Surveillance of vancomycin-resistant enterococci reveals shift in dominating clusters from vanA to vanB Enterococcus faecium clusters, Denmark, 2015 to 2022.

BackgroundVancomycin-resistant enterococci (VRE) are increasing in Denmark and Europe. Linezolid and vancomycin-resistant enterococci (LVRE) are of concern, as treatment options are limited. Vancomycin-variable enterococci (VVE) harbour the vanA gene complex but are phenotypically vancomycin-susceptible.AimThe aim was to describe clonal shifts for VRE and VVE in Denmark between 2015 and 2022 and to investigate genotypic linezolid resistance among the VRE and VVE.MethodsFrom 2015 to 2022, 4,090 Danish clinical VRE and VVE isolates were whole genome sequenced. We extracted vancomycin resistance genes and sequence types (STs) from the sequencing data and performed core genome multilocus sequence typing (cgMLST) analysis for Enterococcus faecium. All isolates were tested for the presence of mutations or genes encoding linezolid resistance.ResultsIn total 99% of the VRE and VVE isolates were E. faecium. From 2015 through 2019, 91.1% of the VRE and VVE were vanA E. faecium. During 2020, to the number of vanB E. faecium increased to 254 of 509 VRE and VVE isolates. Between 2015 and 2022, seven E. faecium clusters dominated: ST80-CT14 vanA, ST117-CT24 vanA, ST203-CT859 vanA, ST1421-CT1134 vanA (VVE cluster), ST80-CT1064 vanA/vanB, ST117-CT36 vanB and ST80-CT2406 vanB. We detected 35 linezolid vancomycin-resistant E. faecium and eight linezolid-resistant VVEfm.ConclusionFrom 2015 to 2022, the numbers of VRE and VVE increased. The spread of the VVE cluster ST1421-CT1134 vanA E. faecium in Denmark is a concern, especially since VVE diagnostics are challenging. The finding of LVRE, although in small numbers, ia also a concern, as treatment options are limited.

Perceptions of society regarding the concept of nurse: A metaphorical study.

INTRODUCTION: Metaphors are one of the most effective linguistic tools that are used to reveal how society describes nursing and what their vision of nursing is and to understand how effective the roles and responsibilities assumed by nurses in a multidisciplinary healthcare team are in protecting and maintaining the health of individuals, families, and society. AIM: The aim of this study was to reveal the perceptions of society about "nurses" through metaphors. METHODS: The study was planned with a mixed design involving qualitative and quantitative research methods. It was carried out with 810 people living in Turkey who were between the ages of 15 and 65 and voluntarily participated in the study. Each participant was asked to fill in the blanks in the sentence, "A nurse is like a/an………………because…………" The data were analyzed by using qualitative (content analysis) and quantitative (chi-squared) data analysis methods. RESULTS: It was determined that the participants produced 194 metaphors related to the concept of a "nurse." It was observed that they frequently used metaphors of "angel," "parent," "doctor's assistant/right hand," "lifesaver," and "confidant" regarding the concept of nurse and conceptualized a nurse as "Beneficial/Helpful/Healer/Facilitator." CONCLUSIONS AND CLINICAL RELEVANCE: The results showed that the awareness and perception of society toward nurses should be improved on the basis of the opportunity created by the COVID-19 pandemic period, and the concepts should be introduced to younger generations in a wider framework under the leadership of nursing faculties.

The Relationship Between Learning Needs and Fatalism Tendency in Women Who Have a Relative with Breast Cancer.

The aim of this study was to determine the information-support needs and level of meeting these needs, the tendency of fatalism trend, and the relationship between these parameters in women having a relative with breast cancer. The research was carried out with 400 women who were the primary relatives of patients treated within oncology units. Participants completed an information form, the information support needs questionnaire and the fatalism tendency scale. There was found to be a high, negative and weak significant relationship between the mean of needs for information-support and the mean of fatalism tendency scale (r = - 343; p < .001) and high, negative and average significant relationship with fulfilling their needs. There was also a negative relationship between the importance for information-support needs, fulfilling their needs and fatalism tendency in women who have relatives with breast cancer.

Transmission of Antimicrobial-Resistant Staphylococcus aureus Clonal Complex 9 between Pigs and Humans, United States.

Transmission of livestock-associated Staphylococcus aureus clonal complex 9 (LA-SA CC9) between pigs raised on industrial hog operations (IHOs) and humans in the United States is poorly understood. We analyzed whole-genome sequences from 32 international S. aureus CC9 isolates and 49 LA-SA CC9 isolates from IHO pigs and humans who work on or live near IHOs in 10 pig-producing counties in North Carolina, USA. Bioinformatic analysis of sequence data from the 81 isolates demonstrated 3 major LA-SA CC9 clades. North Carolina isolates all fell within a single clade (C3). High-resolution phylogenetic analysis of C3 revealed 2 subclades of intermingled IHO pig and human isolates differing by 0-34 single-nucleotide polymorphisms. Our findings suggest that LA-SA CC9 from pigs and humans share a common source and provide evidence of transmission of antimicrobial-resistant LA-SA CC9 between IHO pigs and humans who work on or live near IHOs in North Carolina.

Association between vancomycin-resistant Enterococcus faecium colonization and subsequent infection: a retrospective WGS study.

BACKGROUND: Since 2012, the incidence of vancomycin-resistant Enterococcus faecium (VREfm) has increased dramatically in Copenhagen and vanA E. faecium has become endemic and polyclonal. OBJECTIVES: To examine whether a patient with a positive VRE clinical sample had the same VREfm in a preceding screening sample (within 60 days). METHODS: We performed a 30 month retrospective study. From our laboratory information system (LIS), we identified all patients with an invasive VREfm isolate and a VREfm rectal screening isolate within 60 days before infection. VREfm pairs (screening isolate and invasive isolate) were whole-genome sequenced. All isolates were analysed using SeqSphere and core-genome MLST (cgMLST) types were determined. We examined all isolates for the presence of the three most dominant vanA plasmids in the Capital Region of Denmark. Two novel vanA plasmids were closed by Nanopore/Illumina sequencing. RESULTS: We found a total of 19 VREfm pairs. Of these, 13 patients had pairs with matching cgMLST types and vanA plasmids and a median number of 6 days from identification of carriage to clinical infection. One patient had a pair with non-matching cgMLST types but matching vanA plasmids and 24 days between identification of carriage to clinical infection. Five patients had pairs with non-matching cgMLST types and non-matching vanA plasmids and a median number of 18 days from identification of carriage to clinical infection. CONCLUSIONS: Of our 19 pairs, 13 were a match regarding cgMLST types (68%) and 1 more (5%) had matching vanA plasmids. Infection was thus preceded by colonization with the same isolates in 13 out of 19 patients. The five mismatches (26%) could be explained by the longer interval between colonization and infection.

Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of cases, Denmark, January 2016 to August 2019.

BackgroundCarbapenemase-producing Escherichia coli are increasing worldwide. In recent years, an increase in OXA-244-producing E. coli isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark.AimMolecular characterisation and epidemiological investigation of OXA-244-producing E. coli isolates from January 2016 to August 2019.MethodsFor the epidemiological investigation, data from the Danish National Patient Registry and the Danish register of civil registration were used together with data from phone interviews with patients. Isolates were characterised by analysing whole genome sequences for resistance genes, MLST and core genome MLST (cgMLST).ResultsIn total, 24 OXA-244-producing E. coli isolates were obtained from 23 patients. Among the 23 patients, 13 reported travelling before detection of the E. coli isolates, with seven having visited countries in Northern Africa. Fifteen isolates also carried an extended-spectrum beta-lactamase gene and one had a plasmid-encoded AmpC gene. The most common detected sequence type (ST) was ST38, followed by ST69, ST167, ST10, ST361 and ST3268. Three clonal clusters were detected by cgMLST, but none of these clusters seemed to reflect nosocomial transmission in Denmark.ConclusionImport of OXA-244 E. coli isolates from travelling abroad seems likely for the majority of cases. Community sources were also possible, as many of the patients had no history of hospitalisation and many of the E. coli isolates belonged to STs that are present in the community. It was not possible to point at a single country or a community source as risk factor for acquiring OXA-244-producing E. coli.

A valid and reliable tool in assessing patient education: the Patient Education Implementation Scale.

AIM: This study aimed to develop a valid and reliable tool for assessing the frequency of nurses' implementation of patient education in line with the stages of determining needs, assessment and planning, implementation, and evaluation and documentation. BACKGROUND: Patient education is important in terms of the patient's completion of a reliable and effective treatment process. Patient education is one of the main responsibilities of a nurse. No valid and reliable study that assessed nurses' patient education process implementation was found in the literature. METHODS: This instrument development study was conducted with 583 nurses working at university, private, and research and training hospitals located in the province of Istanbul in Turkey. The items of the Patient Education Implementation Scale were developed in line with the literature and expert opinions. The analyses involved descriptive statistics and psychometric analyses. The level of statistical significance was accepted as P < .05. RESULTS: The content validity index was calculated as 0.96 for the 42-item Patient Education Implementation Scale, which explained 63.37% of the total variance. The scale items whose factor loads were 0.45 or higher were divided into four factors as (a) determining education needs, (b) assessment and planning, (c) implementation, and (d) evaluation and documentation. The Cronbach's alpha coefficients were 0.78-0.95 for the subdimensions and 0.97 for the general scale. CONCLUSION: It was determined that the Patient Education Implementation Scale is a valid and reliable tool.

LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences.

OBJECTIVES: In enterococci, resistance to linezolid is often mediated by mutations in the V domain of the 23S rRNA gene (G2576T or G2505A). Furthermore, four genes [optrA, cfr, cfr(B) and poxtA] encode linezolid resistance in enterococci. We aimed to develop a Web tool for detection of the two mutations and the four genes encoding linezolid resistance in enterococci from whole-genome sequence data. METHODS: LRE-Finder (where LRE stands for linezolid-resistant enterococci) detected the fraction of Ts in position 2576 and the fraction of As in position 2505 of the 23S rRNA and the cfr, cfr(B), optrA and poxtA genes by aligning raw sequencing reads (fastq format) with k-mer alignment. For evaluation, fastq files from 21 LRE isolates were submitted to LRE-Finder. As negative controls, fastq files from 1473 non-LRE isolates were submitted to LRE-Finder. The MICs of linezolid were determined for the 21 LRE isolates. As LRE-negative controls, 26 VRE isolates were additionally selected for linezolid MIC determination. RESULTS: LRE-Finder was validated and showed 100% concordance with phenotypic susceptibility testing. A cut-off of 10% mutations in position 2576 and/or position 2505 was set in LRE-Finder for predicting a linezolid resistance phenotype. This cut-off allows for detection of a single mutated 23S allele in both Enterococcus faecalis and Enterococcus faecium, while ignoring low-level sequencing noise. CONCLUSIONS: A Web tool for detection of the 23S rRNA mutations (G2576T and G2505A) and the optrA, cfr, cfr(B) and poxtA genes from whole-genome sequences from enterococci is now available online.

Surveillance of vancomycin-resistant enterococci reveals shift in dominating clones and national spread of a vancomycin-variable vanA Enterococcus faecium ST1421-CT1134 clone, Denmark, 2015 to March 2019.

We describe clonal shifts in vanA Enterococcus faecium isolates from clinical samples obtained from patients in Denmark from 2015 to the first quarter (Q1) of 2019. During Q1 2019, the vancomycin-variable enterococci (VVE) ST1421-CT1134 vanA E. faecium became the most dominant vanA E. faecium clone and has spread to all five regions in Denmark. Among 174 E. faecium isolates with vanA, vanB or vanA/vanB genes in Q1 2019, 44% belonged to this type.

RUCS: rapid identification of PCR primers for unique core sequences.

MOTIVATION: Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico. RESULTS: Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers. AVAILABILITY AND IMPLEMENTATION: Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS. CONTACT: mcft@cbs.dtu.dk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Personal and professional values held by baccalaureate nursing students.

BACKGROUND: Values are ideals and beliefs that individuals and groups uphold and lie at the core of the diverse world of human behaviour and are expressed in every human decision and action, both consciously and unconsciously. They represent basic beliefs of what is right, good or desirable and motivate both personal and professional behaviour. In the context of nursing profession, values are essential in order to maintain high standards of the nursing care. OBJECTIVES: This study was planned to examine changes in nursing students' personal and professional values between entering and graduating from an undergraduate nursing programme. Ethical considerations: Measures to protect participants included obtaining Deaconship of Nursing Faculty approval, obtaining signed informed consent and maintaining confidentiality. METHODS: This study was designed as longitudinal quality. The research population included 143 students registered at a first grade of a nursing faculty for the 2009-2010 academic year. Data were collected with a Questionnaire Form, the Value Preferences Scale, the Professional Values Precedence Scale and the Nursing Professional Values Scale. FINDINGS: According to the results, social values have statistical differences in 4-year nursing education. Nursing students in second class have higher score in terms of social values than those in third class. Also, majority of students ranked human dignity as first and justice as second and third from first to fourth classes, and they have very high scores on Nursing Professional Values Scale and its subscales and stated that all items of Nursing Professional Values Scale are very important. CONCLUSION: As a result, nursing education has vital role in acquiring and maintaining professional values.

Association Mapping in Turkish Olive Cultivars Revealed Significant Markers Related to Some Important Agronomic Traits.

Olive (Olea europaea L.) is one of the most important fruit trees especially in the Mediterranean countries due to high consumption of table olive and olive oil. In olive breeding, the phenotypic traits associated to fruit are the key factors that determine productivity. Association mapping has been used in some tree species and a lot of crop plant species, and here, we perform an initial effort to detect marker-trait associations in olive tree. In the current study, a total of 96 olive genotypes, including both oil and table olive genotypes from Turkish Olive GenBank Resources, were used to examine marker-trait associations. For olive genotyping, SNP, AFLP, and SSR marker data were selected from previously published study and association analysis was performed between these markers and 5 yield-related traits. Three different approaches were used to check for false-positive results in association tests, and association results obtained from these models were compared. Using the model utilizing both population structure and relative kinship, eleven associations were significant with FDR ≤ 0.05. The largest number of significant associations was detected for fruit weight and stone weight. Our results suggested that association mapping could be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations. This study shows for the first time the use of association mapping for identifying molecular markers linked to important traits in olive tree.

Relationship between self-compassion and emotional intelligence in nursing students.

Nursing focuses on meeting physical, social and emotional health-care needs of individuals, families and society. In health care, nurses directly communicate with patients and try to empathize with them. Nurses give care under emotionally intense conditions where the individual undergoes pain and distress. Research is aimed at analysing the correlation of self-compassion and emotional intelligence of nursing students. The population of the research consisted of all the undergraduate students (571 students) of the 2010-2011 fall semester of the department of nursing. An information form, Self-compassion Scale and Emotional Intelligence Assessment Scale were utilized to obtain data for the research. For the assessment of the findings of research, Statistical Package for Social Sciences 16.0 for Windows was utilized for statistical analysis. Results indicated that there is a correlation between self-compassion and emotional intelligence and that emotional intelligence, which includes the individual perceiving one's emotions and using the knowledge one gained from them to function while directing thoughts, actions and professional applications, has positive contributions to the features of nurses with developed self-compassion.

VirulenceFinder for Enterococcus faecium and Enterococcus lactis: an enhanced database for detection of putative virulence markers by using whole-genome sequencing data.

Enterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.

Metaphors used by in-service training nurses for in-service training nurses in Turkey.

AIM: To report a study conducted using a qualitative and quantitative study pattern with an aim to reveal the perceptions of in-service training nurses about in-service training nurses via metaphors. BACKGROUND: The in-service training nurse assumes great responsibility in the effective and efficient implementation of the educational activities in healthcare. In line with this, determining the perceptions of the in-service training nurses about in-service training nurses via metaphors and taking this into consideration in professional activities are important in terms of developing, changing, or questioning the perspectives of the in-service training nurses about their roles and developing their own training nurse identity. DESIGN: This article was designed as qualitative and quantitative study pattern. METHODS: The population of the study included 93 in-service training nurses. Data were collected between June-September 2009. To collect data, each in-service training nurse was asked to complete the blanks in the sentence, 'The in-service training nurse is like a/an.....................because..................' The data were analysed using qualitative (content analysis) and quantitative (chi-square) data analysis methods. FINDINGS: According to the findings of the study, the in-service training nurses identified 59 metaphors in total. The metaphors were grouped under nine conceptual categories depending on the characteristics they had in common. In cognitive image of the in-service training nurses relating to the concept of in-service training nurse, the outstanding conceptual category was the in-service training nurse as a knowledge provider. CONCLUSION: The metaphors can be used as a strong research tool in understanding, revealing and explaining the cognitive images of the in-service training nurses.

Personal values of baccalaureate nursing students in Turkey.

Value education is aimed at helping students develop a mode of reasoning, enabling them to make decisions and deal with conflicts on a daily basis. For this, it should firstly be assessment personal values of nursing students. The purpose of the study was to determine the personal values of nursing students with respect to certain variables. The population of the study, which had a cross-sectional design, included all undergraduate students (n = 525) attending the nursing school. The sample group comprised 397 nursing students selected from among the nursing students attending a baccalaureate programme in Turkey using the disproportional cluster sampling method. Data were collected utilizing the Personal Information Form and Value Preferences Scale. The personal values of the students were found to be moral, social, financial/economic, aesthetic, political, religious and scientific/theoretical values. The study suggested that the age, year at school and economic level of the family affected the students' values. Values influence behaviours that are an essential component of humanistic nursing care. They are integral to professional socialization, evident in nursing care and fundamental decisions that affect practice.

Do the Lifelong Learning Tendencies of Nursing Students Affect Their Attitudes Toward E-Learning?

AIM: This study aimed to determine the lifelong learning tendencies and e-learning attitudes of prospective nurses and the relationship between these variables. METHOD: This was a descriptive study conducted to find the relationship between lifelong learning tendencies and e-learning attitudes of nurses. The population of the study consisted of a total of 1202 students who were enrolled in the nursing faculty of a state university. The data were collected by an information form, the Lifelong Learning Tendency Scale, and the E-Learning Attitude Scale. The study was conducted between April and May 2018. Continuous variables were presented as arithmetic means, standard deviations, and minimum, maximum, and median values, while categorical variables were presented as frequencies and percentages. Pearson correlation test was used to determine the relationship between the scores of the scales. RESULTS: The minimum score of the nursing students was 70.00 and their maximum scores was 152.00 in the Lifelong Learning Tendency Scale, with a mean score of 122.80 ± 21.35. The minimum score of the participants was 34.00 and their maximum score was 95.00 in the E-Learning Attitude Scale, with a mean score of 62.56 ± 8.72. There was a positive and weak statistically significant relationship between the lifelong learning tendencies and e-learning attitudes of the prospective nurses (r = .238, p > .01). CONCLUSION: As a result of the study, the lifelong learning tendencies of the nursing students were found to be high, and considering the subdimension scores of lifelong learning tendency scale of the nursing students, in general, the participants' motivation, persistence, and deficiency in learning scores were high and curiosity motivation scores were medium. They had medium-level attitudes toward e-learning, and there was a weak, positive relationship between their lifelong learning tendencies and e-learning attitudes. It is recommended that involving nursing students in seminars, conferences, and scientific activities will support their lifelong learning. It is also recommended to organize learning environments where they will experience positive e-learnings.

Complete Genome Sequences of Methicillin-Resistant Staphylococcus aureus Strains 110900 and 128254, Two Representatives of the CRISPR-Cas-Carrying Sequence Type 630/spa Type t4549 Lineage.

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type 630 (ST630) and spa type t4549 is an emerging lineage in Nordic countries, and some representatives carry the CRISPR-Cas system. Here, the complete genome sequences of two isolates from this lineage are presented, comprising chromosomes of 2,918,239 and 2,877,083 nucleotides, respectively, and a 2,473-nucleotide plasmid carrying erm(C).

Molecular characterization of Danish ESBL/AmpC-producing Klebsiella pneumoniae from bloodstream infections, 2018.

OBJECTIVES: The aim of the study was to molecularly characterize third-generation cephalosporin-resistant Klebsiella pneumoniae isolated from bloodstream infections in Denmark in 2018 using whole-genome sequencing (WGS) data, and to compare these isolates to the most common clones detected in 2006 and 2008. METHODS: Sixty-two extended-spectrum beta-lactamase (ESBL)/AmpC-producing K. pneumoniae isolates from Danish blood cultures from 2018 were analysed using WGS to obtain multilocus sequence typing (MLST), core genome MLST (cgMLST), resistance profile and phylogeny. These were compared to the most common ESBL K. pneumoniae clones detected in 2006 and 2008. RESULTS: The most common ESBL clone was ST15 CTX-M-15, the DHA-1 enzyme was the most common in AmpC isolates, and the OXA-48-like group was the most common carbapenemase. Thirty-nine different sequence types (STs) were found, with the most frequent being ST14, ST15 and ST37, accounting for 24% of the isolates. The isolates were subdivided into 55 complex types (CTs) of which 49 were singletons, with the most frequent being ST14-CT2080. Two of the CTX-M-15-producing isolates from 2018 belonged to the ST15-CT105/CT3078 clone, which was first detected in 2006. CONCLUSIONS: The ESBL/AmpC K. pneumoniae isolates detected in Danish blood cultures belonged to many different types. No dominant clones were circulating in Danish hospitals, but the ST15-CT105/CT3078 CTX-M-15 K. pneumoniae clone was seen 13 years after its first detection.

Genome wide association study of 5 agronomic traits in olive (Olea europaea L.).

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.