Degree Of Genetic Relatedness Research Articles

Microbiological monitoring of nasal lavage fluid as a method for early detection and prevention of bacterial lung complications in a patient with cystic fibrosis

The severity of complications in cystic fibrosis are determined by microorganisms colonizing the lower airways. Paranasal sinuses can be a reservoir of aggressive pathogens. We have developed a method for collection and primary inoculation of nasal lavage fluid from cystic fibrosis patients for microbiological investigation. As a clinical case illustrating the feasibility of this technique, we describe the dynamics of the microflora composition in a patient with cystic fibrosis. The patient had a clinical and microbiological picture of P. aeruginosa eradication from the lung tissue, owing to which the antibacterial therapy was stopped. Six months later, the microflora in the nasal lavage fluid and sputum were assessed in parallel. The growth of P. aeruginosa (102 CFU/mL) but not P. aeruginosa in sputum was detected. To determine origin of this strain, the degree of genetic relationship between 5 strains obtained from the patient from 2008 to 2016 was assessed based on bacterial protein profiling. A typical strain of P. aeruginosa ATTS 27853 was used as a control. Strains isolated from the patient in 2009 and 2016 were identical suggesting that the antibacterial therapy led to eradication of P. aeruginosa in the lungs, but not in the upper airways. Four months later, the growth of P. aeruginosa was found in sputum. The patient was prescribed to use antibacterial drugs inhaled into paranasal sinuses. Repeated test performed 3 months later resulted in growth of P. aeruginosa 101 CFU/mL from nasal lavage fluid, but not from sputum. The patient was referred to a risk group on airway colonization by pathogen strains derived from the upper airway tract. The clinical example illustrates relevance of conducting a regular microbiological study of nasal lavage fluid in order to early identify clinically significant pathogens to prevent their spread to the lower airway tract.

Kinship mediates the expression of alternative reproductive tactics in competing spider mite males

Owing to its fitness implications, the degree of genetic relatedness within and between the sexes is a highly significant determinant in mate competition, mate choice and mating success. The role of kinship in the expression of alternative reproductive tactics (ARTs) has been rarely investigated. Here we scrutinized kinship effects on male ARTs in two-spotted spider mites Tetranychus urticae.

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis).

The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

Familial liability to asthma and ADHD: A Swedish national register-based study.

Studies have reported significant associations between asthma and attention-deficit/hyperactivity disorder (ADHD), but whether the association is due to shared etiology such as shared genetic risk factors remains unclear. We aimed to investigate patterns of familial co-aggregation of asthma and ADHD and also to quantify the relative contribution of genetic and environmental influences. Through Swedish register linkages, we obtained a cohort of 927,956 individuals born 1992-2001 and identified monozygotic twins (MZ), dizygotic twins (DZ), full- and half-siblings, and full- and half-cousins. Clinical diagnosis of asthma and ADHD were identified from the Swedish national registers. We used logistic regressions to investigate the within-individual association and familial co-aggregation between asthma and ADHD. We then used bivariate twin modeling to quantify the genetic and environmental correlations and their contributions to the familial liability. Individuals with asthma had significantly higher risk of ADHD (odds ratio [OR], 1.50; 95% confidence interval [CI], 1.47-1.54). Relatives of individuals with asthma had an increased risk of ADHD compared to relatives of individuals without asthma; in familial co-aggregation analysis, the association was strongest in MZ twins (OR, 1.67; 95% CI, 0.99-2.84) and attenuated with degree of genetic relatedness. In the twin modeling, the phenotypic and genetic correlations between asthma and ADHD estimated from the ACE model were 0.09 (95% CI, 0.05-0.14) and 0.12 (95% CI, 0.02-0.21), respectively. The bivariate heritability was 0.88 (95% CI, 0.30-1.46). Estimates for contributions from shared and non-shared environment factors were not statistically significant. Asthma and ADHD co-aggregate in families primarily due to shared genetic risk factors. Within-individual and family history of either disorder should prompt clinical assessment of the other condition. Future studies should further investigate genetic variants underlying the co-occurrence of ADHD and asthma.

Familial Risk of Hashimoto's Thyroiditis Among First-Degree Relatives: A Population-Based Study in Korea.

Background: Few small-scale studies have reported a genetic and familial predisposition in Hashimoto's thyroiditis (HT), however, quantified familial risk estimates from population-level data are unavailable. We aimed to estimate the incidence and familial risk of HT among first-degree relatives (FDR) according to age, sex, and family relationships. Methods: We conducted a population-based study in the general population of Korea from 2002 to 2017. Using the nationwide health insurance database, which has full population coverage and family relationship information, a cohort of 22 million individuals with blood-related FDR comprising 12 million families were followed up for a familial occurrence of HT. Age- and sex-adjusted incidence risk ratios (IRRs) were calculated in individuals with an affected FDR compared with those without an affected FDR. Results: Among 21,940,795 individuals, 234,912 had an HT-affected FDR, of whom 2425 familial cases developed HT with an incidence of 7.12/10,000 person-years. The familial risk for HT was 6.5-fold (95% confidence interval [CI]: 6.24-6.78) higher in individuals with versus without affected FDR. According to relationship, familial risks were IRR 102.71, IRR 7.80, IRR 5.54, and IRR 5.52 with an affected twin, sibling, mother, and father, respectively, and the corresponding incidence (/10,000 person-years) was 115.57, 10.66, 5.73, and 5.91. Same-sex twins had three times higher risk of developing HT than opposite-sex twins (IRR 121.01 vs. 21.46). The sex-specific familial risk was higher in males than females. The risks demonstrated age dependence, being higher in younger age groups. Conclusions: This study represents the largest population-based study of familial HT risk in Asia. We demonstrated elevated familial risk of incident HT among FDR, but with lower magnitude as those observed in previous studies. Familial risk increased with the degree of genetic relatedness among FDR indicating a prominent role of genetic factors in the familial aggregation of HT. Elevated risks in the younger age groups should motivate clinicians to screen people with a family history, especially those <30 years.

Bacterial Cross-Contamination in a Veterinary Ophthalmology Setting.

The present study describes the prevalence of bacterial cross-contamination in a veterinary ophthalmology setting, a serious issue that can result in healthcare-associated (or nosocomial) infections among patients and staff. Retrospective (n = 5 patients) and prospective (n = 23 patients) studies evaluated bacterial isolates in companion animals presenting with ulcerative keratitis, sampling the patients' cornea and surrounding examination room, including the environment (exam table, countertop, floor) and ophthalmic equipment (slit lamp, transilluminator, direct ophthalmoscope, indirect headset, tonometer). Results of bacterial culture and antibiotic susceptibility testing were recorded, and degree of genetic relatedness was evaluated in six pairs of isolates (cornea + environment or equipment) using pulse-field gel electrophoresis (PFGE). Overall contamination rate of ophthalmic equipment, environment, and examination rooms (equipment + environment) was 42.9% (15/35 samples), 23.7% (9/38 samples) and 32.9% (24/73 samples), respectively. Methicillin-resistant Staphylococcus pseudintermedius (MRSP), a multi-drug resistant (MDR) pathogen with zoonotic potential, was isolated in 8.2% (6/73) of samples. The patient's cornea was likely the source of cross-contamination in 50% (3/6) of MRSP pairs as evaluated by PFGE; notably, two of the three similar bacterial strains did not have an exact match of their antibiotic susceptibility profiles, highlighting the importance of advanced diagnostics such as PFGE to assess cross-contamination in healthcare facilities. Future work could examine the contamination prevalence of specific equipment or the efficacy of cleaning protocols to mitigate cross-contamination in veterinary practice.

Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label‐Free Quantitative Proteomics

Escherichia coli and Shigella spp. causing illnesses in humans represent a genotypically and phenotypically diverse group of pathogens. Although E. coli diversity has been studied by comparative genomics, the intra-species variation at the proteome level is currently unknown. The proteomes of 16 pathogenic E. coli, 2 non-pathogenic E. coli, and 5 Shigella strains originating from 18 phylogenetic lineages are investigated. By applying label-free quantitative proteomics on trypsin-digested cell extracts from bacteria grown on blood agar, 4018 proteins are detected, 3285 of which arequantified, and 261 represented virulence factors. Of 753 proteins quantified in all strains, the levels of 153 vary substantially between strains and are functionally associated mostly with stress response and peripheral metabolism. The levels of proteins associated with the central metabolism vary considerably less than the levels of proteins from other metabolic pathways. Hierarchical clustering analysis based on the protein levels results in strains grouping that differ from that obtained by gene-based phylogenetic analysis. Finally, strains of some E. coli pathotypes have more similar protein profiles even when the strains are not genetically closely related. The results suggest that the degree of genetic relatedness may not necessarily be a good predictor of E. coli phenotypic characteristics.

Genotyping oil flax varieties using the microsatellite DNA marker system

The tendency to increase crop acreage of oil flax requires the development of new varieties with high indicators of ecological plasticity, productivity and resistance to biotic and abiotic stresses. The application of modern biotechnolog ical approaches based on the use of molecular markers can accelerate the assessment of genetic differences and the dete rmination of potential of the source material for breeding. The research was aimed at assessment of the genotyping parameters of some oil flax varieties of VNIIMK breeding using the system of microsatellite markers. Seventeen variety samples of flax were used as the material for the research. DNA was isolated using CTAB buffer. Eleven SSR loci were used for the identification of varieties. Ten polymorphic loci were identified during the research. The total number of counted alleles is 32. The size of alleles varied in the range of 111-210 bps. The number of alleles per locus ranged from 2 to 6 with an average value of 3.20. The value of the index of polymorphic information content (PIC) was from 0.29 to 0.75 with an average parameter value of 0.51. The effective number of alleles for different loci is determined in the range of 1.40-3.94 with an average value of 2.28. The level of information content of the marker system (PIC 0.51) corresponds to that for identifying sets of genotypes from collections with a limitation in geographical origin. There were established differences in the frequency of occurrence of alleles. The discriminatory potential of the used marker system allowed to identify 15 variety samples. Two genotypes with common origin were identical. The degree of genetic relatedness of the studied flax genotypes has been evaluated. The obtained results will serve as the basis for the subsequent construction of genetic passports of oil flax varieties of VNIIMK breeding.

Familial Risk for Moyamoya Disease Among First-Degree Relatives, Based on a Population-Based Aggregation Study in Korea

Genetic factors have been known to play a role in the etiology of moyamoya disease (MMD); however, population-level studies quantifying familial risk estimates are unavailable. We aimed to quantify familial incidence and risk for MMD in first-degree relatives (FDR) in the general population of Korea. By using the Korean National Health Insurance database which has complete population coverage and confirmed FDR information, we constructed a cohort of 21 940 795 study subjects constituting 12 million families with blood-related FDR and followed them for a familial occurrence of MMD from 2002 to 2017. Incidence risk ratios were calculated as MMD incidence in individuals with affected FDR compared with those without affected FDR, according to age, sex, and family relationships. Among total study subjects, there were 22 459 individuals with affected FDR, of whom 712 familial cases developed MMD with an incidence of 21.8/104 person-years. Overall, the familial risk for MMD was 132-fold higher in individuals with versus without affected FDR. Familial risk (incidence risk ratio; incidence/104 person-years) increased with the degree of genetic relatedness, being highest in individuals with an affected twin (1254.1; 230.0), followed by a sibling (212.4; 35.6), then mother (87.7; 14.4) and father (62.5; 10.4). Remarkably, there was no disease concordance between spouses. The risks were age-dependent and were particularly high in younger age groups. Familial risks were similar in males and females, and the risk of disease transmission was higher in same-sex parent-offspring and sibling pairs. Our study indicates that genetic predisposition is the predominant driver in MMD pathogenesis, with minimal contribution of environmental factors. These results could be utilized to direct future genetic studies and clinical risk counseling.

GENETIC (RAPD-PCR) VARIABILITY OF STAPHYLOCOCCUS AUREUS STRAINS EXTRACTED FROM LOCUS MORBI AND INTAKT SKIN OF PATIENTS WITH ALLERGODERMATOSIS

The article presents data on the study of genetic relatedness of S. aureus strains growing on the skin and nasal passages of patients with allergodermatoses. A study of the possible correlation between the genotype of the pathogen and the burden of allergodermatoses using the RAPD-PCR method was done. The aim of the research: determination by RAPD-PCR analysis (Random Amplified Polymorphic DNA) of genetic variability and affinity of S. aureus strains extracted from locus morbi, intact areas of skin and nasal mucosa of patients with allergodermatoses (AD and IE). Materials and methods. RAPD-PCR was used to genotype 111 strains of Staphylococcus aureus extracted from the skin and nasal passages of patients with allergodermatoses (AD and IE), as well as 11 strains isolated from the skin of almost healthy individuals to identify genetic links between these strains. These strains were removed from patients with AD and IE who sought medical help in the dermatological department of the State Institution "Institute of Dermatology and Venereology of the National Academy of Medical Sciences of Ukraine" during 2016-2019. Results. When comparing the RAPD spectra of strains extracted from the affected and intact areas of the skin of patients with mild and severe AD, the degree of genetic relatedness of the strains was 75.1±4.4 % and 98.8±0.8 %, (P˂0,001), respectively, indicating a high level of affinity of the strains. Strains of S. aureus removed from the nasal passages of patients with AD had a high level of genetic affinity with strains removed from the affected areas of the skin – 79.5±1.6 %, which indicates the auto-origin of strains growing on the skin of patients. The affinity of strains isolated from patients with IE with the reference culture of S. aureus ATCC 25923 was 27.4±1.8 % and 52.0±5.2 % for strains isolated from patients with AD, indicating their low genetic relatedness. Conclusions. In the study of RAPD spectra of S. aureus strains isolated from patients with both AD and IE, no genotype was identified that would be associated with the disease or its severity. A high level of genetic affinity of strains extracted from locus morbi with strains extracted from the nasal passages of patients with AD, indicating the auto-origin of strains that grow on the skin of patients. It is shown that with increasing severity of AD, the genetic monotype of isolated pathogens increased: in patients with mild AD, 3 genetic clusters of the microorganism were identified, with moderate – 2, and with severe only one.

Mate choice in naturally inbred spiders: testing the role of relatedness

Mate preference based on relatedness may evolve in response to costs and benefits of inbreeding avoidance. Whereas mating with closely related individuals can have negative fitness consequences due to inbreeding depression, it may simultaneously be favoured by inclusive fitness benefits. Variation in the fitness payoff shaped by benefits of inbreeding may even lead to preference for mating with kin. We investigated this hypothesis in the social spider Stegodyphus dumicola, a cooperative species in which reproduction occurs among siblings within the group, premating dispersal is lacking and infrequent encounters with unrelated individuals result in homozygous genetic lineages. We tested whether female mate choice is influenced by male relatedness by pairing females with males that differ in the degree of genetic relatedness, namely nest members, non-nest members from the same population and non-nest members from allopatric populations. We recorded premating (male rejections, latency to mating) and mating (copulation duration and interruptions) behaviours. Females showed no preference for partners on the basis of their relatedness during the premating phase, as frequencies of rejections and successful matings did not differ markedly in encounters with nest and non-nest members. This suggests that selection on discriminatory mechanisms may be weakened or lost in species with inbreeding tolerance and in which relatedness between interacting individuals is very high and variance in relatedness extremely low. Unrelated males from the geographically distant population experienced longer copulations than males from the same population. We interpret this finding as depicting a possible scenario of a between-population reproductive barrier or functional incompatibility, which may be the mechanism causing lower fitness in between-population crosses previously documented in these populations.

Genetic diversity and relatedness in Arabian oryx (Oryx leucoryx) revealed by SSR markers

Information on genetic relatedness can be used to control the rate of inbreeding by applying the sib-avoidance mating strategy. Estimation of genetic relatedness based on molecular markers is a potential technique to infer the degree of genetic relationships among individuals identified as parent–offspring, full-sib, half-sib, and unrelated pairs. The objectives of the study were to assess the genetic variation, the population structure, and the level of inbreeding and relatedness in seven different collections of Oryx leucoryx based on the analysis of 13 polymorphic microsatellite loci, in order to provide information about the impact of captive breeding management. The analysis revealed that the mean number of alleles per locus, the polymorphic information content, and the observed and expected heterozygosity across the loci were 6.46 ± 0.95, 0.523 ± 0.028, 0.391 ± 0.032, and 0.583 ± 0.031, respectively. The inbreeding coefficient was found to be significant in five of the seven collections. The structure analysis identified two groups among the 96 individuals. The pairwise relatedness (rXYW) in the combined sample followed the distributions expected under the unrelated category. A low level of heterozygosity and a high level of inbreeding and relatedness were found in the samples of O. leucoryx collected from Qatar. As individual animals can be identified by tags, this relatedness information can be used to control the rate of inbreeding by avoiding mating between close relatives.

Habitat suitability and the genetic structure of human populations during the Last Glacial Maximum (LGM) in Western Europe.

Human populations in Western Europe during the Last Glacial Maximum were geographically constrained to glacial refugia by the severity of the climate and ecological risk factors. In this research we use an agent-based model of human mobility and interaction, based on ethnographic and archaeological data, to explore the impact of ecological risk on human population structure via a reconstructed landscape of habitat suitability. The agent-based model allows us to evaluate the size and location of glacial refugia, the size of the populations occupying them and the degree of genetic relatedness between people occupying these areas. To do this, we model the probability of an agent foraging groups’ survival as a function of habitat suitability. The model’s simulated “genomes” (composed of regionally specific genetic markers) allow us to track long-term trends of inter-regional interaction and mobility. The results agree with previous archaeological studies situating a large glacial refugium spanning southern France and northeastern Spain, but we expand on those studies by demonstrating that higher rates of population growth in this central refugium led to continuous out-migration and therefore genetic homogeneity across Western Europe, with the possible exception of the Italian peninsula. These results concur with material culture data from known archaeological sites dating to the Last Glacial Maximum and make predictions for future ancient DNA studies.

Genetic and environmental sources of familial coaggregation of obsessive\u2212compulsive disorder and suicidal behavior: a population-based birth cohort and family study

Obsessive−compulsive disorder (OCD) is associated with high risk of suicide. It is yet unknown whether OCD and suicidal behaviors coaggregate in families and, if so, what are the mechanisms underlying this coaggregation. In a population-based birth cohort and family study, we linked individuals born in Sweden in 1967–2003 (n = 3,594,181) to their parents, siblings, and cousins, and collected register-based diagnoses of OCD, suicide attempts, and deaths by suicide and followed them until December 31, 2013. We also applied quantitative genetic modeling to estimate the contribution of genetic and environmental factors to the familial coaggregation of OCD and suicidal behavior. An elevated risk of suicide attempts was observed across all relatives of individuals with OCD, increasing proportionally to the degree of genetic relatedness, with odds ratios (OR) ranging from 1.56 (95% confidence interval (CI) 1.49–1.63) in parents to 1.11 (95% CI 1.07–1.16) in cousins. The risk of death by suicide also increased alongside narrowing genetic distance, but was only significant in parents (OR 1.55; 95% CI 1.40–1.72) and full siblings (OR 1.80; 95% CI 1.43–2.26) of individuals with OCD. Familial coaggregation of OCD and suicide attempts was explained by additive genetic factors (60.7%) and non-shared environment (40.4%), with negligible contribution of shared environment. Similarly, familial coaggregation with death by suicide was attributed to additive genetics (65.8%) and nonshared environment (34.2%). Collectively, these observations indicate that OCD and suicidal behaviors coaggregate in families largely due to genetic factors. The contribution of unique environment is also considerable, providing opportunities to target high-risk groups for prevention and treatment.

Diversidad genética de genotipos partenocarpicos arbustivos de calabaza mediante marcadores genéticos moleculares

La producción de calabaza (Cucurbita pepo L.) para verdura o calabacita bajo cubierta presenta dificultades por la falta de polinización, por tal razón, la partenocarpia es una alternativa para generar variedades de calabacita de invernadero, por lo que actualmente se realizan esfuerzos en la búsqueda de partenocarpia genética que no requiera del estímulo de la polinización, ni por factores fisiológicos a fin de que el fruto se desarrolle en forma normal hasta la madurez fisiológica. Se estudiaron molecularmente 46 genotipos partenocarpicos de calabaza arbustiva tipo round zucchini obtenidos en la Universidad Autónoma Chapingo. El objetivo fue caracterizar e identificar la diversidad genética entre los genotipos a partir de la variabilidad obtenida mediante marcadores genéticos moleculares como los microsatélites del tipo ISSR (inter secuencias simples repetidas) y RAMP (polimorfismo de microsatélites amplificados al azar). Se utilizó (GATA)4 como iniciador de ISSR y la combinación de (GATA)4 con cuatro iniciadores de secuencia aleatoria de la serie A de Operon (OPA05, OPA10, OPA13 Y OPA19) para RAMP. Con las dos técnicas se obtuvo un total de 43 loci polimórficos, seis loci amplificaron con ISSR y 37 loci con RAMP. El porcentaje de loci polimórficos para ISSR fue de 100%, mientras que para RAMP fue de 91.8% de polimorfismo, se encontró alto grado de relación genética entre los genotipos partenocarpicos. Se formaron cinco grupos para ISSR y cuatro para RAMP, con distancias génicas entre 0.72 a 1.&#x0D;

Changing the paradigm for hospital outbreak detection by leading with genomic surveillance of nosocomial pathogens.

The current paradigm for hospital outbreak detection and investigation is based on methodology first developed over 150 years ago. Daily surveillance to detect patients positive for pathogens of particular importance for nosocomial infection is supported by epidemiological investigation to determine their relationship in time and place, and to identify any other factor that could link them. The antibiotic resistance pattern is commonly used as a surrogate for bacterial relatedness, although this lacks sensitivity and specificity. Typing may be used to define bacterial relatedness, although routine methods lack sufficient discriminatory power to distinguish relatedness beyond the level of bacterial clones. Ultimately, the identification of an outbreak remains a predominately subjective process reliant on the intuition of experienced infection control professionals. Here, we propose a redesign of hospital outbreak detection and investigation in which bacterial species associated with nosocomial transmission and infection undergo routine prospective whole-genome sequencing. Further investigation is based on the probability that isolates are associated with an outbreak, which is based on the degree of genetic relatedness between isolates. Evidence is provided that supports this model based on studies of MRSA (methicillin-resistant Staphylococcus aureus), together with the benefits of a ‘Sequence First’ approach. The feasibility of implementation is discussed, together with residual barriers that need to be overcome prior to implementation.

Differentiation of apomictic and sexual genotypes of Brachiaria spp., using molecular markers

Some species of Brachiaria are cultivated in the tropics because of their high productivity and drought resistance; their apomictic hybrids are of interest because of the almost null segregation and xation of the hybrid vigor in seeds. In this research, Amplied Fragment Length Polymorphism (AFLP) and Cleaved Amplied Polymorphic Sequence (CAPS) markers were used to dierentiate apomictic tetraploid and sexual diploid Brachiaria parents and their progeny. Polymorphism detected with AFLP was 91.3% and with CAPS 79.7%. Phenograms dierentiated each genotype and the clustering of parents and their progeny was by their degree of genetic relatedness. AFLP did not separate the apomictic genotypes from the sexual ones, but CAPS markers did so through the C15-8 marker. Some apomictic genotypes of the progeny inherited it from their B. ruziziensis sexual mother, which may be related to some segregating character of the parental line.

Kinship inference for males with identical Y-STR profiles using whole genome SNP data provides a deeper understanding about the level of coancestry in the Swedish male population

Male individuals, from a Swedish reference population, with identical 17 loci Y-chromosomal STR haplotypes were analyzed with more than 900,000 autosomal SNPs in order to estimate their degree of genetic relatedness. This study shows that even though identical Y-STR profiles are shared, there is no evidence that these individuals are related to a higher degree compared with randomly unrelated male individuals in the Swedish population. Based on the results in this study, we conclude that the data do not show any signs of a biased sampling when it comes to the studied male individuals representing the Swedish reference population.

Molecular characterization and phylogenetic analysis of highly pathogenic Vibrio alginolyticus strains isolated during mortality outbreaks in cultured Ruditapes decussatus juvenile

In the summer of 2008 and 2009, a series of mortalities in growing out seeds of R. decussatus juveniles were occurred in the eastern Tunisian littoral. Nine predominant bacterial strains were isolated from dead and moribund juveniles and characterized as Vibrio alginolyticus. These isolates were subjected to biochemical and molecular characterization. All the Vibrio strains were tested for their susceptibility against the most widely used antibiotic in aquaculture as well as, the assessment of the presence of erythromycin (emrB) and tetracycline (tetS) resistance genes among the tested bacteria. The degree of genetic relatedness between V. alginolyticus strains was evaluated on the basis of the Entero-Bacterial Repetitive Intergenic Consensus (ERIC) and the Random Amplification of Polymorphic DNA-PCR (RAPD-PCR) approaches. We also looked for siderophore activity and the ability to grow under iron limitation. Furthermore, the pathogenic potential of the tested isolates was evaluated using R. decussatus larva and juveniles as infection models. On antimicrobial susceptibility test, Vibrio strains exhibited total resistance to at least four antibiotics. The MICs data revealed that flumequine and oxolinic acid were the most effective antibiotics to control the studied bacteria. Results also showed that studied antibiotics resistance genes were widely disseminated in the genome of V. alginolyticus strains. Both ERIC and RAPD-PCR fingerprinting showed the presence of genetic variation among Vibrio isolates. However, RAPD typing exhibited a higher discriminative potential than ERIC-PCR. Besides, we reported here for the first time the co-production of catechol and hydroxamte by V. alginolyticus species. The challenge experiment showed that most of Vibrio isolates caused high mortality rates for both larva and juveniles at 48-h post-exposure to a bacterial concentration of 106 CFU/ml.

Genetic characterization of &lt;i&gt;Salmonella&lt;/i&gt; and &lt;i&gt;Shigella&lt;/i&gt; spp. isolates recovered from water and riverbed sediment of the Apies River, South Africa

Riverbed sediment is a vital component of river ecosystems and plays an important role in many geomorphological and ecological processes. However, when re-suspension occurs, pathogenic bacteria associated with sediment particles may be released into the water column, thus creating a health risk to those who use such water for drinking, household and recreational purposes. The aim of this study was to investigate the presence of bacterial pathogens Salmonella spp. and Shigella spp. in the Apies River and to ascertain whether there was any level of genetic relatedness between river water and riverbed sediment isolates of these pathogenic bacteria. A total of 124 water and sediment samples were collected from a site located on the Apies Rivers upstream of the Daspoort Wastewater Treatment Works, Pretoria, Gauteng, South Africa, between August and November 2014. In order to detect and identify the target bacteria, samples were analysed by culture-dependent and culture-independent techniques (quantitative real-time PCR). Genetic relatedness was established using Sanger sequencing of the invA gene of Salmonella spp. and ipaH of Shigella spp. Results of this study displayed the presence of the target bacteria both in the water and sediment of the river. The phylogenetic tree of Salmonella spp. revealed a ≥ 99% and 99% genetic relatedness between river water and riverbed sediment isolates for Salmonella spp. and Shigella spp., respectively. The degree of genetic relatedness between sediment and water pathogen isolates suggests that these organisms could possibly have a common origin and that there could be possible movement of microorganisms between the water column and the sediments. Keywords: Salmonella spp., Shigella spp., river water, riverbed sediment, genetic relatedness