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2. RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance

Author

Stockdale, Stephen R., Blanchard, Adam M., Nayak, Amit, Husain, Aliabbas, Nashine, Rupam, Dudani, Hemanshi, McClure, C. Patrick, Tarr, Alexander W., Nag, Aditi, Meena, Ekta, Sinha, Vikky, Shrivastava, Sandeep K., Hill, Colin, Singer, Andrew C., Gomes, Rachel L., Acheampong, Edward, Chidambaram, Saravana B., Bhatnagar, Tarun, Vetrivel, Umashankar, Arora, Sudipti, Kashyap, Rajpal Singh, and Monaghan, Tanya M.

Published
2023
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4. Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave

Author

Acheampong, Edward, primary, Husain, Aliabbas A., additional, Dudani, Hemanshi, additional, Nayak, Amit R., additional, Nag, Aditi, additional, Meena, Ekta, additional, Shrivastava, Sandeep K., additional, McClure, Patrick, additional, Tarr, Alexander W., additional, Crooks, Colin, additional, Lade, Ranjana, additional, Gomes, Rachel L., additional, Singer, Andrew, additional, Kumar, Saravana, additional, Bhatnagar, Tarun, additional, Arora, Sudipti, additional, Kashyap, Rajpal Singh, additional, and Monaghan, Tanya M., additional

Published
2024
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7. Protective effects of fecal microbiota transplantation against ischemic stroke and other neurological disorders: an update

Author

Hediyal, Tousif Ahmed, primary, Vichitra, C., additional, Anand, Nikhilesh, additional, Bhaskaran, Mahendran, additional, Essa, Saeefh M., additional, Kumar, Pravir, additional, Qoronfleh, M. Walid, additional, Akbar, Mohammed, additional, Kaul-Ghanekar, Ruchika, additional, Mahalakshmi, Arehally M., additional, Yang, Jian, additional, Song, Byoung-Joon, additional, Monaghan, Tanya M., additional, Sakharkar, Meena Kishore, additional, and Chidambaram, Saravana Babu, additional

Published
2024
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8. Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave

Author

Acheampong, Edward, Husain, Aliabbas A., Dudani, Hemanshi, Nayak, Amit R., Nag, Aditi, Meena, Ekta, Shrivastava, Sandeep K., McClure, Patrick, Tarr, Alexander W., Crooks, Colin, Lade, Ranjana, Gomes, Rachel L., Singer, Andrew, Kumar, Saravana, Bhatnagar, Tarun, Arora, Sudipti, Kashyap, Rajpal Singh, Monaghan, Tanya M., Acheampong, Edward, Husain, Aliabbas A., Dudani, Hemanshi, Nayak, Amit R., Nag, Aditi, Meena, Ekta, Shrivastava, Sandeep K., McClure, Patrick, Tarr, Alexander W., Crooks, Colin, Lade, Ranjana, Gomes, Rachel L., Singer, Andrew, Kumar, Saravana, Bhatnagar, Tarun, Arora, Sudipti, Kashyap, Rajpal Singh, and Monaghan, Tanya M.

Abstract

Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool for predicting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease outbreaks in high-income countries (HICs) with centralized sewage infrastructure. However, few studies have applied WBE alongside epidemic disease modelling to estimate the prevalence of SARS-CoV-2 in low-resource settings. This study aimed to explore the feasibility of collecting untreated wastewater samples from rural and urban catchment areas of Nagpur district, to detect and quantify SARS-CoV-2 using real-time qPCR, to compare geographic differences in viral loads, and to integrate the wastewater data into a modified Susceptible-Exposed-Infectious-Confirmed Positives-Recovered (SEIPR) model. Of the 983 wastewater samples analyzed for SARS-CoV-2 RNA, we detected significantly higher sample positivity rates, 43.7% (95% confidence interval (CI) 40.1, 47.4) and 30.4% (95% CI 24.66, 36.66), and higher viral loads for the urban compared with rural samples, respectively. The Basic reproductive number, R0, positively correlated with population density and negatively correlated with humidity, a proxy for rainfall and dilution of waste in the sewers. The SEIPR model estimated the rate of unreported coronavirus disease 2019 (COVID-19) cases at the start of the wave as 13.97 [95% CI (10.17, 17.0)] times that of confirmed cases, representing a material difference in cases and healthcare resource burden. Wastewater surveillance might prove to be a more reliable way to prepare for surges in COVID-19 cases during future waves for authorities.

Published
2024

9. Sleep apnoea, gut dysbiosis and cognitive dysfunction.

Author

Deyang, Tenzin, Baig, MD Awaise Iqbal, Dolkar, Phurbu, Hediyal, Tousif Ahmed, Rathipriya, Annan Gopinath, Bhaskaran, Mahendran, PandiPerumal, Seithikuruppu R., Monaghan, Tanya M., Mahalakshmi, Arehally M, and Chidambaram, Saravana Babu

Subjects
SLEEP apnea syndromes, COGNITION disorders, SHORT-chain fatty acids, DYSBIOSIS, MICROBIAL metabolites, SLEEP disorders, FRUCTOOLIGOSACCHARIDES
Abstract

Sleep disorders are becoming increasingly common, and their distinct effects on physical and mental health require elaborate investigation. Gut dysbiosis (GD) has been reported in sleep‐related disorders, but sleep apnoea is of particular significance because of its higher prevalence and chronicity. Cumulative evidence has suggested a link between sleep apnoea and GD. This review highlights the gut–brain communication axis that is mediated via commensal microbes and various microbiota‐derived metabolites (e.g. short‐chain fatty acids, lipopolysaccharide and trimethyl amine N‐oxide), neurotransmitters (e.g. γ‐aminobutyric acid, serotonin, glutamate and dopamine), immune cells and inflammatory mediators, as well as the vagus nerve and hypothalamic–pituitary–adrenal axis. This review also discusses the pathological role underpinning GD and altered gut bacterial populations in sleep apnoea and its related comorbid conditions, particularly cognitive dysfunction. In addition, the review examines the preclinical and clinical evidence, which suggests that prebiotics and probiotics may potentially be beneficial in sleep apnoea and its comorbidities through restoration of eubiosis or gut microbial homeostasis that regulates neural, metabolic and immune responses, as well as physiological barrier integrity via the gut–brain axis. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Sleep apnoea, gut dysbiosis and cognitive dysfunction

Author

Deyang, Tenzin, primary, Baig, Awaise Iqbal, additional, Dolkar, Phurbu, additional, Hediyal, Tousif Ahmed, additional, Rathipriya, Annan Gopinath, additional, Bhaskaran, Mahendran, additional, PandiPerumal, Seithikuruppu R., additional, Monaghan, Tanya M., additional, Mahalakshmi, Arehally M, additional, and Chidambaram, Saravana Babu, additional

Published
2023
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13. The Molecular Epidemiology of Clostridioides difficile Infection in Central India: A Prospective Observational Cohort Study

Author

Biswas, Rima, primary, Pinkham, Nick, additional, Walk, Seth T., additional, Wang, Qian, additional, Ambalkar, Shrikant, additional, Satav, Ashish R., additional, Wilcox, Mark H., additional, Reghunath, Rahul, additional, Chawla, Kiran, additional, Shenoy, Padmaja A., additional, Nayak, Amit R., additional, Husain, Aliabbas A., additional, Raje, Dhananjay V., additional, Kashyap, Rajpal Singh, additional, and Monaghan, Tanya M., additional

Published
2023
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14. Gut microbiome-based dietary intervention in Parkinson disease subject: A case report

Author

Sulthana, Ayesha, primary, Paneyala, Shasthara, additional, H.S., Sindhu, additional, Narayan, Meghana Kowlagi, additional, Hediyal, Tousif Ahmed, additional, Sharma, Sonali, additional, Senthilkumar, Arunsaikiran, additional, Dave, Paul, additional, Mahalakshmi, Arehally M., additional, Chidambaram, Saravana Babu, additional, Monaghan, Tanya M., additional, and Sulakhe, Dinanath, additional

Published
2023
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23. Skin

Author

Monaghan, Tanya M., primary and Thomas, James D., additional

Published
2019
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28. Role of Endogenous Lipopolysaccharides in Neurological Disorders

Author

Kalyan, Manjunath, primary, Tousif, Ahmed Hediyal, additional, Sonali, Sharma, additional, Vichitra, Chandrasekaran, additional, Sunanda, Tuladhar, additional, Praveenraj, Sankar Simla, additional, Ray, Bipul, additional, Gorantla, Vasavi Rakesh, additional, Rungratanawanich, Wiramon, additional, Mahalakshmi, Arehally M., additional, Qoronfleh, M. Walid, additional, Monaghan, Tanya M., additional, Song, Byoung-Joon, additional, Essa, Musthafa Mohamed, additional, and Chidambaram, Saravana Babu, additional

Published
2022
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29. Gut dysbiosis, defective autophagy and altered immune responses in neurodegenerative diseases: Tales of a vicious cycle

Author

Chidambaram, Saravana Babu, Rathipriya, A.G., Bishir, Muhammed, Ray, Bipul, Mahalakshmi, Arehally M., Tousif, A.H., Sakharkar, Meena K., Essa, Musthafa Mohamed, Kashyap, Rajpal Singh, Friedland, Robert, and Monaghan, Tanya M.

Subjects
Pharmacology, Pharmacology (medical)
Abstract

The human microbiota comprises trillions of symbiotic microorganisms and is involved in regulating gastrointestinal (GI), immune, nervous system and metabolic homeostasis. Recent observations suggest a bidirectional communication between the gut microbiota and the brain via immune, circulatory and neural pathways, termed the Gut-Brain Axis (GBA). Alterations in gut microbiota composition, such as seen with an increased number of pathobionts and a decreased number of symbionts, termed gut dysbiosis or microbial intestinal dysbiosis, plays a prominent role in the pathogenesis of central nervous system (CNS)-related disorders. Clinical reports confirm that GI symptoms often precede neurological symptoms several years before the development of neurodegenerative diseases (NDDs). Pathologically, gut dysbiosis disrupts the integrity of the intestinal barrier leading to ingress of pathobionts and toxic metabolites into the systemic circulation causing GBA dysregulation. Subsequently, chronic neuroinflammation via dysregulated immune activation triggers the accumulation of neurotoxic misfolded proteins in and around CNS cells resulting in neuronal death. Emerging evidence links gut dysbiosis to the aggravation and/or spread of proteinopathies from the peripheral nervous system to the CNS and defective autophagy-mediated proteinopathies. This review summarizes the current understanding of the role of gut microbiota in NDDs, and highlights a vicious cycle of gut dysbiosis, immune-mediated chronic neuroinflammation, impaired autophagy and proteinopathies, which contributes to the development of neurodegeneration in Alzheimer's disease, Parkinson's disease, Huntington’s disease, multiple sclerosis, amyotrophic lateral sclerosis and frontotemporal lobar degeneration. We also discuss novel therapeutic strategies targeting the modulation of gut dysbiosis through prebiotics, probiotics, synbiotics or dietary interventions, and faecal microbial transplantation (FMT) in the management of NDDs.

Published
2022

31. The Influence of Gut Dysbiosis in the Pathogenesis and Management of Ischemic Stroke

Author

Chidambaram, Saravana Babu, primary, Rathipriya, Annan Gopinath, additional, Mahalakshmi, Arehally M., additional, Sharma, Sonali, additional, Hediyal, Tousif Ahmed, additional, Ray, Bipul, additional, Sunanda, Tuladhar, additional, Rungratanawanich, Wiramon, additional, Kashyap, Rajpal Singh, additional, Qoronfleh, M. Walid, additional, Essa, Musthafa Mohamed, additional, Song, Byoung-Joon, additional, and Monaghan, Tanya M., additional

Published
2022
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33. A Multi-Factorial Observational Study on Sequential Fecal Microbiota Transplant in Patients with Medically Refractory Clostridioides difficile Infection

Author

Monaghan, Tanya M., primary, Duggal, Niharika A., additional, Rosati, Elisa, additional, Griffin, Ruth, additional, Hughes, Jamie, additional, Roach, Brandi, additional, Yang, David Y., additional, Wang, Christopher, additional, Wong, Karen, additional, Saxinger, Lynora, additional, Pučić-Baković, Maja, additional, Vučković, Frano, additional, Klicek, Filip, additional, Lauc, Gordan, additional, Tighe, Paddy, additional, Mullish, Benjamin H., additional, Blanco, Jesus Miguens, additional, McDonald, Julie A. K., additional, Marchesi, Julian R., additional, Xue, Ning, additional, Dottorini, Tania, additional, Acharjee, Animesh, additional, Franke, Andre, additional, Li, Yingrui, additional, Wong, Gane Ka-Shu, additional, Polytarchou, Christos, additional, Yau, Tung On, additional, Christodoulou, Niki, additional, Hatziapostolou, Maria, additional, Wang, Minkun, additional, Russell, Lindsey A., additional, and Kao, Dina H., additional

Published
2021
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36. Multiomics Profiling Reveals Signatures of Dysmetabolism in Urban Populations in Central India

Author

Monaghan, Tanya M., primary, Biswas, Rima N., additional, Nashine, Rupam R., additional, Joshi, Samidha S., additional, Mullish, Benjamin H., additional, Seekatz, Anna M., additional, Blanco, Jesus Miguens, additional, McDonald, Julie A. K., additional, Marchesi, Julian R., additional, Yau, Tung on, additional, Christodoulou, Niki, additional, Hatziapostolou, Maria, additional, Pucic-Bakovic, Maja, additional, Vuckovic, Frano, additional, Klicek, Filip, additional, Lauc, Gordan, additional, Xue, Ning, additional, Dottorini, Tania, additional, Ambalkar, Shrikant, additional, Satav, Ashish, additional, Polytarchou, Christos, additional, Acharjee, Animesh, additional, and Kashyap, Rajpal Singh, additional

Published
2021
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37. Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection Associates With Functional Alterations in Circulating microRNAs

Author

Monaghan, Tanya M., primary, Seekatz, Anna M., additional, Markham, Nicholas O., additional, Yau, Tung On, additional, Hatziapostolou, Maria, additional, Jilani, Tahseen, additional, Christodoulou, Niki, additional, Roach, Brandi, additional, Birli, Eleni, additional, Pomenya, Odette, additional, Louie, Thomas, additional, Lacy, D. Borden, additional, Kim, Peter, additional, Lee, Christine, additional, Kao, Dina, additional, and Polytarchou, Christos, additional

Published
2021
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40. Understanding the mechanisms of efficacy of fecal microbiota transplant in treating recurrent Clostridioides difficile infection and beyond: the contribution of gut microbial-derived metabolites

Author

Martinez-Gili, Laura, McDonald, Julie A.K., Liu, Zhigang, Kao, Dina, Allegretti, Jessica R., Monaghan, Tanya M., Barker, Grace F., Williams, Horace R.T., Holmes, Elaine, Thursz, Mark R., Marchesi, Julian R., and Mullish, Benjamin H.

Subjects
bile acids, Clostridioides difficile infection, trimethylamine, gut microbiome, metabonomics, short chain fatty acids, fecal microbiota transplant
Abstract

Fecal microbiota transplant (FMT) is a highly-effective therapy for recurrent Clostridioides difficile infection (rCDI), and shows promise for certain non-CDI indications. However, at present, its mechanisms of efficacy have remained poorly understood. Recent studies by our laboratory have noted the particular key importance of restoration of gut microbe-metabolite interactions in the ability of FMT to treat rCDI, including the impact of FMT upon short chain fatty acid (SCFAs) and bile acid metabolism. This includes a significant impact of these metabolites upon the life cycle of C. difficile directly, along with potential postulated additional benefits, including effects upon host immune response. In this Addendum, we first present an overview of these recent advancements in this field, and then describe additional novel data from our laboratory on the impact of FMT for rCDI upon several gut microbial-derived metabolites which had not previously been implicated as being of relevance.

Published
2020

42. Variation in Mycobacterium tuberculosis genotype and molecular phenotype influence clinical phenotype of Pulmonary tuberculosis and Tuberculous Meningitis infection in host

Author

Husain, Aliabbas A., primary, Tikariha, Hitesh, additional, Nayak, Amit R., additional, Gupta, Umesh D., additional, Bhullar, Shraddha S., additional, Chandak, Nitin C., additional, Monaghan, Tanya M., additional, Daginawla, Hatim F., additional, Singh, Lokendra R., additional, Purohit, Hemant J., additional, and Kashyap, Rajpal S., additional

Published
2020
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45. Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome

Author

Monaghan, Tanya M., primary, Sloan, Tim J., additional, Stockdale, Stephen R., additional, Blanchard, Adam M., additional, Emes, Richard D., additional, Wilcox, Mark, additional, Biswas, Rima, additional, Nashine, Rupam, additional, Manke, Sonali, additional, Gandhi, Jinal, additional, Jain, Pratishtha, additional, Bhotmange, Shrejal, additional, Ambalkar, Shrikant, additional, Satav, Ashish, additional, Draper, Lorraine A., additional, Hill, Colin, additional, and Kashyap, Rajpal Singh, additional

Published
2020
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46. Decreased Complexity of Serum N-glycan Structures Associates with Successful Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection

Author

Monaghan, Tanya M., primary, Pučić-Baković, Maja, additional, Vučković, Frano, additional, Lee, Christine, additional, Kao, Dina, additional, Wójcik, Iwona, additional, Kliček, Filip, additional, Polytarchou, Christos, additional, Roach, Brandi, additional, Louie, Tom, additional, Kim, Peter, additional, Frankowski, Marcin, additional, and Lauc, Gordan, additional

Published
2019
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48. A Protein Microarray Assay for Serological Determination of Antigen-specific Antibody Responses Following Clostridium difficile Infection

Author

Negm, Ola H., Hamed, Mohamed R., and Monaghan, Tanya M.

Subjects
Adult, Clostridioides difficile, Clostridium Infections, Protein Array Analysis, Humans, Protein, microarray, antibody, Clostridium difficile, intravenous, immunoglobulin, Antibodies, Bacterial, Immunology and Infection
Abstract

We provide a detailed overview of a novel high-throughput protein microarray assay for the determination of anti-Clostridium difficile antibody levels in human sera and in separate preparations of polyclonal intravenous immunoglobulin (IVIg). The protocol describes the methodological steps involved in sample preparation, printing of arrays, assay procedure, and data analysis. In addition, this protocol could be further developed to incorporate diverse clinical samples including plasma and cell culture supernatants. We show how protein microarray can be used to determine a combination of isotype (IgG, IgA, IgM), subclass (IgG1, IgG2, IgG3, IgG4, IgA1, IgA2), and strain-specific antibodies to highly purified whole C. difficile toxins A and B (toxinotype 0, strain VPI 10463, ribotype 087), toxin B from a C. difficile toxin-B-only expressing strain (CCUG 20309), a precursor form of a B fragment of binary toxin, pCDTb, ribotype-specific whole surface layer proteins (SLPs; 001, 002, 027), and control proteins (tetanus toxoid and Candida albicans). During the experiment, microarrays are probed with sera from individuals with C. difficile infection (CDI), individuals with cystic fibrosis (CF) without diarrhea, healthy controls (HC), and from individuals pre- and post-IVIg therapy for the treatment of CDI, combined immunodeficiency disorder, and chronic inflammatory demyelinating polyradiculopathy. We encounter significant differences in toxin neutralization efficacies and multi-isotype specific antibody levels between patient groups, commercial preparations of IVIg, and sera before and following IVIg administration. Also, there is a significant correlation between microarray and enzyme-linked immunosorbent assay (ELISA) for antitoxin IgG levels in serum samples. These results suggest that microarray could become a promising tool for profiling antibody responses to C.difficile antigens in vaccinated or infected humans. With further refinement of antigen panels and a reduction in production costs, we anticipate that microarray technology may help optimize and select the most clinically useful immunotherapies for C. difficile infection in a patient-specific manner.

Published
2018

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