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Article ; Online: Prediction of Phage Virion Proteins Using Machine Learning Methods

Ranjan Kumar Barman / Alok Kumar Chakrabarti / Shanta Dutta

Molecules, Vol 28, Iss 2238, p

2023 Volume 2238

Abstract: Antimicrobial resistance (AMR) is a major problem and an immediate alternative to antibiotics is the need of the hour. Research on the possible alternative products to tackle bacterial infections is ongoing worldwide. One of the most promising ... ...

Abstract	Antimicrobial resistance (AMR) is a major problem and an immediate alternative to antibiotics is the need of the hour. Research on the possible alternative products to tackle bacterial infections is ongoing worldwide. One of the most promising alternatives to antibiotics is the use of bacteriophages (phage) or phage-driven antibacterial drugs to cure bacterial infections caused by AMR bacteria. Phage-driven proteins, including holins, endolysins, and exopolysaccharides, have shown great potential in the development of antibacterial drugs. Likewise, phage virion proteins (PVPs) might also play an important role in the development of antibacterial drugs. Here, we have developed a machine learning-based prediction method to predict PVPs using phage protein sequences. We have employed well-known basic and ensemble machine learning methods with protein sequence composition features for the prediction of PVPs. We found that the gradient boosting classifier (GBC) method achieved the best accuracy of 80% on the training dataset and an accuracy of 83% on the independent dataset. The performance on the independent dataset is better than other existing methods. A user-friendly web server developed by us is freely available to all users for the prediction of PVPs from phage protein sequences. The web server might facilitate the large-scale prediction of PVPs and hypothesis-driven experimental study design.
Keywords	AMR ; bacteriophage ; phage virion protein ; machine learning ; phage therapy ; web server ; Organic chemistry ; QD241-441
Subject code	500
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Neonatal Sepsis

Subhankar Mukherjee / Shravani Mitra / Shanta Dutta / Sulagna Basu

Frontiers in Medicine, Vol

The Impact of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae

2021 Volume 8

Abstract: The convergence of a vulnerable population and a notorious pathogen is devastating, as seen in the case of sepsis occurring during the first 28 days of life (neonatal period). Sepsis leads to mortality, particularly in low-income countries (LICs) and ... ...

Abstract	The convergence of a vulnerable population and a notorious pathogen is devastating, as seen in the case of sepsis occurring during the first 28 days of life (neonatal period). Sepsis leads to mortality, particularly in low-income countries (LICs) and lower-middle-income countries (LMICs). Klebsiella pneumoniae, an opportunistic pathogen is a leading cause of neonatal sepsis. The success of K. pneumoniae as a pathogen can be attributed to its multidrug-resistance and hypervirulent-pathotype. Though the WHO still recommends ampicillin and gentamicin for the treatment of neonatal sepsis, K. pneumoniae is rapidly becoming untreatable in this susceptible population. With escalating rates of cephalosporin use in health-care settings, the increasing dependency on carbapenems, a “last resort antibiotic,” has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP). CRKP is reported from around the world causing outbreaks of neonatal infections. Carbapenem resistance in CRKP is largely mediated by highly transmissible plasmid-encoded carbapenemase enzymes, including KPC, NDM, and OXA-48-like enzymes. Further, the emergence of a more invasive and highly pathogenic hypervirulent K. pneumoniae (hvKP) pathotype in the clinical context poses an additional challenge to the clinicians. The deadly package of resistance and virulence has already limited therapeutic options in neonates with a compromised defense system. Although there are reports of CRKP infections, a review on neonatal sepsis due to CRKP/ hvKP is scarce. Here, we discuss the current understanding of neonatal sepsis with a focus on the global impact of the CRKP, provide a perspective regarding the possible acquisition and transmission of the CRKP and/or hvKP in neonates, and present strategies to effectively identify and combat these organisms.
Keywords	neonatal sepsis ; Klebsiella pneumoniae ; carbapenem resistance ; hypervirulence ; CR-hvKP ; antibiotics ; Medicine (General) ; R5-920
Subject code	572
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Issues and challenges of polypharmacy in the elderly

Abhik Sinha / Shatavisa Mukherjee / Santanu Tripathi / Shanta Dutta

Journal of Family Medicine and Primary Care, Vol 10, Iss 10, Pp 3544-

A review of contemporary Indian literature

2021 Volume 3547

Abstract: The aging population is of growing concern all across the globe as well as in India. Polypharmacy has been defined as the simultaneous use of multiple medications by an individual and the clinical suitability of such use. Polypharmacy is found more ... ...

Abstract	The aging population is of growing concern all across the globe as well as in India. Polypharmacy has been defined as the simultaneous use of multiple medications by an individual and the clinical suitability of such use. Polypharmacy is found more frequently in the geriatric population. Researches in India have also reiterated the fact. Polypharmacy in the geriatric population leads to many negative consequences such as increased adverse drug reactions, falls, frailty, and even increased mortality. Moreover, it leads to increased out-of-pocket expenditure. Polypharmacy also poses risk of poor treatment adherence and missed dose in the geriatric population. Mitigation measures in this regard may include increased awareness among physicians, improved medication management and adherence, efforts to reduce self-medication, and improper crosspathy.
Keywords	elderly ; polypharmacy ; issues and challenges ; Medicine ; R
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Waterborne & foodborne viral hepatitis

Abhik Sinha / Shanta Dutta

Indian Journal of Medical Research, Vol 150, Iss 5, Pp 432-

A public health perspective

2019 Volume 435

Keywords	Medicine ; R
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Fitness gains hamper efforts to tackle drug resistance

Shanta Dutta

eLife, Vol

2013 Volume 2

Abstract: It has long been assumed that resistance to antibiotics reduces the fitness of disease-causing bacteria, but experiments on Salmonella Typhi, the bacteria that causes Typhoid fever, are now challenging this view. ...

Abstract	It has long been assumed that resistance to antibiotics reduces the fitness of disease-causing bacteria, but experiments on Salmonella Typhi, the bacteria that causes Typhoid fever, are now challenging this view.
Keywords	Salmonella ; typhoid ; fitness cost ; epistasis ; fluoroquinolone ; antibiotic resistance ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2013-12-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Covid-19 Infection in India

Arnab Sarkar / Alok Kumar Chakrabarti / Shanta Dutta

Pathogens, Vol 10, Iss 1222, p

A Comparative Analysis of the Second Wave with the First Wave

2021 Volume 1222

Abstract: Coronavirus disease 2019 (COVID-19) is considered as the most dreaded disease that has spread all over the world in the recent past. Despite its outbreak in December 2019–January 2020, a few continents and countries such as India started to experience a ... ...

Abstract	Coronavirus disease 2019 (COVID-19) is considered as the most dreaded disease that has spread all over the world in the recent past. Despite its outbreak in December 2019–January 2020, a few continents and countries such as India started to experience a significant number of COVID-19-positive cases from March 2020. GISAID clade variation analysis in the period March 2020–February 2021 (period I) and March 2021–first week of April 2021 (period II) showed a rapid variation of SARS-CoV-2 in all continents and India over time. Studying the relationship of patient age or gender with viral clades in these two periods revealed that the population under 10 years of age was the least affected, whereas the 11–60-year-old population was the most affected, irrespective of patient gender and ethnicity. In the first wave, India registered quite a low number of COVID-19-positive cases/million people, but the scenario unexpectedly changed in the second wave, when even over 400,000 confirmed cases/day were reported. Lineage analysis in India showed the emergence of new SARS-CoV-2 variants, i.e., B.1.617.1 and B.1.617.2, during April–May 2021, which might be one of the key reasons for the sudden upsurge of confirmed cases/day. Furthermore, the emergence of the new variants contributed to the shift in infection spread by the G clade of SARS-CoV-2 from 46% in period II to 82.34% by the end of May 2021. Along with the management of the emergence of new variants, few factors viz., lockdown and vaccination were also accountable for controlling the upsurge of new COVID-19 cases throughout the country. Collectively, a comparative analysis of the scenario of the first wave with that of the second wave would suggest policymakers the way to prepare for better management of COVID-19 recurrence or its severity in India and other countries.
Keywords	COVID-19 ; SARS-CoV-2 ; first wave ; second wave ; clades ; Medicine ; R
Subject code	950
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Diagnostic validation study of rapid urinary tract infection diagnosis kit at peripheral health facilities of West Bengal, India

Debjit Chakraborty / Falguni Debnath / Agniva Majumdar / Atreyi Chakrabarti / Monica Sharma / Kamini Walia / Alok Kumar Deb / Shanta Dutta

Scientific Reports, Vol 14, Iss 1, Pp 1-

2024 Volume 8

Abstract: Abstract Patients reporting to the outpatient departments of peripheral health care settings in India with symptoms of urinary tract infection (UTI) receive one or the other antibiotic before culture confirmation and out of the total culture confirmed ... ...

Abstract	Abstract Patients reporting to the outpatient departments of peripheral health care settings in India with symptoms of urinary tract infection (UTI) receive one or the other antibiotic before culture confirmation and out of the total culture confirmed UTI cases, in less than one third cases the prescribed antibiotics matches to the antibiotic sensitivity test result. Hence, in this study, an indigenous point-of-care (POCT) rapid diagnostic kit (Rapidogram) for UTI was validated against conventional urine culture and sensitivity to understand its possible applicability at peripheral health care settings. This cross-sectional study was conducted during November 2021 to June 2022 in OPDs of two peripheral hospitals. A sample size of 300 was calculated using prevalence of urinary tract infection (UTI) as 33% for sensitivity and specificity using Buderer’s formula. Urine specimens were collected following standard aseptic procedures from the recruited suspected UTI cases and transferred to laboratory maintaining the cold chain. The validation work up was done in two sections: lab validation and field validation. Out of 300 urine samples, 29 were found positive for the growth of UTI pathogen by both methods and 267 were found negative by both methods. Thus, the kit shows very high specificity (99.6%; 97.9–99.9%) and considerably high sensitivity (90.6%; 74.9–98.0%). We also observed higher PPV, NPV, test accuracy (> 96%). Diagnostic Odds Ratio and Youden index were respectively 2581 and 0.89. Clinical data showed that 44% of the suspected UTI cases were prescribed at least one antibiotic before urine test. Mostly they received Norfloxacin whereas the mostly identified organism E.coli was sensitive to Nitrofurantoin. In the context of absence of microbiology facility at peripheral setting and rampant empirical use of antibiotics in UTI, this highly specific and sensitive POCT for UTI may be used as it not only identifies the organism, also shows the antibiotic sensitivity pattern.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular Analysis of Selected Resistance Determinants in Diarrheal Fecal Samples Collected From Kolkata, India Reveals an Abundance of Resistance Genes and the Potential Role of the Microbiota in Its Dissemination

Rituparna De / Asish Kumar Mukhopadhyay / Shanta Dutta

Frontiers in Public Health, Vol

2020 Volume 8

Abstract: Twenty-five diarrheal fecal samples from Kolkata were examined to determine the relative abundance of antimicrobial resistance genes (ARGs) against eight common classes of antibiotics with polymerase chain reaction (PCR) and Sanger sequencing. Relative ... ...

Abstract	Twenty-five diarrheal fecal samples from Kolkata were examined to determine the relative abundance of antimicrobial resistance genes (ARGs) against eight common classes of antibiotics with polymerase chain reaction (PCR) and Sanger sequencing. Relative abundance of an ARG was calculated as the percentage of fecal samples showing the presence of that particular ARG. The frequency of occurrence of resistance marker against each class of antibiotic was calculated as the percentage of fecal samples carrying at least one resistance marker for that particular class of antimicrobials. Antibiogram of Vibrio cholerae (V. cholerae) O1 strains isolated from four of these samples was obtained by disc diffusion method and was compared with the ARG profile of corresponding fecal samples from which the strains were isolated. A 464 bp amplicon of the V3-V4 region of bacterial 16S rDNA was obtained by PCR from 9 of these 25 samples using the primer pair S-D-Bact-0341-b-S-17 and S-D-Bact-0785-a-A-21 and sequenced to determine the major operational taxonomic unit (OTU). These 9 samples represented diarrhea due to diverse etiology and also unresolved etiology as determined by culture method. We conclude that the diarrheal intestinal microbiome has a common gene pool of ARGs against the major classes of antibiotics and may be serving as a reservoir of ARG dissemination. ARG profile of cholera stool showed that ARGs present in the gut of cholera patients may be transferred to the V. cholerae genome and pose a serious threat to the treatment of cholera by triggering resistance against potential drugs to which contemporary strains of V. cholerae were found to be sensitive in the present study. Fecal samples which were culture negative for diarrheal pathogens we tested also carried ARGs and OTU. Abundance of resistance markers against macrolides, tetracyclines, and aminoglycosides was the highest. Phylum Proteobacteria was the most abundant OTU suggesting proteobacterial blooms characteristic of disturbed gut microflora. Our study is the first comparative study of ARG profile of diarrheal samples with varying etiologic agent revealing the presence of ARGs against the most important classes of antibiotics in the gut of diarrheal patients by common, robust molecular methods, which are easily accessible by molecular epidemiological laboratories worldwide.
Keywords	antimicrobial resistance ; antimicrobial resistance genes ; microbiota ; microbiome ; metagenomics ; diarrhea ; Public aspects of medicine ; RA1-1270
Subject code	630
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Convergence of Biofilm Formation and Antibiotic Resistance in Acinetobacter baumannii Infection

Subhasree Roy / Goutam Chowdhury / Asish K. Mukhopadhyay / Shanta Dutta / Sulagna Basu

Frontiers in Medicine, Vol

2022 Volume 9

Abstract: Acinetobacter baumannii (A. baumannii) is a leading cause of nosocomial infections as this pathogen has certain attributes that facilitate the subversion of natural defenses of the human body. A. baumannii acquires antibiotic resistance determinants ... ...

Abstract	Acinetobacter baumannii (A. baumannii) is a leading cause of nosocomial infections as this pathogen has certain attributes that facilitate the subversion of natural defenses of the human body. A. baumannii acquires antibiotic resistance determinants easily and can thrive on both biotic and abiotic surfaces. Different resistance mechanisms or determinants, both transmissible and non-transmissible, have aided in this victory over antibiotics. In addition, the propensity to form biofilms (communities of organism attached to a surface) allows the organism to persist in hospitals on various medical surfaces (cardiac valves, artificial joints, catheters, endotracheal tubes, and ventilators) and also evade antibiotics simply by shielding the bacteria and increasing its ability to acquire foreign genetic material through lateral gene transfer. The biofilm formation rate in A. baumannii is higher than in other species. Recent research has shown how A. baumannii biofilm-forming capacity exerts its effect on resistance phenotypes, development of resistome, and dissemination of resistance genes within biofilms by conjugation or transformation, thereby making biofilm a hotspot for genetic exchange. Various genes control the formation of A. baumannii biofilms and a beneficial relationship between biofilm formation and “antimicrobial resistance” (AMR) exists in the organism. This review discusses these various attributes of the organism that act independently or synergistically to cause hospital infections. Evolution of AMR in A. baumannii, resistance mechanisms including both transmissible (hydrolyzing enzymes) and non-transmissible (efflux pumps and chromosomal mutations) are presented. Intrinsic factors [biofilm-associated protein, outer membrane protein A, chaperon-usher pilus, iron uptake mechanism, poly-β-(1, 6)-N-acetyl glucosamine, BfmS/BfmR two-component system, PER-1, quorum sensing] involved in biofilm production, extrinsic factors (surface property, growth temperature, growth medium) associated with the process, ...
Keywords	Acinetobacter baumannii ; antimicrobial resistance ; biofilm regulation ; biofilm-associated infections ; adult ; paediatric ; Medicine (General) ; R5-920
Subject code	572
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative Evaluation of Three Diagnostic Tools for the Detection of Hepatitis C Virus among High-risk Individuals in a Tertiary Care Centre of Northeast India

Rajkumar Manojkumar Singh / Smeeta Huidrom / Shanta Dutta / Provash Chandra Sadhukhan / Khumukcham Lokeshwar Singh

Journal of Clinical and Diagnostic Research, Vol 16, Iss 7, Pp DC13-DC

2022 Volume 17

Abstract: Introduction: Hepatitis C virus (HCV) has posed a major public health problem globally. Since majority of HCV infected patients are asymptomatic, diagnosis of HCV infection is mainly based on the detection of anti-HCV antibodies by the Enzyme Linked ... ...

Abstract	Introduction: Hepatitis C virus (HCV) has posed a major public health problem globally. Since majority of HCV infected patients are asymptomatic, diagnosis of HCV infection is mainly based on the detection of anti-HCV antibodies by the Enzyme Linked Immunosorbent Assay (ELISA) or Rapid Diagnostic Tests (RDTs) and HCV Ribonucleic Acid (RNA) by real time Polymerase Chain Reaction (PCR) of serum or plasma samples. Aim: To assess the performance of RDTs and fourth generation ELISA against real time reverse transcriptase PCR for the detection of HCV. Materials and Methods: A hospital-based cross-sectional study was carried out in the Virology Section, Department of Microbiology, Jawaharlal Nehru Institute of Medical Sciences (JNIMS), Imphal, Manipur, India, for a period of two years from June 2019 to May 2021. The study included 3,254 plasma samples from suspected cases of HCV monoinfection, and HCV/HIV co-infection. The plasma samples were subjected to anti-HCV antibodies by RDTs (SD BIOLINE, South Korea) and fourth generation ELISA (Monolisa™ HCV Ag-Ab ULTRA, Bio-Rad, France), and HCV RNA by real time PCR. Data analysis was done using descriptive statistics, and performance of the assays was evaluated by using Cohen kappa test (κ) and Receiver Operating Characteristic (ROC) curve. Results: PCR is considered as the gold standard test. HCV was detected by RDTs in 453 (13.92%), ELISA in 413 (12.69%) and RT-PCR in 367 (11.28%) samples. The present study demonstrated sensitivity of 97.55% and specificity of 96.71% with Positive Predictive Value (PPV) of 79.03% by HCV-RDT. The fourth generation ELISA showed high sensitivity of 99.46% and specificity of 98.34%. Using ROC curve, the area under the curve was 81% for ELISA with diagnostic accuracy of 98.46%. Conclusion: Fourth generation ELISA is more sensitive and specific than RDTs for the detection of HCV infection. Confirmatory HCV-RNA assay could be performed to clear doubts related to false-positive and false-negative findings of the primary screening assays.
Keywords	enzyme linked immunosorbent assay ; rapid diagnostic test ; real time polymerase chain reaction ; Medicine ; R
Subject code	360
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	JCDR Research and Publications Private Limited
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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