Clonal Population Structure Research Articles

Clonal evolution of Candida albicans, Candida glabrata and Candida dubliniensis at oral niche level in health and disease

ABSTRACT Background: Candida species have long been recognised as aetiological agents of opportunistic infections of the oral mucosa, and more recently, as players of polymicrobial interactions driving caries, periodontitis and oral carcinogenesis. Methods: We studied the clonal structure of Candida spp. at oral niche resolution in patients (n = 20) with a range of oral health profiles over 22 months. Colonies from oral micro-environments were examined with multilocus sequencing typing. Results: Candida spp. identified were C. albicans, C. glabrata and C. dubliniensis. Increased propensity for micro-variations giving rise to multiple diploid strain types (DST), as a result of loss of heterozygosity, was observed among C. albicans clade 1 isolates compared to other clades. Micro-variations among isolates were also observed in C. dubliniensis contra to expectations of stable population structures for this species. Multiple sequence types were retrieved from patients without clinical evidence of oral candidosis, while single sequence types were isolated from oral candidosis patients. Conclusion: This is the first study to describe the clonal population structure, persistence and stability of Candida spp. at oral niche level. Future research investigating links between Candida spp. clonality and oral disease should recognise the propensity to micro-variations amongst oral niches in C. albicans and C. dubliniensis identified here.

Molecular basis of drug resistance to bedaquiline and delamanid in Mycobacterium tuberculosis

Aims & objectives: Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), is amongst the most successful pathogens worldwide with a yearly incidence of approximately 10.0 million new cases and a death toll that is well above million people. Even though this is an ancient pathogen affecting humankind since its dawn, as a bacterial species it displays a very low mutation rate and shows a strictly clonal population structure owing to the lack of lateral gene transfer. This latter aspect imposes a limitation on the pathways by which drug resistance can emerge in this species: emergence of resistance must occur through de novo mutations affecting genes that are associated with the action mechanism of a given drug. Methods: The mutations and mechanisms leading to resistance to the drugs that are part of the frontline armamentarium have been extensively studied and the extent of its spectrum is relatively well understood. However, newer drugs such as bedaquiline and delamanid have been introduced to TB treatment in a very recent past. These were the first two drugs to become available in approximately 40 years and, as such, the toxicity and side effects associated with these drugs still pose several challenges. Results: Delamanid, a nitroimidazooxazole, is a pro-drug that requires metabolization to an intermediate metabolite that inhibits the synthesis of methoxy-mycolic acids and keto-mycolic acids. This activation step is mediated by the deazaflavin(F420)-dependent nitroreductase (Ddn) and it is the loss a function of this enzyme that constitutes the main mechanism of resistance acquisition to delamanid. Other gene products susceptible to mutagenesis and part of the F420 metabolism have been implicated in delamanid resistance (fbiABC and fgd1). Conclusions: Several genomic variants occurring in these genes have been reported yielding different resistant levels however, owing to the restricted usage of these drugs, many of these are reported from in vitro studies. The scenario portrayed by clinical strains is somewhat different and the mutational spectrum associated with resistance more limited. Besides covering the mechanisms of action and drug resistance this talk will discern between clinically relevant mutations vs those generated in vitro and the phylogenetic distribution of different polymorphisms in genes associated with resistance.

PyClone-VI: scalable inference of clonal population structures using whole genome data

BackgroundAt diagnosis tumours are typically composed of a mixture of genomically distinct malignant cell populations. Bulk sequencing of tumour samples coupled with computational deconvolution can be used to identify these populations and study cancer evolution. Existing computational methods for populations deconvolution are slow and/or potentially inaccurate when applied to large datasets generated by whole genome sequencing data.ResultsWe describe PyClone-VI, a computationally efficient Bayesian statistical method for inferring the clonal population structure of cancers. We demonstrate the utility of the method by analyzing data from 1717 patients from PCAWG study and 100 patients from the TRACERx study.ConclusionsOur proposed method is 10–100× times faster than existing methods, while providing results which are as accurate. Software implementing our method is freely available https://github.com/Roth-Lab/pyclone-vi.

Molecular characterization of Neisseria meningitidis isolates recovered from patients with invasive meningococcal disease in Colombia from 2013 to 2016.

BackgroundNeisseria meningitidis is a significant cause of morbidity and mortality worldwide. Meningococcal isolates have a highly dynamic population structure and can be phenotypically and genetically differentiated into serogroups and clonal complexes. The aim of this study was to describe the phenotypic and genotypic characteristics of invasive isolates recovered in Colombia from 2013 to 2016.MethodologyA total of 193 invasive isolates were analyzed. Phenotypic and genotypic characteristics were determined by serotyping, antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing.ResultsBased on the results, meningococcal serogroups C, B and Y were responsible for 47.9%, 41.7%, and 9.4% of cases, respectively, and the distribution of serogroups B and C changed over time. Fifteen clonal groups and 14 clonal complexes (cc) were identified by PFGE and genome sequencing. The main clonal group included serogroup B isolates with sequence type (ST)-9493 and its four single-locus variants, which has only been identified in Colombian isolates. The clonal population structure demonstrates that the isolates in this study mainly belong to four clonal complexes: ST-11 cc, ST-32 cc, ST-35 cc and ST-41/44 cc. Thirty-eight penA alleles were identified, but no correlation between MICs and specific sequences was observed.ConclusionThis study shows that most meningococcal isolates recovered from patients with invasive meningococcal disease in Colombia are strains associated with distinct globally disseminated hyperinvasive clones.

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

BackgroundDickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.ResultsHigh quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.ConclusionsThe almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

Multilocus Sequence Typing of Enterocytozoon bieneusi Isolates From Various Mammal and Bird Species and Assessment of Population Structure and Substructure.

Enterocytozoon bieneusi is one of the most common intestinal pathogens in humans and animals. E. bieneusi has been confirmed to be complex microsporidian species. Approximately 500 ITS genotypes of E. bieneusi have been defined. With the establishment and application of multilocus sequencing typing and population genetic tools in E. bieneusi, the studies on these aspects have been carried out worldwide, but little information is available. To understand genetic variation of mini-/micro-satellites and the population structure and substructure of E. bieneusi in northeastern China, 305 E. bieneusi DNA specimens composed of 28 ITS genotypes were from 13 mammal species and five bird species in the investigated areas. They were characterized by nested-PCR amplification and sequencing at four mini-/micro-satellite loci (MS1, MS3, MS4, and MS7). At the MS1, MS3, MS4, and MS7 loci, 153 (50.16%), 131 (42.95%), 133 (43.61%), and 128 (41.97%) DNA specimens were amplified and sequenced successfully with 44, 17, 26, and 24 genotypes being identified, respectively. Multilocus genotypes (MLGs) showed a higher genetic diversity than ITS genotypes. 48 MLGs were produced out of 90 ITS-positive DNA specimens based on concatenated sequences of all the five genetic loci including ITS. Linkage disequilibrium (LD) and limited genetic recombination were observed by measuring LD using both multilocus sequences and allelic profile data, indicating an overall clonal population structure of E. bieneusi in the investigated areas. These data will aid in the longitudinal tracking of the attribution of source of infection/contamination and in elucidating transmission dynamics, and will provide valuable information for making efficient control strategies to intervene with and prevent occurrence of microsporidiosis caused by E. bieneusi among animals and transmission of E. bieneusi from animals to humans in the investigated areas. Phylogenetic and network analyses identified three different subgroups, revealing the presence of host-shaped segregation and the absence of geographical segregation in E. bieneusi population. Meanwhile, the MLGs from zoonotic ITS genotypes were observed to be basically separated from the MLGs from host-adapted ones. Assessment of substructure will have a reference effect on understanding of zoonotic or interspecies transmission of E. bieneusi and evolution direction from zoonotic genotypes to host-adapted genotypes.

Multilocus sequence typing of Enterocytozoon bieneusi in crab-eating macaques (Macaca fascicularis) in Hainan, China

BackgroundEnterocytozoon bieneusi is one of common intestinal pathogens in humans and animals including non-human primates (NHPs). Many zoonotic pathogens including E. bieneusi have been found in these animals. However, there are few studies on the population structure of E. bieneusi in NHPs. To infer the gene diversity and population genetics of E. bieneusi, we selected 88 E. bieneusi-positive samples from crab-eating macaques for multilocus characterizations in this study.MethodsThe E. bieneusi isolates examined belonged to three common genotypes with different host ranges by sequence analysis of the ribosomal internal transcribed spacer (ITS): Type IV (n = 44), Macaque3 (n = 24) and Peru8 (n = 20). They were further characterized by sequence analysis at four microsatellite and minisatellite loci (MS1, MS3, MS4 and MS7). DnaSP, Arlequin and LIAN were used to analyze the sequence data together with those from the ITS locus to infer the population genetics. Subpopulation structure was inferred using phylogenetic and STRUCTURE analyses.ResultsSeventy-two (81.8%), 71 (80.7%), 76 (86.4%) and 79 (89.8%) samples were amplified and sequenced successfully at the MS1, MS3, MS4 and MS7 loci, respectively, with 53 having sequence data at all five MLST loci including ITS. Altogether, 33 multilocus genotypes (MLGs) were produced based on concatenated sequences from the 53 samples. In phylogenetic analyses of sequences and allelic data, four major subpopulations (SPs) were observed with different ITS genotypes in each of them: Type IV and Peru8 in SP1 and SP2; Type IV, Macaque3 and Peru8 in SP3; and Type IV and Macaque3 in SP4. SP3 and SP4 were phylogenetically related and might be NHP-specific based on the fact that Macaque3 is mostly found in NHPs. A strong linkage disequilibrium (LD) was observed among the multilocus sequences and allelic data.ConclusionsThe significant LD in the multilocus sequence analysis indicated the presence of an overall clonal population structure of E. bieneusi in crab-eating macaques. The inconsistent segregation of MLGs among ITS genotypes suggested some occurrence of genetic recombination. These observations should improve our understanding of the population genetics of E. bieneusi in NHPs.

Adaptability of the structure and biomass of Arundinaria spanostachya clonal populations grazing by wild giant pandas.

To understand the defense mechanism of Arundinaria spanostachya clonal populations in response to grazing by giant pandas, dynamic variations in A. spanostachya clonal population structure and biomass allocation in a wild giant panda habitat at the Liziping Nature Reserve were evaluated, as well as whether the clonal populations would be continuously used by the wild giant pandas. The population density of each age-class in the grazed and control plots after grazing (2014a and 2015a) was similar to that before grazing (2013a). The effects of grazing on the size-class and height-class structures were relatively lower. Before and after grazing, the perennial individuals showed the highest total biomass, followed by the biennial and annual individuals, and the maximum dry matter content in each module was found in the culm, followed by the branch and leaf. The dry matter content of A. spanostachya individuals increased as the age class increased, whereas the total water content decreased. The maximum water content allocation in the modules was observed in the culm, and no significant differences were found between the shoot and leaf. Thus, foraging by the wild giant pandas had no impact on the size-class and height-class structures and biomass allocation of A. spanostachya clonal populations, and the clonal populations have established an adaptive mechanism against grazing by giant pandas. After grazing, the A. spanostachya clonal populations showed greater self-adjustment ability to restore the status to that before grazing and, thus, continuously supply food for the giant pandas. Further management intervention of A. spanostachya clonal populations after the foraging of wild giant pandas is not needed, which has implications for understanding the impact of co-evolutionary mechanisms between giant panda and its staple bamboo species.

Molecular Correlates of Central Nervous System Relapse in Diffuse Large B-Cell Lymphoma

Introduction: Central nervous system (CNS) relapse is a rare phenomenon in diffuse large B-cell lymphoma (DLBCL), occurring in less than 5% of all patients, but is associated with disproportionate morbidity and mortality. Indeed, the median survival of patients diagnosed with CNS relapse is as low as 2-4 months. Individual risk factors for CNS relapse are well established, and include clinical parameters such as stage, number/type of extranodal sites and elevated lactate dehydrogenase. These and other clinical risk factors have been integrated into a risk score that is reproducible and easy to calculate (CNS International Prognostic Index). Moreover, molecular attributes such as double-hit translocation status, MYC/BCL2 dual protein expression and the activated B-cell-like subtype have been associated with a higher risk of CNS relapse. However, while experts recommend prophylactic interventions for high-risk patients, the major shortcoming of available risk tools is their limited sensitivity. Herein, we evaluated whether gene expression and/or mutational profiles can identify those patients that will ultimately experience CNS relapse, and whether intratumoral heterogeneity impedes accurate prognostication. Methods: We accrued diagnostic FFPET samples from 230 newly diagnosed DLBCL patients, selected to fall into 3 clinical groups: 1) cases with CNS relapse/CNS involvement at diagnosis (n=58); 2) cases with systemic relapse but without CNS relapse (n=64) and 3) cases without any relapse (n=108). These 230 samples were subjected to microarray-based gene expression profiling and differential gene expression analysis. Pathway analysis was performed using Gene Set Enrichment Analysis on ranked gene lists. We assembled a partially overlapping dataset with mutation data of 45 genes in 213 diagnostic samples (n=65 with CNS relapse, 62 with systemic relapse and 86 without relapse). Lastly, we performed exome sequencing in 5 pairs (peripheral and CNS parenchymal tumors) of patients with CNS relapse or CNS involvement at diagnosis, and reconstructed clonal phylogenies using PyClone. Results: Focusing on gene expression data at first, we did not observe significant differential expression between CNS relapse and non-relapse cases at the individual gene level. This was in contrast to the comparison between systemic relapse vs. non-relapse cases where 368 genes were differentially expressed (adjusted P<0.05). In terms of pathway analysis, minimal gene set enrichment was seen in CNS relapse cases, whereas functional annotations such as translation, ribosome biogenesis and MYC targets were significantly enriched in cases with systemic relapse. In keeping with these observations, the percentage of cases that were positive for the recently published double hit signature was highest in cases with systemic relapse (64% vs. 39% in CNS relapse cases and 27% in cases without relapse, P=0.012). However, CNS relapsing cases were defined by down-regulation of numerous immune signatures (e.g. interferon and multiple T cell signatures), suggesting that an intact immune response may have a protective effect on CNS relapse. Considering mutation data, we found that TP53 and SGK were most commonly mutated in systemic relapse cases, while TNFRSF14 and KTM2D were most commonly mutated in non-relapse cases (all adjusted P<0.05). The only gene mutation with a borderline significant trend for enrichment in CNS relapse cases was MYD88 (adjusted P=0.05). We then performed exome sequencing of 5 tumor pairs. A subset of high-confidence somatic variants and tumor purity were used as input for PyClone to infer clonal population structures. In all pairs, we documented the existence of common ancestral mutations, as well as significant clonal divergence, with CNS-exclusive mutations not identified in diagnostic specimens. Conclusion: In summary, we have documented that CNS and systemic relapse result from distinct biological processes that, in part, may be associated with the underlying taxonomy of DLBCL. Our findings further show that CNS relapse results from the dissemination of sub-clones that may not be readily sampled at the time of diagnosis, and that intratumoral heterogeneity may limit our ability to predict CNS relapse. Large-scale, integrative analyses and in-depth characterization of clonal trajectories hold the promise to increase our ability to predict dissemination of DLBCL into the CNS. Disclosures Kridel: Gilead Sciences: Research Funding. Villa:Roche, Abbvie, Celgene, Seattle Genetics, Lundbeck, AstraZeneca, Nanostring, Janssen, Gilead: Consultancy, Honoraria. Steidl:Nanostring: Patents & Royalties: Filed patent on behalf of BC Cancer; Juno Therapeutics: Consultancy; Bristol-Myers Squibb: Research Funding; Roche: Consultancy; Tioma: Research Funding; Bayer: Consultancy; Seattle Genetics: Consultancy. Savage:BMS, Merck, Novartis, Verastem, Abbvie, Servier, and Seattle Genetics: Consultancy, Honoraria; Seattle Genetics, Inc.: Consultancy, Honoraria, Research Funding. Scott:Celgene: Consultancy; Roche/Genentech: Research Funding; NanoString: Patents & Royalties: Named inventor on a patent licensed to NanoSting [Institution], Research Funding; Janssen: Consultancy, Research Funding.

Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence Factor, ess/Type VII Locus.

Staphylococcus lugdunensis is a commensal bacterium of human skin that has emerged as a virulent Coagulase-Negative Staphylococcus in both community-acquired and healthcare associated infections. Genotyping methods have shown a clonal population structure of this pathogen but failed to identify hypervirulent lineages. Here, complete genomes of three pathogenic and three carriage S. lugdunensis strains were obtained by Single-Molecule sequencing (PacBio) and compared to 15 complete genomes available in GenBank database. The aim was to identify (i) genetic determinants specific to pathogenic or carriage strains or specific to clonal complexes (CCs) defined by MultiLocus Sequence Typing, and (ii) antibiotic resistance genes and new putative virulence factors encoded or not by mobile genetic elements (MGE). Comparative genomic analysis did not show a strict correlation between gene content and the ability of the six strains to cause infections in humans and in a Galleria mellonella infection model. However, this study identified new MGEs (five prophages, two genomic islands and one plasmid) and genetic variations of some putative virulence-associated loci, especially in CC3 strains. For a clonal population, high variability and eight CC-dependent genetic organizations were observed for the ess locus, which encodes a putative type VII secretion system (T7SS) homologous to that of S. aureus. Further phenotypic and functional studies are needed to characterize this particular CC3 and to evaluate the role of T7SS in the virulence of S. lugdunensis.

Molecular Detection, Multilocus Genotyping, and Population Genetics of Enterocytozoon bieneusi in Pigs in Southeastern China.

Enterocytozoon bieneusi is an important opportunistic pathogen widely distributed in humans and animals that causes diarrhea or fatal diarrhea in immunocompromised hosts. To examine the infection status and molecular characteristics of E.bieneusi in pigs, 725 fecal samples were collected from pigs in six areas of Fujian Province. The E.bieneusi genotypes were identified based on the internal transcribed spacer (ITS) regions of the ribosomal RNA (rRNA) gene by nested PCR, and its population genetics were analyzed by multilocus sequence typing (MLST). The results showed that the infection rate of E.bieneusi was 24.4% (177/725), and 11 known genotypes (EbpC, EbpA, CHN-RR2, KIN-1, CHG7, CHS5, CM11, CHG23, G, PigEBITS, and D) and 2 novel genotypes (FJF and FJS) were identified. All the genotypes were found to be clustered into zoonotic Group 1. Moreover, 52 positive samples were successfully amplified at minisatellite and microsatellite loci and formed 48 distinct multilocus genotypes (MLGs). Further population structure analyses showed strong genetic linkage disequilibrium (LD) and several recombination events (Rm), indicating that E.bieneusi has a clonal population structure. This study is the first to investigate the prevalence and molecular characteristics of E.bieneusi in Fujian Province and could provide baseline data to control E.bieneusi infection in pigs and humans and deepen our understanding of the zoonotic risk of E.bieneusi and its distribution in China.

A systematic review of Toxoplasma gondii genotypes and feline: Geographical distribution trends.

Toxoplasma gondii (T.gondii) is well known for its ability to virtually infect all warm-blooded vertebrates. Although felines as the definitive hosts have an important role in the epidemiology of toxoplasmosis, there are few descriptions of genetic diversity in the world. The present review study aimed to describe the population structure of T.gondii in these animal species. For the purpose of the study, five English language databases reporting data on T.gondii genotyping in cats were searched within March-June 2019. This study is registered on the site of CAMARADES-NC3Rs (15-Jan-2018). The searching process resulted in the inclusion of 50 reports published from 1992 to June 2019. The data revealed that 47,390 samples were genotyped into 662 T.gondii DNA/isolates. Globally, atypical genotypes were predominant (47.7%, n=316); in addition, Type II clonal strains were the second most common genotype (37%, n=244). These results suggested an epidemic population structure in America and Asia, and a clonal population structure in Europe and Africa. Genotype #3 was found to be dominant in Africa, Europe and Oceania continents. Furthermore, genotypes #9 and #5 were prevalent in Asia and America, respectively. Additionally, genotypes #2, #3, #5 and #20 were common genotypes in domestic and sylvatic cycles from family Felidae. Collectively, this systematic review indicated a large degree of genetic diversity and circulation of mouse-virulent T.gondii strains in this family. However, further studies are necessary to better understand the population structure of T.gondii in these animal species and determine the significance of their features.

Prevalence and Population Genetics Analysis of Enterocytozoon bieneusi in Dairy Cattle in China.

Enterocytozoon bieneusi, an obligate intracellular pathogen, can infect various hosts. In this study, 3527 dairy cattle fecal specimens were collected from different geographic locations in China (including 673 from Shandong province, 1,440 from Guangdong province and 1,414 from Gansu province) and examined for the presence of E. bieneusi using polymerase chain reactions targeting the ribosomal internal transcribed spacer (ITS). The dominant genotypes identified were further subtyped by multilocus sequence typing. The overall prevalence of E. bieneusi was 14.2% (501/3527), with a significant difference in prevalence among the different geographical locations (P < 0.001). Our logistic regression analysis showed that all four variables (farming model, location, age, and clinical manifestations) had strong effects on the risk of contracting E. bieneusi. Sequence analysis revealed 11 genotypes: eight known genotypes (J, I, BEB4, BEB10, D, EbpC, CM19, and CM21) and three novel genotypes (named here as CGC1, CGC2, and CGC3). Genotypes J and I, the commonest, were found on all farms across the three provinces. Our linkage disequilibrium analysis showed a clonal population structure in the E. bieneusi dairy cattle population but the ITS genotypes had different population structures. Phylogenetic and haplotype network analysis showed the absence of geographical segregation in the E. bieneusi dairy cattle populations. Instead, they revealed the presence of host adaptation to the E. bieneusi populations in various animals. Our findings augment the current understanding of E. bieneusi transmission dynamics.

Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica

BackgroundThe emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium).ResultsAMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6′)-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins.ConclusionsOur data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica.

Sexual reproduction in a natural Trypanosoma cruzi population.

BackgroundSexual reproduction provides an evolutionary advantageous mechanism that combines favorable mutations that have arisen in separate lineages into the same individual. This advantage is especially pronounced in microparasites as allelic reassortment among individuals caused by sexual reproduction promotes allelic diversity at immune evasion genes within individuals which is often essential to evade host immune systems. Despite these advantages, many eukaryotic microparasites exhibit highly-clonal population structures suggesting that genetic exchange through sexual reproduction is rare. Evidence supporting clonality is particularly convincing in the causative agent of Chagas disease, Trypanosoma cruzi, despite equally convincing evidence of the capacity to engage in sexual reproduction.Methodology/ Principle FindingsIn the present study, we investigated two hypotheses that can reconcile the apparent contradiction between the observed clonal population structure and the capacity to engage in sexual reproduction by analyzing the genome sequences of 123 T. cruzi isolates from a natural population in Arequipa, Peru. The distribution of polymorphic markers within and among isolates provides clear evidence of the occurrence of sexual reproduction. Large genetic segments are rearranged among chromosomes due to crossing over during meiosis leading to a decay in the genetic linkage among polymorphic markers compared to the expectations from a purely asexually-reproducing population. Nevertheless, the population structure appears clonal due to a high level of inbreeding during sexual reproduction which increases homozygosity, and thus reduces diversity, within each inbreeding lineage.Conclusions/ SignificanceThese results effectively reconcile the apparent contradiction by demonstrating that the clonal population structure is derived not from infrequent sex in natural populations but from high levels of inbreeding. We discuss epidemiological consequences of this reproductive strategy on genome evolution, population structure, and phenotypic diversity of this medically important parasite.

Novel insights into the genetic diversity and clonal structure of natural trembling aspen (Populus tremuloidesMichx.) populations: A transcontinental study

AbstractAimDistribution‐wide trends in climate variability significantly influence the genetic diversity, differentiation and population structure of tree species. This study investigates the effects of disturbances such as fire, fragmentation and climate on modern‐day genetic patterns and clonal structures of trembling aspen at the transcontinental scale.LocationNorth American boreal zone.TaxonTrembling aspen (Populus tremuloidesMichx.).MethodsOne thousand two hundred individuals in a 30‐site network (40 trees per location) were genotyped with neutral genetic markers and studied in relation to regional differences in climate and surrounding site conditions (aridity, fire cycle, fragmentation). Multiple linear regression models and variance analysis were used to test relationships between genetic indices, structural parameters and the surrounding site factors.ResultsOverall, a high percentage of single ramet clones (SRC) and clonal diversity was detected and assumed to be the consequence of multiple sexual reproduction events that took place at all sites, together with suckering, which shapes the clonal structure of populations. Neutral genetic diversity and clonal structure suggested no substantial differences among sites, which were categorized into climate moisture index (CMI) classes; aspen stands across Canada were highly similar from a genetic point of view. Allelic richness (AR) and the average number of alleles (Na) varied significantly among clonal organization groups, and landscape fragmentation and a higher frequency of fires showed a negative influence on the levels of genetic diversity.Main conclusionsOur results are inconsistent with the idea that the genotypic diversity of trembling aspen is related to the intensity of disturbance within the boreal forest. It appears that species‐specific disturbance responses and post‐fire recruitment mechanisms are more important than dominant ecological factors, such as climate and fire regimes, in shaping distribution‐wide patterns of neutral genetic variation and clonal structure.

Circulating tumor DNA analyses predict progressive disease and indicate trastuzumab-resistant mechanism in advanced gastric cancer.

BackgroundCirculating tumor DNA (ctDNA) isolated from plasma contains genetic mutations that can be representative of those found in primary tumor tissue DNA. These samples can provide insights into tumoral heterogeneity in patients with advanced gastric cancer (AGC). Although trastuzumab has been shown to be effective in first-line therapy for patients with metastatic gastric cancer with overexpression of human epidermal growth factor receptor 2 (HER2), the mechanism of AGC resistance is incompletely understood.MethodsIn this prospective study, we used targeted capture sequencing to analyze 173 serial ctDNA samples from 39 AGC patients. We analyzed cancer cell fractions with PyClone to understand the clonal population structure in cancer, and monitored serial samples during therapy. Serial monitoring of ctDNA using the molecular tumor burden index (mTBI), identified progressive disease before imaging results (mean: 18 weeks).FindingsWe reconstructed the clonal structure of ctDNA during anti-HER2 treatment, and identified 32 expanding mutations potentially related to trastuzumab resistance. Multiple pathways activating in the same patients revealed heterogeneity in trastuzumab resistance mechanisms in AGC. In patients who received chemotherapy, mTBI was validated for the prediction of progressive disease, with a sensitivity of 94% (15/16). A higher mTBI (≥1%) in pretreatment ctDNA was also a risk factor for progression-free survival.ConclusionsAnalysis of ctDNA clones based on sequencing is a promising approach to clinical management, and may lead to improved therapeutic strategies for AGC patients.FundThis work was supported by grants from the National International Cooperation Grant (to J.X.; Project No. 2014DFB33160).

Multilocus sequence typing detects new Piscirickettsia salmonis hybrid genogroup in Chilean fish farms: Evidence for genetic diversity and population structure.

Piscirickettsia salmonisis the causative bacterial pathogen of piscirickettsiosis, a salmonid disease that causes notable mortalities in the worldwide aquaculture industry. Published research describes the phenotypic traits, virulence factors, pathogenicity and antibiotic-resistance potential for various P.salmonisstrains. However, evolutionary and genetic information is scarce for P.salmonis. The present study used multilocus sequence typing (MLST) to gain insight into the population structure and evolution of P.salmonis. Forty-two Chilean P.salmonisisolates, as well as the type strain LF-89T , were recovered from diseased Salmo salar, Oncorhynchus kisutchand Oncorhynchus mykissfrom two Chilean Regions. MLST assessed the loci sequences of dnaK, efp, fumC, glyA, murG, rpoD and trpB. Bioinformatics analyses established the genetic diversity among P.salmonis isolates (H=0.5810). A total of 23 sequence types (ST) were identified, 53.48% of which were represented by ST1, ST5 and ST2. Population structure analysis through polymorphism patterns showed few polymorphic sites (218 nucleotides from 4,010bp), while dN/dS ratio analysis indicated purifying selection for dnaK, epf, fumC, murG, and rpoD but neutral selection for the trpB loci. The standardized index of association indicated strong linkage disequilibrium, suggesting clonal population structure. However, recombination events were detected in a group of seven isolates. Findings included genogroups homologous to the LF-89T and EM-90 strains, as well as a seven-isolate hybrid genogroup recovered from both assessed regions (three O.mykiss and four S.salar isolates). The presented MLST scheme has comparative potential, with promising applications in studying distinct P.salmonis isolates (e.g., from different hosts, farms, geographical areas) and in understanding the epidemiology of this pathogen.

Usefulness of a multiplex PCR for the rapid identification of Candida glabrata species complex in Mexican clinical isolates.

ABSTRACT Candida glabrata complex includes three species identified through molecular biology methods: C. glabrata sensu stricto , C. nivariensis and C. bracarensis . In Mexico, the phenotypic methods are still used in the diagnosis; therefore, the presence of C. nivariensis and C. bracarensis among clinical isolates is still unknown. The aim of this study was to evaluate the utility of a multiplex PCR for the identification of the C. glabrata species complex. DNA samples from 92 clinical isolates that were previously identified through phenotypic characteristics as C. glabrata were amplified by four oligonucleotides (UNI-5.8S, GLA-f, BRA-f, and NIV-f) that generate amplicons of 397, 293 and 223-bp corresponding to C. glabrata sensu stricto , C. nivariensis , and C. bracarensis , respectively. The amplicon sequences were used to perform a phylogenetic analysis through the Maximum Likelihood method (MEGA6), including strains and reference sequences of species belonging to C. glabrata complex. In addition, recombination and linkage disequilibrium were estimated (DnaSP version 5.0) for C. glabrata sensu stricto isolate s . Eighty-eight isolates generated a 397-bp fragment and only in one isolate a 223-bp amplicon was observed. In the phylogenetic tree, the sequences of 397-bp were grouped with C. glabrata reference sequences , and the sequence of 223-bp was grouped with C. bracarensis reference sequences, corroborating the PCR identification. The number of recombination events for the isolates of C. glabrata sensu stricto was zero, suggesting a clonal population structure. Three isolates that did not amplify any of the expected fragments were identified as Saccharomyces cerevisiae through the sequencing of the D1/D2 domain region within the 28S rDNA gene. The multiplex PCR is a fast, cost-effective and reliable tool that can be used in clinical laboratories to identify C. glabrata complex species.

Analyses of the genetic diversity and population structures of Histoplasma capsulatum clinical isolates from Mexico, Guatemala, Colombia and Argentina, using a randomly amplified polymorphic DNA-PCR assay.

We studied the genetic diversity and the population structure of human isolates of Histoplasma capsulatum, the causative agent of histoplasmosis, using a randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) assay to identify associations with the geographic distribution of isolates from Mexico, Guatemala, Colombia and Argentina. The RAPD-PCR pattern analyses revealed the genetic diversity by estimating the percentage of polymorphic loci, effective number of alleles, Shannon's index and heterozygosity. Population structure was identified by the index of association (IA) test. Thirty-seven isolates were studied and clustered into three groups by the unweighted pair-group method with arithmetic mean (UPGMA). Group I contained five subgroups based on geographic origin. The consistency of the UPGMA dendrogram was estimated by the cophenetic correlation coefficient (CCCr = 0.94, P = 0.001). Isolates from Mexico and Colombia presented higher genetic diversity than isolates from Argentina. Isolates from Guatemala grouped together with the reference strains from the United States of America and Panama. The IA values suggest the presence of a clonal population structure in the Argentinian H. capsulatum isolates and also validate the presence of recombining populations in the Colombian and Mexican isolates. These data contribute to the knowledge on the molecular epidemiology of histoplasmosis in Latin America.