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Article ; Online: Primary antibiotic resistance of Helicobacter pylori in India over the past two decades: A systematic review.

Dutta, Spriha / Jain, Surbhi / Das, Kunal / Verma, Prashant / Som, Anup / Das, Rajashree

2024 Volume 29, Issue 1, Page(s) e13057

Abstract: Background: Helicobacter pylori antibiotic resistance has undergone vast changes in the last two decades. No systematic review has been done on the prevalence of antibiotic resistant H. pylori in India in the last two decades. We evaluated the pattern ... ...

Abstract	Background: Helicobacter pylori antibiotic resistance has undergone vast changes in the last two decades. No systematic review has been done on the prevalence of antibiotic resistant H. pylori in India in the last two decades. We evaluated the pattern of resistance rates across various regions of India. Materials and methods: A systematic review of the geographical variations in antibiotic resistance pattern of H. pylori was conducted using PubMed, Google Scholar, Web of Science, Science Direct, etc. for articles published between January 1, 2000 and May 30, 2023. Random effects-model-based Cochran's Q test, I Results: The overall resistance was highest against metronidazole (77.65%) followed by amoxicillin (37.78%), levofloxacin (32.8%), clarithromycin (35.64%), furazolidone (12.03%), and tetracycline (11.63%). 14.7% of the H. pylori isolates were multi-drug resistant. Under meta-analysis of each antibiotic, high heterogeneity levels were observed having I Conclusions: Metronidazole resistance is high in most regions of India except Assam and Mumbai while clarithromycin is found to be ineffective in South India, Gujarat, and Kashmir. As compared to other antibiotics, resistance to amoxicillin is generally low except in certain regions (Hyderabad, Chennai, and the Gangetic belt of North India). Tetracycline and Furazolidone have the least resistance rates and should be part of anti- H. pylori regimens. The resurgence of high single and multidrug resistance to the commonly used drugs suggests the need for newer antibiotics and regular resistance surveillance studies.
MeSH term(s)	Humans ; Metronidazole/pharmacology ; Metronidazole/therapeutic use ; Clarithromycin ; Helicobacter pylori ; Levofloxacin ; Furazolidone ; India/epidemiology ; Helicobacter Infections/drug therapy ; Helicobacter Infections/epidemiology ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Amoxicillin ; Tetracycline ; Antibodies ; Drug Resistance, Microbial
Chemical Substances	Metronidazole (140QMO216E) ; Clarithromycin (H1250JIK0A) ; Levofloxacin (6GNT3Y5LMF) ; Furazolidone (5J9CPU3RE0) ; Anti-Bacterial Agents ; Amoxicillin (804826J2HU) ; Tetracycline (F8VB5M810T) ; Antibodies
Language	English
Publishing date	2024-02-28
Publishing country	England
Document type	Systematic Review ; Meta-Analysis ; Journal Article ; Review
ZDB-ID	1330665-0
ISSN	1523-5378 ; 1083-4389
ISSN (online)	1523-5378
ISSN	1083-4389
DOI	10.1111/hel.13057
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Article: Low abundance of healthy bacteria in the gastric microbiota can be a potential biomarker for gastrointestinal diseases: A pilot study.

Arfi, Safiya / Sharma, Prateek / Das, Kunal / Bhaskar, Yogendra / Goel, Isha / Singh, Harpreet / Das, Rajashree

The Indian journal of medical research

2024 Volume 159, Issue 2, Page(s) 254–258

MeSH term(s)	Humans ; Pilot Projects ; Microbiota ; Bacteria/genetics ; Gastrointestinal Diseases/diagnosis ; Biomarkers ; RNA, Ribosomal, 16S
Chemical Substances	Biomarkers ; RNA, Ribosomal, 16S
Language	English
Publishing date	2024-04-04
Publishing country	India
Document type	Journal Article
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
DOI	10.4103/ijmr.ijmr_864_23
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Article ; Online: Dysbiosis of gut microbiota due to diet, alcohol intake, body mass index, and gastrointestinal diseases in India.

Sharma, Prateek / Singh, Sarika / Das, Kunal / Mahant, Shweta / Das, Rajashree

Applied microbiology and biotechnology

2023 Volume 107, Issue 7-8, Page(s) 2547–2560

Abstract: The human gut is composed of diverse microflora which is influenced by dietary intake. Body mass index (BMI) and lifestyle patterns also play a vital role in human health to alter gut microbial composition. Our study aims to determine the impact of ... ...

Abstract	The human gut is composed of diverse microflora which is influenced by dietary intake. Body mass index (BMI) and lifestyle patterns also play a vital role in human health to alter gut microbial composition. Our study aims to determine the impact of alcohol intake, BMI, and diet on gut microbiota and its relationship with gastrointestinal disorders. Thirty-nine gastric biopsies were taken from patients with various gastrointestinal (GI) diseases, and all the patient's lifestyle behavior were recorded in a written proforma. 16S rRNA metagenome analysis for V3-V4 regions was used to examine microbial compositions. The richness and diversity of gut microbiota were analyzed by PERMANOVA using the Bray-Curtis dissimilarity index and principal component analysis. The difference in relative abundance was calculated by ANOVA (p < 0.05). Alpha diversity indexes between vegetarians and non-vegetarians showed no significant difference based on BMI, alcohol status, and GI diseases. We found that in overweight vegetarian individuals Faecalibacterium and Rumicococcus might play a role in the control of Helicobacter pylori. Similarly, the increased abundance of Akkermansia muciniphila in non-vegetarian individuals with normal BMI might play a role to decrease the level of harmful bacteria like H. pylori, and Corynebacterium sp. Also, the relative abundance of Corynebacterium sp. among the vegetarians and Streptococcus sp. in the non-vegetarians was increased in alcoholics while H. pylori was increased in non-alcoholics irrespective of diet. There is an increased abundance of Faecalibacterium prausnitzii in vegetarians among all categories; however, we did not find any correlation between disease outcomes. Our study shows that alcohol intake and dietary habits have independent effects on gut microbial composition. The relative abundance of F. prausnitzii was high among vegetarians in all categories. KEY POINTS: • The presence of H. pylori is less among alcoholics. • Good bacteria help to maintain a normal body mass index. • Gut microbiota richness is high in vegetarians and diversity in non-vegetarians.
MeSH term(s)	Humans ; Gastrointestinal Microbiome/genetics ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Dysbiosis ; Diet ; Bacteria/genetics ; Alcohol Drinking ; Gastrointestinal Diseases
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2023-03-16
Publishing country	Germany
Document type	Journal Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-023-12470-y
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Article ; Online: Dysbiosis of gut microbiota due to diet, alcohol intake, body mass index, and gastrointestinal diseases in India

Sharma, Prateek / Singh, Sarika / Das, Kunal / Mahant, Shweta / Das, Rajashree

Appl Microbiol Biotechnol. 2023 Apr., v. 107, no. 7-8 p.2547-2560

2023

Abstract	The human gut is composed of diverse microflora which is influenced by dietary intake. Body mass index (BMI) and lifestyle patterns also play a vital role in human health to alter gut microbial composition. Our study aims to determine the impact of alcohol intake, BMI, and diet on gut microbiota and its relationship with gastrointestinal disorders. Thirty-nine gastric biopsies were taken from patients with various gastrointestinal (GI) diseases, and all the patient’s lifestyle behavior were recorded in a written proforma. 16S rRNA metagenome analysis for V3-V4 regions was used to examine microbial compositions. The richness and diversity of gut microbiota were analyzed by PERMANOVA using the Bray–Curtis dissimilarity index and principal component analysis. The difference in relative abundance was calculated by ANOVA (p < 0.05). Alpha diversity indexes between vegetarians and non-vegetarians showed no significant difference based on BMI, alcohol status, and GI diseases. We found that in overweight vegetarian individuals Faecalibacterium and Rumicococcus might play a role in the control of Helicobacter pylori. Similarly, the increased abundance of Akkermansia muciniphila in non-vegetarian individuals with normal BMI might play a role to decrease the level of harmful bacteria like H. pylori, and Corynebacterium sp. Also, the relative abundance of Corynebacterium sp. among the vegetarians and Streptococcus sp. in the non-vegetarians was increased in alcoholics while H. pylori was increased in non-alcoholics irrespective of diet. There is an increased abundance of Faecalibacterium prausnitzii in vegetarians among all categories; however, we did not find any correlation between disease outcomes. Our study shows that alcohol intake and dietary habits have independent effects on gut microbial composition. The relative abundance of F. prausnitzii was high among vegetarians in all categories. KEY POINTS: • The presence of H. pylori is less among alcoholics. • Good bacteria help to maintain a normal body mass index. • Gut microbiota richness is high in vegetarians and diversity in non-vegetarians.
Keywords	Corynebacterium ; Helicobacter pylori ; Streptococcus ; alcohol drinking ; alcohols ; body mass index ; dysbiosis ; food intake ; gastrointestinal system ; human health ; humans ; intestinal microorganisms ; lifestyle ; metagenomics ; overweight ; patients ; principal component analysis ; species diversity ; vegetarian diet ; India
Language	English
Dates of publication	2023-04
Size	p. 2547-2560.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-023-12470-y
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Article ; Online: Analysis of Functional Status of Genetically Diverse OipA Gene in Indian Patients with Distinct Gastrointestinal Disease

Singh, Sarika / Sharma, Prateek / Mahant, Shweta / Das, Kunal / Som, Anup / Das, Rajashree

Curr Microbiol. 2023 Jan., v. 80, no. 1 p.35-35

2023

Abstract: Helicobacter pylori (H. pylori,) a genetically diversified bacteria which colonizes human gastric epithelium, is now established causative agent for gastric cancer worldwide. Outer membrane protein (OMP)-coding genes of H. pylori are responsible for ... ...

Abstract	Helicobacter pylori (H. pylori,) a genetically diversified bacteria which colonizes human gastric epithelium, is now established causative agent for gastric cancer worldwide. Outer membrane protein (OMP)-coding genes of H. pylori are responsible for attachment and colonization of bacteria. These genes which code proteins on outer membrane of H. pylori is a group of 33 genes which with other virulent genes are causative of giving rise to disease-causing factors in the host. OipA (Outer inflammatory protein A), a participant of Hop family of OMP, is effective in acting as a biomarker for studying progression of diseases like gastric cancer. The functionality of oipA gene is regulated by phase variation within CT repeat pattern. It is the expression, i.e., “on”/“off” of oipA gene which is related with the development of distinct gastric diseases. 40 amplified DNA sequences were studied to investigate functional status of oipA. Our results reveal 57.2% isolates with functional oipA along with significant association with cagA (P = 0.0011) and vacAs1m1/s1m2 (P = 0.0034, P = 0.0093) genotypes, respectively. In conclusion, our results indicate diversity in CT repeat pattern among Indian H. pylori strains. The prevalence of functional oipA gene was found to be ranging between 50% and 64.2% though it did not show significant correlation between functional oipA and disease outcome.
Keywords	DNA ; Helicobacter pylori ; biomarkers ; etiological agents ; functional status ; gastric mucosa ; gastrointestinal diseases ; genes ; humans ; outer membrane proteins ; stomach neoplasms ; virulence
Language	English
Dates of publication	2023-01
Size	p. 35.
Publishing place	Springer US
Document type	Article ; Online
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-022-03137-4
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Article ; Online: Clinical and Optical Coherence Tomography Correlation of Recurrence Patterns After Femtosecond Laser-Assisted Anterior Lamellar Keratoplasty in Reis-Bucklers Corneal Dystrophy.

Chaurasia, Sunita / Mishra, Dilip K / Murthy, Somasheila / Das, Rajashree / Edward, Deepak P / Ramappa, Muralidhar

Cornea

2023 Volume 43, Issue 4, Page(s) 459–465

Abstract: Purpose: The aim of this study was to report the clinical profile and patterns of recurrence after femtosecond laser-assisted anterior lamellar keratoplasty (FALK) in Reis-Bucklers corneal dystrophy.: Methods: This is a case series of 5 eyes of 4 ... ...

Abstract	Purpose: The aim of this study was to report the clinical profile and patterns of recurrence after femtosecond laser-assisted anterior lamellar keratoplasty (FALK) in Reis-Bucklers corneal dystrophy. Methods: This is a case series of 5 eyes of 4 patients with Reis-Bucklers corneal dystrophy. Clinical images of recurrence were correlated with the high-resolution optical coherence tomography. Histopathologic examination of excised corneal samples was performed when possible. Results: The median time to recurrence was 2 (1-5) years after FALK. Of the 5 eyes, 1 eye had primary FALK, whereas 4 eyes had secondary interventions, which included previous phototherapeutic keratectomy (once in 1 eye and twice in 2 eyes), and previous penetrating keratoplasty, followed by phototherapeutic keratectomy (1 eye). Recurrence was noted at the level of the subepithelium. In addition, 1 eye showed interface deposits along with epithelial downgrowth at the graft-host bed. Conclusions: The 2 distinct patterns of recurrence noted were at the subepithelial region and the interface. The clinical patterns of recurrence favor an epithelial origin of recurrent deposits.
MeSH term(s)	Humans ; Tomography, Optical Coherence ; Corneal Dystrophies, Hereditary/diagnosis ; Keratoplasty, Penetrating ; Recurrence ; Lasers ; Corneal Transplantation/methods
Language	English
Publishing date	2023-09-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	604826-2
ISSN	1536-4798 ; 0277-3740
ISSN (online)	1536-4798
ISSN	0277-3740
DOI	10.1097/ICO.0000000000003387
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Article: Crosstalk between

Sharma, Prateek / Phatak, Shravani M / Warikoo, Prisha / Mathur, Akshita / Mahant, Shweta / Das, Kunal / Das, Rajashree

3 Biotech

2023 Volume 13, Issue 9, Page(s) 303

Abstract: Gastroduodenal diseases have prevailed for a long time and more so due to dominance of gut ... ...

Abstract	Gastroduodenal diseases have prevailed for a long time and more so due to dominance of gut bacteria
Language	English
Publishing date	2023-08-14
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-023-03734-5
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Article: Development and evaluation of a simple PCR assay and nested PCR for rapid detection of clarithromycin-resistant Helicobacter pylori from culture and directly from the biopsy samples in India.

Karmakar, Bipul Chandra / Paul, Sangita / Basak, Surajit / Ghosh, Manisha / Mukherjee, Piyali / Das, Rajashree / Chaudhuri, Sujit / Dutta, Shanta / Mukhopadhyay, Asish Kumar

Gut pathogens

2023 Volume 15, Issue 1, Page(s) 7

Abstract: Background: Eradication of Helicobacter pylori provides the most effective treatment for gastroduodenal diseases caused by H. pylori infection. Clarithromycin, a member of the macrolide family, still remains the most important antibiotic used in H. ... ...

Abstract	Background: Eradication of Helicobacter pylori provides the most effective treatment for gastroduodenal diseases caused by H. pylori infection. Clarithromycin, a member of the macrolide family, still remains the most important antibiotic used in H. pylori eradication treatment. But the increasing prevalence of clarithromycin resistant H. pylori strains due to point mutations in the V region of the 23S rRNA, poses a great threat in treating the ailing patients. So, we aimed for PCR-mediated rapid detection of the point mutation at 2143 position of 23S rRNA gene in H. pylori that is relevant to clarithromycin resistance from culture and simultaneously from biopsy specimens to avoid the empirical treatment. Results: Newly developed PCR assay using DNA of pure culture detected point mutation in 23S rRNA gene in 21 (8.04%) of 261 clinical strains tested. The agar dilution method showed that all these 21 strains were resistant to clarithromycin indicating the perfect match of the PCR based results. Additionally, the sequencing study also identified the A to G mutation at 2143 position in 23S rRNA gene of the resistant strains only. Consequently, the newly developed Nested-ASP-PCR dealing directly with 50 biopsy specimens demonstrated 100% sensitivity and specificity with the findings of agar dilution method taken as Gold standard. Bioinformatics based analysis such as accessibility analysis and dot plot clearly stated that the base pairing probability has increased due to mutation. Computational studies revealed that the point mutation confers more stability in secondary structure due to conversion of loop to stem. Furthermore, interaction studies showed binding affinity of the CLR to the mutant type is weaker than that to the wild type. Conclusion: This assay outlines a rapid, sensitive and simple approach to identify point mutation that confers clarithromycin resistance as well as clarithromycin sensitive strains, providing rapid initiation of effective antibiotic treatment. Additionally, it is simple to adopt for hospital based diagnostic laboratories to evaluate the degree of regional clarithromycin resistance from biopsy specimens itself. Furthermore, in silico studies provide evidence or a signal that the prevalence of clarithromycin resistance may rise in the near future as a result of this point mutation.
Language	English
Publishing date	2023-02-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2478277-4
ISSN	1757-4749
ISSN	1757-4749
DOI	10.1186/s13099-023-00530-7
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Article: Prevalence of tumor necrosis factor alpha inducing protein (

Mahant, Shweta / Mehra, Shubham / Chhawchharia, Ayushi / Karmakar, Bipul Chandra / Paul, Sangita / Mukhopadhyay, Asish Kumar / Bose, Sudeep / Das, Kunal / Das, Rajashree

3 Biotech

2021 Volume 11, Issue 5, Page(s) 246

Abstract: Helicobacter ... ...

Abstract	Helicobacter pylori
Language	English
Publishing date	2021-04-30
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-021-02804-w
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Article ; Online: The Synergistic Role of Tip α, Nucleolin and Ras in Helicobacter pylori Infection Regulates the Cell Fate Towards Inflammation or Apoptosis.

Mahant, Shweta / Chakraborty, Amlan / Som, Anup / Mehra, Shubham / Das, Kunal / Mukhopadhyay, Asish Kumar / Gehlot, Valentina / Bose, Sudeep / Das, Rajashree

Current microbiology

2021 Volume 78, Issue 10, Page(s) 3720–3732

Abstract: Infection with Helicobacter pylori (H. pylori) leads to a fork in the road situation where it is critical and complex to judge the fate of the cell. We propose for the first time an in silico representation of a protein level network model that can ... ...

Abstract	Infection with Helicobacter pylori (H. pylori) leads to a fork in the road situation where it is critical and complex to judge the fate of the cell. We propose for the first time an in silico representation of a protein level network model that can unfold the mystery behind the cell fate decision between inflammation or cell proliferation or cell death. Upon infection TNF inducible protein α (Tip α) is internalised after binding with the cell surface receptor Nucleolin which is overexpressed on the cell surface thereby activating the Ras pathway. Tip α, Nucleolin and Ras decides the cell fate for apoptosis or abnormal cell proliferation along with ulcers in the gastric tract, hence we term it as the "death triad", which otherwise triggers the inflammatory pathway through downstream signalling of NF-κβ. A series of proteins involved in the signalling cascade are portrayed through compartmentalization of the bacteria and the gut wall. The depicted network works synchronously toward an overarching goal of deciding between apoptosis or inflammation or proliferation. The model has been validated by simulating it with existing transcriptomic data along with clinical findings from patients infected with H. pylori across different regions in India. The results clearly indicate that for a short period of time there is increased binding of Tip α to Nucleolin and the receptor starts to saturate. This increases the tenacity of binding and the cell triggers an inflammatory cascade reaction which involves proinflammatory cytokines such as TNF α thereby progressing to inflammation by activating NF-κβ downstream. On the other hand, Ras involved in interaction with nucleolin can be present both in its activated or inactivated state. Binding of Tip α as a monomer leads to desensitization of Nucleolin leading to cell survival and proliferation.
MeSH term(s)	Apoptosis ; Bacterial Proteins/metabolism ; Gastric Mucosa ; Helicobacter Infections ; Helicobacter pylori ; Humans ; Inflammation ; Phosphoproteins ; RNA-Binding Proteins ; Tumor Necrosis Factor-alpha ; ras Proteins/metabolism ; Nucleolin
Chemical Substances	Bacterial Proteins ; Phosphoproteins ; RNA-Binding Proteins ; Tipalpha protein, Helicobacter pylori ; Tumor Necrosis Factor-alpha ; ras Proteins (EC 3.6.5.2)
Language	English
Publishing date	2021-09-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-021-02626-2
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