Sushim K Gupta | USDA Agricultural Research Service (original) (raw)

Papers by Sushim K Gupta

Antibiotics, Jan 7, 2024

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Genome Announcements, Oct 27, 2016

Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella ente... more Here, we report a 4.87-Mbp draft genome sequence of the multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Bardo strain CRJJGF_00099, isolated from dairy cattle in 2005.

Genome Announcements, Oct 27, 2016

Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar O... more Here, we report a 4.70-Mbp draft genome sequence of Salmonella enterica subsp. enterica serovar Orion strain CRJJGF_00093, isolated from a dog in 2005.

Journal of Food and Drug Analysis, Jul 14, 2020

Botanical root of Flemingia and Glycine of Leguminosae is used as a traditional Chinese medicine ... more Botanical root of Flemingia and Glycine of Leguminosae is used as a traditional Chinese medicine material "I-Tiao-Gung" in Taiwan. It is widely used in both traditional Chinese medicine and folk remedies for the treatment of rheumatism, arthropathy, leukorrhea, menalgia, menopausal syndrome, and chronic nephritis, and the improvement of bone mineral density. The quasi root of Glycine tomentella and Glycine tabacina is substituted and used by some offshore island users, and it is also known as I-Tiao-Gung. Thus, the establishment of an effective method to distinguish the herb from alternative species is a critical issue. In this study, internal transcribed spacer (ITS) region-based analysis was used to ascertain the phylogenetic relationship among the indigenous four Flemingia species and two Glycine species. The length of the ITS regions among the six species ranged from 595 bp to 622 bp and the GC ratio in ITS (ITS 1 þ 5.8S þ ITS 2) regions ranged from 57.17% to 58.86%. The molecular phylogenetic trees were constructed and indicated that Flemingia species and Glycine species were separated into two clusters. These results indicate that ITS regions can be used as a molecular marker to differentiate the four Flemingia species and two Glycine species.

American Journal of Tropical Medicine and Hygiene, Sep 7, 2017

Buruli ulcer is an emerging infectious disease caused by Mycobacterium ulcerans that has been rep... more Buruli ulcer is an emerging infectious disease caused by Mycobacterium ulcerans that has been reported from 33 countries. Antimicrobial agents either alone or in combination with surgery have been proved to be clinically relevant and therapeutic strategies have been deduced mainly from the empirical experience. The genome sequences of M. ulcerans strain AGY99, M. ulcerans ecovar liflandii, and three Mycobacterium marinum strains were analyzed to predict resistance in these bacteria. Fourteen putative antibiotic resistance genes from different antibiotics classes were predicted in M. ulcerans and mutation in katG (R431G) and pncA (T47A, V125I) genes were detected, that confer resistance to isoniazid and pyrazinamide, respectively. No mutations were detected in rpoB, gyrA, gyrB, rpsL, rrs, emb, ethA, 23S ribosomal RNA genes and promoter region of inhA and ahpC genes associated with resistance. Our results reemphasize the usefulness of in silico analysis for the prediction of antibiotic resistance in fastidious bacteria.

Access Microbiology

Francisella tularensis , the causative agent for tularaemia, is a Tier 1 select agent, and a pan-... more Francisella tularensis , the causative agent for tularaemia, is a Tier 1 select agent, and a pan-species pathogen of global significance due to its zoonotic potential. Consistent genome characterization of the pathogen is essential to identify novel genes, virulence factors, antimicrobial resistance genes, for studying phylogenetics and other features of interest. This study was conducted to understand the genetic variations among genomes of F. tularensis isolated from two felines and one human source. Pan-genome analysis revealed that 97.7 % of genes were part of the core genome. All three F. tularensis isolates were assigned to sequence type A based on single nucleotide polymorphisms (SNPs) in sdhA. Most of the virulence genes were part of the core genome. An antibiotic resistance gene coding for class A beta-lactamase was detected in all three isolates. Phylogenetic analysis showed that these isolates clustered with other isolates reported from Central and South-Central USA. Asse...

INSERM U895, C3M, 151 Route de Ginestiere, BP 2 3194, F-06204 NICE Cedex 3, France 13 * Correspon... more INSERM U895, C3M, 151 Route de Ginestiere, BP 2 3194, F-06204 NICE Cedex 3, France 13 * Corresponding author 14 Tel: (33). 04.91.32.43.75, Fax: (33). 04.91.38.77.72 15 E-mail: 1 16 Abstract words: 246 17 Text words: 3685 18 References: 30 19 20 AAC Accepts, published online ahead of print on 21 October 2013Antimicrob. Agents Chemother. doi:10.1128/AAC.01310-13Copyright © 2013, American Society for Microbiology. All Rights Reserved.

Genome announcements, Jan 16, 2017

Here, we present the draft genome sequences of eight streptogramin-resistant Enterococcus species... more Here, we present the draft genome sequences of eight streptogramin-resistant Enterococcus species isolated from animals and an environmental source in the United States from 2001 to 2004. Antimicrobial resistance genes were identified conferring resistance to the macrolide-lincosamide-streptogramins, aminoglycosides, tetracyclines, beta-lactams, and glycopeptides.

Journal of Cystic Fibrosis, 2013

The use of chronic azithromycin treatment has been linked with increased macrolide resistance. Al... more The use of chronic azithromycin treatment has been linked with increased macrolide resistance. Although, Prevotella spp. are one of the most common anaerobes detected in CF pulmonary samples, the effect of chronic azithromycin exposure on this genus is unknown. The aims of this study were to i. investigate if resistance is associated with azithromycin prescription ii. compare azithromycin and clindamycin MICs between Prevotella isolates cultured from CF patients and healthy control subjects. Methods: Isolates were grouped according to source and patient prescription of azithromycin: CF (currently prescribed), n = 27; CF (not currently prescribed), n = 30; healthy controls (none), n = 17. Susceptibility was determined by Etest ® and MICs compared between groups using the Mann-Whitney test. Results: CF isolates had significantly higher azithromycin and clindamycin MICs compared to the healthy control isolates (P < 0.001). Current prescription of azithromycin was associated with significantly higher azithromycin MICs (P = 0.016) in the CF isolates. CF isolates (not currently prescribed) had significantly higher azithromycin MICs (P = 0.009) compared to isolates from healthy control subjects. Isolates from the 2 CF groups had equal resistance to clindamycin (P = 0.228). Conclusions: CF patients harbour isolates with increased resistance to azithromycin and clindamycin. Azithromycin resistance is associated with current azithromycin prescription.

Antibiotics

Comparative genomic sequencing of laboratory-derived vancomycin-intermediate Staphylococcusaureus... more Comparative genomic sequencing of laboratory-derived vancomycin-intermediate Staphylococcusaureus (VISA) (MM66-3 and MM66-4) revealed unique mutations in both MM66-3 (in apt and ssaA6), and MM66-4 (in apt and walK), compared to hetero-VISA parent strain MM66. Transcriptional profiling revealed that both MM66 VISA shared 79 upregulated genes and eight downregulated genes. Of these, 30.4% of the upregulated genes were associated with the cell envelope, whereas 75% of the downregulated genes were associated with virulence. In concordance with mutations and transcriptome alterations, both VISA strains demonstrated reduced autolysis, reduced growth in the presence of salt and reduced virulence factor activity. In addition to mutations in genes linked to cell wall metabolism (ssaA6 and walK), the same mutation in apt which encodes adenine phosphoribosyltransferase, was confirmed in both MM66 VISA. Apt plays a role in both adenine metabolism and accumulation and both MM66 VISA grew better ...

Antibiotics

Physiological experimentation, transcriptomics, and metabolomics were engaged to compare a fusidi... more Physiological experimentation, transcriptomics, and metabolomics were engaged to compare a fusidic acid-resistant Staphylococcus aureus mutant SH10001st-2 to its parent strain SH1000. SH10001st-2 harbored a mutation (H457Y) in the gene fusA which encodes the fusidic acid target, elongation factor G, as well as mutations in a putative phage gene of unknown function. SH10001st-2 grew slower than SH1000 at three temperatures and had reduced coagulase activity, two indicators of the fitness penalty reported for fusA-mediated fusidic acid- resistance in the absence of compensatory mutations. Despite the difference in growth rates, the levels of O2 consumption and CO2 production were comparable. Transcriptomic profiling revealed 326 genes were upregulated and 287 were downregulated in SH10001st-2 compared to SH1000. Cell envelope and transport and binding protein genes were the predominant functional categories of both upregulated and downregulated genes in SH10001st-2. Genes of virulence...

BackgroundSalmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype ... more BackgroundSalmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In the current study, two methods were used to determine serotypes of 225 clinical, environmental, food and veterinary isolates of Salmonella from Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0.ResultsAmong the 225 Salmonella isolates, serotypes for 48 (21.33%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. One hundred and seventy-six new SMART codes were developed for common and uncommon serotypes. Serotypes for a total of 205 (91.1%) isolates wer...

Antibiotics

The emergence of antimicrobial-resistant bacteria in developing countries increases risks to the ... more The emergence of antimicrobial-resistant bacteria in developing countries increases risks to the health of both such countries’ residents and the global community due to international travel. It is consequently necessary to investigate antimicrobial-resistant pathogens in countries such as Burkina Faso, where surveillance data are not available. To study the epidemiology of antibiotic resistance in Salmonella, 102 Salmonella strains isolated from slaughtered chickens were subjected to whole-genome sequencing (WGS) to obtain information on antimicrobial resistance (AMR) genes and other genetic factors. Twenty-two different serotypes were identified using WGS, the most prevalent of which were Hato (28/102, 27.5%) and Derby (23/102, 22.5%). All strains analyzed possessed at least one and up to nine AMR genes, with the most prevalent being the non-functional aac(6′)-Iaa gene, followed by aph(6)-Id. Multi-drug resistance was found genotypically in 36.2% of the isolates for different clas...

Botanical Studies, Jul 1, 2011

Plant secondary metabolites have enormous potential for research and new drug development. Many s... more Plant secondary metabolites have enormous potential for research and new drug development. Many secondary metabolites have complex and unique structure and their production can be enhanced by introducing different types of additives into the basal media. An efficient in vitro callus induction system in Stephania tetrandra S. Moore (Fan fang ji, an important Chinese medicinal herb) was established on MS medium supplemented with 3% sucrose and different concentrations (0.5 to 2.0 mg/L) of plant growth regulators i.e. auxins (2,4D, IAA and NAA) and cytokinins (BA, kinetin, TDZ and zeatin) in the dark. The effects of various auxins and cytokinin on the growth and accumulation of benzylisoquinoline alkaloids i.e. Fangchinoline (Fan) and Tetrandrine (Tet) were investigated. MS medium supplemented with 1.0 mg/L BA and 0.5 mg/L TDZ supported callus growth and its proliferation. A maximum amount of dry biomass (7.8 fold) was produced 45 days after culture. High Performance Liquid Chromatographic analysis of methanol extracts from callus revealed an accumulation of Fan and Tet alkaloids. The addition of casein hydrolysate (500 mg/L) and coconut milk (10%), respectively, enhanced Fan and Tet accumulation. The established in vitro callus induction system in S. tetrandra can be utilized for biomass production of pharmaceutically important alkaloids such as Fan and Tet.

Annals of Microbiology, 2021

Purpose Fish is an excellent source of protein and vitamins for humans, but improperly handled, f... more Purpose Fish is an excellent source of protein and vitamins for humans, but improperly handled, fish can expose consumers to pathogenic bacteria. This study was aimed to isolate and characterize the genomes of Salmonella strains isolated from imported fish sold in the open market in Ouagadougou. Methods One hundred and fifty-nine fish were collected from open markets and were cultured for Salmonella . Antimicrobial susceptibility was determined by broth microdilution. Whole-genome sequencing was done to further study antibiotic resistance genes, plasmid replicons, and MSLT types. Serotyping was done using SeqSero 2. Result Out of the 159 fish samples analyzed, 30 (18.9%) were found to be contaminated with Salmonella . Among the isolated Salmonella strains, six different serotypes, Nima, Liverpool, Kokomlemle, Teshie, Derby, and Tennessee, were found using SeqSero2. Salmonella Tennessee was the predominant serotype. All the isolates possessed at least one resistance gene. The aac6-Ia...

Medicinal Plants - Recent Advances in Research and Development, 2016

The dried, red-colored roots of Salvia miltiorrhiza (Lamiaceae) also called “danshen” in colloqui... more The dried, red-colored roots of Salvia miltiorrhiza (Lamiaceae) also called “danshen” in colloquial language in China have been used in traditional Chinese medicine for thousands of years to treat hypertension and other cardiovascular ailments. The main constituents of danshen are hydrophilic phenolic acids and lipophilic tanshinones. The various uses of danshen in traditional as well as modern medicines have motivated an intensive research on compounds in S. miltiorrhiza. In recent years, more than 110 compounds have been isolated from S. miltiorrhiza and their structure was identified. Tanshinones and their derivatives have been demonstrated to possess properties of slowing down or curing various ailments related to cardiovascular, cerebrovascular, respiratory, liver, nervous system, cancer, Alzheimer’s, and Parkinson’s diseases. With the increasing demand of this herb, an unrestricted collection to supply raw materials and the extraction of its constituents have severely threatened the natural habitats of S miltiorrhiza. This has prompted the researchers to develop alternative strategies for metabolite production. Several in vitro methodologies have been established to generate callus, cell suspension culture, hairy roots, and plant regeneration. Different regulators and elicitors for plant growth have been employed to enhance levels of different constituents. The advent of sequencing technologies, whole genome, and expression data has helped to provide insights and identification of pathway genes involved in the biosynthesis. This book chapter gives a brief description of in vitro methodologies, use of different elicitors, gene functions, genetic modifications, expression profiling for a better understanding, and enhancement of the constituents in S. miltiorrhiza.

Physiology and Molecular Biology of Plants, 2015

Aboitic stress such as drought and salinity are class of major threats, which plants undergo thro... more Aboitic stress such as drought and salinity are class of major threats, which plants undergo through their lifetime. Lignin deposition is one of the responses to such abiotic stresses. The gene encoding Cinnamoyl CoA Reductase (CCR) is a key gene for lignin biosynthesis, which has been shown to be over-expressed under stress conditions. In the present study, developing seedlings of Leucaena leucocephala (Vernacular name: Subabul, White popinac) were treated with 1 % mannitol and 200 mM NaCl to mimic drought and salinity stress conditions, respectively. Enzyme linked immunosorbant assay (ELISA) based expression pattern of CCR protein was monitored coupled with Phlorogucinol/HCl activity staining of lignin in transverse sections of developing L. leucocephala seedlings under stress. Our result suggests a differential lignification pattern in developing root and stem under stress conditions. Increase in lignification was observed in mannitol treated stems and corresponding CCR protein accumulation was also higher than control and salt stress treated samples. On the contrary CCR protein was lower in NaCl treated stems and corresponding lignin deposition was also low. Developing root tissue showed a high level of CCR content and lignin deposition than stem samples under all conditions tested. Overall result suggested that lignin accumulation was not affected much in case of developing root however developing stems were significantly affected under drought and salinity stress condition.

Genome Announcement, American Society For Microbiology (ASM), May 10, 2017

Here, we present the draft genome sequences of nine multidrugresistant Escherichia coli strains i... more Here, we present the draft genome sequences of nine multidrugresistant Escherichia coli strains isolated from humans (n ϭ 6) and chicken carcasses (n ϭ 3) from Lagos, Nigeria, in 2013. Multiple extended-spectrum ␤-lactamase (ESBL) genes were identified in these isolates.

Genes

Salmonella Infantis carrying extended spectrum β-lactamase blaCTX-M-65 on a pESI-like megaplasmid... more Salmonella Infantis carrying extended spectrum β-lactamase blaCTX-M-65 on a pESI-like megaplasmid has recently emerged in United States poultry. In order to determine the carriage rate and gene content variability of this plasmid in U.S. Salmonella Infantis, whole genome sequences of Salmonella isolates from humans and animals in the U.S. and internationally containing the pESI-like plasmid were analyzed. The U.S. Department of Agriculture Food Safety and Inspection Service (FSIS) identified 654 product sampling isolates containing pESI-like plasmids through hazard analysis and critical control point (HACCP) verification testing in 2017 and 2018. The Centers for Disease Control and Prevention identified 55 isolates with pESI-like plasmids in 2016–2018 through the National Antimicrobial Resistance Monitoring System. Approximately 49% of pESI-like plasmids from FSIS verification isolates and 71% from CDC NARMS contained blaCTX-M-65. Pan-plasmid genome analysis was also performed. All ...

Antibiotics, Jan 7, 2024

Genome Announcements, Oct 27, 2016

Journal of Food and Drug Analysis, Jul 14, 2020

American Journal of Tropical Medicine and Hygiene, Sep 7, 2017

Access Microbiology

Genome announcements, Jan 16, 2017

Journal of Cystic Fibrosis, 2013

Antibiotics

Botanical Studies, Jul 1, 2011

Annals of Microbiology, 2021

Medicinal Plants - Recent Advances in Research and Development, 2016

Physiology and Molecular Biology of Plants, 2015

Genome Announcement, American Society For Microbiology (ASM), May 10, 2017

Genes

A PCR based approach to fish out the c-DNA clones of 4CL genes from Leucaena leucocephala was fo... more A PCR based approach to fish out the c-DNA clones of 4CL genes from Leucaena leucocephala was
followed. Primers were designed on the basis of consensus regions of various reported 4CLs from the
NCBI Gen-Bank database. Rapid amplification of cDNA ends (RACE) was performed to fish out the full
length cDNA clones of 4CL. The isolated genes were characterized using different bioinformatics tools.
Ll4CL gene sequence was arranged with Chromas 2.01 software and homology was verified by database
searching at the National Center for Biotechnology Information server using BLAST algorithm
(http://www.ncbi.nlm.nih.gov). The deduction of the amino acid sequences, calculation of the theoretical
molecular mass and pI, was performed with ExPaSy proteomic tools provided at
http://www.expasy.ch/tools/. Alignment of two nucleotide or amino acid sequence and percent identity
were calculated using the EMBOSS pair wise alignment algorithms (http://www.ebi.ac.uk/ emboss/).
Multiple alignments of the amino acid sequences were carried out with the Clustal X program. The
evolutionary history was inferred using the Neighbor-Joining method using MEGA4.

The full length Ll4CL clone in T-vector was subcloned in pET- 30b (+) vector and transformed into... more The full length Ll4CL clone in T-vector was subcloned in pET-
30b (+) vector and transformed into host BL21 (DE3) pLysS cells of E. coli for expression of
recombinant 4CL At 37 degree celcious with 1 mM IPTG. The SDS-PAGE analysis indicated that the soluble and the
pellet fraction of recombinant bacteria contained an over-expressed protein with an apparent molecularmass of 59 kDa, which was in good agreement with the molecular weight deduced from nucleotide
sequence (58874 Da). No corresponding protein was observed in samples extracted from bacteria carrying
control vector. The spatial expression of Ll4CL protein was investigated using protein blot analysis,
which revealed that it is expressed unanimously in stem and root.

The 4CL was immunolocalized in the transverse sections of shoots and roots of 0 5, 10, and 15 da... more The 4CL was immunolocalized
in the transverse sections of shoots and roots of 0 5, 10, and 15 days old seedling. The purified IgG rose
against 4CL protein and anti rabbit goat IgG conjugated with alkaline phosphatase were used as primary
and secondary antibodies respectively. Results revealed 4CL enzyme expression in differentiating xylem
tissues and phloem fibers in stem and root. Comparison of the sections where 4CL was immunolocalized,
with phloroglucinol-HCl stained sections showed that the presence of 4CL was just not restricted at the
locations where lignin was stained 10d stem and root sections. Thus, the immunolacalization studies in
developing seedlings revealed the presence of 4Cls was not only confined to the area of extensive
lignification but to the surrounding tissue too.

The present study focused on spatio-temporal expression of the Ll4CL gene in developing stems an... more The present study focused
on spatio-temporal expression of the Ll4CL gene in developing stems and root. The expression of the
Ll4CL at the level of transcript was recorded from 0 to 60 d for stem and from 5 to 60 d for root in
growing L. leucocephala seedlings. The expression of the Ll4CL transcript in developing seedlings
revealed gradual increase in expression level in stem up to 15 d but decreased drastically in 60 d old
plantlets, however increase in expression level in root was recorded on 5 and 15 d, while decreased
expression was recorded on 10 and 60 d old root. Over all higher expression in 0 to 15 d old developing
seedlings suggests that Ll4CL gene is present mostly in tissues undergoing active lignification
(particularly developing xylem). However, when the tissue matures, the reduced activity of 4CL suggest
that the mature tissues are not undergoing active lignification and at this point of time lignin accumulation
has reached its plateau so 4CL gene maintains a low level of expression (60 d). The quantified 4CL
protein through ELISA using total extracted protein also supported the qRT-PCR evaluation, which
suggests that the expressed gene at transcriptional level was directly in correlation with the 4CL protein
accumulated in stem and root.

Leaf of tobacco and Embryo axes of Leucaena was used as explants for transformed via three differ... more Leaf of tobacco and Embryo axes of Leucaena was used as explants for transformed via three
different methods i.e. particle bombardment, particle bombardment followed by co-cultivation and agroinfusion
method. The Gus assay was done to confirm the transient expression of transferred genes.
Transgenic plants were generated by all three methods and highest frequency of transformation was
obtained with particle bombardment followed by co-cultivation. The integration of genes was confirmed
by PCR. DNA blot analysis of the transformed plants showed strong positive signals confirming the
integration of the genes. ELISA was done to estimate total 4CL protein in the transgenic events.

Les Journées de l’Infectiopôle Sud, Marseille, France

36th European Cystic fibrosis conference, Lisbon, Portugal

In Proceedings of International Symposium on Frontiers of Genetic Engineering and Biotechnology R... more In Proceedings of International Symposium on Frontiers of Genetic Engineering and Biotechnology Retrospect and Prospect, Osmania University, Hyderabad, Andhra Pradesh, India.

In Proceedings of National Symposium on Plant Biotechnology: New Frontiers, CIMAP, Lucknow, Utta... more In Proceedings of National Symposium on Plant Biotechnology: New Frontiers, CIMAP, Lucknow, Uttar Pradesh, India.

In Proceedings of National Symposium on Plant Biotechnology: New Frontiers, CIMAP, Lucknow, Uttar... more In Proceedings of National Symposium on Plant Biotechnology: New Frontiers, CIMAP, Lucknow, Uttar Pradesh. India.

In Proceedings of National Symposium on Biotechnological Interventions for Improvement of Horticu... more In Proceedings of National Symposium on Biotechnological Interventions for Improvement of Horticultural Crops: Issues and Strategies, Kerala Agriculture University- ICAR, Thrissur, Kerala, India.

In Abstract volume of National Science Day, NCL, Pune, India.