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The present study was entitled “Study of genetic variability and character association in elite lines of finger millet [Eleusine coracana (L.)] Suitable for the eastern plain zone of Uttar Pradesh” was carried out to estimate the genetic variability, genetic advance, correlation, between yield and yield contributing traits and direct and indirect effect of yield component on yield through path analysis (18). The present investigation concluded genotype acquiring the less for grain yield per plant were IC NO 0474166 (FIN NO 5126) (0.41 t/ha). The genotype IC NO 0473932 (FIN NO 4980) (2.22 t/ha) was high ear head length. This genotype was the highest grain yield per plant than CHECK GPU 67 (0.55 t/ha). The genotype IC NO 0473932 (FIN NO 4980) (2.22 t/ha) was 1.67 t/ha higher yield than CHECK GPU 67 (0.55 t/ha). The highest genotypic variance observed were finger length, harvest index, grain yield per plant. The highest phenotypic coefficient of variance observed were test weight, finger length, harvest index, grain yield per plant. The highest heritability were recorded in harvest index, grain yield per plant, flag leaf width, plant height, Number of days to 50% flowering, Days to Maturity, finger width, finger length. The traits Number of days to 50% flowering, biological yield per plant, plant height, days to Maturity exhibited moderate genetic advance. The traits were biological yield per plant, test weight, finger width, harvest index, finger length, grain yield per plant recorded high genetic advance as percentage of mean. Genotypic correlation coefficient reveals that single plant yield significantly positive correlation with number of finger fingers per, harvest index, biological yield per plant, finger length, ear head length, finger width, no. of tillers per plant, flag leaf length. For phenotypic correlation traits were harvest index, test weight, biological yield per plant, number of finger per ear, ear head length, flag leaf length, number of tillers per plant, flag leaf width showed significantly positive correlation with grain yield per plant. The traits harvest index, flag leaf length, flag leaf width, number of finger per ear showed higher positive direct effect on grain yield per plant at genotypic level. The traits harvest index, biological yield, plant height showed higher positive direct effect on grain yield per plant at phenotypic level (6).

Wheat is the most important cereal crop in the world that ranks first position in terms of production and trade. In Nepal this is the third most cultivated crop after rice and maize. Various environmental constraints including heat stress have been determined to be a great factor to limit world wheat production. High temperature leaves a devastating impact in wheat production by affecting different stages including germination, plant growth, anthesis and grain filling etc. heat stress also affects photosynthesis process and responsible for the lower biomass yield. Various studies have shown that the reproductive stages of wheat plant are more susceptible to heat stress than vegetative stages. Heat stress hinders germination, reduce plant growth, decrease number of plant population per unit area and causes leaf senescence. Water relation disturbance and oxidative damage to plants are other harmful effects of heat stress in wheat plants. Plant also has tolerance mechanism against such heat induced stresses. Such mechanisms include avoidance against heat stress, production of heat shock protein and antioxidant mechanisms.

Background: Morphological characters are stable across environments owing to oligogeneic nature. Hence, they serve as morphological markers which can be used in varietal or genotypic identification, varietal purification and even in seed production. Genetic diversity analysis is being used to identify the divergent genotypes and to utilize these genotypes to exploit heterosis and also help to select desirable segregants. Methods: A total of 266 pigeonpea germplasm lines along with three checks were evaluated in augmented block design (ABD) at ZARS, Kalaburagi, during kharif, 2020. Observations are recorded on nine quantitative and fourteen morphological triats. Result: Grouping of 266 germplasm lines into twelve clusters indicated a wider genetic diversity for the traits studied, in which cluster I and cluster II are the largest comprising 105 genotypes each, while clusters V, VI, VIII, IX, X, XI, XII were solitary with one entry each. Germplasm lines IC339062, IC343954, IC339074, IC418976, IC343931, IC437078, IC355599 and IC384490 fall into solitary cluster and are more often likely to have some unique characters which make them divergent. The genotypes IC 355599 and IC 343931 are trait specific for both seed weight and pods per plant.

Barnyard millet, Echinochloa sp. is one of the important small millet crops used as food and fodder crop. Utilization of diverse germplasm is important in breeding programme to improve yield of the crop. In the present study, 494 barnyard millet germplasm were characterized using multivariate traits. Wide variation was observed for most of the traits indicated the scope of importance of these characters by direct selection. Phenotypic correlation between grain yield per plant was in significantly positive association with days to 50% flowering, plant height, the number of productive tillers, days to maturity and straw weight whereas, it was negatively associated with length of peduncle. Principle component analysis showed that the first two components contributed about 64% of the total variability. The proportions of the total variance attributed to the first two principle components were 43% and 20% respectively. The characters days to 50% flowering, plant height, days to maturity and straw weight were the most important traits contributing to the total variance in the first two principle components, indicating their importance for the characterization of barnyard millet germplasm accessions and these traits could be effectively used for future breeding programmes to create more variability. K means clustering method based on 7 quantitative traits among 494 barnyard millet germplasm was able to separate and grouped them into 23 clusters. Crossing accessions belonging to different clusters would maximize opportunities for transgressive segregation because of the higher probability that unrelated genotypes will contribute unique desirable alleles at multiple loci. Variability present in barnyard millet germplasm can be effectively used for the selection of specific donor lines for improvement of barnyard millet.

Oxidative reactive species play an important role in pathological conditions such as aging, fatty liver and cancers. Secondary metabolites enriched fraction derived from medicinal plants showed the inhibition of free radical generation by playing an important role in precluding various diseases. The aim of present study was to evaluate the antioxidant activity of different extracts by using the DPPH method. We assayed the free radicals scavenging activity of extracts at 50, 100, 200, 400 and 500 µg/ml concentration and phytochemical study of Petroleum ether, Chloroform, Methanol and Aqueous whole plant extracts of Catharanthus roseus. Amid the five absorption concentrations tested, it was observed that dose of 500 µg/ml showed the higher antioxidant activity for each extract. All samples displayed an increasing antioxidant effect with increase in concentration i.e. concentration dependant. The IC50 value of Petroleum ether, Chloroform, Methanol and Aqueous extract was found as 330.73 µg/ml, 596.13 µg/ml, 801.92 µg/ml and 504.12 µg/ml respectively. The petroleum ether extract at the concentration of 500 µg/ml showed the highest % inhibition of 67.441% compare to other extracts. DPPH method provides an easy and fast way to analyze potential antioxidants. The C. roseus extracts can be considered a rich natural source of antioxidants and can be used to develop pharmaceutical products for therapeutic treatment of various disorders caused by free radicals in human body.

Studies on infection indexing and distribution profiling of seed-borne fungi of sorghum germplasm in india for safe and healthy

Background Molecular mechanisms determining the transmission and prevalence of drug resistant tuberculosis (DR-TB) in Papua New Guinea (PNG) are poorly understood. We used genomic and drug susceptibility data to explore the evolutionary history, temporal acquisition of resistance and transmission dynamics of DR-TB across PNG. Methods We performed whole genome sequencing on isolates from Central Public Health Laboratory, PNG, collected 2017–2019. Data analysis was done on a composite dataset that also included 100 genomes previously sequenced from Daru, PNG (2012–2015). Results Sampled isolates represented 14 of the 22 PNG provinces, the majority (66/94; 70%) came from the National Capital District (NCD). In the composite dataset, 91% of strains were Beijing 2.2.1.1, identified in 13 provinces. Phylogenetic tree of Beijing strains revealed two clades, Daru dominant clade (A) and NCD dominant clade (B). Multi-drug resistance (MDR) was repeatedly and independently acquired, with the first MDR cases in both clades noted to have emerged in the early 1990s, while fluoroquinolone resistance emerged in 2009 (95% highest posterior density 2000–2016). We identified the presence of a frameshift mutation within Rv0678 (p.Asp47fs) which has been suggested to confer resistance to bedaquiline, despite no known exposure to the drug. Overall genomic clustering was significantly associated with rpoC compensatory and inhA promoter mutations (p Conclusions The acquisition and evolution of drug resistance among the major clades of Beijing strain threaten the success of DR-TB treatment in PNG. With continued transmission of this strain in PNG, genotypic drug resistance surveillance using whole genome sequencing is essential for improved public health response to outbreaks. With occurrence of resistance to newer drugs such as bedaquiline, knowledge of full drug resistance profiles will be important for optimal treatment selection.

In this retrospective study, we used whole-genome sequencing (WGS) to delineate transmission dynamics, characterize drug-resistance markers, and identify risk factors of transmission among Papua New Guinea residents of the Torres Strait Protected Zone (TSPZ) who had tuberculosis diagnoses during 2010-2015. Of 117 isolates collected, we could acquire WGS data for 100; 79 were Beijing sublineage 2.2.1.1, which was associated with active transmission (odds ratio 6.190, 95% CI 2.221-18.077). Strains were distributed widely throughout the TSPZ. Clustering occurred more often within than between villages (p = 0.0013). Including 4 multidrug-resistant tuberculosis isolates from Australia citizens epidemiologically linked to the TSPZ into the transmission network analysis revealed 2 probable cross-border transmission events. All multidrug-resistant isolates (33/104) belonged to Beijing sublineage 2.2.1.1 and had high-level isoniazid and ethionamide co-resistance; 2 isolates were extensively drug resistant. Including WGS in regional surveillance could improve tuberculosis transmission tracking and control strategies within the TSPZ.

Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively. Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation. Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC. Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing. Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples. Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.

Background Studies to date show contrasting conclusions when comparing intracorporeal and extracorporeal anastomoses for minimally invasive right colectomy. Large multi-center prospective studies comparing perioperative outcomes between these two techniques are needed. The purpose of this study was to compare intracorporeal and extracorporeal anastomoses outcomes for robotic assisted and laparoscopic right colectomy. Methods Multi-center, prospective, observational study of patients with malignant or benign disease scheduled for laparoscopic or robotic-assisted right colectomy. Outcomes included conversion rate, gastrointestinal recovery, and complication rates. Results There were 280 patients: 156 in the robotic assisted and laparoscopic intracorporeal anastomosis (IA) group and 124 in the robotic assisted and laparoscopic extracorporeal anastomosis (EA) group. The EA group was older (mean age 67 vs. 65 years, p = 0.05) and had fewer white (81% vs. 90%, p = 0.05) and Hispanic (2% vs. 12%, p = 0.003) patients. The EA group had more patients with comorbidities (82% vs. 72%, p = 0.04) while there was no significant difference in individual comorbidities between groups. IA was associated with fewer conversions to open and hand-assisted laparoscopic approaches (p = 0.007), shorter extraction site incision length (4.9 vs. 6.2 cm; p ≤ 0.0001), and longer operative time (156.9 vs. 118.2 min). Postoperatively, patients with IA had shorter time to first flatus, (1.5 vs. 1.8 days; p ≤ 0.0001), time to first bowel movement (1.6 vs. 2.0 days; p = 0.0005), time to resume soft/regular diet (29.0 vs. 37.5 h; p = 0.0014), and shorter length of hospital stay (median, 3 vs. 4 days; p ≤ 0.0001). Postoperative complication rates were comparable between groups. Conclusion In this prospective, multi-center study of minimally invasive right colectomy across 20 institutions, IA was associated with significant improvements in conversion rates, return of bowel function, and shorter hospital stay, as well as significantly longer operative times compared to EA. These data validate current efforts to increase training and adoption of the IA technique for minimally invasive right colectomy.

In a manufacturer-independent laboratory validation study, the Xpert MTB/XDR® assay demonstrated equivalent limit of detection to Xpert MTB/RIF®, detected 100% of tested resistance mutations and showed some utility for resistance detection in strain mixtures. The Xpert MTB/XDR assay is a reliable, sensitive assay for tuberculosis and expanded resistance detection.

Background: Chickpea is the largest produced food legume in South Asia. It is mainly grown in dry or rainfed area, where patchy plant stand often results due to delayed and non-uniform emergence. Moreover, genotypes vary for seed germination and seedling vigour. Therefore, the study was undertaken to find most appropriate seed treatment for enhancement of planting value of desi and kabuli type chickpeas. Methods: Study was conducted at ICAR-IARI, New Delhi with fresh, 2 and 4 years stored seed lots of desi (Pusa 2028) and kabuli (Pusa 1108) varieties. The lots were compared with untreated (control) for quality and vigour parameters after giving seed enhancement treatments (SET); osmopriming, halopriming, solid matrix priming (SMP), thiram and neem khali. Result: Investigations revealed that SMP and thiram seed treatments significantly enhanced germination and field performance of fresh as well as aged seeds in these varieties. Effectiveness of treatments was found more pronounced in kabuli than desi type and thus confirmed the usefulness of SETs for poor vigour seeds. Results also showed that seed quality and vigour of both the types were significantly affected with time in storage. However, desi variety maintained satisfactory germination and field performance up to 2 years under ambient conditions of storage.

Higher-yielding rice varieties adapted to the upland conditions of Yunnan were developed and disseminated during the late 1990s. Using cross-sectional farm-level data of 448 households collected from five prefectures in Southern Yunnan, this paper carries out an econometric analysis of the determinants of variations in the adoption of improved varieties among households and assesses the impact of adoption on rice income and total household income. The two major determinants of adoption were found to be the government programs for extension of improved upland rice varieties and for terracing of sloping fields. The presence of government programs for extension and for terracing contributed to increased adoption of improved varieties. Household-specific factors such as land and labor endowments were less important as these variables had a statistically insignificant impact on adoption. The adoption of improved rice varieties increased both rice income and the average household income. About half of the household income difference observed between the full adopters and non-adopters of improved rice varieties with comparable household characteristics can be attributed directly to the adoption. The results imply that increased investments in promoting improved rice varieties and terracing will generate additional income growth in the uplands of Yunnan.

Sorghum genetic resource conservations involve multiple strategies and collaboration to ensure the continued safeguarding of this valuable genetic resource. Curations of such worldwide collections require commitments to the acquisition, maintenance, distribution, evaluation, and utilization of such collections. In sorghum, a major challenge to its curation has been the standardization of protocols and techniques that each country deploys in evaluating their own collections. Information and documentation of these various collections has been a challenge; however, the two largest collections from the USA and ICRISAT have attempted to update their databases to reflect the rich sources of information available on their collections. In 2007, a panel of sorghum experts met to develop a “Strategy for the Global Ex Situ Conservation of Sorghum Genetic Diversity” and from this a review of the various collections is presented within this chapter. This review looked at various collections and evaluated the collections based on passport and characterization data. Collections reflected sorghum accessions from many different parts of the world and highlight some of the genetic stocks and phenotypic information available for utilization. As world populations increase and climate change challenges our ability to feed our population, the safety and curation of these types of collection allow us to respond to both biotic and abiotic stresses that will put pressure on the world’s population to feed itself. These irreplaceable collections are in greater need of curation than ever before, but in order to understand the needs, one must first understand what is already present in these collections.

Morpho-physiological and biochemical analyses were carried out in eight diverse indigenous muskmelon (Cucumis melo L.) genotypes exposed to different degrees of water deficit (WD). The ability of genotypes MM-7, and especially MM-6, to counteract better the negative effect of WD was associated with maintaining higher relative water content (RWC), photosynthetic rate, efficiency of PSII, and photosynthetic pigments compare to other genotypes. Furthermore, MM-6 showed a better ability to maintain cellular homeostasis than the others. It was indicated by a stimulated antioxidative defense system, i.e., higher activities of antioxidant enzymes, accumulation of nonenzymatic antioxidants together with lower concentration of reactive oxygen species and malondialdehyde. However, the genotypes MM-2 and MM-5 suffered greatly due to WD and showed reduced RWC, photosynthetic rates, pigment content, and exhibited higher oxidative stress observed as lower antioxidant enzyme activities.

The aim of this study was to assess the performance of the GeneXpert MTB/RIF assay on extrapulmonary (EP) and respiratory (non-sputum) clinical samples of patients suspected of having tuberculosis (TB) from Queensland, Australia. A total of 269 EP and respiratory (non-sputum) clinical samples collected from Qld patients who were suspected of having TB were subjected to the GeneXpert MTB/RIF analysis, Ziehl-Neelsen (ZN) staining, Mycobacterium tuberculosis (MTB) culture and drug susceptibility testing. Phenotypic and genotypic data were compared. The overall performance analysis of the GeneXpert MTB/RIF assay for detection of MTB complex demonstrated sensitivity of 89%, specificity of 95%, PPV of 89% and NPV of 95% using culture as a reference standard. The GeneXpert MTB/RIF analysis of acid-fast bacilli (AFB) smear positive samples and AFB smear negative samples showed sensitivities of 100% and 77%, respectively. Looking at individual EP and respiratory (non-sputum) sample types, the sensitivity ranged from 60% to 100% although the specificity ranged from 33% to 100% with the specificity of lymph node tissue biopsy being the lowest. The GeneXpert MTB/RIF assay detected 11% more TB cases than culture and 27% more cases than ZN microscopy. Due to insufficient numbers of presenting rifampicin resistance cases, performance analysis of the GeneXpert MTB/RIF assay on rifampicin resistance could not be carried out. The GeneXpert MTB/RIF assay is potentially valuable for TB diagnosis in the majority of the EP and respiratory (other than sputum) samples in our setting. Although the GeneXpert MTB/RIF assay provides rapid diagnostic results, the overall sensitivity to rule out the disease is suboptimal for some specimen types. Performance varied according to specimen type and AFB smear status. The sensitivity and specificity of lymph node tissue was 63% and 33%. Care must be taken when using the GeneXpert MTB/RIF assay for detection of MTB in lymph node tissue samples. All samples should be cultured regardless of the GeneXpert MTB/RIF assay result.

XpertTo assess the concordance of Xpert with phenotypic drug susceptibility testing (DST) performed at the supranational reference laboratory and to describe the patterns of drug-resistant TB observed.This was a retrospective descriptive study of laboratory data collected from April 2012 to December 2017.In 69 months, 1408 specimens with Xpert results were sent for mycobacterial culture and DST; Mycobacterium tuberculosis was cultured from 63% (884/1408) and DST was completed in 99.4%. The concordance between Xpert and culture for M. tuberculosis detection was 98.6%. Of 760 RR-TB cases, 98.7% were detected using Xpert; 98.5% of 620 MDR-TB cases were identified using phenotypic DST. Phenotypic resistance to second-line drugs was detected in 59.4% (522/879) of specimens tested, including 29 with fluoroquinolone resistance; the majority were from the National Capital District and Daru Island.The high concordance between phenotypic DST and Xpert in identifying RR-TB cases supports the scale-up of initial Xpert testing in settings with high rates of drug resistance. However, rapid DST in addition to the detection of RR-TB is required.L'XpertEvaluer la concordance de l'Xpert avec le test de pharmacosensibilité phénotypique (DST) réalisé au laboratoire de référence supranational et décrire les profils de TB pharmacorésistante observés.Une étude rétrospective descriptive de données de laboratoire recueillies entre avril 2012 et décembre 2017.En 69 mois, 1408 échantillons comportant des résultats d'Xpert ont été envoyés au laboratoire pour une culture de mycobactéries et un DST. Mycobacterium tuberculosis a été cultivé sur 63% (884/1408) et le DST a été réalisé sur 99,4% de ces derniers. La concordance entre l'Xpert et la culture pour la détection de M. tuberculosis a été de 98,6%. L'Xpert a détecté 98,7% de 760 cas de RR-TB et 98,5% de 620 cas de MDR-TB identifiés par DST phénotypique. La résistance phénotypique aux médicaments de deuxième ligne a été détectée dans 59,4% (522/879) des échantillons testés, dont 29 avaient une résistance aux fluoroquinolones, la majorité émanant du district de la capitale nationale et de l'île de Daru, Province de l'Ouest.La concordance entre DST phénotypique et Xpert pour la RR-TB est en faveur de l'accélération du test initial par Xpert dans les contextes de taux élevés de pharmacorésistance. Il y a cependant un besoin de test rapide de pharmacorésistance pour la détection de la résistance aux médicaments autres que la rifampicine.La prueba XpertEvaluar la concordancia de la prueba Xpert con las pruebas fenotípicas de sensibilidad realizadas en el Laboratorio Supranacional de Referencia y describir los tipos de TB farmacorresistente observados.Fue este un estudio descriptivo retrospectivo de los datos de laboratorio recogidos de abril del 2012 a diciembre del 2017.En 69 meses, se enviaron 1408 muestras con resultados de la prueba Xpert para cultivo micobacteriano y pruebas fenotípicas de resistencia. Se cultivó el Mycobacterium tuberculosis del 63% de las muestras (884/1408) y en 99,4% de estas se completaron las pruebas fenotípicas de resistencia. La concordancia entre la prueba Xpert y el cultivo de micobacterias para la detección de M. tuberculosis fue de 98,6%. Con la prueba Xpert se detectó el 98,7% de 760 casos de RR-TBy el 98,5% de 620 casos de MDR-TB detectados con las pruebas fenotípicas. En el 59,4% (522/879) de las muestras examinadas se detectó resistencia fenotípica a los fármacos de segunda línea, incluidos 29 casos con resistencia a fluoroquinolona y la mayor parte provenía del Distrito Capital Nacional y la Isla Daru de la Provincia Occidental.La alta concordancia entre las pruebas fenotípicas de sensibilidad a los medicamentos y la prueba Xpert con respecto a rifampicina respalda la ampliación de escala de la utilización de la prueba Xpert hacia entornos con tasas altas de farmacorresistencia. Sin embargo, se precisan pruebas rápidas de detección de la resistencia a otros fármacos diferentes de la rifampicina.

Objectives Mycobacterium triplex is a slow-growing nontuberculous mycobacteria (NTM) and is a rare cause of human disease. The pathogenicity, natural history and spectrum of disease is unknown. The aim of this study was to review the clinical features, outcomes and drug susceptibility testing (DST) of all M. triplex isolates in Queensland, Australia to guide management of this rare NTM infection in the future. Methods This retrospective study included all patients who isolated M. triplex in Queensland, Australia from the 1st January 2000 to 31st December 2016. Clinical information was obtained from medical records to determine the clinical significance of isolates, natural history of disease and treatment outcomes. DST was performed on 15 isolates. Results Forty-three patients (21 male) had positive cultures for M. triplex. Thirty-nine patients had isolates from pulmonary specimens and 17 (43.6%) met the American Thoracic Society criteria for NTM lung disease. Six patients with pulmonary infection received antimicrobial therapy with 5 patients demonstrating treatment success. Four patients had localised extrapulmonary disease and were cured with surgical management ± antimicrobial therapy. DST suggests 93% of isolates are susceptible to macrolides. Conclusion This is the largest case series of M. triplex isolates and confirms it is a rare human pathogen. Extrapulmonary disease responded well to surgical management. Treatment of M. triplex pulmonary disease is challenging, and the optimal antimicrobial regimen is unknown. However, the DST data suggests macrolide resistance is rare and macrolides should be included in treatment regimens.

BACKGROUND Nano-size and wide-range solubility of amphiphilic polymers (having both hydrophilic and hydrophobic blocks) can improve uniformity in seed coatings. An investigation was carried out to assess the positive effect of amphiphilic polymers over hydrophilic or hydrophobic polymers as seed coating agents and pesticide carriers. RESULTS Amphiphilic polymers with 127.5-354 nm micelle size were synthesized in the laboratory using polyethylene glycols and aliphatic di-acids. After 6 months of storage, germination of uncoated soybean seeds decreased drastically from 97.80 to 81.55%, while polymer-coated seeds showed 89.44-95.92% germination. Similarly, vigour index-1 was reduced from 3841.10 to 2813.06 for control seeds but ranged from 3375.59 to 3844.60 for polymer-coated seeds after 6 months. The developed imidacloprid formulations retained more pesticide on soybean seed coatings than did a commercial formulation (Gaucho(®) 600 FS). The time taken for 50% release of imidacloprid from seed coatings in water was 7.12-9.11 h for the developed formulations and 0.41 h for the commercial formulation. CONCLUSION Nano-range amphiphilic polymers can be used to protect soybean seeds from ageing. Formulations as seed treatments may produce improved and sustained efficacy with minimum environmental contamination. © 2016 Society of Chemical Industry.

Global spread of aggressive mycobacteria Many mycobacteria, in addition to those causing leprosy and tuberculosis, are capable of infecting humans. Some can be particularly dangerous in patients suffering from immunosuppression or chronic disease, such as cystic fibrosis (CF). Bryant et al. observed clusters of near-identical isolates of drug-resistant Mycobacterium abscessus in patients reporting to CF clinics. The similarity of the isolates suggests transmission between patients, rather than environmental acquisition. Although this bacterium is renowned for its environmental resilience, the mechanism for its long-distance transmission among the global CF patient community remains a puzzle. Science , this issue p. 751

Chickpea (Cicer arietinum L.) is the second largest pulse crop grown worldwide and ascochyta blight caused by Ascochyta rabiei (Pass.) Labr. is the most devastating disease of the crop in all chickpea growing areas across the continents. The pathogen A. rabiei is highly variable. The resistant sources available are not sufficient and new sources needs to be identified from time to time as resistance breakdown in existing chickpea varieties is very frequent due to fast evolution of new pathotypes of the pathogen. Therefore, this work was undertaken to evaluate the existing chickpea germplasm diversity conserved in Indian National Genebank against the disease under artificial epiphytotic conditions. An artificial standard inoculation procedure was followed for uniform spread of the pathogen. During the last five winter seasons from 2014-15 to 2018-19, a total of 1,970 accessions have been screened against the disease and promising accessions were identified and validated. Screening has resulted in identification of some promising chickpea accessions such as IC275447, IC117744, EC267301, IC248147 and EC220109 which have shown the disease resistance (disease severity score ≤3) in multiple seasons and locations. Promising accessions can serve as the potential donors in chickpea improvement programs. The frequency of resistant and moderately resistant type accessions was comparatively higher in accessions originated from Southwest Asian countries particularly Iran and Syria than the accessions originated from Indian sub-continent. Further large scale screening of chickpea germplasm originated from Southwest Asia may result in identifying new resistant sources for the disease.

A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the use of the MinION nanopore sequencer (Oxford Nanopore Technologies) to sequence and assemble an extensively drug-resistant (XDR) isolate, which is part of a modern Beijing sub-lineage strain, prevalent in Western Province, Papua New Guinea. Using 238-fold coverage obtained from a single flow-cell, de novo assembly of nanopore reads resulted into one contiguous assembly with 99.92 % assembly accuracy. Incorporation of complementary short read sequences (Illumina) as part of consensus error correction resulted in a 4 404 064 bp genome with 99.98 % assembly accuracy. This assembly had an average nucleotide identity of 99.7 % relative to the reference genome, H37Rv. We assembled nearly all GC-rich repetitive PE/PPE family genes (166/168) and identified variants within these genes. With an estimated genotypic error rate of 5.3 % from MinION data, we demonstrated identification of variants to include the conventional drug resistance mutations, and those that contribute to the resistance phenotype (efflux pumps/transporter) and virulence. Reference-based alignment of the assembly allowed detection of deletions and insertions. MinION sequencing provided a fully annotated assembly of a transmissible XDR strain from an endemic setting and showed its utility to provide further understanding of genomic processes within Mycobacterium tuberculosis.

Introduction. We describe the first detailed case report of human infection with Mycobacterium stomatepiae. Infection with non-tuberculous mycobacteria (NTM) related to M. stomatepiae is well described, despite the lack of previous confirmed reports of M. stomatepiae-related human disease. Localised cervical lymphadenitis is the most common NTM disease in children, with species closely related to M. stomatepiae, such as Mycobacterium triplex and Mycobacterium florentinum, having been shown to be rare causative agents. Case presentation. A 19-month-old girl presented with persistent unilateral neck lumps which developed following a facial laceration. Both lumps were fluctuant with overlying erythema and no fistulae present. Incision and drainage with curettage was performed. The operative sample of purulent fluid revealed pleomorphic bacilli on Ziehl–Neelsen staining. The isolate cultured was referred for further genotypic identification via 16S rRNA gene sequencing, identifying the organism as M. stomatepiae. Conclusion. We describe the first detailed case report of human infection with M. stomatepiae. This organism can now be added to the growing list of NTM that are opportunistic human pathogens, though it is likely to remain a very rare causative agent of this clinical syndrome. Early diagnosis relies on clinical suspicion by the treating doctor, flagging potential cases to the microbiology laboratory and hence allowing correct specimen set-up. Laboratory diagnosis requires incubation of cultures at lower temperatures, and definitive identification is best performed by sequencing methods, including 16S rRNA gene sequencing. The description of novel species of NTM causing human disease is likely to increase with further advancements in diagnostic methods.

A better understanding of the genomic changes that facilitate the emergence and spread of drug resistant M. tuberculosis strains is required. Short-read sequencing methods have limited capacity to identify long, repetitive genomic regions and gene duplications. We sequenced an extensively drug resistant (XDR) Beijing sub-lineage 2.2.1.1 “epidemic strain” from the Western Province of Papua New Guinea using long-read sequencing (Oxford Nanopore MinION®). With up to 274 fold coverage from a single flow-cell, we assembled a 4404947bp circular genome containing 3670 coding sequences that include the highly repetitive PE/PPE genes. Comparison with Illumina reads indicated a base-level accuracy of 99.95%. Mutations known to confer drug resistance to first and second line drugs were identified and concurred with phenotypic resistance assays. We identified mutations in efflux pump genes (Rv0194), transporters (secA1, glnQ, uspA), cell wall biosynthesis genes (pdk, mmpL, fadD) and virulence genes (mce-gene family, mycp1) that may contribute to the drug resistance phenotype and successful transmission of this strain. Using the newly assembled genome as reference to map raw Illumina reads from representative M. tuberculosis lineages, we detect large insertions relative to the reference genome. We provide a fully annotated genome of a transmissible XDR M. tuberculosis strain from Papua New Guinea using Oxford Nanopore MinION sequencing and provide insight into genomic mechanisms of resistance and virulence.Data SummarySample Illumina and MinION sequencing reads generated and analyzed are available in NCBI under project accession number PRJNA386696 (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA386696)The assembled complete genome and its annotations are available in NCBI under accession number CP022704.1 (https://www.ncbi.nlm.nih.gov/sra/?term=CP022704.1)Impact statementWe recently characterized a Modern Beijing lineage strain responsible for the drug resistance outbreaks in the Western province, Papua New Guinea. With some of the genomic markers responsible for its drug resistance and transmissibility are known, there is need to elucidate all molecular mechanisms that account for the resistance phenotype, virulence and transmission. Whole genome sequencing using short reads has widely been utilized to study MTB genome but it does not generally capture long repetitive regions as variants in these regions are eliminated using analysis. Illumina instruments are known to have a GC bias so that regions with high GC or AT rich are under sampled and this effect is exacerbated in MTB, which has approximately 65% GC content. In this study, we utilized Oxford Nanopore Technologies (ONT) MinION sequencing to assemble a high-quality complete genome of an extensively drug resistant strain of a modern Beijing lineage. We were able to able to assemble all PE/PPE (proline-glutamate/proline-proline-glutamate) gene families that have high GC content and repetitive in nature. We show the genomic utility of ONT in offering a more comprehensive understanding of genetic mechanisms that contribute to resistance, virulence and transmission. This is important for settings up predictive analytics platforms and services to support diagnostics and treatment.

An outbreak of multi-drug resistant (MDR) tuberculosis (TB) has been reported on Daru Island, Papua New Guinea. Mycobacterium tuberculosis strains driving this outbreak and the temporal accrual of drug resistance mutations have not been described. Whole genome sequencing of 100 of 165 clinical isolates referred from Daru General Hospital to the Supranational reference laboratory, Brisbane, during 2012-2015 revealed that 95 belonged to a single modern Beijing sub-lineage strain. Molecular dating suggested acquisition of streptomycin and isoniazid resistance in the 1960s, with potentially enhanced virulence mediated by an mycP1 mutation. The Beijing sub-lineage strain demonstrated a high degree of co-resistance between isoniazid and ethionamide (80/95; 84.2 %) attributed to an inhA promoter mutation combined with inhA and ndh coding mutations. Multi-drug resistance, observed in 78/95 samples, emerged with the acquisition of a typical rpoB mutation together with a compensatory rpoC mutation in the 1980s. There was independent acquisition of fluoroquinolone and aminoglycoside resistance, and evidence of local transmission of extensively drug resistant (XDR) strains from 2009. These findings underline the importance of whole genome sequencing in informing an effective public health response to MDR/XDR TB.

Objective: To determine the proportion of non-tuberculous mycobacteria (NTM) in samples of pulmonary tuberculosis (TB) cases from Papua New Guinea who were diagnosed using acid-fast microscopy. Methods: As part of a case detection study for TB, conducted in three provincial hospitals in Papua New Guinea, sputum samples of suspected tuberculous cases aged 15 years or older were collected from November 2010 to July 2012. Mycobacterial species isolated from sputum and grown in culture were examined to distinguish between NTM and the Mycobacterium tuberculosis complex (MTBC). Results: NTM were detected in 4% (9/225) of sputum samples grown in culture. Five (2.2%) of them were identified as NTM only and four (1.8%) were identified as mixed cultures containing both MTBC and NTM. Four different NTM species were identified; M. fortuitum, M. intracellulare, M. terrae and M. avium. Discussion: This is the first report from Papua New Guinea identifying NTM in three different locations. As NTM cannot be distinguished from M. tuberculosis through smear microscopy, the presence of NTM can lead to a false-positive diagnosis of tuberculosis. The prevalence of NTM should be determined and a diagnostic algorithm developed to confirm acid-fast bacilli in a smear as M. tuberculosis.