Comparison among three M. abscessus sub-species. The Venn diagram shows the number of genes in ea... more Comparison among three M. abscessus sub-species. The Venn diagram shows the number of genes in each MAB sub-species type strain. Number of homologous genes (more than 50Â % protein sequence identity using BBH method) are indicated at the intersections of the circles. (PDF 350Â kb)
Remarkable features of M. massiliense strain M139 genome. A Genomic exchanges at erm(41) locus. M... more Remarkable features of M. massiliense strain M139 genome. A Genomic exchanges at erm(41) locus. M. massiliense strain M139 Contig 22. Subspecies identity is indicated (blue: M. massiliense, red: M. abscessus, yellow: M. bolletii, grey: no significant subspecies attribution). Erm(41) (purple). B: non-aligned contig of M. massiliense strain M139 containing an ESX locus similar to M. marinum p-RAW conjugative plasmid (light blue: typeVII/ESX and type IV coding genes). (PDF 35Â kb)
M. abscessus sub-species-specific SNP whole genome density map. A: M. massiliense strain M139. B:... more M. abscessus sub-species-specific SNP whole genome density map. A: M. massiliense strain M139. B: M. abscessus strain 23. C: M. massiliense strain 137. Blue: M. massiliense specific SNPs; red: M. abscessus specific SNPs; yellow: M. bolletii specific SNPs. (PDF 1879 kb)
A. Mstree representing the isolates characterization based on rpoB typing. B. Rates of false iden... more A. Mstree representing the isolates characterization based on rpoB typing. B. Rates of false identification according to rpoB sequencing. Colored histograms correspond to assignments confirmed by the Bayesian algorithm (MLST based), whereas black fractions correspond to conflicting identifications (failure rate). (PDF 184Â kb)
<b>Copyright information:</b>Taken from "Genetic diversity of the obligate intra... more <b>Copyright information:</b>Taken from "Genetic diversity of the obligate intracellular bacterium by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure"http://www.biomedcentral.com/1471-2164/8/355BMC Genomics 2007;8():355-355.Published online 4 Oct 2007PMCID:PMC2092436. These curves represent the frequency distribution of pairwise differences. The dashed plot correspond to the observed data; the smoth curve corresponds to the sudden expansion model and the punctuated lines represent the upper and lower bounds of the 95% confidence interval on this model. value represents the probability that the raggedness of the simulated data set is equal to or greater than the observed data set. The major demographic extension occurred 2 mutations ago for the entire concatenated genes (70 kb). The latter translates into 0.003% sequence divergence, which suggests that the maximum population expansion occurred about 3,300 years (700 to 7,200 years) ago.
Background/Objectives: Parasites of the subgenus Leishmania (Viannia) cause varying clinical symp... more Background/Objectives: Parasites of the subgenus Leishmania (Viannia) cause varying clinical symptoms ranging from cutaneous leishmaniases (CL) with single or few lesions, disseminated CL (DL) with multiple lesions to disfiguring forms of mucocutaneous leishmaniasis (MCL). In this population genetics study, 37 strains of L. (V.) guyanensis, 63 of L. (V.) braziliensis,
Frequent bottlenecks and recent diversification result in relatively low levels of genetic divers... more Frequent bottlenecks and recent diversification result in relatively low levels of genetic diversity and population structure in modern humans, making inferences of their history difficult from classical genetic markers. To get around this drawback, pathogens, which have coevolved with humans and generally present a higher genetic diversity, can illuminate their host history. Following this idea, population structure of several microbes has been investigated by means of phylogenetic, coalescent, and Bayesian methods. However, the utility of such bugs as human tracers varied considerably according to the studied pathogen and targeted molecular markers. Indeed, the efficacy of inferring host history from a pathogen depends on certain life-history traits and genetic characteristics of the pathogen. Recent studies of three important human pathogens have been used to decipher both past and recent human migrations: Helicobacter pylori , which is nowadays the most studied pathogen in this ...
data Supplementary http://www.genome.org/cgi/content/full/gr.6122607/DC1 "Supplemental Resea... more data Supplementary http://www.genome.org/cgi/content/full/gr.6122607/DC1 "Supplemental Research Data" References http://www.genome.org/cgi/content/full/17/11/1647#References This article cites 58 articles, 32 of which can be accessed free at: service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article sign up in the box at the
Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is... more Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is critical to adapting responses against future waves of the pandemic. By combining phylogenetic data of 5,198 SARS-CoV-2 genomes with the chronology of non-pharmaceutical interventions in 57 countries, we examine how interventions and combinations thereof alter the divergence rate of viral lineages, which is directly related to the epidemic reproduction number. Home containment and education lockdown had the largest independent impacts and were predicted to reduce the reproduction number by 35% and 26%, respectively. However, we find that in contexts with a reproduction number >2, no individual intervention is sufficient to stop the epidemic and increasingly stringent intervention combinations may be required. Our phylodynamic approach can complement epidemiological models to inform public health strategies against COVID-19.
Background: The gut microbiome plays a major role in chronic diseases, of which several are chara... more Background: The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenges. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Results: Here, we propose a computational and experimental protocol for whole genome quantitative metagenomics studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatic protocol to analyse ONT sequences taxonomically and functionally and optimized pre-analytic protocols including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for t...
The gut microbiome plays a major role in chronic diseases, of which several are characterized by ... more The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenge. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Here, we propose a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatics protocol to analyze ONT sequences taxonomically and functionally and optimized preanalytic protocols, including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence a...
Mycobacterium bovis is the primary cause of bovine tuberculosis (bTB) and infects a wide range of... more Mycobacterium bovis is the primary cause of bovine tuberculosis (bTB) and infects a wide range of domestic animal and wildlife species and humans. In Germany, bTB still emerges sporadically in cattle herds, free-ranging wildlife, diverse captive animal species, and humans. In order to understand the underlying population structure and estimate the population size fluctuation through time, we analyzed 131 M. bovis strains from animals ( n = 38) and humans ( n = 93) in Germany from 1999 to 2017 by whole-genome sequencing (WGS), mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing, and spoligotyping.
Retracing microbial emergence and spread is essential to understanding the evolution and dynamics... more Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial foodborne pathogenListeria monocytogenesclonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is strongly associated with cattle and dairy products. Here we analysed 2,021Lm-CC1 isolates collected from 40 countries, since the firstLmisolation to the present day, to define its evolutionary history and population dynamics. Our results suggest thatLm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19thcentury and the rapid growth of cattle farming in the 20thcentury.Lm-CC1 then firmly established at a local level, with limited inter-country spread. This study provides an unprecedented insight intoLm-CC1 phylogeography and dynamics and can contribute to effective disease surveillance to red...
Staphylococcus capitis is a coagulase-negative staphylococcus that has been described primarily a... more Staphylococcus capitis is a coagulase-negative staphylococcus that has been described primarily as causing bloodstream infections in neonatal intensive care units (NICUs), but has also recently been described in prosthetic joint infections (PJIs). The multidrug-resistant S. capitis subsp. urealyticus clone NRCS-A, comprising three sublineages, is prevalent in NICUs across the world, but its impact on other patient groups such as those suffering from PJIs or among adults planned for arthroplasty is unknown. Genome sequencing and subsequent analysis were performed on a Swedish collection of PJI isolates (n = 21), nasal commensals from patients planned to undergo arthroplasty (n = 20), NICU blood isolates (n = 9), operating theatre air isolates (n = 4), and reference strains (n = 2), in conjunction with an international strain collection (n = 248). The NRCS-A Outbreak sublineage containing the composite type V SCCmec-SCCcad/ars/cop element was present in PJIs across three Swedish hospi...
Comparison among three M. abscessus sub-species. The Venn diagram shows the number of genes in ea... more Comparison among three M. abscessus sub-species. The Venn diagram shows the number of genes in each MAB sub-species type strain. Number of homologous genes (more than 50Â % protein sequence identity using BBH method) are indicated at the intersections of the circles. (PDF 350Â kb)
Remarkable features of M. massiliense strain M139 genome. A Genomic exchanges at erm(41) locus. M... more Remarkable features of M. massiliense strain M139 genome. A Genomic exchanges at erm(41) locus. M. massiliense strain M139 Contig 22. Subspecies identity is indicated (blue: M. massiliense, red: M. abscessus, yellow: M. bolletii, grey: no significant subspecies attribution). Erm(41) (purple). B: non-aligned contig of M. massiliense strain M139 containing an ESX locus similar to M. marinum p-RAW conjugative plasmid (light blue: typeVII/ESX and type IV coding genes). (PDF 35Â kb)
M. abscessus sub-species-specific SNP whole genome density map. A: M. massiliense strain M139. B:... more M. abscessus sub-species-specific SNP whole genome density map. A: M. massiliense strain M139. B: M. abscessus strain 23. C: M. massiliense strain 137. Blue: M. massiliense specific SNPs; red: M. abscessus specific SNPs; yellow: M. bolletii specific SNPs. (PDF 1879 kb)
A. Mstree representing the isolates characterization based on rpoB typing. B. Rates of false iden... more A. Mstree representing the isolates characterization based on rpoB typing. B. Rates of false identification according to rpoB sequencing. Colored histograms correspond to assignments confirmed by the Bayesian algorithm (MLST based), whereas black fractions correspond to conflicting identifications (failure rate). (PDF 184Â kb)
<b>Copyright information:</b>Taken from "Genetic diversity of the obligate intra... more <b>Copyright information:</b>Taken from "Genetic diversity of the obligate intracellular bacterium by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure"http://www.biomedcentral.com/1471-2164/8/355BMC Genomics 2007;8():355-355.Published online 4 Oct 2007PMCID:PMC2092436. These curves represent the frequency distribution of pairwise differences. The dashed plot correspond to the observed data; the smoth curve corresponds to the sudden expansion model and the punctuated lines represent the upper and lower bounds of the 95% confidence interval on this model. value represents the probability that the raggedness of the simulated data set is equal to or greater than the observed data set. The major demographic extension occurred 2 mutations ago for the entire concatenated genes (70 kb). The latter translates into 0.003% sequence divergence, which suggests that the maximum population expansion occurred about 3,300 years (700 to 7,200 years) ago.
Background/Objectives: Parasites of the subgenus Leishmania (Viannia) cause varying clinical symp... more Background/Objectives: Parasites of the subgenus Leishmania (Viannia) cause varying clinical symptoms ranging from cutaneous leishmaniases (CL) with single or few lesions, disseminated CL (DL) with multiple lesions to disfiguring forms of mucocutaneous leishmaniasis (MCL). In this population genetics study, 37 strains of L. (V.) guyanensis, 63 of L. (V.) braziliensis,
Frequent bottlenecks and recent diversification result in relatively low levels of genetic divers... more Frequent bottlenecks and recent diversification result in relatively low levels of genetic diversity and population structure in modern humans, making inferences of their history difficult from classical genetic markers. To get around this drawback, pathogens, which have coevolved with humans and generally present a higher genetic diversity, can illuminate their host history. Following this idea, population structure of several microbes has been investigated by means of phylogenetic, coalescent, and Bayesian methods. However, the utility of such bugs as human tracers varied considerably according to the studied pathogen and targeted molecular markers. Indeed, the efficacy of inferring host history from a pathogen depends on certain life-history traits and genetic characteristics of the pathogen. Recent studies of three important human pathogens have been used to decipher both past and recent human migrations: Helicobacter pylori , which is nowadays the most studied pathogen in this ...
data Supplementary http://www.genome.org/cgi/content/full/gr.6122607/DC1 "Supplemental Resea... more data Supplementary http://www.genome.org/cgi/content/full/gr.6122607/DC1 "Supplemental Research Data" References http://www.genome.org/cgi/content/full/17/11/1647#References This article cites 58 articles, 32 of which can be accessed free at: service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article sign up in the box at the
Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is... more Quantifying the effectiveness of large-scale non-pharmaceutical interventions against COVID-19 is critical to adapting responses against future waves of the pandemic. By combining phylogenetic data of 5,198 SARS-CoV-2 genomes with the chronology of non-pharmaceutical interventions in 57 countries, we examine how interventions and combinations thereof alter the divergence rate of viral lineages, which is directly related to the epidemic reproduction number. Home containment and education lockdown had the largest independent impacts and were predicted to reduce the reproduction number by 35% and 26%, respectively. However, we find that in contexts with a reproduction number >2, no individual intervention is sufficient to stop the epidemic and increasingly stringent intervention combinations may be required. Our phylodynamic approach can complement epidemiological models to inform public health strategies against COVID-19.
Background: The gut microbiome plays a major role in chronic diseases, of which several are chara... more Background: The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenges. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Results: Here, we propose a computational and experimental protocol for whole genome quantitative metagenomics studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatic protocol to analyse ONT sequences taxonomically and functionally and optimized pre-analytic protocols including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for t...
The gut microbiome plays a major role in chronic diseases, of which several are characterized by ... more The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these communities. However, translating these discoveries into clinical applications remains a challenge. To facilitate routine implementation of microbiome profiling in clinical settings, portable, real-time, and low-cost sequencing technologies are needed. Here, we propose a computational and experimental protocol for whole-genome semi-quantitative metagenomic studies of human gut microbiome with Oxford Nanopore sequencing technology (ONT) that could be applied to other microbial ecosystems. We developed a bioinformatics protocol to analyze ONT sequences taxonomically and functionally and optimized preanalytic protocols, including stool collection and DNA extraction methods to maximize read length. This is a critical parameter for the sequence a...
Mycobacterium bovis is the primary cause of bovine tuberculosis (bTB) and infects a wide range of... more Mycobacterium bovis is the primary cause of bovine tuberculosis (bTB) and infects a wide range of domestic animal and wildlife species and humans. In Germany, bTB still emerges sporadically in cattle herds, free-ranging wildlife, diverse captive animal species, and humans. In order to understand the underlying population structure and estimate the population size fluctuation through time, we analyzed 131 M. bovis strains from animals ( n = 38) and humans ( n = 93) in Germany from 1999 to 2017 by whole-genome sequencing (WGS), mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing, and spoligotyping.
Retracing microbial emergence and spread is essential to understanding the evolution and dynamics... more Retracing microbial emergence and spread is essential to understanding the evolution and dynamics of pathogens. The bacterial foodborne pathogenListeria monocytogenesclonal complex 1 (Lm-CC1) is the most prevalent clonal group associated with listeriosis, and is strongly associated with cattle and dairy products. Here we analysed 2,021Lm-CC1 isolates collected from 40 countries, since the firstLmisolation to the present day, to define its evolutionary history and population dynamics. Our results suggest thatLm-CC1 spread worldwide from North America following the Industrial Revolution through two waves of expansion, coinciding with the transatlantic livestock trade in the second half of the 19thcentury and the rapid growth of cattle farming in the 20thcentury.Lm-CC1 then firmly established at a local level, with limited inter-country spread. This study provides an unprecedented insight intoLm-CC1 phylogeography and dynamics and can contribute to effective disease surveillance to red...
Staphylococcus capitis is a coagulase-negative staphylococcus that has been described primarily a... more Staphylococcus capitis is a coagulase-negative staphylococcus that has been described primarily as causing bloodstream infections in neonatal intensive care units (NICUs), but has also recently been described in prosthetic joint infections (PJIs). The multidrug-resistant S. capitis subsp. urealyticus clone NRCS-A, comprising three sublineages, is prevalent in NICUs across the world, but its impact on other patient groups such as those suffering from PJIs or among adults planned for arthroplasty is unknown. Genome sequencing and subsequent analysis were performed on a Swedish collection of PJI isolates (n = 21), nasal commensals from patients planned to undergo arthroplasty (n = 20), NICU blood isolates (n = 9), operating theatre air isolates (n = 4), and reference strains (n = 2), in conjunction with an international strain collection (n = 248). The NRCS-A Outbreak sublineage containing the composite type V SCCmec-SCCcad/ars/cop element was present in PJIs across three Swedish hospi...
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