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 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 Development of a Tiered Multilocus Sequence Typing Scheme for Members of the Lactobacillus acidophilus Complex

2013 ◽  
Vol 79 (23) ◽  
pp. 7220-7228 ◽  
Author(s):  
Padmini Ramachandran ◽  
David W. Lacher ◽  
Erika A. Pfeiler ◽  
Christopher A. Elkins
Keyword(s):  
Lactobacillus Acidophilus ◽  
Multilocus Sequence Typing ◽  
Random Amplified Polymorphic Dna ◽  
Rflp Analysis ◽  
Housekeeping Genes ◽  
Nucleotide Substitutions ◽  
Content Type ◽  
Mlst Scheme ◽  
Pcr Rflp ◽  
Pcr Targeting

ABSTRACTMembers of theLactobacillus acidophiluscomplex are associated with functional foods and dietary supplements because of purported health benefits they impart to the consumer. Many characteristics of these microorganisms are reported to be strain specific. Therefore, proper strain typing is essential for safety assessment and product labeling, and also for monitoring strain integrity for industrial production purposes. Fifty-two strains of theL. acidophiluscomplex (L. acidophilus,L. amylovorus,L. crispatus,L. gallinarum,L. gasseri, andL. johnsonii) were genotyped using two established methods and compared to a novel multilocus sequence typing (MLST) scheme. PCR restriction fragment length polymorphism (PCR-RFLP) analysis of thehsp60gene with AluI and TaqI successfully clustered 51 of the 52 strains into the six species examined, but it lacked strain-level discrimination. Random amplified polymorphic DNA PCR (RAPD-PCR) targeting the M13 sequence resulted in highly discriminatory profiles but lacked reproducibility. In this study, an MLST scheme was developed using the conserved housekeeping genesfusA,gpmA,gyrA,gyrB,lepA,pyrG, andrecA, which identified 40 sequence types that successfully clustered all of the strains into the six species. Analysis of the observed alleles suggests that nucleotide substitutions within five of the seven MLST loci have reached saturation, a finding that emphasizes the highly diverse nature of theL. acidophiluscomplex and our unconventional application of a typically intraspecies molecular typing tool. Our MLST results indicate that this method could be useful for characterization and strain discrimination of a multispecies complex, with the potential for taxonomic expansion to a broader collection ofLactobacillusspecies.

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

2014 ◽  
Vol 80 (13) ◽  
pp. 3920-3929 ◽  
Author(s):  
Abdur Rahman ◽  
Catherine Cailliez-Grimal ◽  
Cyril Bontemps ◽  
Sophie Payot ◽  
Stéphane Chaillou ◽  
...  
Keyword(s):  
Population Structure ◽  
Lactic Acid ◽  
Multilocus Sequence Typing ◽  
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.

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.

scholarly journals Development of a Multilocus Sequence Typing Scheme for Molecular Typing of Mycoplasma pneumoniae

2015 ◽  
Vol 53 (10) ◽  
pp. 3195-3203 ◽  
Author(s):  
Rebecca J. Brown ◽  
Matthew T. G. Holden ◽  
O. Brad Spiller ◽  
Victoria J. Chalker
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Genomic Sequence ◽  
Variable Number Tandem Repeat ◽  
Housekeeping Genes ◽  
Variable Number ◽  
Respiratory Pathogen ◽  
Content Type ◽  
Mlst Scheme ◽  
Lower Respiratory Disease

Mycoplasma pneumoniaeis a major human respiratory pathogen causing both upper and lower respiratory disease in humans of all ages, and it can also result in other serious extrapulmonary sequelae. A multilocus sequence typing (MLST) scheme forM. pneumoniaewas developed based on the sequences of eight housekeeping genes (ppa,pgm,gyrB,gmk,glyA,atpA,arcC, andadk) and applied to 55M. pneumoniaeclinical isolates and the two type strains M129 and FH. A total of 12 sequence types (STs) resulted for 57M. pneumoniaeisolates tested, with a discriminatory index of 0.21 STs per isolate. The MLST loci used in this scheme were shown to be stable in 10 strains following 10 sequential subculture passages. Phylogenetic analysis of concatenated sequences of the eight loci indicated two distinct genetic clusters that were directly linked to multilocus variable-number tandem repeat analysis (MLVA) type. Genetic MLST clustering was confirmed by genomic sequence analysis, indicating that the MLST scheme developed in this study is representative of the genome. Furthermore, this MLST scheme was shown to be more discriminatory than both MLVA and P1 typing for theM. pneumoniaeisolates examined, providing a method for further and more detailed analysis of observed epidemic peaks ofM. pneumoniaeinfection. This scheme is supported by a public Web-based database (http://pubmlst.org/mpneumoniae).

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 Draft Genome Sequence of Enterococcus faecalis DD14, a Bacteriocinogenic Lactic Acid Bacterium with Anti-Clostridium Activity

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Yanath Belguesmia ◽  
Valérie Leclère ◽  
Matthieu Duban ◽  
Eric Auclair ◽  
Djamel Drider
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacterium ◽  
Enterococcus Faecalis ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Coding Sequences ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Healthy Newborn

ABSTRACT We report the draft genome sequence of Enterococcus faecalis DD14, a strain isolated from meconium of a healthy newborn at Roubaix Hospital (France). The strain displayed antagonism against a set of Gram-positive bacteria through concomitant production of lactic acid and bacteriocin. The genome has a size of 2,893,365 bp and a 37.3% G+C ratio and is predicted to contain at least 2,755 coding sequences and 62 RNAs.

scholarly journals Analysis of Transcriptomic Response to SO 2 by Oenococcus oeni Growing in Continuous Culture

2021 ◽  
Author(s):  
Cristobal A. Onetto ◽  
Peter J. Costello ◽  
Radka Kolouchova ◽  
Charlotte Jordans ◽  
Jane McCarthy ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacterium ◽  
High Sensitivity ◽  
Malolactic Fermentation ◽  
Oenococcus Oeni ◽  
Low Ph ◽  
Transcriptomic Response ◽  
Content Type ◽  
Bacterium Species ◽  
High Ethanol

Malolactic fermentation is an indispensable step in the elaboration of most wines and is generally performed by Oenococcus oeni , a Gram-positive heterofermentative lactic acid bacterium species. While O. oeni is tolerant to many of the wine stresses, including low pH and high ethanol concentrations, it has high sensitivity to SO 2 , an antiseptic and antioxidant compound regularly used in winemaking.

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 Draft Genome Sequences of 12 Leuconostoc carnosum Strains Isolated from Cooked Ham Packaged in a Modified Atmosphere and from Fresh Sausages

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Francesco Candeliere ◽  
Stefano Raimondi ◽  
Gloria Spampinato ◽  
Moon Yue Feng Tay ◽  
Alberto Amaretti ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacterium ◽  
Draft Genome ◽  
Modified Atmosphere ◽  
Genome Sequences ◽  
Content Type ◽  
Cooked Ham ◽  
Leuconostoc Carnosum ◽  
Bacteriocin Genes

Leuconostoc carnosum is a lactic acid bacterium that preferentially colonizes meat. In this work, we present the draft genome sequences of 12 Leuconostoc carnosum strains isolated from modified-atmosphere-packaged cooked ham and fresh sausages. Three strains harbor bacteriocin genes.

Sign in / Sign up

Export Citation Format

Share Document