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Mitra S, Bhagwan J, William A, Siddiqui O, Saxena S. Paeniclostridium sordellii causing liver abscess: A rare case report in India. Indian J Med Microbiol 2024; 49:100595. [PMID: 38641008 DOI: 10.1016/j.ijmmb.2024.100595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Paeniclostridium sordellii, an anaerobic bacterium, causes hepatic infections in alcoholics and post-surgery (liver transplantation). While liver and brain abscesses are rare, drainage procedures and targeted antibiotic therapy assisted by early microbiological diagnosis have reduced mortality rates. We report a rare case of pyogenic liver abscess caused by Paeniclostridium sordellii in India, the early diagnosis of which has led to life saving outcome for the patient. Hence, the microbiological diagnosis and comprehensive medical-surgical treatment are vital for preventing mortality in Paeniclostridium sordellii infections.
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Affiliation(s)
- Srestha Mitra
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Jai Bhagwan
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Ashish William
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Oves Siddiqui
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College and Lok Nayak Hospital, Delhi, India.
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Manchanda V, Siddiqui O, Meena K, Sharma A, Saxena S. Quality assurance of SARS-CoV-2 testing laboratories during the pandemic period in India - An experience from a designated provider laboratory. Indian J Med Microbiol 2024; 49:100577. [PMID: 38588879 DOI: 10.1016/j.ijmmb.2024.100577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/10/2024]
Abstract
PURPOSE Indian Council of Medical Research (ICMR) initiated an Inter-Laboratory Quality Control testing (ILQC) program for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) testing. Under this program, SARS-CoV-2 testing laboratories across the country submit specimens to the assigned State Quality Control (SQCs) laboratories for ILQC testing. This study aimed to investigate the performance of public and private SARS-CoV-2 testing laboratories in Delhi and highlights the country's effort in ramping up testing facility with close monitoring of the quality of Covid-19 testing results. METHODS In the present study, two-years of SARS-CoV-2 testing data is included. During July 2020 through February 2022, a total of 1791 anonymised specimens were received from 56 public and private laboratories. These specimens were processed by reverse transcriptase - polymerase chain reaction (RT-PCR) tests as per National Institute of Virology (NIV) protocol and the results were uploaded on the ICMR quality control/quality assurance (QC/QA) portal without directly conveying the results to respective participating laboratories. This portal generated a final report stating concordance and intimate results to individual laboratories. RESULTS Among the 1791 specimens, 25 were rejected and the remaining 1766 were tested. Among these specimens 1691 (95.75%) revealed concordance, and 75 (4.24%) were discordant. A total of 29 laboratories had 100% concordance, 21 laboratories had over 90% concordance and six laboratories had over 80% concordance. CONCLUSIONS The study demonstrates that the establishment of an inter-laboratory comparison program for SARS-CoV-2 testing helped in monitoring quality of SARS-CoV-2 testing in the country.
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Affiliation(s)
- Vikas Manchanda
- Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India; State Level -Viral Research and Diagnostic Laboratory (VRDL), Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Oves Siddiqui
- Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India; State Level -Viral Research and Diagnostic Laboratory (VRDL), Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Kavita Meena
- Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Anju Sharma
- State Level -Viral Research and Diagnostic Laboratory (VRDL), Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India; State Level -Viral Research and Diagnostic Laboratory (VRDL), Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
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Jairath V, Hunter Gibble T, Potts Bleakman A, Chatterton K, Medrano P, McLafferty M, Klooster B, Saxena S, Moses R. Patient Perspectives of Bowel Urgency and Bowel Urgency-Related Accidents in Ulcerative Colitis and Crohn's Disease. Inflamm Bowel Dis 2024:izae044. [PMID: 38513272 DOI: 10.1093/ibd/izae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Indexed: 03/23/2024]
Abstract
BACKGROUND Bowel urgency is bothersome in patients with ulcerative colitis (UC) or Crohn's disease (CD) and impacts their well-being but remains underappreciated in clinical trials and during patient-healthcare provider interactions. This study explored the experiences of bowel urgency and bowel urgency-related accidents to identify the concepts most relevant and important to patients. METHODS Adults with a diagnosis of moderate-to-severe UC or CD for ≥6 months and experience of bowel urgency in the past 6 months were included. Qualitative, semi-structured interviews were conducted via telephonic/Web-enabled teleconference. Interview transcripts were coded and analyzed in ATLAS.ti 9 using a systematic thematic analysis. RESULTS In total, 30 participants with UC or CD (n = 15 each) (mean age 52 and 50 years, respectively) participated in the interviews. The majority of participants were receiving biologic and/or conventional therapy (80% and 87%, respectively). Most participants with UC (87%) and all with CD experienced bowel urgency-related accidents. The most frequently reported symptoms co-occurring with bowel urgency were abdominal pain, fatigue, and abdominal cramping. Abdominal pain and abdominal cramping were the most bothersome co-occurring symptoms of bowel urgency and bowel urgency-related accidents. In both groups, participants reported decreased frequency of bowel urgency and not wanting to experience bowel urgency-related accidents at all as a meaningful improvement. CONCLUSIONS Participants with UC or CD expressed bowel urgency and bowel urgency-related accidents to be bothersome and impactful on their daily lives despite use of biologic and/or conventional therapy. These findings underscore the need for development of patient-reported outcome measures to assess bowel urgency in clinical settings.
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Affiliation(s)
- Vipul Jairath
- Division of Gastroenterology, Department of Medicine, Western University, London, Ontario, OX3 9DU, Canada
| | | | | | | | - Paolo Medrano
- Patient-Centered Outcomes, Adelphi Values, Boston, Massachusetts, USA
| | - Megan McLafferty
- Patient-Centered Outcomes, Adelphi Values, Boston, Massachusetts, USA
| | - Brittany Klooster
- Patient-Centered Outcomes, Adelphi Values, Boston, Massachusetts, USA
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Manchanda V, Muralidharan J, Nischal N, Aggarwal K, Gupta S, Gupta N, Velayudhan A, Kaur H, Brijwal M, Chhabra M, Vishwanathan R, Dhodapkar R, Mahajan SK, Deol S, Sekhar JC, Mitra S, Saxena S, Kumar J, Garg A, Lodha R, Ravi V, Soneja M, Verghese VP, Rodrigues C. Approach towards surveillance-based diagnosis of acute respiratory illness in India: Expert recommendations. Indian J Med Microbiol 2024; 48:100548. [PMID: 38403268 DOI: 10.1016/j.ijmmb.2024.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND Emerging infectious diseases, often zoonotic, demand a collaborative "One-Health" surveillance approach due to human activities. The need for standardized diagnostic and surveillance algorithms is emphasized to address the difficulty in clinical differentiation and curb antimicrobial resistance. OBJECTIVE The present recommendations are comprehensive diagnostic and surveillance algorithm for ARIs, developed by the Indian Council of Medical Research (ICMR), which aims to enhance early detection and treatment with improved surveillance. This algorithm shall be serving as a blueprint for respiratory infections landscape in the country and early detection of surge of respiratory infections in the country. CONTENT The ICMR has risen up to the threat of emerging and re-emerging infections. Here, we seek to recommend a structured approach for diagnosing respiratory illnesses. The recommendations emphasize the significance of prioritizing respiratory pathogens based on factors such as the frequency of occurrence (seasonal or geographical), disease severity, ease of diagnosis and public health importance. The proposed surveillance-based diagnostic algorithm for ARI relies on a combination of gold-standard conventional methods, innovative serological and molecular techniques, as well as radiological approaches, which collectively contribute to the detection of various causative agents. The diagnostic part of the integrated algorithm can be dealt at the local microbiology laboratory of the healthcare facility with the few positive and negative specimens shipped to linked viral disease research laboratories (VRDLs) and other ICMR designated laboratories for genome characterisation, cluster identification and identification of novel agents.
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Affiliation(s)
- Vikas Manchanda
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Jayshree Muralidharan
- Department of Pediatric Medicine (Advanced Pediatric Centre), PGIMER, Chandigarh, India.
| | - Neeraj Nischal
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Kshitij Aggarwal
- Department of Pulmonary and Critical Care Medicine, Institute of Heart and Lung Diseases, Bahadurgarh, Haryana, India
| | - Swati Gupta
- Department of Radiodiagnosis, Maulana Azad Medical College, Delhi, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, New Delhi, India
| | - Anoop Velayudhan
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, New Delhi, India
| | - Harmanmeet Kaur
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, New Delhi, India
| | - Megha Brijwal
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - Mala Chhabra
- Department of Microbiology, Atal Bihari Vajpayee Institute of Medical Sciences (ABVIMS) and Dr. Ram Manohar Lohia Hospital (RML), Delhi, India
| | | | | | - Sanjay K Mahajan
- Department of Medicine, Indira Gandhi Medical College & Hospital (IGMC), Shimla, India
| | - Saumya Deol
- Division of Epidemiology & Communicable Diseases, ICMR Headquarters, New Delhi, India
| | | | - Srestha Mitra
- Department of Microbiology, Maulana Azad Medical College, Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College, Delhi, India
| | - Jyoti Kumar
- Department of Radiodiagnosis, Maulana Azad Medical College, Delhi, India
| | - Anju Garg
- Department of Radiodiagnosis, Maulana Azad Medical College, Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences (AIIMS), Delhi, India
| | - V Ravi
- Department of Neurovirology, NIMHANS, Bengaluru, India
| | - Manish Soneja
- Department of Medicine, All India Institute of Medical Sciences (AIIMS), Delhi, India
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Skirrow H, Foley K, Bedford H, Lewis C, Whittaker E, Costelloe C, Saxena S. Impact of pregnancy vaccine uptake and socio-demographic determinants on subsequent childhood Measles, Mumps and Rubella vaccine uptake: A UK birth cohort study. Vaccine 2024; 42:322-331. [PMID: 38072757 DOI: 10.1016/j.vaccine.2023.11.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/21/2023] [Accepted: 11/30/2023] [Indexed: 01/01/2024]
Abstract
BACKGROUND We examined the association between socio-demographic determinants and uptake of childhood Measles, Mumps & Rubella (MMR) vaccines and the association between pregnant women's pertussis vaccine uptake and their children's MMR vaccine uptake. METHODS We used nationally-representative linked mother-baby electronic records from the United Kingdom's Clinical-Practice-Research-Datalink. We created a birth cohort of children born between 01.01.2000 and 12.12.2020. We estimated the proportion vaccinated with first MMR vaccine by age 2 years and first and second MMR vaccines by age 5 years. We used survival-analysis and Cox proportional hazard models to examine the association between deprivation, ethnicity and maternal age and pertussis vaccination in pregnancy and children's MMR uptake. RESULTS Overall, 89.4 % (710,797/795,497) of children had first MMR by age 2 years and 92.6 % (736,495/795,497) by age 5 years. Among children still in the cohort when second MMR was due, 85.9 % (478,480/557,050) had two MMRs by age 5 years. Children from the most-deprived areas, children of Black ethnicity and children of mothers aged < 20 years had increased risk of being unvaccinated compared with children from the least-deprived areas, White children and children of mothers aged 31-40 years: first MMR by 5 years, adjusted Hazard Ratios (HR):0.86 (CI:0.85-0.87), HR:0.87 (CI:0.85-0.88) & HR:0.89 (CI:0.88-0.90) respectively. Deprivation was the determinant associated with the greatest risk of missed second MMR: adjusted HR:0.82 (CI:0.81-0.83). Children of mothers vaccinated in pregnancy were more likely than children of unvaccinated mothers to have MMR vaccines after adjusting for ethnicity, deprivation, and maternal age (First and Second MMRs adjusted HRs:1.43 (CI:1.41-1.45), 1.49 (CI:1.45-1.53). CONCLUSION Children from most-deprived areas are less likely to have MMR vaccines compared with children from least-deprived areas. Mothers who take up pregnancy vaccines are more likely to have their children vaccinated with MMR. Healthcare services should promote and facilitate access to both maternal and childhood vaccines during pregnancy.
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Affiliation(s)
- H Skirrow
- School of Public Health, Imperial College London, United Kingdom.
| | - K Foley
- School of Public Health, Imperial College London, United Kingdom
| | - H Bedford
- Population, Policy and Practice, Great Ormond Street Institute of Child Health, University College London, United Kingdom
| | - C Lewis
- Population, Policy and Practice, Great Ormond Street Institute of Child Health, University College London, United Kingdom; London North Genomic Laboratory Hub, Great Ormond Street Hospital, London, United Kingdom
| | - E Whittaker
- Section of Paediatric Infectious Diseases, Imperial College London, United Kingdom; Department of Paediatric Infectious Diseases, Imperial College Healthcare NHS Trust, United Kingdom
| | - C Costelloe
- School of Public Health, Imperial College London, United Kingdom; Institute of Cancer Research, London, United Kingdom
| | - S Saxena
- School of Public Health, Imperial College London, United Kingdom
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Khyati, Manchanda V, Pumma P, Chawla R, Garg S, Saxena S. Diagnostic performance of saliva RT-PCR test as a diagnostic tool and its utility in the detection of SARS-CoV-2 shedding with different patient characteristics: Prospective observational study. Indian J Med Microbiol 2024; 47:100490. [PMID: 37890412 DOI: 10.1016/j.ijmmb.2023.100490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Salivary shedding of SARS-CoV-2 is a known entity and its role has been established in transmission of the disease. The present study was performed to evaluate the duration of viral shedding in saliva in COVID-19 patients and its variation among symptomatic and asymptomatic patients with or without co-morbidities. METHODS The present prospective observational study was conducted at the COVID-19 care hospital associated with primary to tertiary care in New Delhi, India. A total of 124 COVID-19 confirmed cases enrolled in two phases (January-March 2021; April-June 2021) who consented for 48hrly saliva and nasopharyngeal swab (NPS) specimens till discharge from the hospital for SARS-CoV-2 detection were included. The specimens obtained were tested for SARS-CoV-2 by Real-Time PCR. RESULTS The sensitivity and the specificity of RT-PCR on saliva were 81.7 % and 85.0 %, respectively. The sensitivity of saliva-based PCR was comparable in symptomatic and asymptomatic patients (81.6 % vs 82.1 %). The sensitivity of saliva-based PCR markedly increased in the second phase of enrollment as compared to the first phase (92.6 % vs 78.5 %) indicating higher level of salivary shedding by the delta variant of SARS-CoV-2. The sensitivity of PCR on saliva was the highest up to day seven of illness. The median duration of RNA shedding in saliva was comparable among the symptomatic and asymptomatic patients. The severity of the disease was not associated with the duration of SARS-CoV-2 shedding in saliva. CONCLUSIONS SARS-CoV-2 shedding in saliva continued till seven days in large number of patients including asymptomatic patients. Saliva is non-inferior to NPS specimen in the diagnosis of SARS-CoV-2. Saliva specimen is recommended as a good alternate to NPS for SARS-CoV-2 testing.
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Affiliation(s)
- Khyati
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - V Manchanda
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India.
| | - P Pumma
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - R Chawla
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
| | - S Garg
- Department of Medicine, Maulana Azad Medical College, 110002, New Delhi, India
| | - S Saxena
- Department of Microbiology, Maulana Azad Medical College, 110002, New Delhi, India
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Sharma A, Manchanda V, Agarwal A, Kapoor A, Kumar S, Saxena S. Blood borne infections and Hepatitis B virus immunization levels among medical students in India. Indian J Med Microbiol 2024; 47:100525. [PMID: 38160719 DOI: 10.1016/j.ijmmb.2023.100525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Medical students are actively involved in direct patient care during their training and subsequent medical practice, making them susceptible to acquiring blood-borne pathogens, including HBV. This study aimed to assess the occurrence of blood-borne infections and the Hepatitis B immunization status among medical students. Furthermore, it sought to identify gaps in risk assessment for blood-borne pathogens among medical students at a Medical College in New Delhi. METHODS The study included 108 medical students who participated in a blood donation camp. Blood samples collected from these individuals underwent testing for blood-borne pathogens in accordance with standard screening protocols at the blood bank. The quantitative estimation was performed for anti-HBs IgG using ELISA. RESULTS All 108 participants were pursuing their undergraduate or postgraduate medical degrees. All students tested negative for HBsAg and HIV markers and showed no reactivity to Syphilis and Malaria. However, one student tested positive for HCV. Two postgraduate students had a history of needlestick injuries. Eighty-one (75%) students had received Hepatitis B vaccination. Among the vaccinated students, 34 (41.97%) were immunized before the age of five years, 22 (27.16%) after the age of five years, while 25 (30.86%) couldn't recall the exact age of their Hepatitis B vaccination. Protective anti-HBs titer of anti-Hepatitis B antibodies (>10 mIU/ml) were detected in 48.15% (52/108) of students. CONCLUSIONS Over 50% of medical students did not possess sufficient immunity against HBV infection, putting them at a heightened risk of acquiring HBV during their active participation in patient care in the near future. It is imperative to establish a policy for routine anti-HBs titer assessment and ensure easy access to Hepatitis B immunization for medical students, thereby enhancing their protection against this infectious agent.
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Affiliation(s)
- Anju Sharma
- State Level -Viral Research and Diagnostic Laboratory (VRDL), Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Vikas Manchanda
- State Level -Viral Research and Diagnostic Laboratory (VRDL), Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Aman Agarwal
- Maulana Azad Medical College, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Advitiya Kapoor
- Maulana Azad Medical College, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
| | - Sunil Kumar
- Blood Bank, Lok Nayak Hospital, New Delhi, India.
| | - Sonal Saxena
- State Level -Viral Research and Diagnostic Laboratory (VRDL), Department of Microbiology, Maulana Azad Medical College & Associated Lok Nayak Hospital, Bahadur Shah Zafar Marg, New Delhi, 110002, India.
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Singh M, Saxena S, Mohan KN. DNMT1 downregulation as well as its overexpression distinctly affect mostly overlapping genes implicated in schizophrenia, autism spectrum, epilepsy, and bipolar disorders. Front Mol Neurosci 2023; 16:1275697. [PMID: 38125006 PMCID: PMC10731955 DOI: 10.3389/fnmol.2023.1275697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
Data on schizophrenia (SZ), epilepsy (EPD) and bipolar disorders (BPD) suggested an association of DNMT1 overexpression whereas certain variants of the gene were predicted to result in its increased expression in autism spectrum disorder (ASD). In addition, loss of DNMT1 in frontal cortex resulted in behavioral abnormalities in mice. Here we investigated the effects of increased as well as lack of DNMT1 expression using Dnmt1tet/tet neurons as a model for abnormal neurogenesis and 10,861 genes showing transcript level dysregulation in datasets from the four disorders. In case of overexpression, 3,211 (∼ 30%) genes were dysregulated, affecting pathways involved in neurogenesis, semaphorin signaling, ephrin receptor activity, etc. A disproportionately higher proportion of dysregulated genes were associated with epilepsy. When transcriptome data of Dnmt1tet/tet neurons treated with doxycycline that downregulated DNMT1 was used, 3,356 genes (∼31%) were dysregulated with a significant proportion involved in pathways similar to those in untreated cells. Both conditions resulted in ∼68% of dysregulated genes wherein a majority showed similar patterns of transcript level changes. Among the genes with transcripts returning to normal levels, ribosome assembly/biogenesis was most significant whereas in absence of DNMT1, a new set of 903 genes became dysregulated and are involved in similar pathways as mentioned above. These findings provide support for overexpression of DNMT1 as well as its downregulation as risk factor for the four disorders and that its levels within a tight range are essential for normal neurodevelopment/mental health.
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Affiliation(s)
- Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad, India
| | - Sonal Saxena
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani, Hyderabad, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Hyderabad, India
- Centre for Human Disease Research, Birla Institute of Technology and Science, Pilani, Hyderabad, India
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Nathani M, Singh V, Sharma A, Manchanda V, Saxena S, Juneja M. Autoimmune encephalitis: A diagnostic enigma. Indian J Med Microbiol 2023; 46:100477. [PMID: 37742479 DOI: 10.1016/j.ijmmb.2023.100477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
Autoimmune encephalitis with anti-NMDA (N-methyl-D-aspartate) receptor encephalitis is the most common type. This condition can be associated with underlying malignancy, making appropriate screening essential. Prompt identification and intervention of autoimmune encephalitis is essential for a successful outcome and full recovery from this serious and potentially fatal condition. Immunotherapy is typically used to suppress the immune response and reduce brain inflammation. The choice of therapy depends on the type and severity of autoimmune encephalitis, as well as the presence of an underlying tumour.
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Affiliation(s)
| | | | - Anju Sharma
- Maulana Azad Medical College, New Delhi, India.
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Kushala, Pemde H, Kumar V, Datta V, Saxena S. Quality improvement initiative improves the empiric antibiotic prescribing practices in a tertiary care children's hospital in India. BMJ Open Qual 2023; 12:e002181. [PMID: 37863510 PMCID: PMC10603470 DOI: 10.1136/bmjoq-2022-002181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/19/2023] [Indexed: 10/22/2023] Open
Abstract
INTRODUCTION Infections are a common cause of paediatric morbidity. Antibiotics are vital in treating them. Erratic prescribing practices are an important cause for the development of antibiotic resistance. Our objective was to estimate the effectiveness of educational interventions to improve empirical antibiotic prescribing practices among paediatric trainees. We aimed to improve the compliance to antibiotic protocols and to sustain it over 6 months. METHODS It is a time interrupted non-randomised trial conducted in a tertiary hospital in India. Initially, 200 admitted children were selected randomly. Their antibiotic prescriptions, adherence of prescriptions to the then existing antibiotics guidelines, course during hospital stay and the final outcome were noted. The existing antibiotic policy and its use were reviewed. It was then considered essential to prepare a fresh antibiotic policy based on national guidelines, local sensitivity patterns and with inputs from microbiologists. This was distributed to the residents through seminars, posters and cellphone friendly documents. Compliance to the policy was also tracked twice a week. The adherence to guideline was recorded in the subsequent 6 months. RESULTS The adherence of empirical antibiotic prescriptions was 59% before intervention which improved to 72% in the first month, 90% in the second month, 86% and 78% in the third and sixth months, respectively. There was no significant difference in duration of stay and the outcome at discharge in the patients in adherent and non-adherent groups. CONCLUSION Educational interventions and frequent monitoring improved antibiotic prescribing practices among residents with no negative impact on patient outcomes. Quality improvements need persistent reinforcement and frequent monitoring to be sustainable.
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Affiliation(s)
- Kushala
- Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India
| | - Harish Pemde
- Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India
| | - Virendra Kumar
- Department of Pediatrics, Maulana Azad Medical College, New Delhi, India
| | - Vikram Datta
- Department of Neonatology, Dr Ram Manohar Lohia Hospital and Post Graduate Institute of Medical Education and Research, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India
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Manchanda V, Mitra S, Rafique I, Sharma A, Dhakad MS, Saxena S, Kapoor S, Kumar S. Is Omicron really mild? - Comparative analysis of comorbidities and disease outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants. Indian J Med Microbiol 2023; 45:100391. [PMID: 37573055 PMCID: PMC10242243 DOI: 10.1016/j.ijmmb.2023.100391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/10/2023] [Accepted: 05/21/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE Multiple variants of SARS-CoV-2 from Alpha to Omicron have an estimated 6.1 million deaths globally till date. These variants have been found to vary in transmissibility and severity. The present study deals with comparison of morbidity and mortality with SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants. MATERIALS AND METHOD An observational retrospective cohort study was conducted on a cohort of laboratory confirmed patients of SARS-CoV-2 diagnosed by qRT-PCR of nasopharyngeal swabs in periods; April-2021 and January-2022; that were sequenced and variants were recorded. Patients were invited for a telephonic interview after voluntary and informed consent was obtained from each participant wherein, the demographics, co-morbidities, oxygen requirement and mortality outcomes of the patients were enquired about. RESULTS A total of 200 patients, with 100 from each period were included in the study. Major comorbidities in patients included hypertension, diabetes mellitus and pulmonary disease. Patients who succumbed to the Delta variant (26%) were higher as compared to the Omicron variant (10%); with the elderly (68 ± 9.7 years) having significant mortality during the Omicron variant. The mortality was increased in patients with comorbidities as with hypertension (53.8%, 70%), diabetes mellitus (26.9%, 40%), chronic pulmonary disease (30.8%, 20%), and smoking (15.4%, 40%) in the patients infected with both Delta and Omicron variants, respectively. CONCLUSION The study concluded that the newer strains of SARS-CoV-2 have potential of high transmissibility and milder disease for the population by large, however, for patients with comorbidities have a higher proportion of adverse outcomes, irrespective of the variant.
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Affiliation(s)
- Vikas Manchanda
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Srestha Mitra
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Iram Rafique
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Anju Sharma
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Megh Singh Dhakad
- Department of Microbiology, Maulana Azad Medical College, Delhi, India.
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College and Lok Nayak Hospital, Delhi, India.
| | - Seema Kapoor
- Department of Pediatrics, Pediatric Research and Genetic Lab, Maulana Azad Medical College and Lok Nayak Hospital, Delhi, India.
| | - Suresh Kumar
- Department of Medicine, Maulana Azad Medical College and Lok Nayak Hospital, Delhi, India.
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Kumar A, Sharma A, Singh AK, Singh SK, Saxena S. Data Augmentation for Medical Image Classification based on Gaussian Laplacian Pyramid Blending with a Similarity Measure. IEEE J Biomed Health Inform 2023; PP:1-8. [PMID: 37603476 DOI: 10.1109/jbhi.2023.3307216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Breast cancer is a devastating disease that affects women worldwide, and computer-aided algorithms have shown potential in automating cancer diagnosis. Recently Generative Artificial Intelligence (GenAI) opens new possibilities for addressing the challenges of labeled data scarcity and accurate prediction in critical applications. However, a lack of diversity, as well as unrealistic and unreliable data, have a detrimental impact on performance. Therefore, this study proposes an augmentation scheme to address the scarcity of labeled data and data imbalance in medical datasets. This approach integrates the concepts of the Gaussian-Laplacian pyramid and pyramid blending with similarity measures. In order to maintain the structural properties of images and capture inter-variability of patient images of the same category similarity-metric-based intermixing has been introduced. It helps to maintain the overall quality and integrity of the dataset. Subsequently, deep learning approach with significant modification, that leverages transfer learning through the usage of concatenated pre-trained models is applied to classify breast cancer histopathological images. The effectiveness of the proposal, including the impact of data augmentation, is demonstrated through a detailed analysis of three different medical datasets, showing significant performance improvement over baseline models. The proposal has the potential to contribute to the development of more accurate and reliable approach for breast cancer diagnosis.
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Rana N, Sagar T, Saxena S, Chaudhary K. Facial cutaneous phaeohyphomycosis in an immunocompetent individual. INDIAN J PATHOL MICR 2023:00004270-990000000-00050. [PMID: 38391321 DOI: 10.4103/ijpm.ijpm_692_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/17/2022] [Indexed: 02/24/2024] Open
Abstract
ABSTRACT Fungal infection is a rare condition in immunocompetent individuals, and it is associated with high rates of morbidity and mortality. We report on a case of cutaneous phaeohyphomycosis in healthy 25-year-old man. Based on the clinical findings, the case was first thought to be cervico-facial actinomycosis, but Alternaria was identified on the culture after debridement. Simple surgical excision resulted in the complete cure without administration of systemic antifungals.
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Affiliation(s)
- Neha Rana
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India
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Oberoi JK, Sheoran L, Sagar T, Saxena S. Invasive fungal infections in hemato-oncology. Indian J Med Microbiol 2023; 44:100353. [PMID: 37356843 DOI: 10.1016/j.ijmmb.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND Patients with hematologic malignancies (HM) carries a significant risk of developing invasive fungal infection (IFI) and are associated with a high risk of attributable morbidity and mortality. OBJECTIVES This review has highlighted the importance of diagnosis and management of invasive fungal infections in highly immunocompromised Hemato-Oncology patients. CONTENT IFI continues to be a therapeutic issue in immunocompromised HM patients despite of many advancements in the field of fungal diagnosis and therapies. Non-specific and often overlapping signs and symptoms render fungal infections clinically undifferentiated from bacterial infections. Definite diagnosis requires microbiological diagnostic procedures in addition to imaging techniques. Many international committees have formulated definitions to aid in the diagnosis of IFI in immunocompromised patients and assigned 3 levels of probability to the diagnosis "proven," "probable," and "possible" IFI. Early specific risk-based antifungal strategies such as prophylaxis, pre-emptive and empirical therapies, are common practices in HM patients. For low-risk patients, fluconazole is recommended as primary prophylaxis, while, posaconazole and voriconazole are recommended for high-risk patients. Emerging antifungal-resistant IFIs and breakthrough fungal infections are the new threat to these heavily immunosuppressed patients. Antifungal agents such as azoles have variable pharmacokinetics leading to uncertainty in the drug dose-exposure relationship, especially in the initiation phase. TDM (therapeutic drug monitoring) of voriconazole is strongly recommended.
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Affiliation(s)
- Jaswinder Kaur Oberoi
- Institute of Clinical Microbiology & Immunology, Sir Ganga Ram Hospital, Rajinder Nagar, New Delhi, 110060, India.
| | - Lata Sheoran
- Department of Microbiology, Maulana Azad Medical College, New Delhi, 110002, India.
| | - Tanu Sagar
- Department of Microbiology, Maulana Azad Medical College, New Delhi, 110002, India.
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College, New Delhi, 110002, India.
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Chaurasia S, Anand P, Sharma A, Nangia S, Sivam A, Jain K, Gaind R, Kaur R, Sastry AS, Kapil A, Bhatt M, Salhan M, Dudeja A, Plakkal N, Verma A, Jain M, Saxena S, Mohapatra S, Kashyap A, Goel S, Sivanandan S, Arya S, Saini S, Pande T, Saluja S, Sharma M, Vishnubhatla S, Chellani H, Sankar MJ, Agarwal R. Procalcitonin for Detecting Culture-Positive Sepsis in Neonates: A Prospective, Multicenter Study. Neonatology 2023; 120:642-651. [PMID: 37336195 DOI: 10.1159/000529640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 02/05/2023] [Indexed: 06/21/2023]
Abstract
INTRODUCTION It is unclear if serum procalcitonin (PCT) estimated at sepsis suspicion can help detect culture-positive sepsis in neonates. We evaluated the diagnostic performance of PCT in culture-positive sepsis in neonates. METHODS This was a prospective study (February 2016 to September 2020) conducted in four level-3 units in India. We enrolled neonates suspected of sepsis in the first 28 days of life. Neonates with birth weight <750 g, asphyxia, shock, and major malformations were excluded. Blood for PCT assay was drawn along with the blood culture at the time of suspicion of sepsis and before antibiotic initiation. The investigators labeled the neonates as having culture-positive sepsis or "no sepsis" based on the culture reports and clinical course. PCT assay was performed by electrochemiluminescence immunoassay, and the clinicians were masked to the PCT levels while assigning the label of sepsis. Primary outcomes were the sensitivity, specificity, and likelihood ratios to identify culture-positive sepsis. RESULTS The mean birth weight (SD) and median gestation (IQR) were 2,113 (727) g and 36 (32-38) weeks, respectively. Of the 1,204 neonates with eligible cultures, 155 (12.9%) had culture-positive sepsis. Most (79.4%) were culture-positive within 72 h of birth. The sensitivity, specificity, and positive and negative likelihood ratios at 2 ng/mL PCT threshold were 52.3% (95% confidence interval: 44.1-60.3), 64.5% (60.7-68.1), 1.47 (1.23-1.76), and 0.74 (0.62-0.88), respectively. Adding PCT to assessing neonates with 12.9% pretest probability of sepsis generated posttest probabilities of 18% and 10% for positive and negative test results, respectively. CONCLUSION Serum PCT did not reliably identify culture-positive sepsis in neonates.
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Affiliation(s)
- Suman Chaurasia
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Pratima Anand
- Department of Pediatrics, Safdarjung Hospital and VMMC, New Delhi, India
| | - Akash Sharma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India,
| | - Sushma Nangia
- Department of Pediatrics, Kalawati Saran Children's Hospital, LHMC, New Delhi, India
| | - Adhi Sivam
- Department of Neonatology, JIPMER, Puducherry, India
| | - Kajal Jain
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rajni Gaind
- Department of Microbiology, Safdarjung Hospital and VMMC, New Delhi, India
| | - Ravinder Kaur
- Department of Microbiology, Lady Hardinge Medical College (LHMC), New Delhi, India
| | | | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Meenakshi Bhatt
- Department of Pediatrics, Safdarjung Hospital and VMMC, New Delhi, India
| | - Meetu Salhan
- Department of Pediatrics, Safdarjung Hospital and VMMC, New Delhi, India
| | - Ajay Dudeja
- Department of Pediatrics, Kalawati Saran Children's Hospital, LHMC, New Delhi, India
| | | | - Ankit Verma
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Manisha Jain
- Department of Microbiology, Safdarjung Hospital and VMMC, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Lady Hardinge Medical College (LHMC), New Delhi, India
| | - Sarita Mohapatra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Archana Kashyap
- Department of Pediatrics, Safdarjung Hospital and VMMC, New Delhi, India
| | - Srishti Goel
- Department of Pediatrics, Kalawati Saran Children's Hospital, LHMC, New Delhi, India
| | | | - Sugandha Arya
- Department of Pediatrics, Safdarjung Hospital and VMMC, New Delhi, India
| | - Savita Saini
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Tapish Pande
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Sumita Saluja
- Department of Hematology, Safdarjung Hospital and VMMC, New Delhi, India
| | - Monica Sharma
- Department of Hematology, Safdarjung Hospital and VMMC, New Delhi, India
| | | | - Harish Chellani
- Department of Pediatrics, Safdarjung Hospital and VMMC, New Delhi, India
| | - M Jeeva Sankar
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Ramesh Agarwal
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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Jha H, Baveja CP, Kamal V, Agarwal PN, Saxena S, Dhakad MS, Sharma D. Comparative Diagnostic of Cervical Tuberculous Lymphadenitis: PCR is a Fast, Efficient, and Improved Diagnostic Approach. Can J Infect Dis Med Microbiol 2023; 2023:3312250. [PMID: 37346247 PMCID: PMC10281827 DOI: 10.1155/2023/3312250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023]
Abstract
Methods The study included 100 clinically suspected cases of TBLN. Fine needle aspirate (FNA) samples were processed for cytology staining and cultured on LJ & BACTEC 12B media. The biochemical tests were performed to identify the isolates at the species level. Additionally, for PCR, DNA was extracted and used for the diagnosis and identification of mycobacterial species. Results Patients ranged from 2 to 45 years with a mean age of 24.96 ± 9.10 years. Out of 100 patients, 73% had clinical symptoms of weight loss, followed by fever (72%), anorexia (66%), and night sweats (58%). 24% of patients were found to be smear-positive after Ziehl-Neelsen (ZN) staining and statistically highly significant with PCR. On LJ medium 34% and on BACTEC radiometric 45% of samples were smearing positive. Overall, 48% of cases were PCR-positive for TBLN. When compared with culture, the sensitivity and specificity of PCR were 93.75% and 100%, respectively, which are higher than cytology. The true positive predictive value (PPV) and negative predictive value (NPV) were 83.3% and 61.5%, respectively. Conclusion This study suggests that PCR is a rapid, sensitive, and specific tool for correct diagnosis of TBLN cases as compared to staining and culture which lead to the early and proper management of mycobacterial diseases.
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Affiliation(s)
- Himanshu Jha
- Department of Microbiology, Maulana Azad Medical College, New Delhi 110002, India
- Lab Strengthening & Diagnostics, Jhpiego, India
| | | | - Vinay Kamal
- Department of Pathology, Maulana Azad Medical College, New Delhi 110002, India
| | | | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College, New Delhi 110002, India
| | - Megh Singh Dhakad
- Department of Microbiology, Maulana Azad Medical College, New Delhi 110002, India
| | - Divakar Sharma
- Department of Microbiology, Lady Hardinge Medical College, New Delhi 110001, India
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Sharma R, Shrivastava S, Singh SK, Kumar A, Singh AK, Saxena S. Artificial intelligence-based model for predicting the minimum inhibitory concentration of antibacterial peptides against ESKAPEE pathogens. IEEE J Biomed Health Inform 2023; PP:1-10. [PMID: 37115837 DOI: 10.1109/jbhi.2023.3271611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
In response to environmental threats, pathogens make several changes in their genome, leading to antimicrobial resistance (AMR). Due to AMR, the pathogens do not respond to antibiotics. Amongst drug-resistant pathogens, the ESKAPEE group of bacteria poses a major threat to humans, and therefore World Health Organization has given them the highest priority status. Antibacterial peptides (ABPs) are a family of peptides found in nature that play a crucial role in the innate immune systems of organisms. These ABPs offer several advantages over widely used antibiotics. As a result, they have recently received a lot of attention as potential replacements for currently available antibiotics. But it is expensive and time-consuming to identify ABPs from natural sources. Thus, wet lab researchers employ various tools to screen promising ABPs rapidly. However, the main limitation of the existing tools is that they do not provide the minimum inhibitory concentration values against the ESKAPEE pathogens for the identified ABP. To address this, in the current work, we developed ESKAPEE-MICpred, a two-input model that utilizes transfer learning and ensemble learning techniques. The concept of ensemble learning was realized by combining the decisions provided by deep learning algorithms, whereas the concept of transfer learning was realized by utilizing pretrained amino acid embeddings. The proposed model has been deployed as a web server at https://eskapee-micpred.anvil.app/ to aid the scientific community.
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Sharma R, Shrivastava S, Singh SK, Kumar A, Singh AK, Saxena S. EnDL-HemoLyt: Ensemble Deep Learning-based Tool for Identifying Therapeutic Peptides with Low Hemolytic Activity. IEEE J Biomed Health Inform 2023; PP:1-11. [PMID: 37018101 DOI: 10.1109/jbhi.2023.3264941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Low hemolytic therapeutic peptides have gained an edge over small molecule-based medicines. However, finding low hemolytic peptides in laboratory is time-consuming, costly and necessitates the use of mammalian red blood cells. Therefore, wet-lab researchers often perform in-silico prediction to select low hemolytic peptides before proceeding with in-vitro testing. The in-silico tools available for this purpose have following limitations: (i) They do not provide predictions for peptides having N/C terminal modifications. (ii) Data is food for AI; however, datasets used to create existing tools do not contain peptide data generated over past eight years. (iii) Performance of available tools is also low. Therefore, a novel framework has been proposed in current work. Proposed framework utilizes recent dataset and uses ensemble learning technique to combine the decisions produced by bidirectional long short-term memory, bidirectional temporal convolutional network, and 1-dimensional convolutional neural network deep learning algorithms. Deep learning algorithms are capable of extracting features themselves from data. However, instead of relying solely on deep learning-based features (DLF), handcrafted features (HCF) were also provided so that deep learning algorithms can learn features that are missing from HCF, and a better feature vector can be constructed by concatenating HCF and DLF. Additionally, ablation studies were carried out to understand the roles of an ensemble algorithm, HCF, and DLF in the proposed framework. Ablation studies found that the ensemble algorithm, HCF and DLF are crucial components of proposed framework, and there is a decrease in performance on eliminating any of them. Mean value of performance metrics, namely Acc, Sn, Pr, Fs, Sp, Ba, and Mcc obtained by proposed framework for test data is ≈ 87, 85, 86, 86, 88, 87, and 73, respectively. To aid scientific community, model developed from proposed framework has been deployed as a web server at https://endl-hemolyt.anvil.app/.
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Affiliation(s)
- M Gisselbaek
- Department of Anesthesiology and Acute Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - O L Barreto Chang
- Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, CA, USA
| | - S Saxena
- Department of Anesthesia and Reanimation, AZ Sint-Jan Brugge Oostende AV, Brugge, Belgium.
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Shreya S, Chawla R, Anuradha S, Singh MM, Manchanda V, Saxena S. Proportion of syphilis and hepatitis B and C virus infections among the Integrated Counselling and Testing Centre attendees of a tertiary care hospital. Indian J Sex Transm Dis AIDS 2023; 44:35-39. [PMID: 37457542 PMCID: PMC10343129 DOI: 10.4103/ijstd.ijstd_113_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Human Immunodeficiency Virus (HIV) affects the immune system of the body, causing a breakdown in its normal defenses and leaving it vulnerable to a host of life-threatening diseases. High-risk behaviors and routes of transmission for sexually transmitted infections such as syphilis, hepatitis B and hepatitis C are identical with HIV. This study was conducted to assess the proportion of syphilis and hepatitis B and C virus infections in HIV-positive and HIV-negative individuals, and their association with socioeconomic and other factors in Integrated Counselling and Testing Centre (ICTC) attendees, and to determine the association of absolute CD4+ T-lymphocyte count with these co-infections in HIV-positive individuals. Materials and Methods The study was conducted in the Department of Microbiology of a tertiary care hospital. It included 100 HIV-positive individuals and 100 matched HIV-negative controls attending the ICTC. HIV-positive patients on antiretroviral therapy and patients with history of current/past treatment for chronic hepatitis infection were excluded from the study. Blood samples were tested for HIV, syphilis, and hepatitis B and C infections. Results The prevalence of syphilis, hepatitis B, and hepatitis C was observed in 3.5%, 2%, and 10% of patients, respectively. The frequency of hepatitis B virus (HBV) infection in HIV-positive and HIV-negative individuals was 1% and 3%, respectively. Hepatitis C virus (HCV) infection among HIV-positive and HIV-negative patients was 16% and 4%, respectively. Syphilis was seen in 7% of the HIV-infected patients. The mean CD4+ count for the HIV-positive patients with either syphilis, HBV, or HCV infections was 252 ± 137.5 cells/μl. Significant associations between HIV infection and education below high school, IV drug abuse, and multiple sexual partners were observed. Conclusions The HIV-infected patients were observed to be at an increased risk of acquiring syphilis and HCV co-infections through the shared routes of transmission. Routine screening of these patients for concurrent syphilis and viral hepatitis may aid in prompt diagnosis and treatment with improved outcomes, which in turn may decrease the further spread of these infections.
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Affiliation(s)
- Sunidhi Shreya
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Rohit Chawla
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - S. Anuradha
- Department of Medicine, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Mongjam Meghachandra Singh
- Department of Community Medicine, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Vikas Manchanda
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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Muacevic A, Adler JR, Kumar S, Jaisingh K, R. AT, Rao KC, Chhabra K, Saxena S, Manchanda V, Sharma S. Optical Coherence Tomography Angiography Parameters of the Retina in SARS-CoV-2 Recovered Subjects. Cureus 2023; 15:e33548. [PMID: 36779162 PMCID: PMC9907863 DOI: 10.7759/cureus.33548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION This study aims to evaluate retinochoroidal optical coherence tomography angiography (OCTA) parameters in patients recovered from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). METHODS This study was an observational study that included 80 subjects being discharged after having negative reports on the reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2 to evaluate OCTA parameters of the retina. The subjects underwent an ophthalmic evaluation that included best-corrected visual acuity (BCVA), intraocular pressure (IOP), color vision (CV), contrast sensitivity (CS), and optical coherence tomography (OCT) parameters. OCTA was done for all patients and was evaluated for foveal avascular zone (FAZ) area, perimeter, and circularity index, and vessel density (VD) in superficial capillary plexus (SCP), deep capillary plexus (DCP), outer retina (OR), outer retina chorio-capillaries (ORCC), chorio-capillaries (CC), and choroid (C) using 3 x 3 mm scans. The OCTA parameters were compared with normative data of the Indian population for various parameters in question. RESULTS The subjects included 54/80 (67.5%) males and 26/80 (32.5%) females having a mean age of 52.40 ± 15.71 (18-60) years. The systemic evaluation revealed 38.75% of subjects had hypertension, 30% had diabetes, 20% had kidney disease, 5% had tuberculosis, and 3.75% had coronary artery disease. The mean distance BCVA was logarithm of the minimum angle of resolution (LogMAR) (1.17 ± 0.22), mean IOP was 17.0 ± 4.0 mmHg, mean CS was 2.13 ± 0.36, 50.62% of subjects had normal CV on Farnsworth test while 47% had tritanopia, and none of the subjects had red-green CV defect on Ishihara plates. The OCT scan was normal in 90% of eyes while the posterior vitreous detachment was seen in 4% of eyes, broad vitreomacular adhesion in 2.5% of eyes, and the globally adherent epiretinal membrane was seen in 2.5% of eyes. The mean central macular thickness (CMT) measured 245.14 ± 28.41 micrometers. The mean FAZ area measured 0.37 ± 0.15 mm2, the perimeter was 3.28 ± 1.08 mm, and the circularity index measured 0.41 ± 0.10. The average VD in SCP measured 16.06 ± 12.29, in DCP measured 9.11 ± 8.75, in OR measured 6.38 ± 7.37, in ORCC measured 42.53 ± 12.46, in CC measured 25.83 ± 16.31, and in C measured 25.52 ± 17.49. The VD in coronavirus disease 2019 (COVID-19) subjects was significantly lesser than that in the healthy Indian population in all layers except ORCC. CONCLUSIONS The SARS-CoV-2 recovered subjects have a reduced VD in retinochoroidal layers from COVID-19, an underlying systemic disease, or both. The CS values fall within normal limits. Several subjects show tritanopia on the Farnsworth test but no red-green CV defect on Ishihara plates.
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Ravi V, Kapil A, Biswas S, Saxena S. Indian association of medical microbiologists (IAMM) position paper on guidelines for COVID and SARSCoV2 infections. Indian J Med Microbiol 2023; 42:53-54. [PMID: 36967217 PMCID: PMC9896976 DOI: 10.1016/j.ijmmb.2023.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 02/09/2023]
Affiliation(s)
- V. Ravi
- Department of Neurovirology, Registrar & Dean-Basic Sciences, NIMHANS, Bangalore 560029, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Sanjay Biswas
- Dept. of Microbiology, TMH, Tata Memorial Centre and Joint Secretary-IAMM, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India,Corresponding author
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Sagar T, Sheoran L, Prajapati A, khuraijam B, Jana PP, Pandey PN, Saxena S. Aspergillus fumigatus cerebral abscess following hemodialysis: A case report. Curr Med Mycol 2022; 8:32-36. [PMID: 37736610 PMCID: PMC10509493 DOI: 10.32598/cmm.2023.1323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/28/2022] [Accepted: 12/18/2022] [Indexed: 09/23/2023] Open
Abstract
Background and Purpose Cerebral aspergillosis is a notorious disease that causes rapid clinical deterioration and carries a poor prognosis. Therefore, it requires timely diagnosis and prompt management. Case Report This study reports a case of fungal cerebral abscess in a 26years old man following hemodialysis,2 months afterdengue-induced acute kidney disease. Aspergillus fumigatus was recovered from a brain abscess specimen that was subjected to a parietal craniotomy. The patient was successfully treated with oral Voriconazole 400mg BD for 2 days, followed by 200 mg BD for 3months. Conclusion Hemodialysis patients are at high risk offungal infections due to the frequent use of catheters or the insertion of needles to access the bloodstream. Therefore, a high index of suspicion of fungal infection is required in patients with hemodialysis by the clinician for early diagnosis and treatment.
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Affiliation(s)
- Tanu Sagar
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India
| | - Lata Sheoran
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India
| | - Ajay Prajapati
- Department of Neurosurgery, Lok Nayak Hospital, New Delhi, India
| | - Bembem khuraijam
- Department of Pathology, Maulana Azad Medical College, New Delhi, India
| | - Partha Pratin Jana
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India
| | - P. N Pandey
- Department of Neurosurgery, Lok Nayak Hospital, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College, New Delhi, India
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24
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Foley KA, Maile EJ, Bottle A, Neale FK, Viner RM, Kenny SE, Majeed A, Hargreaves DS, Saxena S. How did the covid-19 pandemic affect lower respiratory tract infections in young children in England? Eur J Public Health 2022. [DOI: 10.1093/eurpub/ckac129.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Social distancing policies to reduce transmission of covid-19 also reduced children's exposures to endemic respiratory viruses. We aimed to examine the impact of the covid-19 pandemic on lower respiratory tract infections in under 5s presenting to primary care in England.
Methods
Longitudinal trends analysis using electronic health records from a nationally representative primary care database. Our target population was children aged <5 years registered with a primary care practice from January 2015 to March 2021.
Our main outcome was total weekly contacts with primary care for a lower respiratory tract infection (LRTI). We defined three pandemic phases from March 2020 - March 2021: i) first national lockdown (late March to early June 2020), ii) childcare settings reopened and second national lockdown with schools open (mid-June to mid-December 2020) and iii) third national lockdown with schools closed (late December 2020 to end of March 2021). We compared outcomes during each of the three phases with corresponding calendar weeks during pre-pandemic years 2015 to 2019.
Results
Our study population included 843 020 children <5 years who had 1 076 181 contacts with primary care for LRTIs. During the first phase (first lockdown) there were falls of 79.3% (95% CI: 73.6 to 84.5) from an average of 28 547 primary care contacts for LRTI in 2015 - 2019 to 5915 in 2020; there was a 78.9% (95% CI: 73.7 to 83.9) fall in phase two (childcare settings reopened and second lockdown) from 107 873 to 22 792 contacts; and a 77.7% (95% CI: 73.5 to 81.4) fall in phase three (third lockdown) from 57 200 to 12 764 contacts.
Conclusions
Children under 5 in England had fewer contacts with primary care for LRTIs during the covid-19 pandemic. This change likely reflects lower prevalence of respiratory illness due to fewer social contacts. This may impact on future health service use as these children have had less exposure, and therefore may have less immunity, to respiratory diseases.
Key messages
• Children under 5 had fewer contacts with primary care for lower respiratory tract infections during the covid-19 pandemic in England likely due to the restrictions in place to reduce social contacts.
• The falls in lower respiratory tract infections during the covid-19 pandemic in under 5s may mean they have less immunity to respiratory viruses which may impact upon their future health service use.
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Affiliation(s)
- KA Foley
- Department of Primary Care and Public Health, Imperial College London , London, UK
| | - EJ Maile
- Department of Primary Care and Public Health, Imperial College London , London, UK
| | - A Bottle
- Department of Primary Care and Public Health, Imperial College London , London, UK
| | - FK Neale
- Department of Primary Care and Public Health, Imperial College London , London, UK
| | - RM Viner
- Population, Policy & Practice Department, UCL Great Ormand Street Institute of Child Health , London, UK
| | - SE Kenny
- Department of Women’s and Children’s Health, Alder Hey Children’s NHS Foundation Trust , Liverpool, UK
- NHS England and NHS Improvement, NHS , London, UK
| | - A Majeed
- Department of Primary Care and Public Health, Imperial College London , London, UK
| | - DS Hargreaves
- Mohn Centre for Children’s Health, Imperial College London , London, UK
| | - S Saxena
- Department of Primary Care and Public Health, Imperial College London , London, UK
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25
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Hofmann L, Mandato A, Saxena S, Ruthstein S. The use of EPR spectroscopy to study transcription mechanisms. Biophys Rev 2022; 14:1141-1159. [PMID: 36345280 PMCID: PMC9636360 DOI: 10.1007/s12551-022-01004-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 02/08/2023] Open
Abstract
Electron paramagnetic resonance (EPR) spectroscopy has become a promising structural biology tool to resolve complex and dynamic biological mechanisms in-vitro and in-cell. Here, we focus on the advantages of continuous wave (CW) and pulsed EPR distance measurements to resolve transcription processes and protein-DNA interaction. The wide range of spin-labeling approaches that can be used to follow structural changes in both protein and DNA render EPR a powerful method to study protein-DNA interactions and structure-function relationships in other macromolecular complexes. EPR-derived data goes well beyond static structural information and thus serves as the method of choice if dynamic insight is needed. Herein, we describe the conceptual details of the theory and the methodology and illustrate the use of EPR to study the protein-DNA interaction of the copper-sensitive transcription factor, CueR.
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Affiliation(s)
- L. Hofmann
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat-Gan, Israel
| | - A. Mandato
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA USA
| | - S. Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA USA
| | - S. Ruthstein
- Department of Chemistry and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat-Gan, Israel
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26
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Anne A, Saxena S, Mohan KN. Genome-wide methylation analysis of post-mortem cerebellum samples supports the role of peroxisomes in autism spectrum disorder. Epigenomics 2022; 14:1015-1027. [PMID: 36154275 DOI: 10.2217/epi-2022-0184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: We tested the hypothesis that a subset of patients with autism spectrum disorder (ASD) contains candidate genes with high DNA methylation differences (effective values) that potentially affect one of the two alleles. Materials & methods: Genome-wide DNA methylation comparisons were made on cerebellum samples from 30 patients and 45 controls. Results: 12 genes with high effective values, including GSDMD, MMACHC, SLC6A5 and NKX6-2, implicated in ASD and other neuropsychiatric disorders were identified. Monoallelic promoter methylation and downregulation were observed for SERHL (serine hydrolase-like) and CAT (catalase) genes associated with peroxisome function. Conclusion: These data are consistent with the hypothesis implicating impaired peroxisome function/biogenesis for ASD. A similar approach holds promise for identifying rare epimutations in ASD and other complex disorders.
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Affiliation(s)
- Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Sonal Saxena
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani - Hyderabad Campus, 500 078, India
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Upadhyaya G, Capoor MR, Verma H, Gambhir S, Saxena S, Khungar N. P302 Disseminated histoplasmosis: Rare entity in immunocompromised individuals in India. Med Mycol 2022. [PMCID: PMC9510017 DOI: 10.1093/mmy/myac072.p302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM
Invasive mycoses kill more than one million people every year. The disease burden of mycoses has increased over the last 20 years and the importance of fungal disease is expected to keep increasing in the years to come. One of these mycoses, histoplasmosis, a disease caused by species of dimorphic genera, Histoplasma and is endemic in the USA, Asia, and Africa with sporadic cases reported from India. In the United States alone, 3.4 cases/100 000 people occur yearly. In India, prevalence of histoplasmosis is seen in the eastern part of the country and few cases are reported from north India. Here, we present four cases of classic progressive disseminated histoplasmosis from non-endemic central and northern parts of India.
Cases I and II: Two cases, firstly a 51-year-old male resident of Delhi, came with complaints of fever, generalized weakness and weight loss for the past 6 months, and another a 55-year-old in an apparently immunocompetent female from a non-endemic state in central India. The disease was diagnosed by bone marrow aspirate incidentally.
Cases III and IV: A 25-year-old female and a 29-year-old HIV-infected female, with chief complaints of multiple skins colored swellings on her face, neck, chest, and back and also on both limbs. Physical examination revealed multiple skin-colored papules and nodules coalescing to form large plaques on the face, neck, upper back, and chest which had overlying yellowish-brown crusting (Fig.1). Her entire face was involved with depression of the nasal bridge and madarosis. Multiple discrete 0.1-0.5 mm papules and nodules on bilateral upper and lower limbs. Patient was started on the treatment of cutaneous histoplasmosis with injection of liposomal amphotericin-B 100 mg intravenous (around 3 mg/kg/day) after pre-medication for 10 days. For both cases, capsule itraconazole 200 mg BD started for 4 days. Patient responded well to the treatment and follow-up showed improvement in the condition of the patient.
Results
In all the cases, fine needle aspirate cytology of the lesions showed plenty of inflammatory cells and macrophages in pathological microscopic examination. Microscopic examination of skin tissue revealed that macrophages comprising of yeast forms of Histoplasma have pericellular halo around them. Moreover, on long incubation of biopsy sample on SDA media plate at 27˚C, white/buff colonies with yellow-tan on the back were observed. Furthermore, microscopic examination of grown fungal culture showed mycelial septate hyphae bearing round to pear-shaped, smooth-walled broadly elliptical microconidia, or tuberculate macroconidia. In all the cases, clinical suspicion, histopathological and mycological findings (microscopy, culture and post-culture sequencing) led to a confirmatory diagnosis of progressive disseminated Histoplasmosis by H. capsulatum var. capsulatum was made.
Conclusion
In all, 3 of these cases are of progressive disseminated histoplasmosis in apparently immunocompetent patients from the non-endemic states of north India. On the contrary, one of the cases was HIV positive with mucocutaneous lesions. Disseminated histoplasmosis in immunocompetent individuals is not a rare entity, in India. High clinical suspicion and awareness regarding the pathogen are required. From the point of good patient care, an accurate diagnosis, and timely management in cases of histoplasmosis are warranted.
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Affiliation(s)
| | | | | | | | - S Saxena
- VMMC and Safdarjung Hospital , New Delhi , India
| | - Niti Khungar
- VMMC and Safdarjung Hospital , New Delhi , India
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28
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Singh DK, Kapoor R, Yadav PS, Saxena S, Agarwal K, Solanki RS, Gupta A, Choudhury SR, Chadha R. Morbidity and Mortality of Necrotizing Fasciitis and Their Prognostic Factors in Children. J Indian Assoc Pediatr Surg 2022; 27:577-584. [PMID: 36530832 PMCID: PMC9757794 DOI: 10.4103/jiaps.jiaps_222_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/08/2022] [Accepted: 04/16/2022] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND This is a prospective study of the clinico-etiologic profile and factors affecting outcomes in 40 children managed for necrotizing fasciitis (NF). MATERIALS AND METHODS Demographic details, clinical characteristics, and laboratory parameters were recorded, and the Laboratory Risk Indicator for Necrotizing Fasciitis (LRINEC) score was calculated. Primary outcome (survival vs. nonsurvival) was noted, and prognostic factors were identified. RESULTS Initiating factors included boils (45%), i.v. cannula extravasations (22.5%), and blunt trauma (17.5%). Lesion (s) were predominantly on the lower limbs (35%) and trunk (25%). Twenty-two patients (55%) had <5% body surface area (BSA) involved. Severely deranged clinical and laboratory parameters were common. Ultrasound localized fluid collections. Pus cultures showed methicillin-resistant Staphylococcus aureus (52.5%), methicillin-sensitive S. aureus [27.5%], and polymicrobial growth (20%). Blood culture was positive in 24 patients (60%). Most isolates were sensitive to clindamycin and amoxy-clavulanate. Prognostic factors for mortality (n = 6; 15%) included categorization as "Sick," BSA involvement >10%, thrombocytopenia, raised serum creatinine, late debridement, and polymicrobial blood culture isolates. All six nonsurvivors had a LRINEC score of ≥8 and positive blood cultures. Six patients (20.7%) developed unsightly scars and 5 (17.24%) contractures across joints. CONCLUSIONS Pediatric NF has significant morbidity and mortality. Patients with adverse prognostic factors can benefit from early referral to a facility with a critical care unit. Adequate wound management is essential to minimize residual deformity.
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Affiliation(s)
- Dilip Kumar Singh
- Department of Pediatric Surgery, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Rohit Kapoor
- Department of Pediatric Surgery, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Partap Singh Yadav
- Department of Pediatric Surgery, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Kiran Agarwal
- Department of Pathology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Ravi S. Solanki
- Department of Radiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Amit Gupta
- Department of Pediatric Surgery, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Subhasis Roy Choudhury
- Department of Pediatric Surgery, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Rajiv Chadha
- Department of Pediatric Surgery, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
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29
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Lewis HC, Marcato AJ, Meagher N, Valenciano M, Villanueva‐Cabezas J, Spirkoska V, Fielding JE, Karahalios A, Subissi L, Nardone A, Cheng B, Rajatonirina S, Okeibunor J, Aly EA, Barakat A, Jorgensen P, Azim T, Wijesinghe PR, Le L, Rodriguez A, Vicari A, Van Kerkhove MD, McVernon J, Pebody R, Price DJ, Bergeri I, Alemu MA, Alvi Y, Bukusi EA, Chung PS, Dambadarjaa D, Das AK, Dub T, Dulacha D, Ebrahim F, González‐Duarte MA, Guruge D, Heraud J, Heredia‐Melo DC, Herman‐Roloff A, Herring BL, Inbanathan FY, Islam F, Jeewandara KC, Kant S, Khan W, Lako R, Leite J, Malavige GN, Mandakh U, Mariam W, Mend T, Mize VA, Musa S, Nohynek H, Olu OO, Osorio‐Merchán MB, Pereyaslov D, Randremanana RV, de Dieu Randria MJ, Ransom J, Saxena S, Sharma P, Sreedevi A, Satheesh M, Subhashini KJ, Tippet‐Barr BA, Usha A, Wamala JF, Watare SH, Yadav K. Transmission of SARS-CoV-2 in standardised first few X cases and household transmission investigations: A systematic review and meta-analysis. Influenza Other Respir Viruses 2022; 16:803-819. [PMID: 36825117 PMCID: PMC9343340 DOI: 10.1111/irv.13002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/29/2022] Open
Abstract
We aimed to estimate the household secondary infection attack rate (hSAR) of SARS-CoV-2 in investigations aligned with the WHO Unity Studies Household Transmission Investigations (HHTI) protocol. We conducted a systematic review and meta-analysis according to PRISMA 2020 guidelines. We searched Medline, Embase, Web of Science, Scopus and medRxiv/bioRxiv for "Unity-aligned" First Few X cases (FFX) and HHTIs published 1 December 2019 to 26 July 2021. Standardised early results were shared by WHO Unity Studies collaborators (to 1 October 2021). We used a bespoke tool to assess investigation methodological quality. Values for hSAR and 95% confidence intervals (CIs) were extracted or calculated from crude data. Heterogeneity was assessed by visually inspecting overlap of CIs on forest plots and quantified in meta-analyses. Of 9988 records retrieved, 80 articles (64 from databases; 16 provided by Unity Studies collaborators) were retained in the systematic review; 62 were included in the primary meta-analysis. hSAR point estimates ranged from 2% to 90% (95% prediction interval: 3%-71%; I 2 = 99.7%); I 2 values remained >99% in subgroup analyses, indicating high, unexplained heterogeneity and leading to a decision not to report pooled hSAR estimates. FFX and HHTI remain critical epidemiological tools for early and ongoing characterisation of novel infectious pathogens. The large, unexplained variance in hSAR estimates emphasises the need to further support standardisation in planning, conduct and analysis, and for clear and comprehensive reporting of FFX and HHTIs in time and place, to guide evidence-based pandemic preparedness and response efforts for SARS-CoV-2, influenza and future novel respiratory viruses.
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Affiliation(s)
- Hannah C. Lewis
- World Health OrganizationGenevaSwitzerland,World Health Organization, Regional Office for AfricaBrazzavilleRepublic of Congo
| | - Adrian J. Marcato
- Department of Infectious DiseasesThe University of Melbourne, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Niamh Meagher
- Department of Infectious DiseasesThe University of Melbourne, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneAustralia
| | - Marta Valenciano
- World Health OrganizationGenevaSwitzerland,EpiconceptParisFrance
| | - Juan‐Pablo Villanueva‐Cabezas
- Department of Infectious DiseasesThe University of Melbourne, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia,The Nossal Institute for Global HealthThe University of MelbourneMelbourneAustralia
| | - Violeta Spirkoska
- Department of Infectious DiseasesThe University of Melbourne, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia,Victorian Infectious Diseases Reference LaboratoryRoyal Melbourne Hospital, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - James E. Fielding
- Department of Infectious DiseasesThe University of Melbourne, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneAustralia,Victorian Infectious Diseases Reference LaboratoryRoyal Melbourne Hospital, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Amalia Karahalios
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneAustralia
| | | | - Anthony Nardone
- World Health OrganizationGenevaSwitzerland,EpiconceptParisFrance
| | - Brianna Cheng
- World Health OrganizationGenevaSwitzerland,School of Population and Global HealthMcGill UniversityMontrealQuebecCanada
| | | | - Joseph Okeibunor
- World Health Organization, Regional Office for AfricaBrazzavilleRepublic of Congo
| | - Eman A. Aly
- World Health Organization, Regional Office for the Eastern MediterraneanCairoEgypt
| | - Amal Barakat
- World Health Organization, Regional Office for the Eastern MediterraneanCairoEgypt
| | | | - Tasnim Azim
- World Health Organization, Regional Office for South‐East AsiaNew DelhiIndia
| | | | - Linh‐Vi Le
- World Health Organization, Regional Office for the Western PacificManilaPhilippines
| | - Angel Rodriguez
- World Health Organization, Regional Office for the Americas (Pan American Health Organization)WashingtonDCUSA
| | - Andrea Vicari
- World Health Organization, Regional Office for the Americas (Pan American Health Organization)WashingtonDCUSA
| | | | - Jodie McVernon
- Department of Infectious DiseasesThe University of Melbourne, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneAustralia,Murdoch Children's Research InstituteMelbourneAustralia
| | - Richard Pebody
- World Health Organization Regional Office for EuropeCopenhagenDenmark
| | - David J. Price
- Department of Infectious DiseasesThe University of Melbourne, at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global HealthThe University of MelbourneMelbourneAustralia
| | | | | | | | - Yasir Alvi
- Department of Community Medicine Hamdard Institute of Medical Sciences and Research New Delhi India
| | | | - Pui Shan Chung
- World Health Organization, Regional Office for the Western Pacific Manila Philippines
| | - Davaalkham Dambadarjaa
- School of Public Health Mongolian National University of Medical Sciences Ulaanbaatar Mongolia
| | - Ayan K. Das
- Department of Microbiology Hamdard Institute of Medical Science and Research New Delhi India
- Hakeem Abdul Hameed Centenary Hospital New Delhi India
| | - Timothée Dub
- Department of Health Security Finnish Institute for Health and Welfare Helsinki Finland
| | | | - Faiqa Ebrahim
- World Health Organization Country Office Addis Ababa Ethiopia
| | | | | | | | | | | | - Belinda L. Herring
- World Health Organization, Regional Office for Africa Brazzaville Republic of Congo
| | | | - Farzana Islam
- Hamdard Institute of Medical Sciences and Research (HIMSR) New Delhi India
| | - Kamal Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura Nugegoda Sri Lanka
| | - Shashi Kant
- Centre for Community Medicine All India Institute of Medical Sciences New Delhi India
| | - Wasiq Khan
- World Health Organization, Regional Office for the Eastern Mediterranean Cairo Egypt
| | | | - Juliana Leite
- World Health Organization, Regional Office for the Americas (Pan American Health Organization) Washington DC USA
| | | | - Undram Mandakh
- Mongolian National University of Medical Sciences Ulaanbaatar Mongolia
| | - Warisha Mariam
- Department of Community Medicine Maulana Azad Medical College New Delhi India
| | - Tsogt Mend
- National Center for Communicable Diseases Ulaanbaatar Mongolia
| | | | - Sanjin Musa
- Institute for Public Health of the Federation of Bosnia and Herzegovina Sarajevo Bosnia and Herzegovina
- Sarajevo School of Science and Technology Sarajevo Bosnia and Herzegovina
| | - Hanna Nohynek
- Department of Health Security Finnish Institute for Health and Welfare Helsinki Finland
| | | | | | | | | | | | - James Ransom
- Centers for Disease Control and Prevention Juba South Sudan
| | - Sonal Saxena
- Department of Microbiology Maulana Azad Medical College New Delhi India
| | - Pragya Sharma
- Department of Community Medicine Maulana Azad Medical College New Delhi India
| | - Aswathy Sreedevi
- Department of Community Medicine Amrita Institute of Medical Sciences Kochi Kerala India
| | - Mini Satheesh
- Kerala University of Health Sciences Kerala India
- Government Medical College Thiruvananthapuram Kerala India
| | - K. J. Subhashini
- Centre for Community Medicine All India Institute of Medical Sciences New Delhi India
| | - Beth A. Tippet‐Barr
- U.S. Centers for Disease Control and Prevention Nairobi Kenya
- Nyanja Health Research Institute Salima Malawi
| | - Anuja Usha
- Regional Prevention of Epidemic and Infectious Disease Cell Government of Kerala Kerala India
| | | | | | - Kapil Yadav
- Centre for Community Medicine All India Institute of Medical Sciences New Delhi India
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30
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Roy AK, Chakraborti M, Radhakrishna A, Dwivedi KK, Srivastava MK, Saxena S, Paul S, Khare A, Malaviya DR, Kaushal P. Alien genome mobilization and fixation utilizing an apomixis mediated genome addition (AMGA) strategy in Pennisetum to improve domestication traits of P. squamulatum. Theor Appl Genet 2022; 135:2555-2575. [PMID: 35726065 DOI: 10.1007/s00122-022-04138-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
An approach to release 'frozen' variability in apomictic species using sexuality of another species, eventually its utilization in crop improvement and de-novo domestication of crop wild relatives is presented. Pennisetum squamulatum, a secondary gene pool species of pearl millet (P. glaucum), harbours many desirable traits. However, it was neither utilized to improve pearl millet fodder traits nor improvement of its own domestication traits was attempted, due to the complexities of genomes and apomictic reproduction. To overcome this, we followed an Apomixis Mediated Genome Addition (AMGA) strategy and utilized the contrasting reproductive capacities (sexuality and apomixis) of both the species to access the otherwise un-available variability embedded in P. squamulatum. Segregating population of interspecific hybrids exhibited significant variability and heterosis for desired morphological, agronomical, and nutritional traits. Elite apomictic and perennial hybrids were evaluated in breeding trials, and eventually a novel grass cultivar was released for commercial cultivation in India. The performance of newly developed cultivar was superior to other adapted perennial grasses of arid and semi-arid rangelands. Through AMGA, the sexuality of one species was successfully utilized to 'release' the 'frozen' variability embedded in another species. Subsequently, the hybrids representing desirable trait combinations were again 'fixed' utilizing the apomixis alleles from the male parent in a back-and-forth apomixis-sexual-apomixis selection cycle. This study also demonstrated the potential of AMGA to improve crop relatives through genomes introgression as well as de novo domestication of new crops from wild species.
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Affiliation(s)
- A K Roy
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M Chakraborti
- ICAR - National Rice Research Institute, Cuttack, 753006, India
| | - A Radhakrishna
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - K K Dwivedi
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - M K Srivastava
- ICAR - Indian Institute of Soybean Research, Indore, 452001, India
| | - S Saxena
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - S Paul
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - Aarti Khare
- ICAR - Indian Grassland and Fodder Research Institute, Jhansi, 284003, India
| | - D R Malaviya
- ICAR - Indian Institute of Sugarcane Research, Lucknow, 226002, India
| | - P Kaushal
- ICAR - National Institute of Biotic Stress Management, Raipur, 493225, India.
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Irungbam M, Chitkara A, Singh VK, Sonkar SC, Dubey A, Bansal A, Shrivastava R, Goswami B, Manchanda V, Saxena S, Saxena R, Garg S, Husain F, Talukdar T, Kumar D, Koner BC. Evaluation of Performance of Detection of Immunoglobulin G and Immunoglobulin M Antibody Against Spike Protein of SARS-CoV-2 by a Rapid Kit in a Real-Life Hospital Setting. Front Microbiol 2022; 13:802292. [PMID: 35558113 PMCID: PMC9087894 DOI: 10.3389/fmicb.2022.802292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/26/2022] [Indexed: 12/04/2022] Open
Abstract
Background Antibody testing is often used for serosurveillance of coronavirus disease 2019 (COVID-19). Enzyme-linked immunosorbent assay and chemiluminescence-based antibody tests are quite sensitive and specific for such serological testing. Rapid antibody tests against different antigens are developed and effectively used for this purpose. However, their diagnostic efficiency, especially in real-life hospital setting, needs to be evaluated. Thus, the present study was conducted in a dedicated COVID-19 hospital in New Delhi, India, to evaluate the diagnostic efficacy of a rapid antibody kit against the receptor-binding domain (RBD) of the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods Sixty COVID-19 confirmed cases by reverse transcriptase–polymerase chain reaction (RT-PCR) were recruited and categorized as early, intermediate, and late cases based on the days passed after their first RT-PCR–positive test report, with 20 subjects in each category. Twenty samples from pre-COVID era and 20 RT-PCR–negative collected during the study period were taken as controls. immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against the RBD of the spike (S) protein of SARS-CoV-2 virus were detected by rapid antibody test and compared with the total antibody against the nucleocapsid (N) antigen of SARS-CoV-2 by electrochemiluminescence-based immunoassay (ECLIA). Results The detection of IgM against the RBD of the spike protein by rapid kit was less sensitive and less specific for the diagnosis of SARS-CoV-2 infection. However, diagnostic efficacy of IgG by rapid kit was highly sensitive and specific when compared with the total antibody against N antigen measured by ECLIA. Conclusion It can be concluded that detection of IgM against the RBD of S protein by rapid kit is less effective, but IgG detection can be used as an effective diagnostic tool for SARS-CoV-2 infection in real-life hospital setting.
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Affiliation(s)
- Monica Irungbam
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Anubhuti Chitkara
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Vijay Kumar Singh
- Multidisciplinary Research Unit (MRU), Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Subash Chandra Sonkar
- Multidisciplinary Research Unit (MRU), Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Abhisek Dubey
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Aastha Bansal
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Ritika Shrivastava
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Binita Goswami
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India.,Multidisciplinary Research Unit (MRU), Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Vikas Manchanda
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Ritu Saxena
- Emergency Department, Lok Nayak Jai Prakash Narayan (LNJP) Hospital, New Delhi, India
| | - Sandeep Garg
- Department of Medicine, Lok Nayak Jai Prakash Narayan (LNJP) Hospital, New Delhi, India
| | - Farah Husain
- Department of Anesthesiology, Lok Nayak Jai Prakash Narayan (LNJP) Hospital, New Delhi, India
| | - Tanmay Talukdar
- Department of TB & Chest Diseases/Pulmonary Medicine, Lady Hardinge Medical College (LHMC), New Delhi, India
| | - Dinesh Kumar
- Food Safety and Standards Authority of India, Ministry of Health and Family Welfare (MoHFW), New Delhi, India
| | - Bidhan Chandra Koner
- Department of Biochemistry, Maulana Azad Medical College and Associated Hospitals, New Delhi, India.,Multidisciplinary Research Unit (MRU), Maulana Azad Medical College and Associated Hospitals, New Delhi, India
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Kumar R, Singh M, Sagar T, Bharanidharan , Khurana N, Kumar V, Meher R, Malhotra V, Goel R, Saxena S, Kumar J. Sensitivity of liquid-based cytology in the diagnosis of mucormycosis in COVID-19 treated patients. Cytopathology 2022; 33:454-462. [PMID: 35436358 PMCID: PMC9111708 DOI: 10.1111/cyt.13131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) infection caused by the novel severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is associated with a wide range of disease patterns, ranging from mild to life-threatening pneumonia. COVID-19 can be associated with a suppressed immune response and/or hyperinflammatory state due to cytokine storm. Reduced immunity, combined with steroid usage to prevent cytokine storm along with various pre-existing co morbidities can prove to be a fertile ground for various secondary bacterial and fungal infection, including mucormycosis. Diagnosis of mucor is a challenging task given high negativity rate of various detection methods. While histopathology is considered the gold standard, the acquisition of necessary tissue biopsy specimens requires invasive procedures and is time consuming. METHOD In this study various methods of mucor detection, like conventional cytopathology (CCP), liquid-based cytology (LBC, BD SurepathTM ), potassium hydroxide mount (KOH) preparation, culture and histopathology were analysed. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for various methods. RESULTS This study showed that LBC has sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 72.4%,100%,100% and 38.4% respectively. CONCLUSION This study showed that, liquid-based cytology (LBC) can be a rapid and effective alternative to histopathology in mucor diagnosis.
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Affiliation(s)
- Rabish Kumar
- Department of PathologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Meeta Singh
- Department of PathologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Tanu Sagar
- Department of MicrobiologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Bharanidharan
- Department of PathologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Nita Khurana
- Department of PathologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Vikas Kumar
- Department of OtorhinolaryngologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Ravi Meher
- Department of OtorhinolaryngologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Vikas Malhotra
- Department of OtorhinolaryngologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Ruchi Goel
- Department of OphthalmologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Sonal Saxena
- Department of MicrobiologyMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
| | - Jyoti Kumar
- Department of RadiodiagnosisMaulana Azad Medical College and Associated HospitalsNew DelhiIndia
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Saxena S, Pirracchio R, Krombach JW. Beyond miracles and heroes: time for an anaesthesia checklist mandate. Anaesthesia 2022; 77:735-738. [PMID: 35343589 DOI: 10.1111/anae.15724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022]
Affiliation(s)
- S Saxena
- Department of Anaesthesia, CHU de Charleroi, Université Libre de Bruxelles, Belgium
| | - R Pirracchio
- Department of Anaesthesia and Peri-operative Care, Zuckerberg San Francisco General Hospital and Trauma Centre, University of California San Francisco, CA, USA
| | - J W Krombach
- Department of Anaesthesiology, Medical College of Wisconsin, Milwaukee, WI, USA
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Singh V, Shrivastava S, Kumar Singh S, Kumar A, Saxena S. Accelerating the discovery of antifungal peptides using deep temporal convolutional networks. Brief Bioinform 2022; 23:6526725. [DOI: 10.1093/bib/bbac008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/27/2021] [Accepted: 01/06/2022] [Indexed: 02/02/2023] Open
Abstract
Abstract
The application of machine intelligence in biological sciences has led to the development of several automated tools, thus enabling rapid drug discovery. Adding to this development is the ongoing COVID-19 pandemic, due to which researchers working in the field of artificial intelligence have acquired an active interest in finding machine learning-guided solutions for diseases like mucormycosis, which has emerged as an important post-COVID-19 fungal complication, especially in immunocompromised patients. On these lines, we have proposed a temporal convolutional network-based binary classification approach to discover new antifungal molecules in the proteome of plants and animals to accelerate the development of antifungal medications. Although these biomolecules, known as antifungal peptides (AFPs), are part of an organism’s intrinsic host defense mechanism, their identification and discovery by traditional biochemical procedures is arduous. Also, the absence of a large dataset on AFPs is also a considerable impediment in building a robust automated classifier. To this end, we have employed the transfer learning technique to pre-train our model on antibacterial peptides. Subsequently, we have built a classifier that predicts AFPs with accuracy and precision of 94%. Our classifier outperforms several state-of-the-art models by a considerable margin. The results of its performance were proven as statistically significant using the Kruskal–Wallis H test, followed by a post hoc analysis performed using the Tukey honestly significant difference (HSD) test. Furthermore, we identified potent AFPs in representative animal (Histatin) and plant (Snakin) proteins using our model. We also built and deployed a web app that is freely available at https://tcn-afppred.anvil.app/ for the identification of AFPs in protein sequences.
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Affiliation(s)
- Vishakha Singh
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Sameer Shrivastava
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
| | - Sanjay Kumar Singh
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Abhinav Kumar
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Sonal Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
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Meher R, Wadhwa V, Kumar V, Shisha Phanbuh D, Sharma R, Singh I, Rathore PK, Goel R, Arora R, Garg S, Kumar S, Kumar J, Agarwal M, Singh M, Khurana N, Sagar T, Manchanda V, Saxena S. COVID associated mucormycosis: A preliminary study from a dedicated COVID Hospital in Delhi. Am J Otolaryngol 2022; 43:103220. [PMID: 34547717 PMCID: PMC8432976 DOI: 10.1016/j.amjoto.2021.103220] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/05/2021] [Indexed: 11/28/2022]
Abstract
Background It is an incontrovertible fact that the Rhino Orbital Cerebral Mucormycosis (ROCM) upsurge is being seen in the context of COVID-19 in India. Briefly presented is evidence that in patients with uncontrolled diabetes, a dysfunctional immune system due to SARS-COV-2 and injudicious use of corticosteroids may be largely responsible for this malady. Objective To find the possible impact of COVID 19 infection and various co-morbidities on occurrence of ROCM and demonstrate the outcome based on medical and surgical interventions. Methodology. Prospective longitudinal study included patients diagnosed with acute invasive fungal rhinosinusitis after a recent COVID-19 infection. Diagnostic nasal endoscopy (DNE) was performed on each patient and swabs were taken and sent for fungal KOH staining and microscopy. Medical management included Injection Liposomal Amphotericin B, Posaconazole and Voriconazole. Surgical treatment was restricted to patients with RT PCR negative results for COVID-19. Endoscopic, open, and combined approaches were utilized to eradicate infection. Follow-up for survived patients was maintained regularly for the first postoperative month. Results Out of total 131 patients, 111 patients had prior history of SARS COVID 19 infection, confirmed with a positive RT-PCR report and the rest 20 patients had no such history. Steroids were received as a part of treatment in 67 patients infected with COVID 19. Among 131 patients, 124 recovered, 1 worsened and 6 died. Out of 101 known diabetics, 98 recovered and 3 had fatal outcomes. 7 patients with previous history of COVID infection did not have any evidence of Diabetes mellitus, steroid intake or any other comorbidity. Conclusion It can be concluded that ROCM upsurge seen in the context of COVID-19 in India was mainly seen in patients with uncontrolled diabetes, a dysfunctional immune system due to SARS-COV-2 infection and injudicious use of corticosteroids.
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Affiliation(s)
- Ravi Meher
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Vikram Wadhwa
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Vikas Kumar
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India.
| | | | - Raman Sharma
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Ishwar Singh
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - P K Rathore
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Ruchi Goel
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Ritu Arora
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Sandeep Garg
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Suresh Kumar
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Jyoti Kumar
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Munisha Agarwal
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Meeta Singh
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Nita Khurana
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Tanu Sagar
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Vikas Manchanda
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
| | - Sonal Saxena
- Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India
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Sharma P, Chawla R, Basu S, Saxena S, Mariam W, Bharti PK, Rao S, Tanwar N, Rahman A, Ahmad M. Seroprevalence of SARS-CoV-2 and Risk Assessment Among Healthcare Workers at a Dedicated Tertiary Care COVID-19 Hospital in Delhi, India: A Cohort Study. Cureus 2021; 13:e20805. [PMID: 35145765 PMCID: PMC8810309 DOI: 10.7759/cureus.20805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2021] [Indexed: 11/05/2022] Open
Abstract
Background Healthcare workers (HCWs) have a substantially higher risk of Covid-19 infection but there is a paucity of information on the risk factors of disease transmission in high-burden real-world settings. The study objective was to determine the seroprevalence of SARS-CoV-2 among healthcare workers in a high-burden Covid-19 setting and to estimate the incidence and identify the risk factors of infection. Methods This was a prospective observational cohort study amongst doctors and nurses working at a dedicated Covid-19 tertiary care government hospital in Delhi, India. A baseline blood sample (2-3ml) was collected from all the participants to test for the presence of total SARS-CoV-2 antibodies. The HCWs that were seronegative (non-reactive) at baseline were followed-up for ≥21≤28 days with the collection of a second blood sample to assess for the incidence of SARS-CoV-2 infection. Results A total of 321 (51.3%, 95% C.I 47.4, 55.3) HCWs were detected with SARS-CoV-2 antibodies on baseline examination. The seroprevalence, when adjusted for assay characteristics, was 54.5% (95% C.I 50.3, 58.6). On bivariate analysis, SARS-CoV-2 antibody positivity lacked statistically significant association with either age, sex, occupation, cumulative duty duration, and smoking status. The incidence of seroconversion in the baseline seronegative cohort on follow-up after 21-28 days was observed in 35 (14.9%) HCWs (n=245). Furthermore, the self-reported adherence to infection prevention and control measures did not show a statistically significant association with antibody positivity in the HCWs, neither at baseline nor on follow-up. Conclusions The high risk of SARS-CoV-2 transmission in HCWs may be substantially reduced by adherence to Infection Prevention Control (IPC) and protective measures.
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Boomadevi S, Kundu A, Anthony SP, Pandiyan K, Sastikumar D, Saxena S, Bagchi S, Chakera J. Investigations on synthesis, growth, crystal structure, thermal, Dielectric and Terahertz Transmission properties of Organic NLO Crystal : (2-(2-hydroxy-3-methoxystyryl)-1-methylquinolinium-4-methylbenzenesulfonate (O-HMQ). J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.131099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Sharma R, Shrivastava S, Singh SK, Kumar A, Singh AK, Saxena S. Deep-AVPpred: Artificial intelligence driven discovery of peptide drugs for viral infections. IEEE J Biomed Health Inform 2021; 26:5067-5074. [PMID: 34822333 DOI: 10.1109/jbhi.2021.3130825] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Rapid increase in viral outbreaks has resulted in the spread of viral diseases in diverse species and across geographical boundaries. The zoonotic viral diseases have greatly affected the well-being of humans, and the COVID-19 pandemic is a burning example. The existing antivirals have low efficacy, severe side effects, high toxicity, and limited market availability. As a result, natural substances have been tested for antiviral activity. The host defense molecules like antiviral peptides (AVPs) are present in plants and animals and protect them from invading viruses. However, obtaining AVPs from natural sources for preparing synthetic peptide drugs is expensive and time-consuming. As a result, an in-silico model is required for identifying new AVPs. We proposed Deep-AVPpred, a deep learning classifier for discovering AVPs in protein sequences, which utilises the concept of transfer learning with a deep learning algorithm. The proposed classifier outperformed state-of-the-art classifiers and achieved approximately 94% and 93% precision on validation and test sets, respectively. The high precision indicates that Deep-AVPpred can be used to propose new AVPs for synthesis and experimentation. By utilising Deep-AVPpred, we identified novel AVPs in human interferons- family proteins. These AVPs can be chemically synthesised and experimentally verified for their antiviral activity against different viruses. The Deep-AVPpred is deployed as a web server and is made freely available at https://deep-avppred.anvil.app, which can be utilised to predict novel AVPs for developing antiviral compounds for use in human and veterinary medicine.
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Singh V, Shrivastava S, Kumar Singh S, Kumar A, Saxena S. StaBle-ABPpred: a stacked ensemble predictor based on biLSTM and attention mechanism for accelerated discovery of antibacterial peptides. Brief Bioinform 2021; 23:6423526. [PMID: 34750606 DOI: 10.1093/bib/bbab439] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/06/2021] [Accepted: 09/24/2021] [Indexed: 01/29/2023] Open
Abstract
Due to the rapid emergence of multi-drug resistant (MDR) bacteria, existing antibiotics are becoming ineffective. So, researchers are looking for alternatives in the form of antibacterial peptides (ABPs) based medicines. The discovery of novel ABPs using wet-lab experiments is time-consuming and expensive. Many machine learning models have been proposed to search for new ABPs, but there is still scope to develop a robust model that has high accuracy and precision. In this work, we present StaBle-ABPpred, a stacked ensemble technique-based deep learning classifier that uses bidirectional long-short term memory (biLSTM) and attention mechanism at base-level and an ensemble of random forest, gradient boosting and logistic regression at meta-level to classify peptides as antibacterial or otherwise. The performance of our model has been compared with several state-of-the-art classifiers, and results were subjected to analysis of variance (ANOVA) test and its post hoc analysis, which proves that our model performs better than existing classifiers. Furthermore, a web app has been developed and deployed at https://stable-abppred.anvil.app to identify novel ABPs in protein sequences. Using this app, we identified novel ABPs in all the proteins of the Streptococcus phage T12 genome. These ABPs have shown amino acid similarities with experimentally tested antimicrobial peptides (AMPs) of other organisms. Hence, they could be chemically synthesized and experimentally validated for their activity against different bacteria. The model and app developed in this work can be further utilized to explore the protein diversity for identifying novel ABPs with broad-spectrum activity, especially against MDR bacterial pathogens.
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Affiliation(s)
- Vishakha Singh
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Sameer Shrivastava
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
| | - Sanjay Kumar Singh
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Abhinav Kumar
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Sonal Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
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Goldstein M, Saxena S. M285 EXERCISE-INDUCED LARYNGOPHARYNGEAL REFLUX (EILPR). Ann Allergy Asthma Immunol 2021. [DOI: 10.1016/j.anai.2021.08.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Venkatraman T, Honeyford K, van Sluijs EMF, Costelloe C, Saxena S. Are children at schools registered to The Daily Mile™ more physically active? Eur J Public Health 2021. [DOI: 10.1093/eurpub/ckab164.214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The Daily Mile (TDM) is among the most popular school-based running programmes recommended globally by governments and the WHO to meet the shortfalls in children's physical activity. In England, it has been adopted by 1 in 5 primary schools. However, its impact on children's physical activity has not been assessed at scale. We aimed to compare a)minutes (mins) of moderate to vigorous physical activity (MVPA) in and outside school hours and b)meeting physical activity guidelines in primary school children in England, comparing those in schools registered with TDM with those that were not.
Methods
This was a cross-sectional study. We used self-reported data of 49,561 English primary school children(5-11 years) from the Active Lives Children and Young People Survey and TDM registration data of their school. We compared mins of MVPA in and outside school hours between children in TDM-registered and non-registered schools using a multilevel zero-inflated negative binomial model; and the differences in the likelihood of meeting physical activity guidelines based on TDM registration with a multilevel logistic regression model. All models included a random effect for school and adjusted for potential confounders.
Results
Children attending TDM-registered schools reported an extra 36 mins of MVPA a week overall, including 10 additional mins (95%CI:3,16) MVPA/week during school hours and 26 additional (95%CI:4,44) mins MVPA/week outside school hours. Children in TDM-registered schools were 6% more likely to meet physical activity guidelines compared to those who were not(RR:1.06 (95%CI:1.02,1.11)).
Conclusions
Children in primary schools registered to TDM report more physical activity that is not compensated for outside school hours. However, the absolute differences fall considerably short of international guidelines across the whole child population. Therefore, a whole school and systems-based approach is required, embedding school-based running programmes.
Key messages
Children in schools registered to TDM report more MVPA overall, inside, and outside school hours; suggesting no compensation of activity in those who are registered. TDM is a potential solution to increase children’s physical activity during the school day.
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Affiliation(s)
- T Venkatraman
- Department of Primary Care and Public Health, Imperial College London, London, UK
| | - K Honeyford
- Department of Primary Care and Public Health, Imperial College London, London, UK
| | - EMF van Sluijs
- Centre for Diet and Activity Research, MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - C Costelloe
- Department of Primary Care and Public Health, Imperial College London, London, UK
| | - S Saxena
- Department of Primary Care and Public Health, Imperial College London, London, UK
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Creese H, Saxena S, Nicholls D, Pascual-Sanchez A, Hargreaves D. Internalized weight bias in the relationship between mental health and obesity in UK adolescents. Eur J Public Health 2021. [DOI: 10.1093/eurpub/ckab165.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
It is crucial to promote mental and physical health during adolescence to protect against lifetime risks of mental health problems and obesity. Internalized weight bias (self-directed stigmatizing attitudes about perceived weight status) and bullying are implicated as potential mechanisms in the relationship between mental health and obesity in adolescence. We examined internalized weight bias and bullying as potential mediators of the relationship between mental health and weight status across adolescence in the United Kingdom (UK).
Methods
We analysed data on 8,688 adolescents from the UK Millennium Cohort Study. Weight status was defined using sex and age specific International Obesity Taskforce cut points for body-mass index (not overweight/obese; overweight; obese) at 11 and 17 years. Mental health was defined using parental reported emotional (anxiety and depression), and externalizing (aggression and impulsivity) symptoms at 11 and 17 years (low; moderate; high). Self-reported measures of internalized weight bias captured via body-dissatisfaction and self-esteem and bullying at 14 years were tested as mediators. We used Generalized Structural Equation Models to examine longitudinal pathways between weight status and mental health across 11 and 17 years, whilst accounting for concurrent associations and potential confounders.
Results
Adolescents with high emotional (relative risk (RR) 1.98, 95% CI 1.28 to 3.07) or externalizing symptoms (RR 2.07, 95% CI 1.23 to 3.48) at 11 years were twice as likely to be obese at 17 years compared with those who had low symptoms. The impact of emotional and externalizing symptoms on weight status was found to be partially attributable to internalized weight bias, but not bullying, with significant mediation for body-dissatisfaction and low self-esteem.
Conclusions
Internalized weight bias partially explains the relationship between mental health and weight status across adolescence.
Key messages
There is a need for a holistic, early prevention strategy to focus on reducing weight stigma to encourage healthy mental and physical development of children. The relationship between mental health and weight status across adolescence is partly attributable to internalized weight bias.
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Affiliation(s)
- H Creese
- Department of Primary Care and Public Health, Imperial College London, London, UK
| | - S Saxena
- Department of Primary Care and Public Health, Imperial College London, London, UK
| | - D Nicholls
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - D Hargreaves
- Department of Primary Care and Public Health, Imperial College London, London, UK
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43
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Ram B, Foley K, van Sluijs E, Hargreaves D, Viner R, Saxena S. A core outcome set for school-based physical activity interventions: an international consensus. Eur J Public Health 2021. [DOI: 10.1093/eurpub/ckab164.751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Studies of school-based physical activity interventions vary in the outcomes they measure. This prevents comparisons of results to establish impacts. We aimed to develop a core outcome set agreed by key stakeholders for future studies of school-based physical activity interventions.
Methods
We used a modified-Delphi consensus method. First, we conducted a systematic review to identify outcomes measured in relevant studies and listed these in a Delphi survey. Next, we recruited key stakeholders to complete 2 survey rounds: Round 1 was to rate each outcome from ‘not important' to ‘critical', and Round 2 was to re-rate the outcomes based on feedback from Round 1. Outcomes rated ‘critical' by 70% of stakeholders (i.e., reaching consensus) were highlighted. Then, using the full list of outcomes, we conducted a children's workshop to include their views. Finally, we held a stakeholder meeting to discuss results and agree consensus.
Results
We identified 50 outcomes from the systematic review. Sixty-five stakeholders (16 educators, 13 health professionals, 12 parents, 24 researchers) representing 9 countries completed both survey rounds; 13/50 outcomes reached consensus. Children (n = 16) identified 8 outcomes of importance; 3 were consistent with the survey results. Stakeholders attending the meeting (n = 13) reached consensus on 14 outcomes to be included in the core outcome set: fitness, physical activity intensity, energy, sleep, diet, happiness, stress, depression, anxiety, wellbeing, self-esteem, enjoyment, concentration, and focus. These core outcomes were reviewed and agreed by all 65 stakeholders.
Conclusions
Our core outcome set agreed by international stakeholders includes physical and mental health, and cognitive function. We recommend its use in future studies of school-based physical activity interventions. Findings from future studies can be compared and combined which will be relevant to public health policy makers and educators.
Key messages
School-based physical activity interventions should measure physical and mental health, and cognitive function. Wide use of this core outcome set will enable findings to be compared and combined.
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Affiliation(s)
- B Ram
- Primary Care and Public Health, Imperial College London, London, UK
| | - K Foley
- Primary Care and Public Health, Imperial College London, London, UK
| | - E van Sluijs
- Centre for Diet & Activity Research & MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - D Hargreaves
- Primary Care and Public Health, Imperial College London, London, UK
- Department for Education, London, UK
| | - R Viner
- Institute for Child Health, University College London, London, UK
| | - S Saxena
- Primary Care and Public Health, Imperial College London, London, UK
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44
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Sharma R, Shrivastava S, Kumar Singh S, Kumar A, Saxena S, Kumar Singh R. Deep-AFPpred: identifying novel antifungal peptides using pretrained embeddings from seq2vec with 1DCNN-BiLSTM. Brief Bioinform 2021; 23:6404058. [PMID: 34670278 DOI: 10.1093/bib/bbab422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/12/2021] [Indexed: 01/04/2023] Open
Abstract
Fungal infections or mycosis cause a wide range of diseases in humans and animals. The incidences of community acquired; nosocomial fungal infections have increased dramatically after the emergence of COVID-19 pandemic. The increase in number of patients with immunodeficiency / immunosuppression related diseases, resistance to existing antifungal compounds and availability of limited therapeutic options has triggered the search for alternative antifungal molecules. In this direction, antifungal peptides (AFPs) have received a lot of interest as an alternative to currently available antifungal drugs. Although the AFPs are produced by diverse population of living organisms, identifying effective AFPs from natural sources is time-consuming and expensive. Therefore, there is a need to develop a robust in silico model capable of identifying novel AFPs in protein sequences. In this paper, we propose Deep-AFPpred, a deep learning classifier that can identify AFPs in protein sequences. We developed Deep-AFPpred using the concept of transfer learning with 1DCNN-BiLSTM deep learning algorithm. The findings reveal that Deep-AFPpred beats other state-of-the-art AFP classifiers by a wide margin and achieved approximately 96% and 94% precision on validation and test data, respectively. Based on the proposed approach, an online prediction server is created and made publicly available at https://afppred.anvil.app/. Using this server, one can identify novel AFPs in protein sequences and the results are provided as a report that includes predicted peptides, their physicochemical properties and motifs. By utilizing this model, we identified AFPs in different proteins, which can be chemically synthesized in lab and experimentally validated for their antifungal activity.
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Affiliation(s)
- Ritesh Sharma
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Sameer Shrivastava
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
| | - Sanjay Kumar Singh
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Abhinav Kumar
- Department of Computer Science and Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Sonal Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
| | - Raj Kumar Singh
- Former Director & Vice Chancellor, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
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45
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Ram B, Chalkley A, van Sluijs E, Hargreaves D, Viner R, Saxena S. Implementation of The Daily Mile™: survey of primary schools in Greater London. Eur J Public Health 2021. [DOI: 10.1093/eurpub/ckab164.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The Daily Mile™ is a free school-based active mile intervention. Its main features include that children run or jog for 15 minutes at least 3 times a week (3x/wk) during school hours. The Daily Mile Foundation recommends 10 principles for successful implementation. These are it is (1) quick (15 minutes), (2) fun, (3) whole school participates, (4) it takes place in all weathers, (5) 3x/wk in addition to curricular lessons (not during PE, breaks, before/after school), (6) ideally in the school playground, (7) safe, (8) simple (no equipment), (9) children go at their own pace and (10) no change of clothes or shoes is needed. The aim of this study was to identify how many Greater London primary schools adopting The Daily Mile implement its 10 principles.
Methods
In September 2020, we sent all state-funded primary schools (n = 1721) in every Greater London borough (n = 32) a survey to find out if and how they implemented The Daily Mile.
Results
By June 2021, 368 (21%) schools responded to our survey (at least one from every London borough). Of these, 195 (53%) schools adopted The Daily Mile of which only 7 (4%) reported implementing all 10 principles; a median 7 (IQR: 6,8) principles were reported implemented. Whole school participation was reported by 93 (48%) Daily Mile schools, 104 (53%) reported implementing The Daily Mile for 15 minutes, 127 (65%) implemented it at least 3x/wk, and 149 (76%) schools reported that the children ran or jogged during The Daily Mile. A large proportion of schools reported implementing The Daily Mile in the school playground and that it was done simply (both n = 171, 88%), but only 85 (44%) schools reported implementing it during lessons.
Conclusions
Daily Mile schools in Greater London implement 7/10 principles on average. Whether implementing all the principles limits the success of its desired effect is unclear. Studies assessing effects of The Daily Mile should consider its implementation when reporting results.
Key messages
Of The Daily Mile’s 10 principles, an average of 7 are implemented in London schools. Studies examining The Daily Mile should consider implementation which may impact its desired effect.
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Affiliation(s)
- B Ram
- Primary Care and Public Health, Imperial College London, London, UK
| | - A Chalkley
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - E van Sluijs
- Centre for Diet & Activity Research & MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - D Hargreaves
- Primary Care and Public Health, Imperial College London, London, UK
- Department for Education, London, UK
| | - R Viner
- Institute of Child Health, University College London, London, UK
| | - S Saxena
- Primary Care and Public Health, Imperial College London, London, UK
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46
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Saxena S, Choudhury S, Maroju PA, Anne A, Kumar L, Mohan KN. Dysregulation of schizophrenia-associated genes and genome-wide hypomethylation in neurons overexpressing DNMT1. Epigenomics 2021; 13:1539-1555. [PMID: 34647491 DOI: 10.2217/epi-2021-0133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To study the effects of DNMT1 overexpression on transcript levels of genes dysregulated in schizophrenia and on genome-wide methylation patterns. Materials & methods: Transcriptome and DNA methylome comparisons were made between R1 (wild-type) and Dnmt1tet/tet mouse embryonic stem cells and neurons overexpressing DNMT1. Genes dysregulated in both Dnmt1tet/tet cells and schizophrenia patients were studied further. Results & conclusions: About 50% of dysregulated genes in patients also showed altered transcript levels in Tet/Tet neurons in a DNA methylation-independent manner. These neurons unexpectedly showed genome-wide hypomethylation, increased transcript levels of Tet1 and Apobec 1-3 genes and increased activity and copy number of LINE-1 elements. The observed similarities between Tet/Tet neurons and schizophrenia brain samples reinforce DNMT1 overexpression as a risk factor.
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Affiliation(s)
- Sonal Saxena
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Sumana Choudhury
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Pranay Amruth Maroju
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Anuhya Anne
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Lov Kumar
- Computer Science & Information Systems, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
| | - Kommu Naga Mohan
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India.,Centre for Human Disease Research, Birla Institute of Technology & Science, Pilani, Hyderabad, 500078, India
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Gautam G, Gogoi S, Saxena S, Kaur R, Dhakad MS. Nitrofurantoin Susceptibility Pattern in Gram-Negative Urinary Isolates: In Need of Increased Vigilance. J Lab Physicians 2021; 13:252-256. [PMID: 34602790 PMCID: PMC8478500 DOI: 10.1055/s-0041-1731106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Nitrofurantoin is the first-line drug in the treatment of uncomplicated urinary tract infections (UTIs) and its use has increased exponentially in recent years. Objectives
This study aims to determine the susceptibility pattern of nitrofurantoin in gram-negative urinary isolates and to evaluate their bacteriological and epidemiological profile along with co-existing resistance to other important urinary antimicrobials.
Material and Methods
This was a retrospective study conducted in a tertiary care hospital in New Delhi in which 500 gram-negative bacterial urinary isolates were evaluated. Records of antimicrobial susceptibility were reviewed from July to September 2019. Antimicrobial susceptibility was performed using the Kirby–Bauer disk diffusion method on Mueller Hinton agar and interpreted using CLSI 2019. Test for extended spectrum β-lactamase (ESBL) producers was done using double disk approximation test.
Statistical Analysis
Data analysis was performed using the SPSS windows version 25.0 software.
Results
Out of total 500 isolates, 20.17% (94) isolates were resistant (R) to nitrofurantoin and 9.01% (42) were found to be intermediate (I). Highest resistance was seen in
Klebsiella
sp. (44.61%) and
Escherichia coli
(8.12%). About 28.82% of the I/R isolates were of the pediatrics age group and most of the isolates belonged to females (64.69%). High resistance was also seen against ampicillin (92.30%), cefazolin (88.46%), ceftazidime (73.0%), and fluoroquinolones (65.38%). Carbapenemase co-resistance was seen in 57.15% isolates whereas ESBL production was seen in 30.76% of
E. coli
and 12.06% of
Klebsiella
sp.
Conclusion
Increase in multidrug resistance uropathogens along with a near absence of novel oral antibiotics has led to increased consumption of nitrofurantoin since its resistance has increased.
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Affiliation(s)
- Garima Gautam
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Sanjib Gogoi
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Sonal Saxena
- Department of Microbiology, Maulana Azad Medical College and Associated Hospitals, New Delhi, India
| | - Ravinder Kaur
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
| | - Megh Singh Dhakad
- Department of Microbiology, Lady Hardinge Medical College and Associated Hospitals, New Delhi, India
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Verma IK, Randhawa V, Saxena S, Andley M. Susceptibility profile of bacteria isolated from cases having health care acquired catheter -associated urinary tract infection. Indian J Med Microbiol 2021. [DOI: 10.1016/j.ijmmb.2021.08.271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Yadav A, Manchanda V, Tuteja S, Puri D, Saxena S. Invention is the need of the hour: A unique Data Accumulation and Analysis Platform for covid reporting. Indian J Med Microbiol 2021. [DOI: 10.1016/j.ijmmb.2021.08.200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Puri D, Manchanda V, Saxena S, Garg S. Mortality review of COVID-19 patients: An experience from the largest dedicated COVID hospital in Delhi. Indian J Med Microbiol 2021. [PMCID: PMC8594420 DOI: 10.1016/j.ijmmb.2021.08.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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