scholarly journals Identification of Hidden Population Structure in Time-Scaled Phylogenies

2020 ◽  
Vol 69 (5) ◽  
pp. 884-896 ◽  
Author(s):  
Erik M Volz ◽  
Wiuf Carsten ◽  
Yonatan H Grad ◽  
Simon D W Frost ◽  
Ann M Dennis ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Phylogenetic Trees ◽  
Statistical Tests ◽  
Host Population ◽  
Rapid Expansion ◽  
Outbreak Detection ◽  
Hidden Population ◽  
New Methods ◽  
Fitness Advantage

Abstract Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealized genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance. [Antimicrobial resistance; coalescent; HIV; population structure.]

scholarly journals Identification of hidden population structure in time-scaled phylogenies

2019 ◽  
Author(s):  
Erik M. Volz ◽  
Carsten Wiuf ◽  
Yonatan H. Grad ◽  
Simon D.W. Frost ◽  
Ann M. Dennis ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Phylogenetic Trees ◽  
Statistical Tests ◽  
Host Population ◽  
Rapid Expansion ◽  
Outbreak Detection ◽  
Hidden Population ◽  
New Methods ◽  
Fitness Advantage

AbstractPopulation structure influences genealogical patterns, however data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission patterns and detect outbreaks. Discrepancies between observed and idealised genealogies, such as those generated by the coalescent process, can be quantified, and where significant differences occur, may reveal the action of natural selection, host population structure, or other demographic and epidemiological heterogeneities. We have developed a fast non-parametric statistical test for detection of cryptic population structure in time-scaled phylogenetic trees. The test is based on contrasting estimated phylogenies with the theoretically expected phylodynamic ordering of common ancestors in two clades within a coalescent framework. These statistical tests have also motivated the development of algorithms which can be used to quickly screen a phylogenetic tree for clades which are likely to share a distinct demographic or epidemiological history. Epidemiological applications include identification of outbreaks in vulnerable host populations or rapid expansion of genotypes with a fitness advantage. To demonstrate the utility of these methods for outbreak detection, we applied the new methods to large phylogenies reconstructed from thousands of HIV-1 partial pol sequences. This revealed the presence of clades which had grown rapidly in the recent past, and was significantly concentrated in young men, suggesting recent and rapid transmission in that group. Furthermore, to demonstrate the utility of these methods for the study of antimicrobial resistance, we applied the new methods to a large phylogeny reconstructed from whole genome Neisseria gonorrhoeae sequences. We find that population structure detected using these methods closely overlaps with the appearance and expansion of mutations conferring antimicrobial resistance.

scholarly journals Genetic diversity and population structure of Rhipicephalus sanguineus sensu lato across different regions of Colombia

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Luisa Páez-Triana ◽  
Marina Muñoz ◽  
Giovanny Herrera ◽  
Darwin A. Moreno-Pérez ◽  
Gabriel A. Tafur-Gómez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Statistical Tests ◽  
Population Expansion ◽  
Rhipicephalus Sanguineus ◽  
Tick Population ◽  
12S Rdna ◽  
Haplotype Networks

Abstract Background There has been a long-standing debate over the taxonomic status of Rhipicephalus sanguineus sensu lato. Different studies worldwide have reported the occurrence of different well-defined lineages, in addition to Rhipicephalus sanguineus sensu stricto. To date, there are very few studies examining the diverse aspects of this tick in Colombia. We assessed the population structure and genetic diversity of R. sanguineus s.l. in eight departmental regions across Colombia. Methods A total of 170 ticks were collected from dogs in different departments of Colombia. All specimens were morphologically compatible with R. sanguineus s.l. and subjected to genetic analysis. DNA sequences were obtained for the 12S rDNA, cytochrome oxidase I (COI) and internal transcribed spacer 2 (ITS2) markers. A concatenated set of all mitochondrial markers was also constructed. Next, maximum likelihood phylogenetic trees were constructed using the sequences generated herein and sequences available in GenBank. Finally, we assessed different summary statistics and analysed population structure and divergence with Fst and Dxy and demographic changes with Tajima's D and Fu and Li’s statistical tests. Results Analysis of the 12S rDNA and COI revealed that all R. sanguineus s.l. specimens collected across different regions of Colombia clustered within the tropical lineage. Micro-geographical analyses showed that the tick population from Amazonas formed a distinct cluster separated from the other sequences, with moderate Fst and Dxy values. However, no signs of a robust population structure were found within the country. The results of Fu’s FS tests, together with the haplotype networks and diversity values, signal a possible population expansion of this tick species in Colombia. Conclusions Evidence provided herein supports the tropical lineage as the main circulating lineage in Colombia, exhibiting a general lack of genetic structure except for the Amazonas region. Graphical Abstract

scholarly journals Employing phylogenetic tree shape statistics to resolve the underlying host population structure

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hassan W. Kayondo ◽  
Alfred Ssekagiri ◽  
Grace Nabakooza ◽  
Nicholas Bbosa ◽  
Deogratius Ssemwanga ◽  
...  
Keyword(s):  
Population Structure ◽  
Phylogenetic Trees ◽  
Host Population ◽  
Structured Populations ◽  
Basic Reproductive Number ◽  
Support Vector ◽  
Model Parameters ◽  
Classification Procedure ◽  
Machine Learning Classification ◽  
Structured Population

Abstract Background Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal the population structure underlying an epidemic. Determining whether a population is structured or not is useful in informing the type of phylogenetic methods to be used in a given study. We employ tree statistics derived from phylogenetic trees and machine learning classification techniques to reveal an underlying population structure. Results In this paper, we simulate phylogenetic trees from both structured and non-structured host populations. We compute eight statistics for the simulated trees, which are: the number of cherries; Sackin, Colless and total cophenetic indices; ladder length; maximum depth; maximum width, and width-to-depth ratio. Based on the estimated tree statistics, we classify the simulated trees as from either a non-structured or a structured population using the decision tree (DT), K-nearest neighbor (KNN) and support vector machine (SVM). We incorporate the basic reproductive number ($$R_0$$ R 0 ) in our tree simulation procedure. Sensitivity analysis is done to investigate whether the classifiers are robust to different choice of model parameters and to size of trees. Cross-validated results for area under the curve (AUC) for receiver operating characteristic (ROC) curves yield mean values of over 0.9 for most of the classification models. Conclusions Our classification procedure distinguishes well between trees from structured and non-structured populations using the classifiers, the two-sample Kolmogorov-Smirnov, Cucconi and Podgor-Gastwirth tests and the box plots. SVM models were more robust to changes in model parameters and tree size compared to KNN and DT classifiers. Our classification procedure was applied to real -world data and the structured population was revealed with high accuracy of $$92.3\%$$ 92.3 % using SVM-polynomial classifier.

scholarly journals Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

2013 ◽  
Vol 368 (1614) ◽  
pp. 20120198 ◽  
Author(s):  
Tanja Stadler ◽  
Sebastian Bonhoeffer
Keyword(s):  
Population Structure ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Intravenous Drug User ◽  
Host Population ◽  
Major Influence ◽  
Parameter Estimates ◽  
Sexually Transmitted ◽  
Sex With Men ◽  
The Impact

Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states).

The population structure, antimicrobial resistance, and pathogenicity of Streptococcus suis cps31

2021 ◽  
pp. 109149
Author(s):  
Xiaoming Wang ◽  
Junjie Sun ◽  
Chen Bian ◽  
Jianping Wang ◽  
Zijing Liang ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Streptococcus Suis

scholarly journals Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

2019 ◽  
Vol 29 (1) ◽  
pp. 149-157.e3 ◽  
Author(s):  
Thomaz Pinotti ◽  
Anders Bergström ◽  
Maria Geppert ◽  
Matt Bawn ◽  
Dominique Ohasi ◽  
...  
Keyword(s):  
Population Structure ◽  
Native American ◽  
Y Chromosome ◽  
Rapid Expansion

scholarly journals Geographic Information System (GIS) and Its Application in Urban Planning and Environment

2014 ◽  
Vol 3 (6) ◽  
pp. 78-85
Author(s):  
Masood Safari Ali Akbari
Keyword(s):  
Urban Planning ◽  
Environmental Issues ◽  
Point Of View ◽  
Land Evaluation ◽  
Rapid Expansion ◽  
Land Uses ◽  
Urban Green Spaces ◽  
New Methods ◽  
Clear Point ◽  
Data Layers

Using satellite data and GIS, the location of various urban land uses, including new methods for locating is quick. This study, based on a method of analysis - descriptive, and benefit from the resources in this area to assess the effectiveness of GIS in urban planning and environment, is discussed, and attempted to make a clear point of view, this can provide. Our results indicate that, nowadays, several researchers, from capabilities of GIS are used for localization. Because GIS is able to analyze large amounts of data layers is. Use of GIS in urban planning, with the rapid expansion of cities and increased levels of SAM binding information that must be processed for urban management, is clear. Abnormal location for the development of suitable sites for the establishment of urban green spaces, places for waste disposal and land evaluation, and its features and many other environmental issues, it can be pointed out.

scholarly journals Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence

2021 ◽  
Author(s):  
Emeli Månsson ◽  
Thor Bech Johannesen ◽  
Åsa Nilsdotter-Augustinsson ◽  
Bo Söderquist ◽  
Marc Stegger
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Staphylococcus Epidermidis ◽  
Type Species ◽  
Genetic Traits ◽  
Content Type ◽  
Link Type ◽  
Joint Infections ◽  
Prosthetic Joint ◽  
Prosthetic Joint Infections

There is increased awareness of the worldwide spread of specific epidemic multidrug-resistant (MDR) lineages of the human commensal Staphylococcus epidermidis . Here, using bioinformatic analyses accounting for population structure, we determined genomic traits (genes, SNPs and k-mers) that distinguish S. epidermidis causing prosthetic-joint infections (PJIs) from commensal isolates from nares, by analysing whole-genome sequencing data from S. epidermidis from PJIs prospectively collected over 10 years in Sweden, and contemporary S. epidermidis from the nares of patients scheduled for arthroplasty surgery. Previously suggested virulence determinants and the presence of genes and mutations linked to antimicrobial resistance (AMR) were also investigated. Publicly available S. epidermidis sequences were used for international extrapolation and validation of findings. Our data show that S. epidermidis causing PJIs differed from nasal isolates not by virulence but by traits associated with resistance to compounds used in prevention of PJIs: β-lactams, aminoglycosides and chlorhexidine. Almost a quarter of the PJI isolates did not belong to any of the previously described major nosocomial lineages, but the AMR-related traits were also over-represented in these isolates, as well as in international S. epidermidis isolates originating from PJIs. Genes previously associated with virulence in S. epidermidis were over-represented in individual lineages, but failed to reach statistical significance when adjusted for population structure. Our findings suggest that the current strategies for prevention of PJIs select for nosocomial MDR S. epidermidis lineages that have arisen from horizontal gene transfer of AMR-related traits into multiple genetic backgrounds.

scholarly journals Mass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx

2020 ◽  
Author(s):  
Rebecca A. Gladstone ◽  
Ebrima Bojang ◽  
John Hart ◽  
Emma M Harding-Esch ◽  
David Mabey ◽  
...  
Keyword(s):  
Population Structure ◽  
Streptococcus Pneumoniae ◽  
Antimicrobial Resistance ◽  
Drug Administration ◽  
Mass Drug Administration ◽  
Macrolide Resistance ◽  
P Value ◽  
Cross Sectional ◽  
The Third ◽  
Before And After

ABSTRACTBackgroundMass drug administration (MDA) with azithromycin for trachoma elimination reduces nasopharyngeal carriage of Streptococcus pneumoniae in the short term. We evaluated S. pneumoniae carried in the nasopharynx before and after a round of azithromycin MDA to determine whether MDA was associated with changes in pneumococcal population structure.MethodsWe analysed 514 pneumococcal isolates cultured from nasopharyngeal samples collected in Gambian villages that received MDA for trachoma elimination. The samples were collected during three cross-sectional surveys conducted before the third round of MDA (CSS-1) and at one (CSS-2) and six (CSS-3) months after MDA. Whole genome sequencing was conducted on randomly selected isolates. Bayesian Analysis of Population Structure (BAPS) was used to cluster related isolates by capturing variation in the core genome. Serotype and multi-locus sequence type were inferred from the genotype. The Antimicrobial Resistance Identification by Assembly (ARIBA) tool was used to identify macrolide resistance genes.ResultsTwenty-seven BAPS clusters were assigned. These consisted of 81 sequence types (STs), 15 of which were novel additions to pubMLST. Two BAPS clusters, BAPS20 (p-value<=0.016) and BAPS22 (p-value<=0.032) showed an increase in frequency at CSS-3 not associated with antimicrobial resistance. Macrolide resistance within BASP17 increased after treatment (p<0.05) and was carried on a mobile transposable element that also conferred resistance to tetracycline.ConclusionsLimited changes in pneumococcal population structure were observed after the third round of MDA suggesting treatment had little effect on the circulating lineages. An increase in macrolide resistance within one BAPS highlights the need for antimicrobial resistance surveillance in treated villages.

scholarly journals Differences in Neisseria gonorrhoeae population structure and antimicrobial resistance pattern between men who have sex with men and heterosexuals

2016 ◽  
Vol 145 (2) ◽  
pp. 379-385 ◽  
Author(s):  
J. SERRA-PLADEVALL ◽  
M. J. BARBERÁ ◽  
A. E. CALLARISA ◽  
R. BARTOLOMÉ-COMAS ◽  
A. ANDREU
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Antimicrobial Susceptibility ◽  
Sexual Practices ◽  
Resistance Pattern ◽  
High Prevalence ◽  
Sex With Men ◽  
Resistance Rates ◽  
Sequence Types

SUMMARYThis study compared the antimicrobial susceptibility and genotypes of strains of Neisseria gonorrhoeae isolated from men who have sex with men (MSM) and from heterosexuals. One hundred and eleven strains were characterized from 107 patients, comprising 57 strains from 54 heterosexuals and 54 strains from 53 MSM. Antimicrobial resistance rates were higher in strains from heterosexual patients, with resistance to cefixime (P = 0·0159) and ciprofloxacin (P = 0·002) being significantly higher. Typing by N. gonorrhoeae multi-antigen sequence typing (NG-MAST) showed that the most prevalent sequence types (ST) and genogroups (G) respectively were ST2400, ST2992, and ST5793, and G1407, G2992, and G2400. A statistically significant association was observed for MSM and genogroups G2400 (P = 0·0005) and G2992 (P = 0·0488), and G1407 with heterosexuals (P = 0·0002). We conclude that in our region distinct populations of gonococci are circulating among subjects with different sexual practices, with their corresponding transmission patterns. Furthermore, the high prevalence of genotype G2400 in MSM, has not to our knowledge been previously described.

Sign in / Sign up

Export Citation Format

Share Document