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A considerable amount of food waste generated globally could be upcycled to synthesise platform chemicals to enhance environmental sustainability and realise a circular economy. This study investigates the catalytic production of the vital platform molecule levulinic acid (LA) from bread waste, a typical stream of starch-rich food waste generated worldwide. Gamma-valerolactone (GVL), isopropanol (IPA), and propylene carbonate (PC) were evaluated as bio-derived and CO2-derived green co-solvents for LA synthesis. In-vessel pressure generated in PC/H2O (1 : 1) solvent was conducive to rapid LA production from bread waste compared to GVL/H2O and IPA/H2O. In PC/H2O, 72 mol% total soluble product yield was observed quickly within 1 min in moderate reaction conditions (130 °C, 0.5 M H2SO4), whereas ∼15–20 mol% of LA could be obtained when the reaction was prolonged for 10–20 min at 130 °C. The yield of LA could be significantly enhanced in GVL/H2O through phase separation using NaCl (30 wt%(aq)). LA yield increased up to a maximum of ∼2.5 times in the biphasic system (28 mol%, 150 °C, 15 min) (representing a theoretical yield of 66%) in GVL/H2O (1 : 1) compared to the monophasic system (∼11 mol%) under the same reaction conditions. The partition coefficient for LA achieved was 4.2 in the GVL/H2O (1 : 1) biphasic medium, indicating that the system was efficient for simultaneous production and extraction of LA. Biphasic GVL/H2O facilitated selective LA production, which could be optimised by tuning the reaction conditions. These new insights can foster the development of high-performance LA production and sustainable biorefinery. [ABSTRACT FROM AUTHOR]

The transmembrane pattern recognition receptor, Toll-like receptor (TLR), are best known for their roles in innate immunity via recognition of pathogen and initiation of signaling response. Mammalian TLRs recognize molecular patterns associated with pathogens and initiate innate immune response. We have studied the evolutionary diversity of mammalian TLR genes for differences in immunological response. Reconstruction of ancestral sequences is a key aspect of the molecular evolution of TLR to track changes across the TLR genes. The comprehensive analysis of mammalian TLRs revealed a distinct pattern of evolution of TLR9. Various sequence-based features such as amino acid usage, hydrophobicity, GC content, and evolutionary constraints are found to influence the divergence of TLR9 from other TLRs. Ancestral sequence reconstruction analysis also revealed that the gradual evolution of TLR genes in several ancestral lineages leads to the distinct pattern of TLR9. It demonstrates evolutionary divergence with the progressive accumulation of mutations results in the distinct pattern of TLR9. [ABSTRACT FROM AUTHOR]

Introduction: Nosocomial infections caused by Multidrug Resistant (MDR) Pseudomonas aeruginosa (P. aeruginosa) have become a major clinical and public health concern. Moreover, the biofilm production protects the bacteria from antibiotics and thereby makes the drugs ineffective. Aim: To find out the β-lactamases profile of antimicrobial resistance and biofilm production of P. aeruginosa isolated from different clinical specimens of patients attending a tertiary care hospital of Kolkata, West Bengal, India. Materials and Methods: A total of 394 consecutive, nonduplicate isolates of P. aeruginosa were identified from 3559 Gram negative bacilli over a period of two years from July 2016 to June 2018. Identification of the isolates and antibiotic sensitivity testing was performed by using automated method and interpreted. Extended Spectrum β-Lactamases (ESBLs), Amp-C β-lactamase (AmpC) and Metallo-β-Lactamases (MBLs) were phenotypically detected by disk synergy test and MBLencoding genes were detected by multiplex Polymerase Chain Reaction (PCR). Biofilm production was done by tissue culture plate assay. Laboratory data and test results were statistically analysed in counts and percentages using MS Excel 2010 version. Results: Out of 394 strains of P. aeruginosa 288 (73.10%) were isolated from male patients whereas 106 (26.90%) were isolated from female patients. Maximum number of cases (67.26%) were from adult populations. The resistance pattern showed 72.33% resistance to ticarcillin-clavulanic acid followed by ciprofloxacin (53.80%), levofloxacin (50.25%), gentamicin (51.52%), ceftazidime (CAZ) (45.93%), cefoperazone-sulbactam (40.1%), aztreonam (34.77%), imipenem (33.5%), piperacillin/tazobactum (30.96%) and Meropenem (MRP) (29.18%). Out of 394 Pseudomonas spp isolates, 204 (51.77%) were MDR. Overall, ESBLs, AmpC and carbapenemase (MBL) production was detected in 145 (36.80%), 51 (12.94%) and 49 (12.43%) isolates by phenotypic methods. By genotypic method 53.34% were carbapenemase producing and blaNDM-1 (68.75%) was the most prevalent carbapenemase gene detected followed by blaVIM (18.75%) and co-production of blaNDM-1+ blaVIM was 12.5%. Biofilm production was observed in 158 (40.10%) isolates. Conclusion: Early detection of these ß-lactamases production is crucial not only for epidemiological study and effective infection control practices to limit the spread of infection but also for planning appropriate therapy according to the resistance mechanisms of the MDR strains. [ABSTRACT FROM AUTHOR]

Although the current pandemic of cholera originated in Asia, reports of cholera cases and outbreaks in the region are sparse. To provide a sub-regional assessment of cholera in South and Southeast Asia, we collated published and unpublished data from existing surveillance systems from Bangladesh, Cambodia, India, Malaysia, Nepal, Pakistan, Philippines, Thailand and Vietnam. Data from existing country surveillance systems on diarrhea, acute watery diarrhea, suspected cholera and/or confirmed cholera in nine selected Asian countries (Bangladesh, Cambodia, India, Malaysia, Nepal, Pakistan, Philippines, Thailand and Vietnam) from 2011 to 2015 (or 2016, when available) were collated. We reviewed annual cholera reports from WHO and searched PubMed and/or ProMED to complement data, where information is not completely available. From 2011 to 2016, confirmed cholera cases were identified in at least one year of the 5- or 6-year period in the countries included. Surveillance for cholera exists in most countries, but cases are not always reported. India reported the most number of confirmed cases with a mean of 5964 cases annually. The mean number of cases per year in the Philippines, Pakistan, Bangladesh, Malaysia, Nepal and Thailand were 760, 592, 285, 264, 148 and 88, respectively. Cambodia and Vietnam reported 51 and 3 confirmed cholera cases in 2011, with no subsequent reported cases. We present consolidated results of available surveillance in nine Asian countries and supplemented these with publication searches. There is paucity of readily accessible data on cholera in these countries. We highlight the continuing existence of the disease even in areas with improved sanitation and access to safe drinking water. Continued vigilance and improved surveillance in countries should be strongly encouraged. [ABSTRACT FROM AUTHOR]

Viral hepatitis is a hepatic disorder of public health importance. and it can be waterborne/foodborne or bloodborne[[1]]. Waterborne or foodborne hepatitis caused by hepatitis A virus (HAV) and hepatitis E virus (HEV), has faeco-oral route of transmission[[2]]. Diagnosis of HEV infection in immunocompromised patients and solid organ transplant recipients in whom seroconversion to anti-HEV antibodies is delayed or may not occur at all, is often challenging. Clinical course and duration of viremia in vertically transmitted hepatitis E virus (HEV) infection in babies born to HEV-infected mothers. [Extracted from the article]

• Gamma-valerolactone is a precursor for valuable chemicals and potential fuel additive. • Non-noble metals can be used in catalytic transfer hydrogenation (CTH) to produce GVL. • Dispersion of metal particles on catalysts influences hydrogenation efficiency. • Lewis acid and base sites are needed for obtaining high GVL yield and selectivity. • Metal leaching from catalysts is significant in aqueous conditions. The distinct physicochemical properties and renewable origin of gamma-valerolactone (GVL) have provided opportunities for diversifying its applications, particularly as a green solvent, excellent fuel additive, and precursor to valuable chemicals. Among the related publications found in the SCOPUS database (≈172 in the last 10 years), we focused our effort to review the conversion of levulinic acid (LA) to GVL over non-noble metal catalysts and the corresponding mechanisms (≈30 publications) as well as the applications of GVL as a solvent, fuel additive, and platform chemical (≈30 publications) mostly in the last five years (some preceding publications have also been included due to their relevance and importance in the field). The use of non-noble metals (e.g. , Cu and Zr) presents a greener route of GVL synthesis than the conventional practice employing noble metals (e.g. , Pd and Ru), in view of their higher abundance and milder reaction conditions needed (e.g. , low pressure and temperature without H 2 involved). The significance of the catalyst characteristics in promoting catalytic transfer hydrogenation of LA to GVL is critically discussed. Structural features and acid-base properties are found to influence the activity and selectivity of catalysts. Furthermore, metal leaching in the presence of water in catalytic systems is an important issue, resulting in catalyst deactivation. Various endeavors for developing catalysts using well-dispersed metal particles along with a combination of Lewis acid and base sites are suggested for efficiently synthesizing GVL from LA. [ABSTRACT FROM AUTHOR]

Background: Campylobacter is a well-known bacterial pathogen for triggering acute gastroenteritis in humans both in developed and developing countries. This organism is highly resistant to fluoroquinolones. Macrolides are very much useful for the treatment of campylobacteriosis when clinical therapy is necessary. However, increasing resistance to azithromycin, a potent macrolide has been reported in Campylobacter in recent years. Macrolide resistance in Campylobacter is found mainly due to point mutation in V region of 23S rRNA. Results: We have developed a PCR based assay, which can detect the azithromycin resistant and sensitive Campylobacter strains utilizing mutation responsible for the phenotype. This PCR was validated using 359 Campylobacter strains isolated from diarrhoeal patients at Kolkata, India. Antimicrobial resistance through disk diffusion method was also performed on these strains as a gold standard. Studies through sequencing analysis further confirmed the PCR result. Conclusion: This study describes a simple and rapid method for detection of mutation conferring macrolide resistance with additional feature of identification of sensitive strains. [ABSTRACT FROM AUTHOR]

This research explored the possibility of making fertilizer at a laboratory from source separated and untreated human urine added to ash and lime by drying at low temperatures. A mixture of ash and lime (1:1) was used as drying agent and human urine was applied as undiluted and fresh. Ash and lime were chosen as drying agents for maintaining a pH > 10 during the drying process, which should inhibit urea hydrolysis in urine, and thereby urea should be retained in the drying agent. The drying technique was developed and drying capacity of the system was quantified; three specific temperatures (20 °, 35 °, 60 °C) and two airflow rates (1 L/min and 5 L/min) were used in the experiment. A mass balance for nitrogen in the system was obtained. It was evident from the experiment that urea can be retained by maintaining a high pH (>10). Urine drying at 20 °C was not a feasible option, since rate of evaporation was very low. The highest retention of inflow nitrogen at 35 °C and 60 °C were 74% and 54%, respectively, in the produced fertilizer. Reduced evaporation rate, flooding of urine over drying agent, and blockage in airflow influenced nitrogen loss and concentration of nitrogen in the final product. [ABSTRACT FROM AUTHOR]

[Display omitted] • Paper wastes possess distinct characteristics yet viable for platform chemical production. • Cellulose content and crystallinity highly influence the levulinic acid yield. • Thermally stable cellulosic fibres in papers require higher energy for hydrolysis. • Alkaline mineral fillers in papers adversely affect the acid-catalysed conversion. • FeCl 3 is a safe and efficient catalyst for valorising lignocellulosic paper wastes. Lignocellulosic paper waste constitutes a major waste stream globally, which should be valorised for chemical production. However, paper properties (e.g. , feedstock composition, cellulosic crystallinity, and thermal stability/degradability) vary with raw materials and pulping processes. This study investigated levulinic acid (LA), hydroxymethylfurfural (HMF), and furfural production by H 2 SO 4 and FeCl 3 catalysed conversion of nine types of paper wastes in a green solvent system (1:1 γ‐valerolactone/water). At 160–180 °C for 1–20 min, ∼23–27 wt% LA yield was achieved from sanitary papers, tracing/parchment paper, and paper food box mainly containing crystalline cellulose, while a lower LA yield (∼10–20 wt%) was obtained from other paper wastes with high contents of ash and lignin. A higher selectivity towards HMF (∼12 mol%) was achieved in the presence of FeCl 3. A furfural yield of ∼ 4–7.5 wt% was also obtained from the hemicellulose content. This study elucidates crucial factors and desirable characteristics of paper waste for catalytic valorisation. [ABSTRACT FROM AUTHOR]

Enteric fever, caused by Salmonella enterica, remains an unresolved public health problem in India and antimicrobial therapy is the main mode of treatment. The objective of this study was to characterize the Salmonella enterica isolates from Kolkata with respect to their antimicrobial resistance (AMR), virulence profiles and molecular subtypes. Salmonella enterica blood isolates were collected from clinically suspected enteric fever patients attending various hospitals in Kolkata, India from January 2009 to June 2013 and were tested for AMR profiles by standard protocols; for resistance gene transfer by conjugation; for resistance and virulence genes profiles by PCR; and for molecular subtypes by Pulsed Field Gel Electrophoresis (PFGE). A total of 77 Salmonella enterica serovar Typhi (S. Typhi) and 25 Salmonella enterica serovar Paratyphi A (S. Paratyphi A) from Kolkata were included in this study. Although multidrug resistance (resistance to chloramphenicol, ampicillin, co-trimoxazole) was decreasing in S. Typhi (18.2%) and absent in S. Paratyphi A, increased resistance to fluoroquinolone, the current drug of choice, caused growing concern for typhoid treatment. A single, non-conjugative non-IncHI1 plasmid of 180 kb was found in 71.4% multidrug resistant (MDR) S. Typhi; the remaining 28.6% isolates were without plasmid. Various AMR markers (blaTEM-1, catA, sul1, sul2, dfrA15, strA-strB) and class 1 integron with dfrA7 gene were detected in MDR S. Typhi by PCR and sequencing. Most of the study isolates were likely to be virulent due to the presence of virulence markers. Major diversity was not noticed among S. Typhi and S. Paratyphi A from Kolkata by PFGE. The observed association between AMR profiles and S. Typhi pulsotypes might be useful in controlling the spread of the organism by appropriate intervention. The study reiterated the importance of continuous monitoring of AMR and molecular subtypes of Salmonella isolates from endemic regions for better understanding of the disease epidemiology. [ABSTRACT FROM AUTHOR]

A resilient health system necessitates strong governance, political commitment, effective administrative entities and inter-organisational collaboration. This paper examines India's current health policy landscape and explores the analytical and operational capacities required to establish a robust post-pandemic health system using the policy capacity framework described by Wu et al. (2015). We emphasised the need for a coordinated policy response to strengthen health information systems, health service management, human resource management and healthcare financing. The role that the planned implementation of Indian public health management cadres would play in the coming era, the importance of a comprehensive health information management system and the need for operational coordination between government and non-governmental organisations has also been emphasised. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] • Food waste digestate (FWD) should be valorised for sustainable waste management. • FWD can be valorised for biofertilisers, carbon-based materials, and solid biofuel. • Pyrolysis and Hydrothermal carbonisation (HTC) of FWD can offer diverse applications. • HTC can significantly enhance the dewaterability of high-moisture FWD. • Integration of anaerobic digestion and HTC is recommended to close the resource loop. Anaerobic digestion (AD) is a widely used technology to valorise food waste for biogas production yet a considerable amount of digestate remains under-utilised. Sustainable management and recycling of the nutrient-rich food waste anaerobic digestate (FWD) is highly desirable for closing resource loop and actualising circular economy. This work reviews the distinct properties of FWD and the existing treatment technologies. FWD shows great prospects as a nutrient source for microalgal cultivation and biofuel production. Emerging technologies such as thermal conversion (e.g., pyrolysis and hydrothermal treatment) of FWD into value-added products such as functionalised biochar/hydrochar with diverse applications would be attractive and warrant further research investigation. Integrated AD with subsequent valorisation facilities is highly encouraged to achieve complete utilisation of resources and reduce carbon emissions. [ABSTRACT FROM AUTHOR]

Background: Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a major health problem especially in developing countries. Vaccines against typhoid are commonly used by travelers but less so by residents of endemic areas. Methodology: We used single nucleotide polymorphism (SNP) typing to investigate the population structure of 372 S. Typhi isolated during a typhoid disease burden study and Vi vaccine trial in Kolkata, India. Approximately sixty thousand people were enrolled for fever surveillance for 19 months prior to, and 24 months following, Vi vaccination of one third of the study population (May 2003–December 2006, vaccinations given December 2004). Principal Findings: A diverse S. Typhi population was detected, including 21 haplotypes. The most common were of the H58 haplogroup (69%), which included all multidrug resistant isolates (defined as resistance to chloramphenicol, ampicillin and co-trimoxazole). Quinolone resistance was particularly high among H58-G isolates (97% Nalidixic acid resistant, 30% with reduced susceptibility to ciprofloxacin). Multiple typhoid fever episodes were detected in 22 households, however household clustering was not associated with specific S. Typhi haplotypes. Conclusions: Typhoid fever in Kolkata is caused by a diverse population of S. Typhi, however H58 haplotypes dominate and are associated with multidrug and quinolone resistance. Vi vaccination did not obviously impact on the haplotype population structure of the S. Typhi circulating during the study period. Author Summary: Typhoid fever is caused by the bacterium Salmonella enterica serovar Typhi (S. Typhi) and is a major health problem especially in developing countries. Vaccines against typhoid are commonly used by travelers but less so by residents of endemic areas. We used single nucleotide polymorphism (SNP) typing to investigate the population structure of 372 S. Typhi bacteria isolated from typhoid patients during a typhoid disease burden study and Vi anti-typhoid vaccine trial in Kolkata, India. Approximately sixty thousand people were enrolled for fever surveillance for 19 months prior to, and 24 months following, vaccination of one third of the study population against typhoid (May 2003–December 2006, vaccinations given December 2004). We detected a diverse population of S. Typhi, including 21 different genetic forms (haplotypes) of the bacteria. The most common (69%) were of a haplogroup known as H58, which included all multidrug resistant isolates (bacteria resistant to the antibiotics chloramphenicol, ampicillin and co-trimoxazole). Resistance to quinolones, a class of antibiotics commonly used to treat typhoid fever, was particularly high among a subgroup of H58 (H58-G). Vi vaccination did not obviously impact on the haplotype distribution of the S. Typhi circulating during the study period. [ABSTRACT FROM AUTHOR]

Background: Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a major health problem especially in developing countries. Vaccines against typhoid are commonly used by travelers but less so by residents of endemic areas. Methodology: We used single nucleotide polymorphism (SNP) typing to investigate the population structure of 372 S. Typhi isolated during a typhoid disease burden study and Vi vaccine trial in Kolkata, India. Approximately sixty thousand people were enrolled for fever surveillance for 19 months prior to, and 24 months following, Vi vaccination of one third of the study population (May 2003-December 2006, vaccinations given December 2004). Principal Findings: A diverse S. Typhi population was detected, including 21 haplotypes. The most common were of the H58 haplogroup (69%), which included all multidrug resistant isolates (defined as resistance to chloramphenicol, ampicillin and co-trimoxazole). Quinolone resistance was particularly high among H58-G isolates (97% Nalidixic acid resistant, 30% with reduced susceptibility to ciprofloxacin). Multiple typhoid fever episodes were detected in 22 households, however household clustering was not associated with specific S. Typhi haplotypes. Conclusions: Typhoid fever in Kolkata is caused by a diverse population of S. Typhi, however H58 haplotypes dominate and are associated with multidrug and quinolone resistance. Vi vaccination did not obviously impact on the haplotype population structure of the S. Typhi circulating during the study period. [ABSTRACT FROM AUTHOR]

Enteric fever (typhoid and paratyphoid fever) is a major human bacterial infection. Although the disease is not common in industrialised countries, it remains an important and persistent health problem in developing nations. Hospital-based studies and outbreak reports from India indicate that enteric fever is a major public health problem in this country, with Salmonella enterica serovar Typhi (S. Typhi) the most common aetiologic agent but with an apparently increasing number of cases due to S. Paratyphi A (SPA). Because risk factors such as poor sanitation, lack of a safe drinking water supply and low socio economic conditions in resource-poor countries are amplified by the evolution of multidrug resistant salmonellae with reduced susceptibility to fluoroquinolone, treatment failure cases have been reported in India, which is associated with increased mortality and morbidity. Vaccination, which requires strict planning and proper targeting of the vulnerable age groups, is considered to be an effective tool in controlling this disease in endemic areas, given there is development of a conjugate vaccine against both serovars (S. Typhi and S. Para A). [ABSTRACT FROM AUTHOR]

Abstract: Although typhoid fever is confirmed by culture of Salmonella enterica serotype Typhi, rapid and simple diagnostic serologic tests would be useful in developing countries. We examined the performance of Widal test in a community field site and compared it with Typhidot and Tubex tests for diagnosis of typhoid fever. Blood samples were collected from 6697 patients with fever for ≥3 days for microscopy, culture, and serologic testing and from randomly selected 172 consenting healthy individuals to assess the baseline Widal anti-Typhi O lipopolysaccharide antibody (anti-TO) and anti-Typhi H flagellar antibody (anti-TH) titers. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the 3 serologic tests were calculated using culture-confirmed typhoid fever cases as “true positives” and paratyphoid fever and malaria cases as “true negatives”. Comparing cutoff values for the Widal test, an anti-TO titer of 1/80 was optimal with 58% sensitivity, 85% specificity, 69% PPV, and 77% NPV. Sensitivity was increased to 67% when the Widal test was done on the 5th day of illness and thereafter. The sensitivity, specificity, PPV, and NPV of Typhidot and Tubex were not better than Widal test. There is a need for more efficient rapid diagnostic test for typhoid fever especially during the acute stage of the disease. Until then, culture remains the method of choice. [Copyright &y& Elsevier]

Since July 2002, bacteriologically confirmed shigellosis cases have increased, and multidrug-resistant Shigella dysenteriae serotype 1 strains have reemerged in patients hospitalized with diarrhea in Kolkata, India. The isolated strains of S. dysentedae 1 showed resistance to chloramphenicol (80%), ampicillin (100%), tetracycline (100%), co-trimoxazole (100%), nalidixic acid (100%), norfloxacin (100%), and ciprofloxacin (100%). Emergence of fluoroquinolone resistance in S. dysenteriae 1 strains complicated treatment of shigellosis patients. Six strains belonging to provisional serovars of S. dysenteriae were also identified for the first time in patients hospitalized with diarrhea in Kolkata, India. [ABSTRACT FROM AUTHOR]

The conversion of food waste and sludge into biogas via anaerobic digestion technology is gaining attention in recent years, which plays a significant role in waste valorization into bioenergy and promotes environmental sustainability. Biochar is a carbonaceous material produced via thermochemical conversion of biomass waste, and tailoring biochar for diverse environmental applications adheres to the principle of circular economy. The emerging application of biochar as an additive in the anaerobic digestion of food waste and sludge has been intensively investigated in the last few years. However, a comprehensive understanding of multifunctional roles of biochar and its mechanisms in the production of biogas via miscellaneous/complex anaerobic digestion process is yet to be attained. This review scrutinizes the key roles of biochar as an additive and emphasizes the influences of biochar characteristics on the anaerobic digestion processes and their capability to address the foremost challenges. This review also evaluates the techno-economic and environmental impacts of biochar synthesis and its emerging application for biogas production via anaerobic digestion to make the integrated process more economical and environmentally sustainable, and identifies challenges and prospects for future studies. [Display omitted] • Biochar manifests tunable physicochemical properties for diverse applications. • Biochar facilitates efficient anaerobic digestion (AD) of food waste and sludge. • Microbial functions and enzymatic activity can be enhanced by biochar addition. • A closed-loop material flow can be realized by integrating AD and pyrolysis. [ABSTRACT FROM AUTHOR]

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 RDT and 4th 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 RDT (SD BIOLINE, South Korea) and 4th 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 (1) and Receiver Operating Characteristic (ROC) curve. Results: PCR is considered as the gold standard test. HCV was detected by RDT 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 4th 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: 4th generation ELISA is more sensitive and specific than RDT 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. [ABSTRACT FROM AUTHOR]

The global spread of SARS‐CoV‐2 is fast moving and has caused a worldwide public health crisis. In the present article, we analyzed spike protein sequences of SARS‐CoV‐2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS‐CoV‐2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented about foodborne outbreaks of Shigella sonnei in India in 2009-10.

• Green co-solvent systems enhanced cellulose depolymerization and product yield. • Maximum 32% of levulinic acid (LA) yielded in GVL/H 2 O solvent at 200 °C. • GVL/H 2 O system maintained high availability of soluble sugars. • Acetone/H 2 O solvent generated 17 Cmol% of LA at a lower temperature (180 °C) • Higher temperature induced polymerization of sugars in acetone/H 2 O solvent. Lignocellulosic wastes constitute a significant portion of the municipal solid waste, which should be valorised for the synthesis of value-added chemicals to achieve circular bioeconomy. This study evaluates the use of γ-valerolactone (GVL) and acetone as green co-solvents to produce levulinic acid (LA) from lignocellulosic paper towel waste at different temperatures using dilute H 2 SO 4. At the highest reaction temperature (200 °C), H 2 O-only system achieved ~15 Cmol% of LA at maximum. while GVL/H 2 O and acetone/H 2 O co-solvent systems enhanced the depolymerisation of paper towel waste and the subsequent conversion to LA, with the highest yield amounted to ~32 Cmol%. Acetone/H 2 O solvent system generated ~17 Cmol% LA at a lower temperature (180 °C), while higher temperature induced polymerisation of soluble sugars and intermediates, hindering further conversion to LA. In contrast, the availability of soluble sugars was higher in the GVL/H 2 O system, which favoured the production of LA at higher temperatures. [ABSTRACT FROM AUTHOR]

Background: Coronavirus disease-2019 (COVID-19) continues to pose serious challenges to healthcare systems globally with the disease progressing over time in crest-trough pattern of waves. We compared the patient characteristics and outcomes of critically ill patients admitted during the first and second waves of COVID-19 pandemic. Materials and Methods: We did a retrospective analysis of medical records of critically ill patients admitted to intensive care unit (ICU) at the peak period of both waves. The data on demographics, symptoms, treatment received, and outcomes of patients were recorded. Results: Compared to first wave, significantly more females, younger age group, and those without underlying comorbidities required ICU admission during the second wave. The treatments received during both periods were similar except for preferential use of methylprednisolone over dexamethasone and proclivity of bilevel positive airway pressure (BiPAP) ventilation over high-flow nasal cannula (HFNC). There was no significant difference in the duration of ICU stay and mortality of patients. During the first wave, the factors associated with nonsurvival of patients were advanced age, comorbidities, severe disease, and a lesser number of days on HFNC. All these factors along with higher Sequential Organ Failure Assessment (SOFA) score were observed to be linked with patient nonsurvival during the second wave. Conclusion: In India, the second wave of COVID-19 significantly influenced ICU demographics with a predominance of females and young adults requiring critical care. During both time periods, patients received similar treatment except for the propensity to use methylprednisolone and BiPAP as opposed to dexamethasone and HFNC in second wave. No significant difference in ICU mortality was noted. [ABSTRACT FROM AUTHOR]

Background The clinical relevance of Acinetobacter pittii is increasing, but reports of this organism causing neonatal sepsis are rare. Objectives To understand the mechanisms of resistance and virulence of A. pittii isolated from neonatal blood belonging to a novel sequence type. Materials and methods Antibiotic susceptibility, MLST, WGS, phylogenomic comparison with a global collection of carbapenemase-harbouring A. pittii were done. To study the pathogenic potential of novel A. pittii , in vitro and in vivo assays were carried out. Results and discussion Two novel multidrug-resistant A. pittii from neonatal blood belonging to a novel sequence type 1451 (ST1451) were isolated. WGS revealed that the isolates were almost similar (147 SNP distant) and harbouring two carbapenem resistance genes bla NDM-1 with upstream IS Aba125 and downstream ble MBL along with bla OXA-58 with upstream IS Aba3. Other resistance genes included bla ADC-25, bla OXA-533, aph(3″)-Ib , aph(3′)-VIa , aph(6)-Id , aac(3)-IId , mph(E) , msr(E) , sul2 and tet(39) , different efflux pump genes and amino acid substitutions within GyrA (Ser81Leu) and ParC (Ser84Leu; Glu88Ala) were detected among the isolates. The study genomes were closely related to four strains belonging to ST119. The isolates showed biofilm production, serum resistance, growth under iron limiting condition, surface-associated motility and adherence to host cell. Isolates induced cytokine production in the host cell and showed mice mortality. Discussion and conclusions This study is the first report of the presence of bla NDM-1 in A. pittii from India along with another carbapenemase bla OXA-58. Emergence of highly virulent, multidrug-resistant A. pittii with attributes similar to A. baumannii calls for surveillance to identify the novel strains and their pathogenic and resistance potential. [ABSTRACT FROM AUTHOR]

Background: The primary aim of this study was to investigate the occurrence, characteristics, and antimicrobial resistance patterns of various Shigella serotypes isolated from patients with acute diarrhea of the Infectious Diseases Hospital in Kolkata from 2011–2019. Principal findings: During the study period, Shigella isolates were tested for their serotypes, antibiotic resistance pattern and virulence gene profiles. A total of 5.8% of Shigella spp. were isolated, among which S. flexneri (76.1%) was the highest, followed by S. sonnei (18.7%), S. boydii (3.4%), and S. dysenteriae (1.8%). Antimicrobial resistance against nalidixic acid was higher in almost all the Shigella isolates, while the resistance to β-lactamases, fluoroquinolones, tetracycline, and chloramphenicol diverged. The occurrence of multidrug resistance was found to be linked with various genes encoding drug-resistance, multiple mutations in the topoisomerase genes, and mobile genetic elements. All the isolates were positive for the invasion plasmid antigen H gene (ipaH). Dendrogram analysis of the plasmid and pulsed-field electrophoresis (PFGE) profiles revealed 70–80% clonal similarity among each Shigella serotype. Conclusion: This comprehensive long-term surveillance report highlights the clonal diversity of clinical Shigella strains circulating in Kolkata, India, and shows alarming resistance trends towards recommended antibiotics. The elucidation of this study's outcome is helpful not only in identifying emerging antimicrobial resistance patterns of Shigella spp. but also in developing treatment guidelines appropriate for this region. Author summary: Shigella spp. is one of the WHO-designated "antibiotic-resistant priority pathogens" that is the leading cause of bacterial diarrhea among children worldwide. The distribution of Shigella species varies depending on the geographic location, particularly in regions where environmental risk factors like substandard water quality, limited healthcare accessibility, and insufficient sanitation are widespread. The presence of serotype diversity and drug resistance combinations often leads to treatment failures. Therefore, it is crucial to comprehend the prevailing serogroups and antimicrobial resistance patterns of Shigella species in different geographical areas to implement effective treatment strategies. We have identified 535 Shigella positive cases from 9276 diarrheal cases. Multidrug-resistant (MDR) Shigella globally requires a profound understanding of its genetic diversity, as there is significant regional variation in MDR strains. In our study, we observed a broad spectrum of resistance among the Shigella strains, with over 53.6% of the isolates demonstrating multidrug resistance. Representative isolates were evaluated for antimicrobial resistance encoding and virulence-associated genes as they enact significantly in disease development and interaction with the host immune system. This report marks the initial presentation of the outcomes from long-term surveillance and molecular characterization of antimicrobial resistances in clinical Shigella strains in Kolkata since 2011. The outcome of this investigations will guide in identifying emerging antimicrobial resistance trend, formulating suitable treatment guidelines tailored to the community's needs, and establishing baseline data for comparison with potential outbreak strains in the future. [ABSTRACT FROM AUTHOR]

Background: Worldwide, noroviruses are the leading cause of acute gastroenteritis (AGE) in people of all age groups. In India, norovirus rates between 1.4 to 44.4% have been reported. Only a very few complete norovirus genome sequences from India have been reported. Objective: To perform full genome sequencing of noroviruses circulating in India during 2017–2021, identify circulating genotypes, assess evolution including detection of recombination events. Methodology: Forty-five archived norovirus-positive samples collected between October 2017 to July 2021 from patients with AGE from two hospitals in Kolkata, India were processed for full genome sequencing. Phylogenetic analysis, recombination breakpoint analysis and comprehensive mutation analysis were also performed. Results: Full genome analysis of norovirus sequences revealed that strains belonging to genogroup (G)I were genotyped as GI.3[P13]. Among the different norovirus capsid-polymerase combinations, GII.3[P16], GII.4 Sydney[P16], GII.4 Sydney[P31], GII.13[P16], GII.16[P16] and GII.17 were identified. Phylogenetic analysis confirmed phylogenetic relatedness with previously reported norovirus strains and all viruses were analyzed by Simplot. GII[P16] viruses with multiple residue mutations within the non-structural region were detected among circulating GII.4 and GII.3 strains. Comprehensive mutation analysis and selection pressure analysis of GII[P16] viruses showed positive as well as negative selection sites. A GII.17 strain (NICED-BCH-11889) had an untypeable polymerase type, closely related to GII[P38]. Conclusion: This study highlights the circulation of diverse norovirus strains in eastern India. These findings are important for understanding norovirus epidemiology in India and may have implications for future vaccine development. [ABSTRACT FROM AUTHOR]

Background Oral cholera vaccine (OCV) and incremental improvements in household water, sanitation, and hygiene (WASH) within cholera-endemic areas can reduce cholera risk. However, we lack empiric evaluation of their combined impact. Methods We evaluated a cluster-randomized, placebo-controlled trial of OCV (Shanchol) in Kolkata, India. The study population included 108 777 individuals, and 106 879 nonpregnant individuals >1 year of age were eligible to receive 2 doses of OCV or placebo. We measured cholera risk in all household members assigned to OCV vs placebo and in all members of households with "Better" vs "Not Better" WASH, where WASH was classified according to validated criteria. Protection was measured by Cox proportional hazard models. Results Residence in an OCV household was associated with protective effectiveness (PE) of 54% (95% CI, 42%–64%; P <.001) and was similar regardless of Better (PE, 57%; 95% CI, 26%–75%; P =.002) or Not Better (PE, 53%; 95% CI, 40%–64%; P <.001) household WASH. Better WASH household residence was associated with PE of 30% (95% CI, 5%–48%; P =.023) and was similar in OCV (PE, 24%; 95% CI, −26% to 54%; P =.293) and placebo (PE, 29%; 95% CI, −3% to 51%; P =.069) households. When assessed conjointly, residence in OCV households with Better WASH was associated with the greatest PE against cholera at 69% (95% CI, 49%–81%; P <.001). Conclusions These findings suggest that the combination of a vaccine policy and improved WASH reduces cholera risk more than either would alone, although the magnitude of either intervention was not affected by the other. Future randomized trials investigating OCV and WASH interventions separately and together are recommended to further understand the interaction between OCV and WASH. [ABSTRACT FROM AUTHOR]

Understanding the genetic dynamics of circulating Human Adenovirus (HAdV) types is pivotal for effectively managing outbreaks and devising targeted interventions. During the West Bengal outbreak of 2022–2023, an investigation into the genetic characteristics and outbreak potential of circulating HAdV types was conducted. Twenty-four randomly selected samples underwent whole-genome sequencing. Analysis revealed a prevalent recombinant strain, merging type 3 and type 7 of human mastadenovirus B1 (HAd-B1) species, indicating the emergence of recent strains of species B in India. Furthermore, distinctions in VA-RNAs and the E3 region suggested that current circulating strains of human mastadenovirus B1 (HAd-B1) possess the capacity to evade host immunity, endure longer within hosts, and cause severe respiratory infections. This study underscores the significance of evaluating the complete genome sequence of HAdV isolates to glean insights into their outbreak potential and the severity of associated illnesses. [ABSTRACT FROM AUTHOR]

Recurrent Tuberculosis patients contribute to a significant proportion of TB burden in India. A nationwide survey was conducted during 2019–2021 across India among adults to estimate the prevalence of TB. A total of 322480 individuals were screened and 1402 were having TB. Of this, 381 (27.1%) had recurrent TB. The crude prevalence (95% CI) of recurrent TB was 118 (107–131) per 100,000 population. The median duration between episodes of TB was 24 months. The proportion of drug resistant TB was 11.3% and 3.6% in the recurrent group and new TB patients respectively. Higher prevalence of recurrent TB was observed in elderly, males, malnourished, known diabetics, smokers, and alcohol users. (p<0.001). To prevent TB recurrence, all treated tuberculosis patients must be followed at least for 24 months, with screening for Chest X-ray, liquid culture every 6 months, smoking cessation, alcohol cessation, nutritional interventions and good diabetic management. [ABSTRACT FROM AUTHOR]

Background: The burden of the COVID-19 pandemic on healthcare systems worldwide has been compromising the progress made in the fight against HIV. This paper aims to determine how the COVID-19 pandemic has impacted HIV comprehensive care service delivery globally as well as to consolidate the evidence and recommendations that may be useful in averting future crisis. Methods: This review adheres to PRISMA guidelines. PubMed, DOAJ, Science Direct and other sources like Google Scholar and citations from included studies were searched methodically to locate studies evaluating the effects of COVID on services for HIV care. The NIH and JBI quality assessment tools were used for the quality assessment of individual studies. Results: In the present review 31 eligible studies were included and the impact on HIV care cascade were summarised under six themes: Lab services, Treatment and allied services, Counselling services, Outreach services, Psycho-social impact and Implementation of sustainable strategies. The studies also presented many innovative alternatives which were lucidly highlighted in the present article. Conclusion: Current evidence depicts multiple factors are responsible for the interruption of HIV care service delivery during the pandemic, especially in low resources settings. The prospective, alternative solutions that have been used to circumvent the threat have also been addressed in this review, in addition to the negative aspects that have been observed. Transition with new innovative, sustainable care paradigms may prove to be the building blocks in removing HIV-AIDS as a public health threat. Registration: Open Science Framework (DOI: 10.17605/OSF.IO/74GHM). [ABSTRACT FROM AUTHOR]

Background: Salmonella enterica serotype Typhi is one of the major pathogens causing typhoid fever and a public health burden worldwide. Recently, the increasing number of multidrug-resistant strains of Salmonella spp. has made this utmost necessary to consider bacteriophages as a potential alternative to antibiotics for S. Typhi infection treatment. Salmonella phage STWB21, isolated from environmental water, has earlier been reported to be effective as a safe biocontrol agent by our group. In this study, we evaluated the efficacy of phage STWB21 in reducing the burden of salmonellosis in a mammalian host by inhibiting Salmonella Typhi invasion into the liver and spleen tissue. Results: Phage treatment significantly improved the survival percentage of infected mice. This study also demonstrated that oral administration of phage treatment could be beneficial in both preventive and therapeutic treatment of salmonellosis caused by S. Typhi. Altogether the result showed that the phage treatment could control tissue inflammation in mice before and after Salmonella infection. Conclusions: To the best of our knowledge, this is the first report of phage therapy in a mouse model against a clinically isolated Salmonella Typhi strain that includes direct visualization of histopathology and ultrathin section microscopy images from the liver and spleen sections. [ABSTRACT FROM AUTHOR]

The prevalence and genetic diversity of the protozoan pathogen Giardia duodenalis have been extensively studied worldwide. There is currently a lack of data regarding the genetic variability of the organism in eastern India. Understanding the circulating genotypes and associated risk factors is crucial for effective planning and implementing control measures. Therefore, the objective of the study was to conduct an epidemiological study to determine the prevalence and identify the various genotypes present. This survey adds to our knowledge on the occurrence and distribution of Giardia genotypes in the studied region. The overall prevalence was found to be 6.8%. This parasitic infection was significantly associated with two age groups, i.e., >0–5 years and >5–12 years. Using a multilocus genotyping method, we genotyped 52 human Giardia isolates that were obtained from diarrheal patients. Two distinct assemblages were found in the population—30.8% belonged to assemblage A; 63.5% belonged to assemblage B, prevalent in the population; and 5.7% belonged to a combined assemblage A+B. Sub-assemblage AII was found in 17.3% of the cases, followed by sub-assemblage AI (13.5%). High levels of genetic diversity were found within the population of assemblage B undergoing balancing selection. Overall, the high prevalence of the parasite observed, particularly among children, raises a major concern and necessitates implementation of robust control measures. Furthermore, we report the presence of numerous unique genotypes, circulating in this limited geographical boundary, which can be useful dataset for future studies. [ABSTRACT FROM AUTHOR]

Amoebiasis is an infection caused by enteric protozoa, most commonly Entamoeba histolytica, and is globally considered a potentially severe and life-threatening condition. To understand the impact of the parasite genome on disease outcomes, it is important to study the genomes of infecting strains in areas with high disease prevalence. These studies aim to establish correlations between parasite genotypes and the clinical presentation of amoebiasis. We employ a strain typing approach that utilizes multiple loci, including SREHP and three polymorphic non-coding loci (tRNA-linked array N-K2 and loci 1-2 and 5-6), for high-resolution analysis. Distinct clinical phenotype isolates underwent amplification and sequencing of studied loci. The nucleotide sequences were analysed using Tandem Repeats Finder to detect short tandem repeats (STRs). These patterns were combined to assign a genotype, and the correlation between clinical phenotypes and repetitive patterns was statistically evaluated. This study found significant polymorphism in the size and number of PCR fragments at SREHP and 5-6 locus, while the 1-2 locus and NK2 locus showed variations in PCR product sizes. Out of 41 genotypes, two (I6 and I41) were significantly associated with their respective disease outcomes and were found in multiple isolates. We observed that I6 was linked with a symptomatic outcome, with a statistically significant p-value of 0.0183. Additionally, we found that I41 was associated with ALA disease outcome, with a p-value of 0.0089. Our study revealed new repeat units not previously reported, unveiling the genetic composition of E. histolytica strains in India, associated with distinct disease manifestations. [ABSTRACT FROM AUTHOR]

Background Global cholera control efforts rely heavily on effective water, sanitation, and hygiene (WASH) interventions in cholera-endemic settings. Methods Using data from a large, randomized controlled trial of oral cholera vaccine conducted in Kolkata, India, we evaluated whether natural variations in WASH in an urban slum setting were predictive of cholera risk. From the control population (n = 55 086), baseline WASH data from a randomly selected "training subpopulation" (n = 27 634) were analyzed with recursive partitioning to develop a dichotomous ("better" vs "not better") composite household WASH variable from several WASH features collected at baseline, and this composite variable was then evaluated in a mutually exclusive "validation population" (n = 27 452). We then evaluated whether residents of better WASH households in the entire population (n = 55 086) experienced lower cholera risk using Cox regression models. Better WASH was defined by a combination of 4 dichotomized WASH characteristics including safe source of water for daily use, safe source of drinking water, private or shared flush toilet use, and always handwashing with soap after defecation. Results Residence in better WASH households was associated with a 30% reduction in risk of cholera over a 5-year period (adjusted hazard ratio, 0.70 [95% confidence interval,.49–.99]; P =.048). We also found that the impact of better WASH households on reducing cholera risk was greatest in young children (0–4 years) and this effect progressively declined with age. Conclusions The evidence suggests that modest improvements in WASH facilities and behaviors significantly modify cholera risk and may be an important component of cholera prevention and elimination strategies in endemic settings. Clinical Trials Registration. NCT00289224. [ABSTRACT FROM AUTHOR]

• Outer membrane vesicles were isolated from five pathotypes of diarrhoeagenic E. coli (DEC) and mixed in equal proportions for formulation of pentavalent outer-membrane vesicles (POMVs) based immunogen. • Intraperitoneal administration of three doses of 10 µg POMVs in adult BALB/c mice activated both the humoral and cellular arms of immune response. • POMVs immunized adult BALB/c mice sera elicited significant bactericidal effect against five pathotypes of DEC. • Passive transfer of POMVs immunized adult mice sera significantly protected neonatal mice against DEC infections. Diarrhoeagenic Escherichia coli (DEC) pathotypes are one of the major causative agents of diarrhoea induced childhood morbidity and mortality in developing countries. Licensed vaccines providing broad spectrum protection against DEC mediated infections are not available. Outer membrane vesicles (OMVs) are microvesicles released by gram-negative bacteria during the growth phase and contain multiple immunogenic proteins. Based on prevalence of infections, we have formulated a pentavalent outer-membrane vesicles (POMVs) based immunogen targeting five main pathotypes of DEC responsible for diarrhoeal diseases. Following isolation, OMVs from five DEC pathotypes were mixed in equal proportions to formulate POMVs and 10 µg of the immunogen was intraperitoneally administered to adult BALB/c mice. Three doses of POMVs induced significant humoral immune response against whole cell lysates (WCLs), outer membrane proteins (OMPs) and lipopolysaccharides (LPS) isolated from DEC pathotypes along with significant induction of cellular immune response in adult mice. Passive transfer of POMVs immunized adult mice sera protected neonatal mice significantly against DEC infections. Overall, this study finds POMVs to be immunogenic in conferring broad-spectrum passive protection to neonatal mice against five main DEC pathotypes. Altogether, these findings suggest that POMVs can be used as a potent vaccine candidate to ameliorate the DEC-mediated health burden. [ABSTRACT FROM AUTHOR]

Background: Metagenomic analysis of the gut microbiome and resistome is instrumental for understanding the dynamics of diarrheal pathogenesis and antimicrobial resistance transmission (AMR). Metagenomic sequencing of 20 diarrheal fecal samples from Kolkata was conducted to understand the core and variable gut microbiota. Five of these samples were used for resistome analysis. The pilot study was conducted to determine a microbiota signature and the source of antimicrobial resistance genes (ARGs) in the diarrheal gut. Results: 16S rRNA amplicon sequencing was performed using Illumina MiSeq platform and analysed using the MGnify pipeline. The Genome Taxonomy Database (GTDB-Tk) was used for bacterial taxonomic identification. Diarrheal etiology was determined by culture method. Phylum Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria were consistently present in 20 samples. Firmicutes was the most abundant phylum in 11 samples. The Bacteroidetes/Firmicutes ratio was less than 1 in 18 samples. 584 genera were observed. 18 of these were present in all the 20 samples. Proteobacteria was the dominant phylum in 6 samples associated with Vibrio cholerae infection. Conservation of operational taxonomic units (OTUs) among all the samples indicated the existence of a core microbiome. Asymptomatic carriage of pathogens like Vibrio cholerae and Helicobacter pylori was found. Signature of Candidate phyla or "microbial dark matter" occurred. Significant correlation of relative abundance of bacterial families of commensals and pathogens were found. Whole-genome sequencing (WGS) on Illumina MiSeq system and assembly of raw reads using metaSPAdes v3.9.1 was performed to study the resistome of 5 samples. ABRicate was used to assign ARG function. 491 resistance determinants were identified. In 80% of the samples tetracycline resistance was the most abundant resistance determinant. High abundance of ARGs against β-lactams, aminoglycosides, quinolones and macrolides was found. Eschericia sp. was the major contributor of ARGs. Conclusions: This is the first comparative study of the gut microbiome associated with different diarrheal pathogens. It presents the first catalogue of different bacterial taxa representing the core and variable microbiome in acute diarrheal patients. The study helped to define a trend in the gut microbiota signature associated with diarrhea and revealed which ARGs are abundantly present and the metagenome-assembled genomes (MAGs) contributing to AMR. [ABSTRACT FROM AUTHOR]

Annual flu led by influenza viruses is contemplated to be one of the foremost global health challenges due to its rapid spread leading to the life-threatening epidemic or pandemic. An enormous number of people die due to flu and its associated intricacies every year. Annual vaccination is considered to be the gold standard strategy to protect the individual from acquiring infection and further decimation, although recent estimates suggest that overall flu vaccine effectiveness was within 19% to 53% in last five years. A significant weakness of current vaccination is its inability to protect an individual from different or mutant flu strain. Host immune system performs a vital role during natural infection or after vaccination leading to influenza-specific immunities. Previous imprints of common flu or vaccination may alter the outcomes of the current vaccination. Current flu vaccine regime does not consider the host immune status before vaccination. Irrespective of the previous influenza exposure history or prior flu vaccination, individual get flu vaccination based on WHO recommendation with selected strains which may be the reason why induction of broad immunities does not transpire with their testimonial. Over the last few decades, scientific research had identified the role of preexisting immunities on vaccination or natural infection outcome. In this review, we are proposing the concept of personalized flu vaccines depending on individual immune status. We will also discuss why individual was unable to induce broader immunities to protect itself from diverse influenza viruses and how we can accomplish that goal with the current findings. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus) has constantly been evolving into different forms throughout its spread in the population. Emerging SARS-CoV-2 variants, predominantly the variants of concern (VOCs), could have an impact on the virus spread, pathogenicity, and diagnosis. The recently emerged "Omicron" variant has exhibited rapid transmission and divergence. The spike protein of SARS-CoV-2 has consistently been appearing as the mutational hotspot of all these VOCs. In order to determine a deeper understanding of the recently emerged and extremely divergent "Omicron", a study of amino acid usage patterns and their substitution patterns was performed and compared with those of the other four successful variants of concern ("Alpha", "Beta", "Gamma", and "Delta"). We observed that the amino acid usage of "Omicron" has a distinct pattern that distinguishes it from other VOCs and is significantly correlated with the increased hydrophobicity in spike proteins. We observed an increase in the non-synonymous substitution rate compared with the other four VOCs. Considering the phylogenetic relationship, we hypothesized about the functional interdependence between recombination and the mutation rate that might have resulted in a shift in the optimum of the mutation rate for the evolution of the "Omicron" variant. The results suggest that for improved disease prevention and control, more attention should be given to the significant genetic differentiation and diversity of newly emerging variants. [ABSTRACT FROM AUTHOR]

• Bivalent bacterial ghost based vaccine was developed by chemical treatment against Salmonella Typhi and Paratyphi A. • Robust humoral and cell mediated immunity was found in vaccinated mice after intraperitoneal administration of three doses. • Vaccinated mice were conferred 80–100 % protection against clinical isolates of Salmonella Typhi and Paratyphi A. • Vaccinated mice serum has significant bactericidal effect through complement mediated lysis and hinder bacterial motility. • Adoptive transfer of vaccinated mice serum and splenocytes significantly lower the bacterial colonization in naïve animals. Typhoid and emerging paratyphoid fever are a severe enteric disease worldwide with high morbidity and mortality. Licensed typhoid vaccines are in the market, but no paratyphoid vaccine is currently available. In the present study we developed a bivalent vaccine against Salmonella Typhi and Paratyphi A using a bacterial ghost platform. Bacterial ghost cells (BGs) are bacteria-derived cell membranes without cytoplasmic contents that retain their cellular morphology, including all cell surface features. Furthermore, BGs have inherent adjuvant properties that promote an enhanced humoral and cellular immune reaction to the target antigen. Sodium hydroxide was used to prepare ghost cells of Salmonella Typhi and Paratyphi A. The bacterial ghost cells were characterised using electron microscopy. Then BALB/c mice were immunized three times (0th, 14th and 28th day) with the bivalent typhoidal bacterial ghost cells. Haematological study of adult mice throughout immunization period reflected that the immunogen was safe to administer and does not affect the animals' health. After complete immunization, we found significant serum antibody titter against whole cell lysate, outer membrane protein and lipopolysaccharide of both bacteria, and cell-mediated immunity was observed in an ex-vivo experiment. CD4+, CD8a+ and CD19+ splenic cell populations were increased in immunized animals. Bivalent Typhoidal ghost cell immunized mice showed better survival, less bacterial colonization in systemic organs, and less inflammation and/or destruction of tissue in histopathological analysis than non-immunized control mice. Serum antibodies of immunized animals can significantly inhibit bacterial motility and mucin penetration ability with better killing properties against Salmonella Typhi and Paratyphi A. Furthermore, significant passive protection was observed through the adoptive transfer of serum antibody and lymphocytes of immunized animals to naïve animals after bacterial infection. In summary, Bivalent Typhoidal Bacterial Ghost cells (BTBGs) enhances immunogenic properties and serves as a safe and effective prevention strategy against Salmonella Typhi and Paratyphi A. [ABSTRACT FROM AUTHOR]

Background: In the Bengal Delta, research has shown that climate and cholera are linked. One demonstration of this is the relationship between interannual ocean-atmospheric oscillations such as the El Niño Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD). What remains unclear in the present literature is the nature of this relationship in the specific context of Kolkata, and how this relationship may have changed over time. Results: In this study, we analyse the changing relationship between ENSO and IOD with cholera in Kolkata over recent (1999–2019) and historical (1897–1941) time intervals. Wavelet coherence analysis revealed significant non-stationary association at 2–4 year and 4–8 year periods between cholera and both interannual timeseries during both time intervals. However, coherence was notably weakened in the recent interval, particularly with regards to ENSO, a result supported by a complementary SARIMA analysis. Similar coherence patterns with temperature indicate it could be an important mediating factor in the relationship between cholera and oscillating climate phenomena in Kolkata. Conclusions: This study reveals a shifting relationship between cholera and climate variables (ENSO and IOD) in Kolkata, suggesting a decoupling between environmental influences and cholera transmission in recent years. Our results therefore do not suggest that an intensification of ENSO is likely to significantly influence cholera in the region. We also find that the relationship between cholera and interannual climate variables is distinct to Kolkata, highlighting the spatial heterogeneity of the climate-cholera relationship even within the Bengal Delta. [ABSTRACT FROM AUTHOR]

Background: Cholera in Kolkata remains endemic and the Indian city is burdened with a high number of annual cases. Climate change is widely considered to exacerbate cholera, however the precise relationship between climate and cholera is highly heterogeneous in space and considerable variation can be observed even within the Indian subcontinent. To date, relatively few studies have been conducted regarding the influence of climate on cholera in Kolkata. Methods: We considered 21 years of confirmed cholera cases from the Infectious Disease Hospital in Kolkata during the period of 1999–2019. We used Generalised Additive Modelling (GAM) to extract the non-linear relationship between cholera and different climatic factors; temperature, rainfall and sea surface temperature (SST). Peak associated lag times were identified using cross-correlation lag analysis. Results: Our findings revealed a bi-annual pattern of cholera cases with two peaks coinciding with the increase in temperature in summer and the onset of monsoon rains. Variables selected as explanatory variables in the GAM model were temperature and rainfall. Temperature was the only significant factor associated with summer cholera (mean temperature of 30.3 °C associated with RR of 3.8) while rainfall was found to be the main driver of monsoon cholera (550 mm total monthly rainfall associated with RR of 3.38). Lag time analysis revealed that the association between temperature and cholera cases in the summer had a longer peak lag time compared to that between rainfall and cholera during the monsoon. We propose several mechanisms by which these relationships are mediated. Conclusions: Kolkata exhibits a dual-peak phenomenon with independent mediating factors. We suggest that the summer peak is due to increased bacterial concentration in urban water bodies, while the monsoon peak is driven by contaminated flood waters. Our results underscore the potential utility of preventative strategies tailored to these seasonal and climatic patterns, including efforts to reduce direct contact with urban water bodies in summer and to protect residents from flood waters during monsoon. [ABSTRACT FROM AUTHOR]

Background: HCV infection is very common in multi-transfused β-thalassemia patients who need regular blood transfusions. Aim: The study was conducted to determine the epidemiology of HCV in multi-transfused β-thalassemia patients in West Bengal, India. Methods: Over a span of six years, blood samples were collected from HCV sero-reactive β-thalassemia patients and processed for viral RNA isolation followed by nested RT-PCR for qualitative viremia detection. The HCV genotype was determined by amplifying the partial HCV core gene by nested RT-PCR followed by DNA sequencing and NCBI genotyping tools. Phylogenetic and phylogeographic studies were performed with MEGA-X and BEAST software, respectively. Results: Out of 917 multi-transfused HCV sero-reactive β-thalassemia patients, 598 (65.21%) were HCV RNA positive while 250 (41.80%) had spontaneously cleared the virus. A significant percentage of male patients from rural areas (p = 0.042) and economically backward class (p = 0.002) were at higher risk of HCV infection. Female thalassemia patients and individuals belonging to ages 11–15 years had higher chances of spontaneous clearance. The most prevalent circulatory HCV genotype was 3a (78.26%) followed by 1b (12.04%). Phylogeographic analyses revealed that the 3a strains share genomic similarities with strains from Pakistan, Sri Lanka, and Thailand, whereas the 1b strains share similarities with strains from Thailand, Vietnam, Russia, and China. Uncommon HCV subtypes 3g and 3i were also detected. Conclusion: The high prevalence of HCV infection among β-thalassemia patients of West Bengal, India indicates NAT-based assays should be implemented for HCV screening in donor blood to eliminate HCV by 2030. [ABSTRACT FROM AUTHOR]

Cyclospora cayetanensis, a recently described coccidian parasite causes severe gastroenteric disease worldwide. Limited studies are found on the incidence of C. cayetanensis infection from India; hence remains largely unknown. To date, no case of cyclosporiasis from eastern India has been reported. In this study, we described an incidental case of C. cayetanensis in a 30 years old Bengali female patient with no travel history from eastern India. In June 2022, the patient presented with a history of diarrhoea persisting for more than two months with continuous passage foul smelling stools for which she took multiple antibiotics that were ineffective. There were no Salmonella, Shigella, or Vibrio-like organisms in the patient's faecal sample, and Toxin A/B of Clostridium difficile was also not detected by ELISA. The patient was HIV-negative. Finally, UV autofluorescence and DNA-based diagnosis confirmed the presence of C. cayetanensis, and the treatment with a combination of appropriate antibiotics was successful. This case report could raise awareness about C. cayetanensis associated diarrhoeal cases in India. [ABSTRACT FROM AUTHOR]

Background: Importance of the amphizoic amoeba Entamoeba moshkovskii is increasing in the study of amoebiasis as a common human pathogen in some settings. Limited studies are found on the genetic and phylogenetic characterization of E. moshkovskii from India; hence remain largely unknown. In this study, we determined the prevalence and characterized the E. moshkovskii isolates in eastern India. Methods: A three-year systemic surveillance study among a total of 6051 diarrhoeal patients from ID Hospital and BC Roy Hospital, Kolkata was conducted for E. moshkovskii detection via a nested PCR system targeting 18S rRNA locus. The outer primer set detected the genus Entamoeba and the inner primer pair identified the E. moshkovskii species. The 18S rRNA locus of the positive samples was sequenced. Genetic and phylogenetic structures were determined using DnaSP.v5 and MEGA-X. GraphPad Prism (v.8.4.2), CA, USA was used to analyze the statistical data. Result: 4.84% (95%CI = 0.0433–0.0541) samples were positive for Entamoeba spp and 3.12% (95%CI = 0.027–0.036) were infected with E. moshkovskii. E. moshkovskii infection was significantly associated with age groups (X2 = 26.01, P<0.0001) but not with gender (Fisher's exact test = 0.2548, P<0.05). A unique seasonal pattern was found for E. moshkovskii infection. Additionally, 46.56% (95%CI = 0.396–0.537) were sole E. moshkovskii infections and significantly associated with diarrheal incidence (X2 = 335.5,df = 9; P<0.0001). Sequencing revealed that the local E. moshkovskii strains were 99.59%-100% identical to the prototype (GenBank: KP722605.1). The study found certain SNPs that showed a correlation with clinical features, but it is not necessarily indicative of direct control over pathogenicity. However, SNPs in the 18S rRNA gene could impact the biology of the amoeba and serve as a useful phylogenetic marker for identifying pathogenic E. moshkovskii isolates. Neutrality tests of different coinfected subgroups indicated deviations from neutrality and implied population expansion after a bottleneck event or a selective sweep and/or purifying selection in co-infected subgroups. The majority of FST values of different coinfected subgroups were <0.25, indicating low to moderate genetic differentiation within the subgroups of this geographical area. Conclusion: The findings reveal the epidemiological significance of E. moshkovskii infection in Eastern India as the first report in this geographical area and expose this species as a possible emerging enteric pathogen in India. Our findings provide useful knowledge for further research and the development of future control strategies against E. moshkovskii. Author summary: Although Entamoeba genus consists of many different species, not all are pathogenic. Entamoeba histolytica is the only species recognized as a definite pathogen associated with intestinal and extraintestinal infections. Nowadays, the importance of other morphologically identical Entamoeba species, like amphizoic E. moshkovskii is increasing, as it has been reported in human patients over the years from different countries. Investigations into the pathogenic potential of E. moshkovskii are ongoing, and only limited studies have been conducted on genetic characterization from India. This study reveals the epidemiology and population structure of E. moshkovskii in diarrhoeal patients from eastern India. Our study showed that the prevalence of E. moshkovskii in diarrhoeal patients is higher than E. histolytica in the studied region. In addition, there was a unique seasonal pattern, found for the infection. The high prevalence rate of sole infection in patients suggests that it is one of the definite etiological agents for diarrhoeal disease in eastern India. The further study identified two SNPs in the 18S rRNA locus, significantly associated with the sole infection cases and hence they can be regarded as a marker for identifying pathogenic isolates of E. moshkovskii. Many novel genotypes were obtained in the study indicating high genetic diversity in E. moshkovskii population conferring adaptability in a changing environment. Further research is needed to ensure proper control measures for this infection for better health care. [ABSTRACT FROM AUTHOR]