LeCuyer ◽

Barbara A. Byrne ◽

Joshua B. Daniels ◽

Dubraska V. Diaz-Campos ◽

G. Kenitra Hammac ◽

...

Keyword(s):

Population Structure ◽

Antimicrobial Resistance ◽

Companion Animals ◽

Sequence Type ◽

Content Type ◽

E Coli ◽

Extraintestinal Disease ◽

Human Infections ◽

ABSTRACTEscherichia coliis the most common cause of human and canine urinary tract infection (UTI). Clonal groups, often with high levels of antimicrobial resistance, are a major component of theE. colipopulation that causes human UTI. While little is known about the population structure ofE. colithat causes UTI in dogs, there is evidence that dogs and humans can share fecal strains ofE. coliand that human-associated strains can cause disease in dogs. In order to better characterize theE. colistrains that cause canine UTI, we analyzed 295E. coliisolates obtained from canine urine samples from five veterinary diagnostic laboratories and analyzed their multilocus sequence types, phenotypic and genotypic antimicrobial resistance profiles, and virulence-associated gene repertoires. Sequence type 372 (ST372), an infrequent human pathogen, was the predominant sequence type in dogs at all locations. Extended-spectrum β-lactamase-producing isolates withblaCTX-Mgenes were uncommon in canine isolates but when present were often associated with sequence types that have been described in human infections. This provides support for occasional cross-host-species sharing of strains that cause extraintestinal disease and highlights the importance of understanding the role of companion animals in the overall transmission patterns of extraintestinal pathogenicE. coli.

Genetic diversity in Italian Lactobacillus sanfranciscensis strains assessed by multilocus sequence typing and pulsed-field gel electrophoresis analyses

Microbiology ◽

10.1099/mic.0.037341-0 ◽

2010 ◽

Vol 156 (7) ◽

pp. 2035-2045 ◽

Cited By ~ 54

Author(s):

Claudia Picozzi ◽

Gaia Bonacina ◽

Ileana Vigentini ◽

Roberto Foschino

Keyword(s):

Geographical Area ◽

Housekeeping Genes ◽

Processing Conditions ◽

Clonal Population ◽

Factors Affecting ◽

Lactobacillus Sanfranciscensis ◽

Mlst Scheme ◽

Lactobacillus sanfranciscensis is a lactic acid bacterium that characterizes the sourdough environment. The genetic differences of 24 strains isolated in different years from sourdoughs, mostly collected in Italy, were examined and compared by PFGE and multilocus sequence typing (MLST). The MLST scheme, based on the analysis of six housekeeping genes (gdh, gyrA, mapA, nox, pgmA and pta) was developed for this study. PFGE with the restriction enzyme ApaI proved to have higher discriminatory power, since it revealed 22 different pulsotypes, while 19 sequence types were recognized through MLST analysis. Notably, restriction profiles generated from three isolates collected from the same firm but in three consecutive years clustered in a single pulsotype and showed the same sequence type, emphasizing the fact that the main factors affecting the dominance of a strain are correlated with processing conditions and the manufacturing environment rather than the geographical area. All results indicated a limited recombination among genes and the presence of a clonal population in L. sanfranciscensis. The MLST scheme proposed in this work can be considered a useful tool for characterization of isolates and for in-depth examination of the strain diversity and evolution of this species.

A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera

Journal of Bacteriology ◽

10.1128/jb.00086-20 ◽

2020 ◽

Vol 202 (24) ◽

Cited By ~ 2

Author(s):

Kevin Y. H. Liang ◽

Fabini D. Orata ◽

Mohammad Tarequl Islam ◽

Tania Nasreen ◽

Munirul Alam ◽

...

Keyword(s):

Vibrio Cholerae ◽

Core Genome ◽

Geographic Origin ◽

Data Set ◽

Epidemiological Research ◽

Content Type ◽

Typing Scheme ◽

Subspecies Level ◽

Allelic Differences

ABSTRACT Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/). IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae. Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae. In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.