scholarly journals Multilocus Sequence Typing Scheme for Bacteria of the Bacillus cereus Group

2004 ◽  
Vol 70 (1) ◽  
pp. 191-201 ◽  
Author(s):  
Erlendur Helgason ◽  
Nicolas J. Tourasse ◽  
Roger Meisal ◽  
Dominique A. Caugant ◽  
Anne-Brit Kolstø
Keyword(s):  
Population Structure ◽  
Bacillus Cereus ◽  
Multilocus Sequence Typing ◽  
Sequence Data ◽  
Housekeeping Genes ◽  
Industrial Applications ◽  
Enzyme Electrophoresis ◽  
Mlst Scheme ◽  
High Level ◽  
Sequence Types

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.

scholarly journals A Stenotrophomonas maltophilia Multilocus Sequence Typing Scheme for Inferring Population Structure

2009 ◽  
Vol 191 (9) ◽  
pp. 2934-2943 ◽  
Author(s):  
Sabine Kaiser ◽  
Klaus Biehler ◽  
Daniel Jonas
Keyword(s):  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Stenotrophomonas Maltophilia ◽  
Sequence Data ◽  
Clinical Isolates ◽  
Mlst Scheme ◽  
Tree Topologies ◽  
Significant Linkage ◽  
Sequence Types ◽  
Selection Of

ABSTRACT Stenotrophomonas maltophilia is an opportunistic, highly resistant, and ubiquitous pathogen. Strains have been assigned to genogroups using amplified fragment length polymorphism. Hence, isolates of environmental and clinical origin predominate in different groups. A multilocus sequence typing (MLST) scheme was developed using a highly diverse selection of 70 strains of various ecological origins from seven countries on all continents including strains of the 10 previously defined genogroups. Sequence data were assigned to 54 sequence types (ST) based on seven loci. Indices of association for all isolates and clinical isolates of 2.498 and 2.562 indicated a significant linkage disequilibrium, as well as high congruence of tree topologies from different loci. Potential recombination events were detected in one-sixth of all ST. Calculation of the mean divergence between and within predicted clusters confirmed previously defined groups and revealed five additional groups. Consideration of the different ecological origins showed that 18 out of 31 respiratory tract isolates, including 12 out of 19 isolates from cystic fibrosis (CF) patients, belonged to genogroup 6. In contrast, 16 invasive strains isolated from blood cultures were distributed among nine different genogroups. Three genogroups contained isolates of strictly environmental origin that also featured high sequence distances to other genogroups, including the S. maltophilia type strain. On the basis of this MLST scheme, isolates can be assigned to the genogroups of this species in order to further scrutinize the population structure of this species and to unravel the uneven distribution of environmental and clinical isolates obtained from infected, colonized, or CF patients.

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

Microbiology ◽  
2010 ◽  
Vol 156 (7) ◽  
pp. 2035-2045 ◽  
Author(s):  
Claudia Picozzi ◽  
Gaia Bonacina ◽  
Ileana Vigentini ◽  
Roberto Foschino
Keyword(s):  
Multilocus Sequence Typing ◽  
Geographical Area ◽  
Housekeeping Genes ◽  
Processing Conditions ◽  
Clonal Population ◽  
Factors Affecting ◽  
Lactobacillus Sanfranciscensis ◽  
Mlst Scheme ◽  
Sequence Types

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.

scholarly journals Determination of Molecular Phylogenetics of Vibrio parahaemolyticus Strains by Multilocus Sequence Typing

2008 ◽  
Vol 190 (8) ◽  
pp. 2831-2840 ◽  
Author(s):  
Narjol González-Escalona ◽  
Jaime Martinez-Urtaza ◽  
Jaime Romero ◽  
Romilio T. Espejo ◽  
Lee-Ann Jaykus ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Vibrio Parahaemolyticus ◽  
Molecular Phylogenetics ◽  
Clonal Complex ◽  
Housekeeping Genes ◽  
The United States ◽  
Health Concern ◽  
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.

scholarly journals Differentiation of Bacillus anthracis and other Bacillus cereus group bacterial strains using multilocus sequence typing method

2020 ◽  
Vol 16 ◽  
pp. 12-21
Author(s):  
Grzegorz Graniak ◽  
Alina Olender ◽  
Katarzyna Naylor
Keyword(s):  
Bacillus Cereus ◽  
Phylogenetic Relationship ◽  
Multilocus Sequence Typing ◽  
Sequence Data ◽  
Animal Health ◽  
Housekeeping Genes ◽  
Negative Control ◽  
Bacterial Strains ◽  
Bacillus Cereus Group ◽  
Typing Method

The study describes the preparation of the phylogenetic differentiation of Bacillus cereus strains. The Bacillus cereus group of bacteria is very important for human and animal health. The multilocus sequence typing scheme has been used to present this group of bacteria’s phylogenetic relationship and structure. The MLST system was established using 60 isolates of B. anthracis, B. cereus sensu stricto, B. thuringiensis, and transitional environment strains of Bacillus spp. As a negative control, five strains of B. subtilis and B. megaterium were used. Primers for amplification and sequencing were designed to target highly conserved internal fragment of seven housekeeping genes: glpF, gmk, ilvD, pta, pur, pycA, and tpi. A total of 22 different sequence types (STs) were distinguished. Analysis of the sequence data showed that all of the Bacillus cereus strains are very closely related. The MLST scheme exhibited a high level of resolution that can be used as an excellent tool for studying the phylogenetic relationship, epidemiology, and population structure of the Bacillus cereus group strains. The MLST method additionally allows us to define the phylogenetic relationship between very closely related strains based on a combination of the sequences of all seven alleles fragments and each of them separately. Thus, this genetic investigation tool is very useful in epidemiological investigation of potential military/ bioterrorist use of B. anthracis.

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

2015 ◽  
Vol 81 (7) ◽  
pp. 2474-2480 ◽  
Author(s):  
Riitta Rahkila ◽  
Per Johansson ◽  
Elina Säde ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Population Structure ◽  
Lactic Acid ◽  
Lactic Acid Bacterium ◽  
Multilocus Sequence Typing ◽  
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.

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

2021 ◽  
Author(s):  
Signe Nedergaard ◽  
Anne B. Jensen ◽  
Dorte Haubek ◽  
Niels Nørskov-Lauritsen
Keyword(s):  
Population Structure ◽  
Multilocus Sequence Typing ◽  
Housekeeping Genes ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Content Type ◽  
Typing Scheme ◽  
Sequence Types

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.

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

2011 ◽  
Vol 57 (12) ◽  
pp. 982-986 ◽  
Author(s):  
Michelle L. Shuel ◽  
Kathleen E. Karlowsky ◽  
Dennis K.S. Law ◽  
Raymond S.W. Tsang
Keyword(s):  
Nucleotide Sequence ◽  
Haemophilus Influenzae ◽  
Dna Sequencing ◽  
Multilocus Sequence Typing ◽  
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.

scholarly journals The Possible Transmission and Potential Enterotoxicity of Bacillus cereus on Lettuce Farms in Five Chinese Provinces

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Qu ◽  
Chao Wei ◽  
Xiaohang Dai ◽  
Yalong Bai ◽  
Xin Zhao ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Potential Risk ◽  
Trace Analysis ◽  
Multilocus Sequence Typing ◽  
Soil Samples ◽  
Foodborne Diseases ◽  
Human Pathogen ◽  
Toxin Genes ◽  
Positive Rate ◽  
Sequence Types

Bacillus cereus is a well-characterized human pathogen that produces toxins associated with diarrheal and emetic foodborne diseases. To investigate the possible transmission of B. cereus on lettuce farms in China and determine its enterotoxicity, (I) a total of 524 samples (lettuce: 332, soil: 69, water: 57, manure: 57, pesticide: 9) were collected from 46 lettuce farms in five Chinese provinces, (II) multilocus sequence typing (MLST) was used to classify B. cereus isolates and for trace analysis, and (III) the presence of toxin genes and enterotoxins (Hbl and Nhe) was detected in 68 strains. The results showed that one hundred and sixty-one lettuce samples (48.5%) tested positive for B. cereus at levels ranging from 10 to 5.3 × 104 CFU/g. Among the environmental sample categories surveyed, the highest positive rate was that of the pesticide samples at 55.6%, followed by soil samples at 52.2% and manure samples at 12.3%. Moreover, one hundred isolates of B. cereus yielded 68 different sequence types (STs) and were classified into five phylogenetic clades. Furthermore, Nhe toxin genes (nheA, nheB, nheC) were broadly distributed and identified in all 68 strains (100%), while Hbl toxin genes (hblA, hblC, hblD) were present in 61 strains (89.7%), entFM was detected in 62 strains (91.2%), and cytK was found in 29 strains (42.6%). All strains were negative for ces. As for the enterotoxin, Nhe was observed in all 68 isolates carrying nheB, while Hbl was present in 76.5% (52/68) of the strains harboring hblC. This study is the first report of possible B. cereus transmission and of its potential enterotoxicity on lettuce farms in China. The results showed that soil and pesticides are the main sources of B. cereus on lettuce farms in China, and the possible transmission routes are as follows: soil-lettuce, manure-lettuce, pesticide-lettuce, manure-soil-lettuce, and water-manure-soil-lettuce. Furthermore, the B. cereus isolates, whether from lettuce or the environment, pose a potential risk to health.

Genetic variation in the mitochondrial cytochrome c oxidase subunit 1 within Progamotaenia festiva (Cestoda: Anoplocephalidae) from macropodid marsupials

Parasitology ◽  
2007 ◽  
Vol 134 (10) ◽  
pp. 1465-1476 ◽  
Author(s):  
I. BEVERIDGE ◽  
S. SHAMSI ◽  
M. HU ◽  
N. B. CHILTON ◽  
R. B. GASSER
Keyword(s):  
Genetic Variation ◽  
Host Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Enzyme Electrophoresis ◽  
Single Strand Conformational Polymorphism ◽  
Oxidase Subunit ◽  
Single Host ◽  
Distinct Sequence ◽  
Sequence Types

SUMMARYGenetic variation was examined in the anoplocephalid cestode Progamotaenia festiva, from Australian marsupials, in order to test the hypothesis that P. festiva, is a complex of sibling species and to assess the extent of host switching reported previously based on multilocus enzyme electrophoresis (MEE). Polymerase chain reaction (PCR)-based single-strand conformational polymorphism (SSCP) was used for the analysis of sequence variation in the cytochrome c oxidase subunit 1 (cox1) gene among 179 specimens of P. festiva (identified based on morphology and predilection site in the host) from 13 different host species, followed by selective DNA sequencing. Fifty-three distinct sequence types (haplotypes) representing all specimens were defined. Phylogenetic analyses of these sequence data (utilizing maximum parsimony and neighbour-joining methods) revealed 12 distinct clades. Other heterologous species, P. ewersi and P. macropodis, were used as outgroups and the remaining bile-duct inhabiting species, P. diaphana and P. effigia, were included in the analysis for comparative purposes. The latter 2 species were nested within the clades representing P. festiva. Most clades of P. festiva identified were restricted to a single host species; one clade primarily in Macropus robustus was also found in the related host species M. antilopinus in an area of host sympatry; another clade occurring primarily in M. robustus occurred also in additional kangaroo species, M. rufus and M. dorsalis. High levels of genetic divergence, the existence of distinct clades and their occurrence in sympatry provide support for the hypothesis that P. festiva represents a complex of numerous species, most of which, but not all, are host specific. Three distinct clades of cestodes were found within a single host, M. robustus, but there was no evidence of within-host speciation.

Epidemic population structure of clinical Klebsiella aerogenes inferred by multilocus sequence typing

2019 ◽  
Author(s):  
Sheng Chen ◽  
Yu Wang ◽  
Lijun Zeng ◽  
Wenbo Luo ◽  
Wei Feng ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Homologous Recombination ◽  
Key Words ◽  
Multilocus Sequence Typing ◽  
Bacterial Population ◽  
Purifying Selection ◽  
Klebsiella Aerogenes ◽  
Sequence Types

Abstract Background: Multilocus sequence typing (MLST) act as an accurate approach to characterize bacterial population genetics, phylogeny and epidemiology, and has not yet been applied to Klebsiella aerogenes. Results: A MLST scheme was established for a collection of 213 isolates of K. aerogenes. These strains exhibited considerable sequence diversity under purifying selection, and could be assigned into 135 sequence types, which were further divided into 8 clonal complexes and a lot of doubletons and singletons scatterred in the population snapshot. Five separately clustering lineages were presented in the population, which displayed evident homologous recombination occurred within and across lineages, with a tendency of linkage disequilibrium. Conclusions: K. aerogenes shows an epidemic population structure displaying high levels of recombination occurring more frequently than point mutation. Key words: Klebsiella aerogenes; multilocus sequence typing; sequence types; purifying selection; linkage disequilibrium; population structure

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