Indian Isolates Research Articles

New record of mungbean yellow mosaic India virus in Desmodium laxiflorum and association of bhendi yellow vein mosaic betasatellite in Abelmoschus moschatus in Andhra Pradesh, India.

Mungbean yellow mosaic India virus (MYMIV) is one of the most serious commonly occurring yellow mosaic virus (YMV's) group in majority of the pulses especially black gram and green gram in southern India compared to previously reported mungbean yellow mosaic virus. In January 2020 Desmodium laxiflorum and Abelmoscus moschatus showing mosaic symptoms and vein yellowing were collected from Guntur and Prakasam districts respectively in Andhra Pradesh. PCR analysis using MYMIV and betasatellite specific primers gave desired expected amplification from the infected samples of A. moschatus (YMV-ABEL) whereas only MYMIV specific amplification was obtained in D. laxiflorum (YMV-DES). However, no PCR amplification was obtained in respective healthy leaf samples of both plants. Sequence analysis showed that the CP sequence of YMV-ABEL and YMV-DES showed a similarity of 99.19% with MYMIV (KP677496) and 99.75% with MYMIV (JN181003) respectively. The full-length betasatellite (1356bp) showed highest identity of 90% with bhendi yellow vein mosaic betasatellite (BYVMB) (GU111977). Phylogenetic analysis clustered the test isolates with south Indian isolates of MYMIV whereas the betasatellite sequence clustered with various isolates of BYVMB, tomato leaf curl New Delhi virus betasatellite and okra leaf curl betasatellite reported from India and Pakistan. To the best of our knowledge, this is the first report of a MYMIV in D. laxiflorum and A. moschatus and MYMIV betasatellite complex in A. moschatus.

Comment on: Multicentre validation of a EUCAST method for the antifungal susceptibility testing of microconidia-forming dermatophytes

In 2020, we published a multicentre study validating a new EUCAST method for the antifungal susceptibility testing of microconidia-forming dermatophytes.1 We included molecularly confirmed terbinafine-resistant and -susceptible Trichophyton rubrum and Trichophyton interdigitale isolates and established wild-type upper MIC limits (WT-UL) for both species. Since then, the taxonomy for the Trichophyton mentagrophytes/T. interdigitale complex has been revised and a new species Trichophyton indotineae proposed for the highly terbinafine-resistant Indian isolates.2,3 These species cannot be distinguished by phenotypic tests although T. indotineae isolates are most often lighter in colour and less often positive in Tween-80 opacity, urea hydrolysis and hair perforation tests than T. mentagrophytes and T. interdigitale.3 Consequently, T. indotineae has been reported in the literature under all three species names and susceptibility data reported for the species complex cannot be reliably linked to the individual species unless identification to the sensu stricto level has...

Sequence polymorphism within erythrocyte binding domain of EBA175 in Indian and African field isolates

Invasion of erythrocyte by Plasmodium merozoites is mediated by specific molecular interactions between proteins expressed on merozoite surface and the receptors present on erythrocytes. Erythrocyte binding antigen 175 (EBA175) is one such protein that interacts with the sialic acid residues on glycophorin A present on erythrocytes’ surface during invasion. The FII region (PfFII) of EBA175 has been mapped to be critical for binding to erythrocytes. It is reported that antibodies against FII region blocks binding. Polymorphisms in FII region of EBA175 are already reported. The goal of this study was to investigate whether polymorphism in FII region of African P. falciparum field isolates has any effect on erythrocyte binding and also to find whether antibodies raised against FII region from P. falciparum Malayan Camp strain (Camp) can inhibit erythrocyte binding. Genomic DNA of parasites from the blood samples of P. falciparum infected individuals was isolated and PfFII region from these genomic DNA were amplified, cloned and sequenced. Following sequence analysis, we selected three isolates harboring higher PfFII polymorphisms, expressed them on the surface of COS cells as chimeric proteins using secretory signal and transmembrane segments of Herpex simplex virus glycoprotein D (HSVg D) and tested for their erythrocyte binding ability. We further tested the inhibition of erythrocyte binding of these polymorphic FII regions using anti-campPfF2 antibodies. Our results reveal that the polymorphisms in different field isolates included in this study do not have any significant effect on erythrocyte binding and antibodies raised against FII region of camp strain could inhibit erythrocyte binding by all the polymorphic PfFII. This observation strengthens the possibility that PfFII can be a potential candidate vaccine.

Genetic variations in the long control region of human papillomavirus type 16 isolates from India: implications for cervical carcinogenesis.

Introduction. Infection with high-risk human papillomavirus (HPV) types, specifically HPV type 16 (HPV16), is considered to be the most important risk factor in the development of cervical intraepithelial neoplasia and cancer. The long control region (LCR) is a noncoding region that comprises approximately 10 % of the HPV genome and contains regulatory elements for viral transcription and replication. Sequence variations in LCR may impact on the replication efficiency and oncogenic potential of the virus.Gap statement. Studies documenting variations in LCR of HPV16 isolates pertaining to cervical neoplastic status in India are limited.Aim. The present study was designed to characterize variations in the LCR of Indian isolates of HPV16 and study their association with cervical disease grades.Methodology. The LCR was amplified and sequenced from HPV16 positive cervical samples belonging to different cervical disease grades. Sequences were aligned to identify variations and potential transcription factor binding sites (TFbs) were predicted using the JASPAR database in addition to phylogenetic studies.Results. Among the 163 HPV16 isolates analysed, 47 different nucleotide variations were detected in the LCR, of which 25 are reported for first time in Indian isolates. Point mutations were detected in 35/54 (64.8 %) samples with normal cervical status, 44/50 (88 %) samples with low-grade cervical disease and 53/59 (89.8 %) samples with high-grade cervical disease. Variations T6586C, G6657A and T6850G were significantly associated with high-grade cervical status. Thirteen LCR variations were detected in the binding sites for CEBPB, ETS1, JUN, MYB, NFIL3, PHOX2A and SOX9 transcription factors.Conclusion. The present study helped to identify unique variations in the LCRs of HPV16 Indian isolates. The variations in the A4 sub-lineage were significantly associated with high-grade disease status. The isolates belonging to the A4 and D3 sub-lineages harboured mutations in putative TFbs, implying a potential impact on viral replication and progression to cervical cancer.

Detection of a New Variant in Outbreak of Bovine Ephemeral Fever in Turkey, 2020

Background: In this study, partial nucleotide sequence analysis of the G gene was performed for the molecular characterization of the virus that caused the bovine ephemeral fever virus (BEFV) epidemic in Turkey in 2020. Phylogenetic analysis of these nucleotide sequences was performed with the virus nucleotide sequences of the epidemics seen in 2008 and 2012. These sequences were announced in GenBank. Phylogenetic analysis of these nucleotide sequences was performed with the virus nucleotide sequences of the epidemics seen in 2008 and 2012. Methods: The study was conducted in dairy cattle holdings located in Diyarbakır Sur, Çınar and Dicle regions in South-eastern Turkey in August-November 2020. The number of animals in the holdings consisted of 750 (n=750), 150 (n=150) and 200 (n=200) cattle, respectively. Result: Severe respiratory symptoms and high mortality in the affected animals were notable symptoms. As a result of the phylogenetic analysis, it was determined that the virus that caused the epidemic in Turkey in 2020 was formed by a new variant in the Turkey-2 group, which was similar to the Indian isolates, unlike the Turkey-1 group, which was close to the Middle East variants in 2008 and 2012 isolates.

Development of PCR-Based Race-Specific Markers for Differentiation of Indian Fusarium oxysporum f. sp. cubense, the Causal Agent of Fusarium Wilt in Banana.

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc), is the most lethal soil-borne fungal pathogen infecting bananas. Foc race 1 (R1) and 4 (R4) are the two most predominant races affecting the economically important Cavendish group of bananas in India. A total of seven vegetative compatibility groups (VCGs) from three pathogenic races were isolated during our field survey and were found to be highly virulent towards cv. Grande Naine. According to comparative genome analyses, these Indian Foc VCGs were diverse in genomic organization and effector gene profiles. As a result, false-positive results were obtained with currently available molecular markers. In this context, the study has been initiated to develop PCR-based molecular markers for the unambiguous identification of Indian Foc R1 and R4 isolates. Whole-genome sequences of Foc R1 (GCA_011316005.3), Foc TR4 (GCA_014282265.3), and Foc STR4 (GCA_016802205.1), as well as the reference genomes of Foc (ASM799451v1) and F. oxysporum f. sp. lycopersici (Fol; ASM14995v2), were aligned to identify unique variable regions among the Foc races. Using putative chromosome and predicted gene comparison, race-specific unique Foc virulence genes were identified. The putative lineage-specific identified genes encoding products secreted in xylem (SIX) that may be necessary for disease development in the banana. An in silico analysis was performed and primers were designed from a region where sequences were dissimilar with other races to develop a specific marker for Foc R1, R4, TR4, and STR4. These race-specific markers allowed target amplification in the characterized highly virulent Foc isolates, and did not show any cross-amplification to any other Foc races, VCGs or banana pathogens, Fusarium species, and non-pathogenic Fusarium oxysporum isolates. The study demonstrated that the molecular markers developed for all the three Foc races of India could detect the pathogen in planta and up to 0.025 pg µL−1 DNA levels. Thus, the markers developed in this study are novel and could potentially be useful for the accurate diagnosis and detection of the Indian Foc races which are important for the effective management of the disease.

Highly divergent isolates of chrysanthemum virus B and chrysanthemum virus R infecting chrysanthemum in Russia.

BackgroundChrysanthemum is a popular ornamental and medicinal plant that suffers from many viruses and viroids. Among them, chrysanthemum virus B (CVB, genus Carlavirus, family Betaflexiviridae) is widespread in all chrysanthemum-growing regions. Another carlavirus, chrysanthemum virus R (CVR), has been recently discovered in China. Information about chrysanthemum viruses in Russia is very scarce. The objective of this work was to study the prevalence and genetic diversity of CVB and CVR in Russia.MethodsWe surveyed the chrysanthemum (Chrysanthemum morifolium Ramat.) germplasm collection in the Nikita Botanical Gardens, Yalta, Russia. To detect CVB and CVR, we used RT-PCR with virus-specific primers. To reveal the complete genome sequences of CVB and CVR isolates, metatransciptomic analysis of the cultivars Ribonette, Fiji Yellow, and Golden Standard plants, naturally co-infected with CVB and CVR, was performed using Illumina high-throughput sequencing. The recombination detection tool (RDP4) was employed to search for recombination in assembled genomes.ResultsA total of 90 plants of 23 local and introduced chrysanthemum cultivars were surveyed. From these, 58 and 43% plants tested positive for CVB and CVR, respectively. RNA-Seq analysis confirmed the presence of CVB and CVR, and revealed tomato aspermy virus in each of the three transcriptomes. Six near complete genomes of CVB and CVR were assembled from the RNA-Seq reads. The CVR isolate X21 from the cultivar Golden Standard was 92% identical to the Chinese isolate BJ. In contrast, genomes of the CVR isolates X6 and X13 (from the cultivars Ribonette and Fiji Yellow, respectively), were only 76% to 77% identical to the X21 and BJ, and shared 95% identity to one another and appear to represent a divergent group of the CVR. Two distantly related CVB isolates, GS1 and GS2, were found in a plant of the cultivar Golden Standard. Their genomes shared from 82% to 87% identity to each other and the CVB genome from the cultivar Fiji Yellow (isolate FY), as well as to CVB isolates from Japan and China. A recombination event of 3,720 nucleotides long was predicted in the replicase gene of the FY genome. It was supported by seven algorithms implemented in RDP4 with statistically significant P-values. The inferred major parent was the Indian isolate Uttar Pradesh (AM765837), and minor parent was unknown.ConclusionWe found a wide distribution of CVB and CVR in the chrysanthemum germplasm collection of the Nikita Botanical Gardens, which is the largest in Russia. Six near complete genomes of CVR and CVB isolates from Russia were assembled and characterized for the first time. This is the first report of CVR in Russia and outside of China thus expanding the information on the geographical distribution of the virus. Highly divergent CVB and CVR isolates have been identified that contributes the better understanding the genetic diversity of these viruses.

Izolati iz smole "Boswellia serrata" - hemijski sastav i farmakološke aktivnosti

Frankincense is an aromatic resin obtained from a tree of various species of the genus Boswellia, family Burseraceae. Boswellia serrata, which is characteristic for the Indian subcontinent and whose pharmacological effects have been proven in numerous studies, has the greatest medical importance. The aim of this paper is a detailed literature review of the chemical composition and biological activity of Indian frankincense resin isolates (B. serrata). In vitro studies and numerous clinical trials have shown promising beneficial effects in the treatment of inflammatory diseases, such as rheumatoid arthritis, ulcerative colitis, inflammatory bowel disease (ileitis), Crohn's disease and asthma, as well as in the reduction of peritumoral edema. The resin obtained from B. serrata which has both religious and medical significance is today widely used in the cosmetics industry due to its high content of essential oil.

Biological Resistance to Okra yellow vein mosaic virus Using Three Biological Agents on Three Okra Cultivars

Jadoua, J.A. and M.A.W. Al-Fahd. 2022. Biological Resistance to Okra yellow vein mosaic virus Using Three Biological Agents on Three Okra Cultivars. Arab Journal of Plant Protection, 40(2): 148-157. https://doi.org/10.22268/AJPP-40.2.148157 A study was conducted in Al-Alam District, Salah Al-Din Governorate, Iraq, during the fall season 2019-2020, with the goal of diagnosing the local isolate of Okra yellow vein mosaic virus (OYVMV) from infected plants using polymerase chain reaction. A genomic segment of OYVMV with a size of 750 was amplified using polymerase chain reaction (PCR) and a set of specific primers. By amplifying a 750 bp band on agarose gel, the field isolate tested was identified as a member of the genus Begomovirus, which was related to an Indian isolate of the same virus. The study included determining the efficacy of three biological factors: (A) a medicinal plant preparation from A. Paniculara, (H) a preparation from Lion's mushroom (H. erinaceus and (P) a preparation from P. florescence bacteria which has impact on virus infection, as well as determining the response of three okra varieties to virus infection. The use of the three combined factors (A+H+P) outperformed other treatments reducing virus infection rate of the Petra okra variety to 26.67 % and severity to 10.66 % as compared to 100% for the control. The findings showed that there were substantial variation in the peroxidase enzyme activity and chlorophyll content, with the A+H+P treatment producing 59.14 units/mg protein for the Petra variety and 40.81 Spad for the Hasnawi variety. The results also showed that there were extremely significant differences in yield, with the triple treatment (A+H+P) yielding 833.96 gm/plant for the Star variety compared to 537.44 gm/plant for the infected control that was not treated. Keywords: Biological control, viruses, okra

Weeds as Reservoirs for Viruses Infecting Brinjal in its Ecosystem

Brinjal is the most important vegetable crop cultivated in both tropical and sub-tropical regions due to its high adaptability and the prevailing demand for edible purpose. Brinjal crop expressing viral disease like symptoms viz., mosaic, severe mosaic, vein banding, blistering, stunting were collected. The weed plants in brinjal ecosystem viz., Euphorbia spp. Parthenium hysterophorus, Trianthema portulacastrum, Tridax procumbens and Eclipta prostrata were observed with similar symptoms and these symptoms were also collected. The preliminary detection of viruses was carried for Cucumber mosaic virus (CMV) and Tomato leaf curl New Delhi virus (ToLCNDV) antisera resulted in positive reaction for CMV and ToLCNDV infection in Euphorbia spp. and Parthenium hysterophorus confirmed the infection of CMV and ToLCNDV on these weed plants. The molecular characterization of CMV and ToLNDV was done and positive amplicon covering coat protein regions of both the viruses were cloned and sequenced. Sequences revealed 98% identity of CMV between the weed species and 97% homology with other vegetable CMV isolates of India. 99% of identity was observed between TN isolates of ToLCNDV and 98% identity with other ToLCNDV Indian isolates. Upon phylogenetic analysis the CMV weed host isolates clustered in single clade, separated from CMV brinjal isolate, while all the three isolates of ToLCNDV claded in single clade. The results exemplified that Euphorbia spp. and Parthenium hysterophorus act as reservoirs of CMV and ToLCNDV in the brinjal ecosystem during cropping and offseason of the crop in Tamil Nadu.

CIRCUMSPOROZOITE PROTEIN (CSP) GENETIC DIVERSITY IN INDIAN PLASMODIUM VIVAX

India is one of the Plasmodium vivax endemic countries and contributes the highest number of malaria cases worldwide. P. vivax CSP (PvCSP) is one of the most extensively studied antigen and is considered to be a leading malaria vaccine candidate gene. VK210 and VK247 are the two variants described in the central repeat region of P. vivax CSP gene. VK210 (98%) is found to be more prevalent as compared to VK247 (2%) in Indian context. It was noticed that different geographical regions show diversity in nucleotides as well as in haplotype with respect to PvCSP gene of Indian isolates. As natural selection always plays an important role in shaping genomic diversity in Indian P. vivax, the central repeat region of PvCSP gene of all the five-populations found to be under strong purifying selection. In this region, a number of synonymous mutations were found to be higher in number as compared to non-synonymous mutation, which clearly indicated that PvCSP gene is involved in invasion of hepatocytes in the host body and the parasite can't afford non-synonymous changes in this region. The present study helps us to understand the nature of P. vivax population in India, and also that might be helpful in planning the development of PvCSP-based vaccine in India.

Lumpy Skin Disease: Pathomorphological Features and Molecular Detection in Dairy Cattle of West Coastal India

Lumpy skin disease (LSD) is an emerging pox viral disease affecting cattle population worldwide. Present investigation designed to study the prevalence, pathomorphological changes and molecular detection of LSD virus in naturally infected cat-tle. The overall morbidity of LSD was 4.48% among 30 dairy farms. Skin nodular biopsy, whole blood and serum samples (n= 66) were collected for the diagnosis of LSD by histopathology, PCR and gene sequencing. The envelope protein (P32), Fusion protein (F) and DNA dependent RNA polymerase 30 kDa subunit (RPO30) genes were targeted for PCR testing. Out of 66, 46 cattle showed generalized skin nodules and papules of various sizes on the skin particularly at neck, face, nose, tail, perineum and udder. Microscopically, skin nodule biopsy revealed presence of diffuse granulomatous inflammation, hyperkeratosis, focal to diffuse vasculitis and lymphangitis, vacuolar degeneration, spongiosis and acanthosis. The inflammatory cells along with diffuse necrosis seen in the dermis. Gel-PCR assay detected P32 gene in 80%, F gene in 70% and RPO30 gene in 75% of skin biopsy samples. Three blood samples were also found positive for P32 gene by PCR. Whereas, TaqMan™probe Real Time PCR targeting EEV glycoprotein gene (LSDV126) detected LSDV in 94% of biopsy samples and three blood samples which indicated its higher sensitive for the diagnosis of LSDV. Phylogenetic analysis of RPO30 gene sequence showed that the isolates from this study were grouped in same cluster with LSDV isolates of Bangladesh, Kenya and other Indian isolates detected during 2019-20.

OSSEIN EFFLUENT AS WATER AND NUTRIENTS FOOTPRINT FOR BIODIESEL FEEDSTOCK PRODUCTION IN CHLORELLA VULGARIS BDU G91771

India’s national policy on biofuels has proposed a non-mandatory target of 20% blend of biodiesel and ethanol to meet the country’s energy demand. The microalgae is one of the most promising feedstock of biodiesel. The research has identified an Indian marine isolate Chlorella sp. that can produce about 17% lipid and can be grown in ossein effluent containing low total dissolved solid and to use it as microalgal growth medium, reducing the water and nutrient footprint. This gives us lead for largescale microalgal technology, where Chlorella sp. can be grown in a sustained manner. The effluent composition almost mimics the essential algal nutrients (growth medium) and alternatives to the nutrient uptake processes. The lipid content of the control (ASN III medium) was 16%, followed by the ossein effluent comprised of high total dissolved solids (HTDS) 15% and low total dissolved solids LTDS 17%, respectively, which implies the relative lipid production of the strain grown in the effluent. The fatty acid profile of Chlorella vulgaris BDU G91771 in the selected effluent condition indicated its suitability for biodiesel production.

16S rDNA and ITS Sequence Diversity of Burkholderia mallei Isolated from Glanders-Affected Horses and Mules in India (2013-2019).

Glanders is a highly contagious and fatal infection of equids caused by the bacteria known as Burkholderia mallei. It is one of the notifiable equine diseases and is still present in Asia, South America and Africa. In India, glanders re-emerged in 2006, and thereafter, increasing numbers of cases were reported in different regions of the country. Between 2013 and 2019, 39 B. mallei were isolated from glanders-affected horses (n = 30) and mules (n = 9) from seven states of India such as Uttar Pradesh, Haryana, Delhi, Himachal Pradesh, Gujarat, Maharashtra and Tamil Nadu. In this study, the phylogenetic relationships of these isolates were assessed by sequence analysis of 16S rDNA gene and ITS region. Purified PCR-amplified products of 16S rDNA gene and ITS region were sequenced, aligned and phylogenetic trees were constructed using MEGA 11 software. Additionally, B. mallei 16S rDNA (n = 36) and ITS (n = 18) sequences available in the GenBank were also included for analysis to determine the diversity of older B. mallei isolates with recent Indian isolates. Both the phylogeny showed that the majority of the recent isolates from India are closely related to each other, but are genetically diverse from older isolates that originated from India. Nucleotide substitutions were also observed in a single and double position in 12 recent and two old Indian isolates. The study also indicates that similar B. mallei strains were responsible for glanders outbreaks in different states (Uttar Pradesh- Himachal Pradesh and Uttar Pradesh- Haryana) and this is due to the migration of infected animals from one state to another state. This study implies that 16S rDNA and ITS region may be used for molecular characterization of B. mallei associated with glanders in resource-limited settings.

A Multi-class Machine Learning Framework to Predict Ampicillin-Sulbactam Resistance of Acinetobacter baumannii

Acinetobacter baumannii is a serious pathogen responsible for many of the hospital-acquired infections. The emergence of multi-drug and pan-drug resistant strains of A. baumannii has been a growing concern. Ampicillin-sulbactam combination has proven to be effective in treatment of several resistant strains. However, strains resistant to ampicillin-sulbactam combination have also emerged necessitating other combination therapy. Rapid and accurate identification of the phenotype of the organism is essential for starting the right treatment. To this end, genome-based approaches have garnered much attention. In this work, we report a multi-class machine-learning based approach to predict the ampicillin-sulbactam resistance phenotype and MIC of Acinetobacter baumannii based on the presence/absence of AMR genes in the genome of strains isolated in the USA region. Our model achieves an accuracy of about 94% indicating that the gene presence/absence itself can capture the resistance phenotype. Further, we show that our model, built based on the USA strains, does not predict reliably the AMR phenotypes of Indian isolates pointing to the need for building machine learning models from region-specific data.

Whole genome analysis and molecular characterization of chicken infectious anemia virus from an outbreak in a layer flock reveals circulation of genogroup IIIb in South India

The complete genome (2298 nucleotides) of the economically important and immunosuppressive, chicken infectious anemia virus (CAV), from a disease outbreak in a layer flock is discussed. This is the first report of a complete genome sequence of CAV from India. The phylogenetic analyses grouped this isolate with CAV genogroup IIIb based on both complete genome and capsid protein (VP1) sequences. The analyses further revealed the presence of CAV genogroups II, IIIa and IIIb in India. The VP1 sequence identity ranged between 84.4 to 99.3% with that of the Indian isolates and carried a unique substitution at position 447 (serine instead of threonine). Two novel amino acid substitutions were observed at position 52 of VP1 (serine instead of proline) and at position 26 of VP2 (asparagine instead of serine). Sequence analyses of VP1, VP2 and VP3 suggested that the isolate could be attenuated. Comparison with CAV variants, isolated from mammalian species, showed similarities in the numbers of certain transcription factor binding sites in the non-coding regions. Recombination analysis detected no recombination events in this isolate. Further investigations are needed to understand the implications of the unique features of this isolate on viral virulence.

Emerging genetic diversity of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) alters its B-cell epitopes

The RNA dependent RNA polymerase (RdRp) plays crucial role in virus life cycle by replicating the viral genome. The SARS-CoV-2 is an RNA virus that rapidly spread worldwide and acquired mutations. This study was carried out to identify mutations in RdRp as the SARS-CoV-2 spread in India. We compared 50217 RdRp sequences reported from India with the first reported RdRp sequence from Wuhan, China to identify 223 mutations acquired among Indian isolates. Our protein modelling study revealed that several mutants can potentially alter stability and flexibility of RdRp. We predicted the potential B cell epitopes contributed by RdRp and identified thirty-six linear continuous and twenty-five discontinuous epitopes. Among 223 RdRp mutants, 44% of them localises in the B cell epitopes region. Altogether, this study highlights the need to identify and characterize the variations in RdRp to understand the impact of these mutations on SARS-CoV-2.

Antimicrobial resistance in Indian isolates of non typhoidal Salmonella of livestock, poultry and environmental origin from 1990 to 2017

A retrospective antimicrobial resistance study of nontyphoidal Salmonella enterica isolates from India during 1990–2017 was conducted to study the microbial susceptibility to antibiotics. A total of 271 Salmonella enterica isolates from poultry (n = 146), farm animals (n = 55) and environmental sources (n = 70) were tested for susceptibility using 15 antimicrobial drugs. The drug classes include aminoglycosides, phenicols, cephalosporins, penicillins, carbapenems, fluoroquinolones, and sulphonamide-trimethoprim. Study revealed that overall, 133 (49.08%) of 271 isolates were resistant to ≥ 1 antimicrobial drugs and 81 (29.89%) out of 271 isolates were multidrug resistant (resistance to ≥ 3 drugs). Majority (68.96%) of Typhimurium serovars (n = 87) were susceptible to all antibiotics tested, whereas only 5% Kentucky serovars (n = 40) were pan susceptible. All the drugs revealed decreasing trend of susceptibility from 1990 towards 2017 except cephalosporins and carbapenems. Statistical analysis of association between time period and antimicrobial resistance revealed a significance of < 0.05. Molecular detection of genetic determinants associated with antimicrobial resistance revealed the presence of genes like class I integrons, sul1, sul2, catIII, cmlA, dfrA, blaTEM, blaAmpC in the resistant isolates. Furthermore, plasmid mediated quinolone resistant determinants like qnrD and qnrS were also reported in the current study.

Identification of molecular marker linked to resistance gene loci against Indian isolate of Phytophthora capsici L. causing root rot in chilli (Capsicum annuum L.)

Identification of molecular marker linked to resistance gene loci against Indian isolate of Phytophthora capsici L. causing root rot in chilli (Capsicum annuum L.)

Molecular epidemiology of Burkholderia mallei isolates from India (2015-2016): New SNP markers for strain tracing.

Glanders, caused by a bacterium called B. mallei, is primarily an infectious horse and human disease. Although its incidence is rare in developed countries, it is nonetheless prevalent in several geographical areas of the world. There is a lack of cost-effective, rapid and specific molecular typing tools for epidemiological tracing of glanders cases. We previously reported an SNP-based typing method that categorizes global B. mallei strains into three lineages (L1 to L3), as well as additional branches, sub-branches and groups. However, further discrimination of the Indian and Pakistani isolates within the L2B2sB2 sub-branch was not possible due to the lack of sufficient epidemiological markers. In this study, 10 B. mallei strains isolated from four states in India during 2015-2016 were whole genome sequenced; SNP analysis further confirmed their position in the L2B2sB2 branch. To better track the strains, four new markers targeting Indian or Pakistani strains, and specifically targeting sub-groups within the Indian strains, were identified. The new SNP markers were tested and validated on the 10 Indian isolates included in this study as well as on 6 contemporary B. mallei Pakistani strains. These rapid and discriminating typing tools will contribute to the epidemiological monitoring of B. mallei infections, particularly in South Asia and the Middle East, endemic regions of the disease.