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Article ; Online: Comparative genomics of an extensively drug resistant strain Klebsiella pneumoniae IITR008 with international high-risk clonal lineage ST147 isolated from river water.

Singh, Deeksha / Pal, Shilpee / Subramanian, Srikrishna / Manickam, Natesan

2024 Volume 117, Issue 1, Page(s) 57

Abstract: Carbapenem resistant Klebsiella pneumoniae causing severe infection resulting in morbidity and mortality have become a global health concern. K. pneumoniae with sequence type ST147 is an international high-risk clonal lineage, genomic studies have been ... ...

Abstract	Carbapenem resistant Klebsiella pneumoniae causing severe infection resulting in morbidity and mortality have become a global health concern. K. pneumoniae with sequence type ST147 is an international high-risk clonal lineage, genomic studies have been done on K. pneumoniae ST147 isolated from clinical origin but genomic data for environmental K. pneumoniae ST147 is very scarce. Herein, K. pneumoniae IITR008, an extensively drug resistant and potentially hypervirulent bacterium, was isolated from Triveni Sangam, the confluence of three rivers where religious congregations are organized. Phenotypic, genomic and comparative genomic analysis of strain IITR008 was performed. Antibiotic susceptibility profiling revealed resistance to 9 different classes of antibiotics including ß-lactams, ß-lactam combination agents, carbapenem, aminoglycoside, macrolide, quinolones, cephams, phenicol, and folate pathway antagonists and was found to be susceptible to only tetracycline. The strain IITR008 possesses hypervirulence genes namely, iutA and iroN in addition to numerous virulence factors coding for adherence, regulation, iron uptake, secretion system and toxin. Both the IITR008 chromosome and plasmid pIITR008_75 possess a plethora of clinically relevant antibiotic-resistant genes (ARGs) including bla
MeSH term(s)	Humans ; Klebsiella pneumoniae/genetics ; Phylogeny ; Rivers ; Klebsiella Infections/drug therapy ; Klebsiella Infections/epidemiology ; Klebsiella Infections/microbiology ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Carbapenems ; Plasmids ; Genomics ; Iron ; Water ; beta-Lactamases/genetics ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents ; Carbapenems ; Iron (E1UOL152H7) ; Water (059QF0KO0R) ; beta-Lactamases (EC 3.5.2.6)
Language	English
Publishing date	2024-03-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	214861-4
ISSN	1572-9699 ; 0003-6072
ISSN (online)	1572-9699
ISSN	0003-6072
DOI	10.1007/s10482-024-01955-z
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Article ; Online: Characterization and complete genome analysis of Klebsiella phage Kp109 with lytic activity against Klebsiella pneumoniae.

Singh, Deeksha / Pal, Shilpee / Subramanian, Srikrishna / Manickam, Natesan

Virus genes

2024 Volume 60, Issue 2, Page(s) 222–234

Abstract: Klebsiella pneumonia is a serious pathogen involved in a range of infections. The increasing frequency of infection associated with K. pneumoniae and accelerated development of antimicrobial resistance has limited the available options of antibiotics for ...

Abstract	Klebsiella pneumonia is a serious pathogen involved in a range of infections. The increasing frequency of infection associated with K. pneumoniae and accelerated development of antimicrobial resistance has limited the available options of antibiotics for the treatment of infection. Bacteriophages are an attractive substitute to alleviate the problem of antibiotic resistance. In this study, isolation, microbiological and genomic characterization of bacteriophage Kp109 having the ability to infect K. pneumoniae has been shown. Phage Kp109 showed good killing efficiency and tolerance to a broad range of temperatures (4-60 °C) and pH (3-9). Transmission electron microscopy and genomic analysis indicated that phage Kp109 belongs to the genus Webervirus and family Drexlerviridae. Genomic analysis showed that the Kp109 has a 51,630 bp long double-stranded DNA genome with a GC content of 51.64%. The absence of known lysogenic, virulence, and antibiotic-resistant genes (ARGs) in its genome makes phage Kp109 safer to be used as a biocontrol agent for different purposes including phage therapy. The computational analysis of the putative endolysin gene revealed a binding energy of - 6.23 kcal/mol between LysKp109 and ligand NAM-NAG showing its potential to be used as an enzybiotic. However, future research is required for experimental validation of the in silico work to further corroborate the results obtained in the present study. Overall, phenotypic, genomic, and computational characterization performed in the present study showed that phages Kp109 and LysKp109 are promising candidates for future in vivo studies and could potentially be used for controlling K. pneumoniae infection.
MeSH term(s)	Bacteriophages ; Klebsiella pneumoniae ; Klebsiella ; Genomics ; Anti-Bacterial Agents/pharmacology
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-01-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	639496-6
ISSN	1572-994X ; 0920-8569
ISSN (online)	1572-994X
ISSN	0920-8569
DOI	10.1007/s11262-024-02053-y
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Article ; Online: Insights into the phylogenetic inconsistencies of the genus

Kumar, Naresh / Saraf, Aniket / Pal, Sagarika / Mishra, Deeksha / Singh, Prashant

International journal of systematic and evolutionary microbiology

2023 Volume 72, Issue 12

Abstract: A dark-coloured thin film of cyanobacteria growing on the bottom of a submerged stone was isolated from Basantgarh village in Udhampur district, Jammu and Kashmir, India. The isolated strain (designated 19C- ... ...

Abstract	A dark-coloured thin film of cyanobacteria growing on the bottom of a submerged stone was isolated from Basantgarh village in Udhampur district, Jammu and Kashmir, India. The isolated strain (designated 19C-PS
MeSH term(s)	Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; Base Composition ; Fatty Acids/chemistry ; Nostoc ; India
Chemical Substances	RNA, Ribosomal, 16S ; DNA, Bacterial ; Fatty Acids
Language	English
Publishing date	2023-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	2002336-4
ISSN	1466-5034 ; 1466-5026
ISSN (online)	1466-5034
ISSN	1466-5026
DOI	10.1099/ijsem.0.005658
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Article ; Online: Corrigendum to "Association between ZIP10 gene expression and tumor aggressiveness in renal cell carcinoma" [Gene 552(1) (2014) 195-198].

Pal, Deeksha / Sharma, Ujjawal / Singh, Shrawan Kumar / Prasad, Rajendra

Gene

2022 Volume 819, Page(s) 146311

Language	English
Publishing date	2022-02-23
Publishing country	Netherlands
Document type	Published Erratum
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2022.146311
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Article: Mitophagy: An Emergence of New Player in Alzheimer's Disease.

Sharma, Bunty / Pal, Deeksha / Sharma, Ujjawal / Kumar, Aman

Frontiers in molecular neuroscience

2022 Volume 15, Page(s) 921908

Abstract: Mitochondria provide neurons not only energy as ATP to keep them growing, proliferating and developing, but they also control apoptosis. Due to their high bioenergetic demand, neurons which are highly specific terminally differentiated cells, essentially ...

Abstract	Mitochondria provide neurons not only energy as ATP to keep them growing, proliferating and developing, but they also control apoptosis. Due to their high bioenergetic demand, neurons which are highly specific terminally differentiated cells, essentially depend on mitochondria. Defective mitochondrial function is thus related to numerous age-linked neurodegenerative ailments like Alzheimer's disease (AD), in which the build-up of impaired and malfunctioning mitochondria has been identified as a primary sign, paying to disease development. Mitophagy, selective autophagy, is a key mitochondrial quality control system that helps neurons to stay healthy and functional by removing undesired and damaged mitochondria. Dysfunctional mitochondria and dysregulated mitophagy have been closely associated with the onset of ADs. Various proteins associated with mitophagy were found to be altered in AD. Therapeutic strategies focusing on the restoration of mitophagy capabilities could be utilized to strike the development of AD pathogenesis. We summarize the mechanism and role of mitophagy in the onset and advancement of AD, in the quality control mechanism of mitochondria, the consequences of dysfunctional mitophagy in AD, and potential therapeutic approaches involving mitophagy modulation in AD. To develop new therapeutic methods, a better knowledge of the function of mitophagy in the pathophysiology of AD is required.
Language	English
Publishing date	2022-07-06
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2452967-9
ISSN	1662-5099
ISSN	1662-5099
DOI	10.3389/fnmol.2022.921908
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Article ; Online: IL-23/IL-17 in a Paradoxical Association with Primary Membranous Nephropathy.

Kaur, Prabhjot / Prabhahar, Arun / Pal, Deeksha / Nada, Ritambhra / Kohli, Harbir Singh / Kumar, Vinod / Ramachandran, Raja

Inflammation

2024

Abstract: Primary membranous nephropathy (PMN), an autoimmune disease, is the most common cause of nephrotic syndrome in middle-aged non-diabetic adults. PMN pathophysiology includes Th1/Th2 paradigm. The IL-23/IL-17 pathway is implicated in autoimmune kidney ... ...

Abstract	Primary membranous nephropathy (PMN), an autoimmune disease, is the most common cause of nephrotic syndrome in middle-aged non-diabetic adults. PMN pathophysiology includes Th1/Th2 paradigm. The IL-23/IL-17 pathway is implicated in autoimmune kidney disorders, but no study has examined its relationship with PMN. In several unrelated studies, PMN patients reported to have paradoxical IL-17 levels. This manuscript describes the best possible association of IL-23/IL-17 axis with PMN. Biopsy-proven PMN patients and age, gender-matched healthy controls were enrolled. Serum-PLA2R (Euroimmune, Germany), IL-23 and IL-17 (R&D; USA), was measured using ELISA along with biochemical parameters. Appropriate statistical tools were used for analysis. One hundred eighty-nine PMN patients (mean age 41.70 ± 12.53 years) and 100 controls (mean age 43.92 ± 10.93 years) were identified. One hundred forty were PLA2R-related. PMN patients had median proteinuria, serum albumin, and creatinine of 6.12 (3.875, 9.23) g/day, 2.32 (1.96, 2.9) g/dl, and 0.89 (0.7, 1.1) mg/dl, respectively. IL-17, but not IL-23, was significantly increased in PMN patients compared to controls (IL-17, median: 12.07 pg/ml (9.75, 24.56) vs median: 9.75 pg/ml (8.23, 17.03) p = 0.0002); (IL23, median: 6.04 pg/ml (4.22, 10.82) vs median: 5.46 pg/ml (3.34, 9.96) p = 0.142). IL-17 and IL-23 correlated significantly (p 0.05) in PMN patients, and similar trend was seen when grouped into PLA2R-related and -unrelated groups. The levels of IL-23 (p = 0.057) and IL-17 (p = 0.004) were high in MN patients that did not respond to the treatment. The current finding may indicate or suggest the involvement of IL-23/IL-17 PMN pathogenesis. A comprehensive investigation is needed to evaluate IL-23/IL-17 axis with renal infiltrating immune cells, and external stimuli.
Language	English
Publishing date	2024-02-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	434408-x
ISSN	1573-2576 ; 0360-3997
ISSN (online)	1573-2576
ISSN	0360-3997
DOI	10.1007/s10753-024-01992-w
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Article ; Online: Circumscription of Fulbrightiella gen. nov. and Sherwoodiella gen. nov., Two Novel Genera in the Calotrichaceae (Nostocales, Cyanobacteria)

Kumar, Naresh / Saraf, Aniket / Pal, Sagarika / Mishra, Deeksha / Singh, Prashant / Johansen, Jeffrey R.

Journal of Phycology. 2023 Feb., v. 59, no. 1 p.204-220

2023

Abstract: Three novel strains in Calotrichaceae from tropical habitats were isolated and characterized with regard to their morphology, phylogenetic placement, and secondary structures of conserved domains in the 16S‐23S internal transcribed spacer (ITS). The ... ...

Abstract	Three novel strains in Calotrichaceae from tropical habitats were isolated and characterized with regard to their morphology, phylogenetic placement, and secondary structures of conserved domains in the 16S‐23S internal transcribed spacer (ITS). The strains fell into two clades formerly identified as Calothrix from freshwater and brackish habitats. Based on both morphology and ecology, they differed from the type species of Calothrix, C. confervicola, which is marine, has wide trichomes with short cells, and narrows abruptly to a hyaline hair. The first clade grouped species with heteropolar filaments widened at the base and narrowed gradually toward the apex but not ending in a hair, with basal heterocytes that are formed in series as the apically placed heterocytes senesce; this clade is being named Fulbrightiella gen. nov., with two named species, F. bharadwajae sp. nov. and F. oahuensis sp. nov. The second clade was comprised of a single species with isopolar trichomes that are untapering as hormogonia, but which widen midfilament and taper toward both ends following growth. These trichomes develop pairs of heterocyte mid‐filament, causing fragmentation into heteropolar trichomes with basal heterocytes and ends that taper, but not to a hair. This clade consists of a single species at present, Sherwoodiella mauiensis. With this action, four clades in the Calotrichaceae have been named: Macrochaete, Dulcicalothrix, Fulbrightiella, and Sherwoodiella. Calothrix sensu stricto is truly marine, morphologically distinct, and unsequenced; finding and sequencing the generitype for Calothrix remains as the most important and unfinished task in the revision of the Calotrichaceae.
Keywords	Calothrix ; algology ; ecology ; freshwater ; internal transcribed spacers ; phylogeny ; trichomes
Language	English
Dates of publication	2023-02
Size	p. 204-220.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	281226-5
ISSN	1529-8817 ; 0022-3646
ISSN (online)	1529-8817
ISSN	0022-3646
DOI	10.1111/jpy.13297
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Article ; Online: The potential role of gut microbiota in the pathogenesis of type 2 diabetes mellitus via epigenetics and inflammasome.

Sharma, Bunty / Kumar, Aman / Sharma, Ujjawal / Pal, Deeksha / Prashar, Sourabh

Endocrine, metabolic & immune disorders drug targets

2022

Abstract: The gut microbiota that comprises over 100 trillion microorganisms with a weight of about 1-2 kg is regarded as one of the most crucial players in the regulation of the metabolic health of host organisms. In recent years, the incidence of type 2 diabetes ...

Abstract	The gut microbiota that comprises over 100 trillion microorganisms with a weight of about 1-2 kg is regarded as one of the most crucial players in the regulation of the metabolic health of host organisms. In recent years, the incidence of type 2 diabetes mellitus (T2DM), characterized by high levels of sugar in the blood, is exponentially increasing due to obesity and other lifestyle risk factors. It was shown that dysbiosis, change in the overall composition, and diversity of gut microflora can result in T2DM. Conversely, the microbial composition can also influence the epigenetics of the host organism (DNA methylation as well as histone modifications), which might have a potential effect on the metabolic health of the individual. Another mechanism of gut microbiota in the development of T2DM is through the involvement of nucleotide-binding oligomerization domain, Leucine-rich Repeat, and Pyrin domain containing 3 (NLRP3) inflammasome, a part of the innate immune system. NLRP3 inflammasome results in the production of inflammatory cytokines, promoting the secretion of microbial antigens in the intestinal epithelium. Therefore, it is important to understand the possible connecting link between gut microbiota and T2DM that might help in the modulation of gut microflora to better understand the disease. In this review, the role of gut microbiota in the pathogenesis of T2DM will be discussed.
Language	English
Publishing date	2022-03-31
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	2228325-0
ISSN	2212-3873 ; 1871-5303
ISSN (online)	2212-3873
ISSN	1871-5303
DOI	10.2174/1871530322666220331152809
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Article ; Online: Issues in cyanobacterial taxonomy: comprehensive case study of unbranched, false branched and true branched heterocytous cyanobacteria.

Mishra, Deeksha / Saraf, Aniket / Kumar, Naresh / Pal, Sagarika / Singh, Prashant

FEMS microbiology letters

2021 Volume 368, Issue 4

Abstract: The order Nostocales is represented by morphologically diverse forms with respect to the branching patterns and polarity of the filaments. With growing understanding of taxonomy and systematics, members of the order Nostocales have also undergone ... ...

Abstract	The order Nostocales is represented by morphologically diverse forms with respect to the branching patterns and polarity of the filaments. With growing understanding of taxonomy and systematics, members of the order Nostocales have also undergone multiple taxonomic revisions. The last decade has seen a surge in the description of new genera and families within the order Nostocales. In this study, we discuss the taxonomic status of all the newly described and reclassified taxa of some of the prominent morphological forms within the order Nostocales by constructing comprehensive phylogenetic trees. Further, we propose certain strategies that would contribute to resolving the taxonomic complexities arising due to inadequate taxon sampling.
MeSH term(s)	Cyanobacteria/classification ; Cyanobacteria/cytology ; Cyanobacteria/genetics ; Phylogeny
Language	English
Publishing date	2021-01-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	752343-9
ISSN	1574-6968 ; 0378-1097
ISSN (online)	1574-6968
ISSN	0378-1097
DOI	10.1093/femsle/fnab005
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Article ; Online: Circumscription of Fulbrightiella gen. nov. and Sherwoodiella gen. nov., Two Novel Genera in the Calotrichaceae (Nostocales, Cyanobacteria).

Kumar, Naresh / Saraf, Aniket / Pal, Sagarika / Mishra, Deeksha / Singh, Prashant / Johansen, Jeffrey R

Journal of phycology

2022 Volume 59, Issue 1, Page(s) 204–220

Abstract: Three novel strains in Calotrichaceae from tropical habitats were isolated and characterized with regard to their morphology, phylogenetic placement, and secondary structures of conserved domains in the 16S-23S internal transcribed spacer (ITS). The ... ...

Abstract	Three novel strains in Calotrichaceae from tropical habitats were isolated and characterized with regard to their morphology, phylogenetic placement, and secondary structures of conserved domains in the 16S-23S internal transcribed spacer (ITS). The strains fell into two clades formerly identified as Calothrix from freshwater and brackish habitats. Based on both morphology and ecology, they differed from the type species of Calothrix, C. confervicola, which is marine, has wide trichomes with short cells, and narrows abruptly to a hyaline hair. The first clade grouped species with heteropolar filaments widened at the base and narrowed gradually toward the apex but not ending in a hair, with basal heterocytes that are formed in series as the apically placed heterocytes senesce; this clade is being named Fulbrightiella gen. nov., with two named species, F. bharadwajae sp. nov. and F. oahuensis sp. nov. The second clade was comprised of a single species with isopolar trichomes that are untapering as hormogonia, but which widen midfilament and taper toward both ends following growth. These trichomes develop pairs of heterocyte mid-filament, causing fragmentation into heteropolar trichomes with basal heterocytes and ends that taper, but not to a hair. This clade consists of a single species at present, Sherwoodiella mauiensis. With this action, four clades in the Calotrichaceae have been named: Macrochaete, Dulcicalothrix, Fulbrightiella, and Sherwoodiella. Calothrix sensu stricto is truly marine, morphologically distinct, and unsequenced; finding and sequencing the generitype for Calothrix remains as the most important and unfinished task in the revision of the Calotrichaceae.
MeSH term(s)	Phylogeny ; RNA, Ribosomal, 16S ; DNA, Bacterial ; Ecosystem ; Cyanobacteria/genetics ; Sequence Analysis, DNA
Chemical Substances	RNA, Ribosomal, 16S ; DNA, Bacterial
Language	English
Publishing date	2022-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	281226-5
ISSN	1529-8817 ; 0022-3646
ISSN (online)	1529-8817
ISSN	0022-3646
DOI	10.1111/jpy.13297
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