Endemic Genotypes Research Articles

Screening Iranian endemic coriander genebank germplasm for drought tolerance using a new multivariate statistical method

Drought is one of the serious abiotic factors influencing crop production such as coriander. Development of tolerant genotypes is prevented by the lack of effective selection criterion. Objectives of this study were evaluation of coriander accessions for water deficit stress and introduce a new multivariate method to select drought tolerant genotypes. For investigation of 19 traits, 16 Iranian endemic coriander genotypes were grown in a glasshouse under control and water deficit stress conditions. Shoot dry weight (SDW), fruit weight per plant (FWPP), fruit number per plant (FNPP) and umbel number per plant (UNPP) were decreased (Susceptibility Index>38%) under water deficit stress condition compared with the control condition. While the mean values of root dry weight (RDW) and root to shoot ratio (RTSR) were increased 1.49% and 97.33% under water stress condition, respectively. Because of high inheritance, high expected genetic gain, high genotypic correlation with together, well response to drought stress and high explanation of FWPP variation in regression model, the FWPP, branch number per plant (BNPP), FNPP and SPAD chlorophyll content in grain filing stage (SCCIGFS) traits were selected to screen coriander genotypes for drought tolerance in coriander. The principal component analysis mediated method (PCAMM) indicated as comprehensive criterion to screen drought tolerant genotypes. This method was highly heritabl, able to separate the Fernandez described A, B, C and D groups, no multicollinear and using multiple drought tolerance related traits. The PCAMM results showed that G13, G16, G2 and G12 genotypes belonged to Fernandez described A, B, C and D groups, respectively.

Genotypic Diversity of Candida parapsilosis Complex in Invasive Candidiasis at a Pediatric Tertiary Hospital: A 5-Year Retrospective Study.

Invasive candidiasis (IC) contributes to the morbidity and mortality of hospitalized patients and represents a significant burden to the healthcare system. Previous Brazilian studies have reported the presence of endemic Candida parapsilosis sensu stricto genotypes causing candidemia and clonal transmission involving fluconazole-resistant isolates. We performed a 5-year retrospective analysis of IC cases in a Brazilian tertiary pediatric hospital and conducted a molecular investigation of C. parapsilosis sensu stricto. Non-duplicate C. parapsilosis sensu stricto genotyping was performed by microsatellite analysis. Antifungal susceptibility and biofilm formation were also evaluated. A total of 123 IC episodes were identified, with an IC incidence of 1.24 cases per 1000 hospital admissions and an overall mortality of 34%. The main species were the C. parapsilosis complex (35.8%), Candida albicans (29.2%), and Candida tropicalis (21.9%). All C. parapsilosis sensu stricto were recovered from blood cultures, and 97.5% were biofilm producers. Microsatellite typing identified high genotypic diversity among the isolates. We observed that all isolates were sensitive to amphotericin B, and although one isolate was non-sensitive to fluconazole, only a silent mutation on ERG11 gene was identified. No clear evidence of clonal outbreak or emergence of fluconazole-resistant isolates was found, suggesting that multiple sources may be involved in the epidemiology of IC in children.

Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

SummaryBackgroundTyphoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji.MethodsGenomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases.FindingsGenomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted.InterpretationCyclones and flooding drove ‘waves’ of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries.FundingThis work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.

Genetic Diversity of Flavescence Dorée Phytoplasmas in Vineyards of Serbia: From the Widespread Occurrence of Autochthonous Map-M51 to the Emergence of Endemic Map-FD2 (Vectotype II) and New Map-FD3 (Vectotype III) Epidemic Genotypes

Flavescence dorée (FD) is a European quarantine disease of grapevine caused by FD phytoplasma (FDp) transmitted by the leafhopper of North American origin Scaphoideus titanus. The disease affects the most important viticultural regions of Europe and all wine-growing regions of Serbia. Unlike the insect vector, the pathogen is native to Europe and associated with several wild host plants among which alder trees as the main source of two out of three map genetic clusters of pathogen variants (Map-FD1 and FD2). Heretofore, the FDp epidemic in Serbian vineyards was thought to be monotypic, i.e., caused by the single genotype of the Map-FD3 cluster, M51, and correlated with clematis as the natural source plant. This study aimed to provide data on genetic diversity, through map and vmpA gene typing, and insights into ecological properties of epidemiological cycles driving the epidemic outbreaks of FD in Serbia today. Map genotyping of 270 grapevine isolates collected from 2017 to 2019 confirmed M51 as autochthonous genotype widespread in all wine producing regions of Serbia and the dominant FDp epidemic genotype in most of the districts (75%, 202/270 isolates), except in north Serbia where multiple outbreaks of M12 Map-FD3 were recorded (54 isolates). Tree of heaven is reported as a new FDp plant reservoir for the Serbian vineyards, hosting the M51 genotype, along with clematis. An outbreak of a new endemic Map-FD3 genotype M144 was documented in grapevine samples from east Serbia (5 isolates), correlating with previous findings of the same genotype in clematis. In addition, single grapevine infections with five new Map-FD3 genotypes (M150-M154) were recorded in central Serbia, thus indicating high endemic potential for new outbreaks. The vmpA typing placed all Map-FD3 isolates into the VmpA-III cluster, i.e., Vectotype III. Finally, we found direct evidence that at least two FDp endemic genotypes, M89 and M148, of the Map-FD2/VmpA-II have escaped from alders and propagated in the grapevine-S. titanus pathosystem in Serbia (Vectotype II). Our findings confirm the high complexity of the FDp ecological cycle and provide evidence of a unique, autochthonous Balkan epidemiology sourced endemically.

A clinical and molecular epidemiological survey of hepatitis C in Blantyre, Malawi, suggests a historic mechanism of transmission.

Hepatitis C virus (HCV) is a leading cause of liver disease worldwide. There are no previous representative community HCV prevalence studies from Southern Africa, and limited genotypic data. Epidemiological data are required to inform an effective public health response. We conducted a household census‐based random sampling serological survey, and a prospective hospital‐based study of patients with cirrhosis and hepatocellular carcinoma (HCC) in Blantyre, Malawi. We tested participants with an HCV antigen/antibody ELISA (Monolisa, Bio‐Rad), confirmed with PCR (GeneXpert, Cepheid) and used line immunoassay (Inno‐LIA, Fujiribio) for RNA‐negative participants. We did target‐enrichment whole‐genome HCV sequencing (NextSeq, Illumina). Among 96,386 censused individuals, we randomly selected 1661 people aged ≥16 years. Population‐standardized HCV RNA prevalence was 0.2% (95% CI 0.1–0.5). Among 236 patients with cirrhosis and HCC, HCV RNA prevalence was 1.9% and 5.0%, respectively. Mapping showed that HCV RNA+ patients were from peri‐urban areas surrounding Blantyre. Community and hospital HCV RNA+ participants were older than comparator HCV RNA‐negative populations (median 53 vs 30 years for community, p = 0.01 and 68 vs 40 years for cirrhosis/HCC, p < 0.001). Endemic HCV genotypes (n = 10) were 4v (50%), 4r (30%) and 4w (10%). In this first census‐based community serological study in Southern Africa, HCV was uncommon in the general population, was centred on peri‐urban regions and was attributable for <5% of liver disease. HCV infection was observed only among older people, suggesting a historic mechanism of transmission. Genotype 4r, which has been associated with treatment failure with ledipasvir and daclatasvir, is endemic.

Can transplanting seedlings with protection against herbivory be a cost-effective restoration strategy for seasonally flooded environments?

Transplantation of naturally regenerating seedlings (hereafter wildlings) has great potential as a restoration tool as it involves the use of acclimatized individuals and preservation of local and endemic genotypes. When successfully used, this technique has the added benefits of increasing structural and compositional diversity, preserving local and endemic genotypes, and reducing ecological restoration costs. In wetland ecosystems, flooding is an abiotic filter that may hinder success of restoration efforts. We hypothesized that transplanting “ecologically toughened” wildlings from low-lying, flooded areas into restoration areas of higher relief and lower frequency of flooding, would be a successful strategy. In this study, we transplanted wildlings from periodically flooded areas upslope to test the effect of topographic position (where they were collected and outplanted), and protection against herbivory on seedling survival and growth. The experimental design included two collection times and planting areas (high and low topography), two seedling height, use of protection against mammalian herbivory, and four species that represent different functional types. We also evaluated the costs involved. The best experimental outcome for the four study species (most abundance floodplain species) was found with small seedlings (10–39 cm) collected at low relief and outplanted to higher elevations, with protection against herbivory. Even under unusually extreme flood events (high flooding over 7 months) the tree legume Inga vera has emerged with the highest survival rate. The costs of transplantation are lower (USD 739 ha−1) than those found in previous studies and the use of protection against herbivory was also considerably low (USD 2484 ha−1). That said, these estimated costs are on an experimental scale and do not represent large-scale operations, which could reduce and improve cost-benefits significantly. In remote places such as the Pantanal, the lack of nursery infrastructure, high associated costs of seedling production and vulnerability to herbivory are the main challenges for restoration. Hence, wildling collection can be a useful strategy to overcome such obstacles.

Molecular Epidemiology of B3 and D8 Measles Viruses through Hemagglutinin Phylogenetic History.

Of the 24 known measles genotypes, only D8 and B3 are responsible for outbreaks in the last years in Europe, Asia, and America. In this study the H gene of 92 strains circulating between 2015 and 2019 in Lombardy, Northern Italy, and 1273 H sequences available in GenBank were analyzed in order to evaluate the genetic variability and to assess the conservation of the immunodominant sites. Overall, in Lombardy we observed the presence of four different B3 and three different D8 clusters, each one of them including sequences derived from viruses found in both vaccinated and unvaccinated subjects. Worldwide, the residue 400 within the H protein, a position located within the main immune epitope, is mutated in all circulating strains that belong to the two globally endemic genotypes, B3 and D8. Our data demonstrate the usefulness of measles virus (MV) H gene sequencing. Indeed, the monitoring the H protein epitopes of circulating strains could be included in the measles laboratory surveillance activities in order to improve and optimize strategies for measles control, as countries go towards elimination phase.

Molecular Characterization of Candida parapsilosis by Microsatellite Typing and Emergence of Clonal Antifungal Drug Resistant Strains in a Multicenter Surveillance in China.

Candida parapsilosis is an important species causing invasive candidiasis (IC) in China. The present survey was a national multicenter study of the molecular epidemiology and antifungal susceptibility profiles of C. parapsilosis. Non-duplicate C. parapsilosis isolates were collected from 10 hospitals across China in the CHIF-NET program 2016–2017. Isolates were genotyped using four highly polymorphic microsatellite markers, and susceptibility profiles determined using Sensititre YeastOneTM YO10. A total of 319 C. parapsilosis from separate patients with IC were studied; 49.2, 17.9, and 10.3% isolates were from patients in surgical departments, general intensive care units (ICUs) and neonatal ICUs (NICU), respectively. C. parapsilosis showed good susceptibility to nine antifungal drugs. Microsatellite analysis identified 122 microsatellite (MT) types. Most MT types had sporadic distribution. However, we identified 32 clusters across 10 hospitals; seven clusters were caused by seven endemic genotypes involving five or more isolates in hospitals designated as H01, H02, H06, and H10. These clusters mainly affected surgical departments and ICUs, except for genotype MT42 which was seen in 22 patients from NICU (hospital H06). Of 16 fluconazole-resistant isolates, seven from hospital H02 shared the same genotype MT70, and three from hospital H04 were of genotype MT47. For 37 isolates with non-wild type MICs to 5-flucytosine, 29 were from hospital H01 (genotype MT48). Here we present the first nationwide molecular epidemiology study of C. parapsilosis in China, identified several previously unrecognized clusters, which included antifungal drug resistant isolates. These findings provide important data for control of IC in China.

Genotyping of Candidaalbicans isolates from oropharyngeal candidiasis in head and neck cancer patients in Iran: Molecular epidemiology and SAP2 gene expression

ObjectiveMultilocus sequence typing is a powerful method for genotyping of clinical isolates of Candidaalbicans. Cross-contamination between the patients is an important reason for nosocomial infections. Oropharyngeal candidiasis (OPC) caused by C. albicans is an important problem in patients with head and neck cancer, in Cancer Institute of Tehran. Here we studied the endemic genotypes of C. albicans isolates and the relationship between geographic distributions, potential cross-contaminations and the expression of SAP2 gene, an important gene in oral candidiasis, with MLST groups. Material and methodsA total of 32 clinical strains of C. albicans isolated from head and neck cancer patients with oropharyngeal candidiasis were subjected to MLST analysis and SAP2 gene expression was analyzed by Real-time PCR. ResultsWe identified 75 polymorphic sites in 7 loci of C. albicans isolates and 30 diploid sequence types which 27 of them were found as new. After eBURST analysis, our results determined that CC 124 was the most prevalent group among all CCs. SAP2 gene showed high expression in almost all OPC patients’ isolates, compared to the control. ConclusionWe found few genetically-related as well as identical isolates among the 32 Candida strains which indicated low cross-contaminations among the patients. There was no relationship between C. albicans MLST profiles and their geographic distribution, cancer type and SAP2 gene expression. This lack of correlation was possibly due to the small understudy population; hence, finding more relevance requires studies with a higher number of samples.

ارزیابی تنوعپذیری ژنوتیپهای گندم نان تحت شرایط مختلف رطوبتی با استفاده از روشهای متنوع آماری

از بین تنش‌های محیطی، تنش خشکی مهم‌ترین عامل کاهش تولیدات گیاهان در سراسر جهان است. جهت مطالعه تنوع ژنتیکی و ارتباط بین صفات مختلف با عملکرد دانه در 17 ژنوتیپ (شامل ارقام و لاین‌های مختلف) گندم نان، آزمایشی در قالب طرح بلوک‌های کامل تصادفی با سه تکرار تحت دو شرایط عدم تنش خشکی و شرایط دیم در سال زراعی 90-1389 در مزرعه آموزشی-پژوهشی دانشگاه پیام‌نور اسدآباد اجرا گردید. در این آزمایش صفات عملکرد دانه، تعداد دانه در سنبله، طول سنبله، طول برگ پرچم، عرض برگ پرچم، وزن صد دانه، ارتفاع بوته، محتوی نسبی آب برگ، میزان نسبی آب ازدست‌رفته، درصد سبزینگی برگ (میزان کلروفیل) و مساحت برگ پرچم اندازه‌گیری شدند. نتایج تجزیه واریانس ساده تنوع بالا و معنی‌داری را در هر دو شرایط رطوبتی (مکان) نشان داد. نتایج تجزیه واریانس مرکب اثر ژنوتیپ را برای اکثر صفات معنی‌دار نشان داد. نتایج تجزیه همبستگی نیز بیانگر این بود که بین عملکرد دانه و درصد سبزینگی برگ (اسپاد) در شرایط دیم و بین عملکرد دانه و میزان آب ازدست‌رفته برگ در شرایط عدم تنش خشکی همبستگی مثبت و معنی‌داری (P<0.05) مشاهده گردید. نتایج تجزیه خوشه‌ای ژنوتیپ‌های موردمطالعه را در هر دو شرایط محیطی در سه گروه مجزا و متفاوت قرار داد. به‌طوری‌که بیشترین فاصله ژنتیکی در هر دو شرایط رطوبتی بین خوشه اول و سوم مشاهده گردید. تجزیه به مؤلفه‌های اصلی در شرایط عدم تنش خشکی و شرایط دیم به ترتیب 71% و 76% از تنوع موجود را توجیه نمودند. با توجه به مقایسه میانگین عملکرد دانه، ژنوتیپ‌های 7 (3790 کیلوگرم در هکتار)، 8 (3525 کیلوگرم در هکتار) و 13 (3305 کیلوگرم در هکتار) در شرایط عدم تنش خشکی و ژنوتیپ‌های‌ 13 (2147 کیلوگرم در هکتار)، 14 (2440 کیلوگرم در هکتار) و 17 (2254 کیلوگرم در هکتار) در شرایط دیم بیش‌ترین عملکرد دانه را تولید کردند.

High-resolution fingerprinting of Candida parapsilosis isolates suggests persistence and transmission of infections among neonatal intensive care unit patients in Kuwait

Candida parapsilosis causes ~35% of all candidemia cases in neonates. High-resolution fingerprinting of C. parapsilosis isolates from neonatal intensive care unit (NICU) patients in Maternity Hospital (MH) was performed to identify epidemiologically related strains. Sixty-eight bloodstream/colonizing strains isolated from 59 NICU patients, two isolates from health care workers (HCWs) from MH and 18 bloodstream isolates from two other hospitals were used. Six microsatellite markers were employed, isolates were assigned a numerical microsatellite genotype (MSG), dendrogram was constructed and similarities between genotypes were visualized by minimum spanning tree. Fifty bloodstream isolates from MH yielded 37 MSGs with 20 isolates clustering in 7 MSGs. Duplicate isolates and colonizing strains yielded same/highly similar MSG as bloodstream isolates. Colonizing strains from two non-candidemia patients yielded unique MSGs while others belonged to a cluster. All isolates from HCWs and from two other hospitals belonged to unique MSGs. Cluster isolates came from patients in NICU-1 or from neonates in NICU-1 and other NICUs. Clonal complexes comprising closely related genotypes indicative of microevolution were also detected. Our data show that some C. parapsilosis strains have persisted in MH environment over several years and these endemic genotypes were transmitted to other patients in NICU-1 and/or other nearby NICUs.

Genetic diversity analysis and character associations in black cumin (Nigella sativa L.) based on agro-morphological and phytochemical traits

ABSTRACTBlack cumin (Nigella sativa L.) is one of the important medicinal plants that used in food and pharmaceutical industries. In the present study, 32 Iran endemic black cumin genotypes were evaluated through randomized complete block design with three replications in 2016 and 2017 growing seasons to determine the extent of genetic diversity and character associations for agro-morphological and phytochemical traits. Results showed the significant differences between genotypes for all traits studied. Clustering analysis using agro-morphological and phytochemical traits grouped genotypes into the two distinct groups. The values of percentage of essential oil and fatty oil content varied from 0.65 to 0.1.36% and 25.30% to 35.02% between genotypes, respectively. The highest seed yield and fatty oil yield obtained for Arak genotype. GC and GC/MS analyses of essential oil and fatty oil compositions of the Arak genotype revealed that p-cymene and linoleic acid were main components, respectively. Stepwise regression analysis revealed that shoot dry mass, days to ripening and seed length were the most important traits associated with seed yield, fatty oil yield and essential oil yield. Hence, these traits can be considered as important indicators for early selection for seed yield and quality in black cumin breeding programs.

The Amino-Terminal Region of Hepatitis E Virus ORF1 Containing a Methyltransferase (Met) and a Papain-Like Cysteine Protease (PCP) Domain Counteracts Type I Interferon Response.

Hepatitis E virus (HEV) is responsible for large waterborne epidemics of hepatitis in endemic countries and is an emerging zoonotic pathogen worldwide. In endemic regions, HEV-1 or HEV-2 genotypes are frequently associated with fulminant hepatitis in pregnant women, while with zoonotic HEV (HEV-3 and HEV-4), chronic cases of hepatitis and severe neurological disorders are reported. Hence, it is important to characterize the interactions between HEV and its host. Here, we investigated the ability of the nonstructural polyprotein encoded by the first open reading frame (ORF1) of HEV to modulate the host early antiviral response and, in particular, the type I interferon (IFN-I) system. We found that the amino-terminal region of HEV-3 ORF1 (MetYPCP), containing a putative methyltransferase (Met) and a papain-like cysteine protease (PCP) functional domain, inhibited IFN-stimulated response element (ISRE) promoter activation and the expression of several IFN-stimulated genes (ISGs) in response to IFN-I. We showed that the MetYPCP domain interfered with the Janus kinase (JAK)/signal transducer and activator of the transcription protein (STAT) signalling pathway by inhibiting STAT1 nuclear translocation and phosphorylation after IFN-I treatment. In contrast, MetYPCP had no effect on STAT2 phosphorylation and a limited impact on the activation of the JAK/STAT pathway after IFN-II stimulation. This inhibitory function seemed to be genotype-dependent, as MetYPCP from HEV-1 had no significant effect on the JAK/STAT pathway. Overall, this study provides evidence that the predicted MetYPCP domain of HEV ORF1 antagonises STAT1 activation to modulate the IFN response.

1214. High Frequency of Genes Encoding Resistance to Heavy Metals in Methicillin-Resistant Staphylococcus aureus (MRSA) Endemic Lineages From South America

BackgroundMRSA-USA300 is a community-associated clone that has spread worldwide, becoming the most successful clone in the USA. Since 2005, the MRSA-USA300 Latin-American Variant (USA300-LV) has disseminated in community and hospitals in Northern South America. Phylogenetic analysis revealed that USA300-LV is not derived from the USA300 (NA-USA300) but rather, the two clones diverged from a common ancestor. During their evolution, NA-USA300 strains incorporated the ACME element and USA300-LV acquired a copper and mercury resistance mobile element designated COMER. Interestingly, contamination by heavy metals in South American has been recently highlighted and could be driving the selection of resistant genetic lineages. We investigated the frequency of merA, merB, and copB in genomes of clinical isolates of S. aureus from Latin America (LA).MethodsThe presence of merA/merB and copB encoding mercury and copper resistance, respectively, were investigated in 515 S. aureus sequenced genomes recovered from bacteremic patients in hospitals from nine Latin American hospitals trough BLAST searches.ResultsThe prevalence of merAB in S. aureus was 35% (181 out of 515 genomes). Interestingly, among 181 merAB-positive S. aureus, 174 were MRSA (96%). Moreover, 71%, 60%, 59%, and 51% of MRSA genomes from Peru, Ecuador, Colombia, and Venezuela, respectively, harbored mercury resistance genes. Similarly, 65%, 60%, and 22% of MRSA genomes from Ecuador, Colombia, and Venezuela, contained the copB gene. Among 174 MRSA harboring merAB, ST8 and ST5 were the most predominant lineages in (43% and 45% of genomes, respectively). In contrast, among 95 MRSA carrying copB, ST8 was the most frequent lineage (96% of isolates). MRSA from countries with high prevalence of mercury genes showed association with ST5 and ST8. 88% of Colombian and 87% of Ecuadorian MRSA harboring merAB belonged to ST8 lineage, whereas ST5 was predominant in 88% of Peruvian MRSA. In Venezuela, ST5 and ST8 were found in 44% and 33%, respectively, of MRSA positive for merAB.ConclusionHigh levels of mercury in rivers of Colombia, Ecuador and Peru has been reported. Thus, the prevalence of heavy metal resistance genes in MRSA clinical isolates suggest an adaptation of endemic genotypes to heavy metal contamination caused by activities like metal mining.Disclosures J. M. Munita, Pfizer: Grant Investigator, Research grant. C. Arias, Merck & Co., Inc.: Grant Investigator, Research support. MeMed: Grant Investigator, Research support. Allergan: Grant Investigator, Research support.

Grape phylloxera (Daktulosphaira vitifoliaeFitch) in Argentina: ecological associations to diversity, population structure and reproductive mode

Background and Aims The North American insect pest grape phylloxera was introduced into Europe in the 19th century and devastated the Vitis vinifera-based vineyards. It has since become widely distributed among the world’s vineyards. Although it is present in Argentina, it has not caused any major damage. This work aims: to characterise the genetic diversity of Argentinean phylloxera; to determine population structure and reproductive mode; to compare Argentinean genotypes with samples from seven other countries; and to examine relationships between the infestation level and genetic profile with ecological factors. Methods and Results One hundred and twenty-nine samples of phylloxera from Argentinean provinces were analysed with 21 microsatellite markers. Seventeen multilocus genotypes were identified. Unweighted pair group method with arithmetic mean analysis identified two major groups. Principal coordinates analysis grouped together Peruvian, California biotypes A and B and Argentinean phylloxera, showing dissimilarity with other foreign samples. Associations between infestation level, berry colour and climatic region, and associations between genetic clusters and climatic region were established. Conclusions Endemic Argentinean phylloxera genotypes showed genetic diversity and were different from other samples assessed. Parthenogenesis is proposed as the main reproductive mode, but rare sexual reproduction is not ruled out. No particular structure was observed in the phylloxera populations. Significance of the Study This is the first detailed report on the genetic characterisation of phylloxera populations in Argentina using microsatellites markers. It provides the foundation for further studies.

Genotyping of clinical isolates of Candida glabrata from Iran by multilocus sequence typing and determination of population structure and drug resistance profile.

Candida glabrata is often the second most common causative agent for candidiasis following Candida albicans. Despite the importance of C. glabrata infections, few epidemiological studies have been conducted on this issue. The goal of this study was genotyping of clinical isolates of C. glabrata by multilocus sequence typing (MLST) technique for determination of the endemic prevalent genotypes and any association between isolation source and drug resistance. A total of 50 C. glabrata clinical isolates from Iran were analyzed by MLST and tested for in-vitro susceptibilities to amphotericin-B, caspofungin, fluconazole, and voriconazole according to the Clinical Laboratory Standards Institute (CLSI) M27-A4 document guidelines. Among these isolates, 16 distinct STs were identified, indicating a discriminatory power index of 0.9029. The three major sequence types (STs) were ST-59, ST-74, and ST-7 with 10, 8, and 7 isolates, respectively. Furthermore, a total of 11 new sequences were found, to which no allele numbers were assigned in the MLST database. All the isolates were susceptible to amphotericin B and caspofungin. Fluconazole resistance was shown in four isolates. Also, a sole isolate was voriconazole resistant. This study shows that the population structure of C. glabrata in Iran consists of groups closely related to the global database as well as to some new clonal clusters and STs. Regarding the high prevalence of 11 new sequences found in this study, it can be concluded that, these new alleles are among the endemic genotypes of Iran. The genotypes or STs were independent of drug susceptibility and anatomic sources.

Molecular Fingerprinting Studies Do Not Support Intrahospital Transmission of Candida albicans among Candidemia Patients in Kuwait.

Candida albicans, a constituent of normal microbial flora of human mucosal surfaces, is a major cause of candidemia in immunocompromised individuals and hospitalized patients with other debilitating diseases. Molecular fingerprinting studies have suggested nosocomial transmission of C. albicans based on the presence of clusters or endemic genotypes in some hospitals. However, intrahospital strain transmission or a common source of infection has not been firmly established. We performed multilocus sequence typing (MLST) on 102 C. albicans bloodstream isolates (representing 92% of all culture-confirmed candidemia patients over a 31-month period at seven major hospitals) to identify patient-to-patient transmission or infection from a common source in Kuwait, a small country in the Middle East where consanguineous marriages are common. Repeat bloodstream isolates from six patients and nine surveillance cultures from other anatomic sites from six patients were also analyzed. Fifty-five isolates belonged to unique genotypes. Forty-seven isolates from 47 patients formed 16 clusters, with each cluster containing 2–9 isolates. Multiple isolates from the same patient from bloodstream or other anatomical sites yielded identical genotypes. We identified four cases of potential patient-to-patient transmission or infection from a common source based on association analysis between patients' clinical/epidemiological data and the corresponding MLST genotypes of eight C. albicans isolates. However, further fingerprinting by whole genome-based amplified fragment length polymorphism (AFLP) analysis yielded 8 different genotypes, ruling out intrahospital transmission of infection. The findings suggest that related strains of C. albicans exist in the community and fingerprinting by MLST alone may complicate hospital infection control measures during outbreak investigations.

Assessing Potential of Iranian Chicory Genotypes for Industrial Application

Chicory (Cichoriumintybus L.) is an important industrial crop which is used for inulin production. Inulin is widely applied as food ingredient due to its health promoting properties. For the first time, attempts were made to investigate thirteen endemic chicory genotypes including three pumilum populations, along with five root chicory cultivars, four witloof chicory varieties and a crispum endive to find their phylogenic relationships based on some diagnostic morphological traits as well as comparing their fresh root yield, total carbohydrate content as indicator of inulin percentage, and inulin yield in RCBD with three replications, 2013-14. In general, with the exception of Firizi landrace which was classified in C. intybus class, the other endemic genotypes exhibited the maximum similarity with C. endivia, as all formed a monophyletic clade. The highest inulin yield was obtained for ‘Orchies’, after that for ‘Schepens’, ‘Tilda’ and ‘Hera’, respectively, due to firstly their higher root yield and secondly their high inulin percentage. On the whole, fault of flowering at the first year of life cycle of endemic genotypes made intensive selection and breeding of Iranian genotypes for bolting resistance priority work before applying them to build root chicory varieties

Filling a gap in the distribution of Batrachochytrium dendrobatidis: evidence in amphibians from northern China.

Chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd) has been recognized as a major driver of amphibian declines worldwide. Central and northern Asia remain as the greatest gap in the knowledge of the global distribution of Bd. In China, Bd has recently been recorded from south and central regions, but areas in the north remain poorly surveyed. In addition, a recent increase in amphibian farming and trade has put this region at high risk for Bd introduction. To investigate this, we collected a total of 1284 non-invasive skin swabs from wild and captive anurans and caudates, including free-ranging, farmed, ornamental, and museum-preserved amphibians. Bd was detected at low prevalence (1.1%, 12 of 1073) in live wild amphibians, representing the first report of Bd infecting anurans from remote areas of northwestern China. We were unable to obtain evidence of the historical presence of Bd from museum amphibians (n = 72). Alarmingly, Bd was not detected in wild amphibians from the provinces of northeastern China (>700 individuals tested), but was widely present (15.1%, 21 of 139) in amphibians traded in this region. We suggest that urgent implementation of measures is required to reduce the possibility of further spread or inadvertent introduction of Bd to China. It is unknown whether Bd in northern China belongs to endemic and/or exotic genotypes, and this should be the focus of future research.

Genotyping of circulating measles strains in Italy in 2010.

The European Regional Office of the World Health Organization developed a strategic approach to stop the indigenous transmission of measles in its 53 Member States by 2015. In Italy, laboratory surveillance activity is implemented by the National Reference Laboratory for Measles and Rubella at the Italian National Institute of Health (Istituto Superiore di Sanità, Rome). The role of the National Reference Laboratory is to strengthen surveillance systems through rigorous case investigation and laboratory confirmation of suspected sporadic cases and outbreaks. Genetic characterization of wild-type measles virus is an essential component of the laboratory-based surveillance. This study describes the molecular characterization of measles virus strains isolated during 2010. Dried blood spots, urine and oral fluid samples were collected from patients with a suspected measles infection. Serological tests were performed on capillary blood, and viral detection was performed on urine and oral fluid samples through molecular assay. Positive samples were sequenced and phylogenetically analysed. The phylogenetic analysis showed a co-circulation of genotypes D4 and D8, and sporadic cases associated to genotypes D9 and B3. Then, molecular epidemiology of measles cases permitted to establish that D4 and D8 were the endemic genotypes in Italy during 2010.