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

scholarly journals Dispersion of Multidrug-Resistant Enterococcus faecium Isolates Belonging to Major Clonal Complexes in Different Portuguese Settings

2009 ◽  
Vol 75 (14) ◽  
pp. 4904-4908 ◽  
Author(s):  
Ana R. Freitas ◽  
Carla Novais ◽  
Patricia Ruiz-Garbajosa ◽  
Teresa M. Coque ◽  
Luísa Peixe
Keyword(s):  
Population Structure ◽  
Enterococcus Faecium ◽  
Multilocus Sequence Typing ◽  
Multidrug Resistant ◽  
Human Infections ◽  
Sequence Types

ABSTRACT The population structure of 56 Enterococcus faecium isolates selected from a collection of enterococci from humans, animals, and the environment in Portugal (1997 to 2007) was analyzed by multilocus sequence typing. We identified 41 sequence types clustering into CC17, CC5, CC9, CC22 and CC94, all clonal lineages comprising isolates from different hosts. Our findings highlight the role of community-associated hosts as reservoirs of enterococci able to cause human infections.

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 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 More Than a Moggy; A Population Genetics Analysis of the United Kingdom’s Non-Pedigree Cats

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1619
Author(s):  
Jennifer Irving McGrath ◽  
Wengang Zhang ◽  
Regina Hollar ◽  
Alison Collings ◽  
Roger Powell ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Health Risks ◽  
Domestic Cat ◽  
Domestic Cats ◽  
Single Nucleotide ◽  
The World ◽  
Components Analysis ◽  
The Uk

The domestic cat is one of the most popular pets in the world. It is estimated that 89–92% of domestic cats in the UK are non-pedigree Domestic shorthair (DSH), Domestic longhair (DLH), or Domestic semi-longhair cats (DSLH). Despite their popularity, little is known of the UK non-pedigree cats’ population structure and breeding dynamics. Using a custom designed single nucleotide variant (SNV) array, this study investigated the population genetics of 1344 UK cats. Principal components analysis (PCA) and fastSTRUCTURE analysis verified that the UK’s DSH, DLH, and DSLH cats are random-bred, rather than admixed, mix breed, or crossbred. In contrast to pedigree cats, the linkage disequilibrium of these random-bred cats was least extensive and decayed rapidly. Homozygosity by descent (HBD) analysis showed the majority of non-pedigree cats had proportionally less of their genome in HBD segments compared to pedigree cats, and that these segments were older. Together, these findings suggest that the DSH, DLH, and DSLH cats should be considered as a population of random-bred cats rather than a crossbred or pedigree-admixed cat. Unexpectedly, 19% of random-bred cat genomes displayed a higher proportion of HBD segments associated with more recent inbreeding events. Therefore, while non-pedigree cats as a whole are genetically diverse, they are not impervious to inbreeding and its health risks.

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 Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals A Genealogical Interpretation of Linkage Disequilibrium

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 987-991 ◽  
Author(s):  
Gilean A T McVean
Keyword(s):  
Monte Carlo Simulation ◽  
Population Structure ◽  
Linkage Disequilibrium ◽  
Population Bottlenecks ◽  
Neutral Model ◽  
Demographic Models ◽  
Degree Of Association ◽  
Different Parts ◽  
Direct Correspondence ◽  
Coalescence Times

Abstract The degree of association between alleles at different loci, or linkage disequilibrium, is widely used to infer details of evolutionary processes. Here I explore how associations between alleles relate to properties of the underlying genealogy of sequences. Under the neutral, infinite-sites assumption I show that there is a direct correspondence between the covariance in coalescence times at different parts of the genome and the degree of linkage disequilibrium. These covariances can be calculated exactly under the standard neutral model and by Monte Carlo simulation under different demographic models. I show that the effects of population growth, population bottlenecks, and population structure on linkage disequilibrium can be described through their effects on the covariance in coalescence times.

scholarly journals Phenotypic and Molecular Analysis of Penicillin-Nonsusceptible Streptococcus pneumoniae Isolates in Poland

2006 ◽  
Vol 51 (1) ◽  
pp. 40-47 ◽  
Author(s):  
Ewa Sadowy ◽  
Radosław Izdebski ◽  
Anna Skoczyńska ◽  
Paweł Grzesiowski ◽  
Marek Gniadkowski ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Molecular Analysis ◽  
Gel Electrophoresis ◽  
Multilocus Sequence Typing ◽  
Susceptibility Testing ◽  
Bacterial Pathogen ◽  
Pulsed Field Gel Electrophoresis ◽  
Pulsed Field ◽  
Related Clone ◽  
Sequence Types

ABSTRACT β-Lactams are the drugs of choice for the treatment of infections caused by the important bacterial pathogen Streptococcus pneumoniae. The recent growth of resistance of this organism to penicillin observed worldwide is of the highest concern. In this study, using 887 surveillance pneumococcal isolates recovered in Poland from 1998 to 2002, we observed the increase in penicillin nonsusceptibility from 8.7% to 20.3%. All of the 109 penicillin-nonsusceptible S. pneumoniae (PNSP) isolates identified, together with 22 archival PNSP isolates from 1995 to 1997, were subsequently analyzed by susceptibility testing, serotyping, profiling of pbp genes, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Four predominant serotypes, serotypes 6B, 9V, 14, and 23F, characterized 85.5% of the isolates. MLST revealed the presence of 34 sequence types, 15 of which were novel types. Representatives of seven multiresistant international clones (Spain23F-1, Spain6B-2, Spain9V-3, Taiwan23F-15, Poland23F-16, Poland6B-20, and Sweden15A-25) or their closely related variants comprised the majority of the study isolates. The spread of Spain9V-3 and its related clone of serotype 14/ST143 has remarkably contributed to the recent increase in penicillin resistance in pneumococci in the country.

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