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Parkins MD, Lee BE, Acosta N, Bautista M, Hubert CRJ, Hrudey SE, Frankowski K, Pang XL. Wastewater-based surveillance as a tool for public health action: SARS-CoV-2 and beyond. Clin Microbiol Rev 2024; 37:e0010322. [PMID: 38095438 PMCID: PMC10938902 DOI: 10.1128/cmr.00103-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2024] Open
Abstract
Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.
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Affiliation(s)
- Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- O’Brien Institute of Public Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Bonita E. Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nicole Acosta
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria Bautista
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Casey R. J. Hubert
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Steve E. Hrudey
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin Frankowski
- Advancing Canadian Water Assets, University of Calgary, Calgary, Alberta, Canada
| | - Xiao-Li Pang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Provincial Health Laboratory, Alberta Health Services, Calgary, Alberta, Canada
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Yu X, Wang F, Ren R, Dong L, Xue Y, Zhao L, Jia J, Huang H. Xpert MTB/RIF Ultra Assay Using Stool: an Effective Solution for Bacilli Identification from Adult Pulmonary Tuberculosis Suspects without Expectorated Sputum. Microbiol Spectr 2023; 11:e0126523. [PMID: 37378554 PMCID: PMC10434112 DOI: 10.1128/spectrum.01265-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
This study evaluated the diagnostic performance of stool-based Xpert MTB/RIF Ultra assay (Xpert-Ultra, Cepheid, USA) against other tests using respiratory tract specimens (RTS) and stool for diagnosing adult pulmonary tuberculosis. A prospective study on patients with presumptive pulmonary tuberculosis was conducted in Beijing Chest Hospital from June to November 2021. The smear test, MGIT960 liquid culture, and Xpert MTB/RIF (Xpert, Cepheid, USA) were performed simultaneously on RTS, and smear, culture Xpert, and Xpert-Ultra were performed simultaneously using stool. Patients were grouped based on the outcomes of RTS examination and other tests. In total, 130 eligible patients were enrolled that included 96 pulmonary tuberculosis and 34 non-TB patients. The sensitivity of smear, culture, Xpert, and Xpert-Ultra using stool was 10.96%, 23.28%, 60.27%, and 79.45%, respectively. The specificities of Xpert and Xpert-Ultra using RTS and stool were all 100% (34/34). Notably, all five confirmed cases detected by bronchoalveolar lavage fluid (BALF) examination yielded Xpert-Ultra positive outcomes with the stool specimens. Xpert-Ultra assay on stool sample harbors comparable sensitivity with Xpert on RTS. Thus, the Xpert-Ultra testing on stool specimens could be a very promising and practical strategy to improve pulmonary tuberculosis (PTB) diagnosis, especially among patients who could not expectorate sputum. IMPORTANCE This study is aimed at assessing the value of Xpert MTB/RIF Ultra (Xpert-Ultra) in PTB on stool in adult in low HIV settings and Xpert-Ultra assay on stool sample harboring comparable sensitivity with Xpert MTB/RIF on respiratory tract specimens. Although the yield in stool samples by Xpert-Ultra is lower than RTS, it may be useful in detecting disease in presumptive TB patients who cannot expectorate sputum and are not open to BALF collection. In addition, Xpert-Ultra with a "trace call" on stool in adult was highly supportive of PTB.
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Affiliation(s)
- Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
| | - Fen Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
| | - Ruyan Ren
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
| | - Lingling Dong
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
| | - Yi Xue
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
| | - Liping Zhao
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
| | - Junnan Jia
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, Beijing, China
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Holcomb DA, Monteiro V, Capone D, António V, Chiluvane M, Cumbane V, Ismael N, Knee J, Kowalsky E, Lai A, Linden Y, Mataveia E, Nala R, Rao G, Ribeiro J, Cumming O, Viegas E, Brown J. Long-term impacts of an urban sanitation intervention on enteric pathogens in children in Maputo city, Mozambique: study protocol for a cross-sectional follow-up to the Maputo Sanitation (MapSan) trial 5 years postintervention. BMJ Open 2023; 13:e067941. [PMID: 37290945 PMCID: PMC10254709 DOI: 10.1136/bmjopen-2022-067941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
INTRODUCTION We previously assessed the effect of an onsite sanitation intervention in informal neighbourhoods of urban Maputo, Mozambique on enteric pathogen detection in children after 2 years of follow-up (Maputo Sanitation (MapSan) trial, ClinicalTrials.gov: NCT02362932). We found significant reductions in Shigella and Trichuris prevalence but only among children born after the intervention was delivered. In this study, we assess the health impacts of the sanitation intervention after 5 years among children born into study households postintervention. METHODS AND ANALYSIS We are conducting a cross-sectional household study of enteric pathogen detection in child stool and the environment at compounds (household clusters sharing sanitation and outdoor living space) that received the pour-flush toilet and septic tank intervention at least 5 years prior or meet the original criteria for trial control sites. We are enrolling at least 400 children (ages 29 days to 60 months) in each treatment arm. Our primary outcome is the prevalence of 22 bacterial, protozoan, and soil transmitted helminth enteric pathogens in child stool using the pooled prevalence ratio across the outcome set to assess the overall intervention effect. Secondary outcomes include the individual pathogen detection prevalence and gene copy density of 27 enteric pathogens (including viruses); mean height-for-age, weight-for-age, and weight-for-height z-scores; prevalence of stunting, underweight, and wasting; and the 7-day period prevalence of caregiver-reported diarrhoea. All analyses are adjusted for prespecified covariates and examined for effect measure modification by age. Environmental samples from study households and the public domain are assessed for pathogens and faecal indicators to explore environmental exposures and monitor disease transmission. ETHICS AND DISSEMINATION Study protocols have been reviewed and approved by human subjects review boards at the Ministry of Health, Republic of Mozambique and the University of North Carolina at Chapel Hill. Deidentified study data will be deposited at https://osf.io/e7pvk/. TRIAL REGISTRATION NUMBER ISRCTN86084138.
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Affiliation(s)
- David A Holcomb
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Vanessa Monteiro
- Centro de Investigação e Treino em Saúde da Polana Caniço, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Drew Capone
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, Indiana, USA
| | - Virgílio António
- Division of Biotechnology and Genetics, Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Márcia Chiluvane
- Centro de Investigação e Treino em Saúde da Polana Caniço, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Victória Cumbane
- Centro de Investigação e Treino em Saúde da Polana Caniço, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Nália Ismael
- Division of Biotechnology and Genetics, Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Jackie Knee
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Erin Kowalsky
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Amanda Lai
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Yarrow Linden
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Elly Mataveia
- Centro de Investigação e Treino em Saúde da Polana Caniço, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Rassul Nala
- Division of Parasitology, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jorge Ribeiro
- Centro de Investigação e Treino em Saúde da Polana Caniço, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Edna Viegas
- Centro de Investigação e Treino em Saúde da Polana Caniço, Instituto Nacional de Saúde, Maputo, Mozambique
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
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Sultana S, Afrin S, Hasan M, Ansar A, Saif-Ur-Rahman KM. Stool specimen for diagnosis of pulmonary tuberculosis in adults: a systematic review. BMJ Open 2023; 13:e062135. [PMID: 37105702 PMCID: PMC10151869 DOI: 10.1136/bmjopen-2022-062135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
OBJECTIVE To assess the diagnostic accuracy of stool specimens to diagnose pulmonary tuberculosis (PTB) in adults. DESIGN Systematic review. DATA SOURCES MEDLINE (Ovid), Embase (Ovid), Web of Science and the Cochrane database were searched from inception to 9 March 2023-10 March 2023 using a comprehensive search strategy; reference lists of selected articles and relevant review articles were manually searched. ELIGIBILITY CRITERIA FOR SELECTING STUDIES Studies in English reporting diagnostic performance of stool specimens against respiratory specimens using mycobacterial culture or smear microscopy or Xpert assay to diagnose PTB in adults were eligible for this systematic review. DATA EXTRACTION AND SYNTHESIS Two reviewers independently screened the retrieved citations and extracted data. The risk of bias and applicability of results were assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Narrative data synthesis was performed. RESULTS A total of 1658 citations were screened, and 28 full-text articles were assessed. Nine studies met the inclusion criteria. The reported sensitivity and specificity of stool culture varied between 21.4% and 63.9%, and 61.5% and 100%, respectively. In stool smear microscopy, sensitivities and specificities ranged from 12.1% to 53.9%, and from 79.5% to 100%, respectively. The reported sensitivities of PCR assays, including Xpert assays, ranged from 69.7% to 100%, with specificities ranging from 69.8% to 100%. Most of the studies had a low risk of bias and a low applicability concern in all domains. CONCLUSION This systematic review could not conclude on the diagnostic accuracy of stool specimens for PTB diagnosis in adults. Further studies are required to evaluate the accuracy of stool specimens in adults to enable meta-analyses in updates of this review as well as other systematic reviews. PROSPERO REGISTRATION NUMBER CRD42021245203.
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Affiliation(s)
| | - Sadia Afrin
- Health Systems and Population Studies Division, ICDDRB, Dhaka, Bangladesh
| | | | - Adnan Ansar
- School of Nursing and Midwifery, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria, Australia
| | - K M Saif-Ur-Rahman
- Health Systems and Population Studies Division, ICDDRB, Dhaka, Bangladesh
- Evidence Synthesis Ireland and Cochrane Ireland, University of Galway, Galway, Ireland
- College of Medicine, Nursing and Health Sciences, University of Galway, Galway, Ireland
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Li S, Chen W, Feng M, Liu Y, Wang F. Drug Resistance and Molecular Characteristics of Mycobacterium tuberculosis: A Single Center Experience. J Pers Med 2022; 12:jpm12122088. [PMID: 36556308 PMCID: PMC9783070 DOI: 10.3390/jpm12122088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/11/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
In recent years, the incidence of tuberculosis (TB) and mortality caused by the disease have been decreasing. However, the number of drug-resistant tuberculosis patients is increasing rapidly year by year. Here, a total of 380 Mycobacterium tuberculosis (MTB)-positive formalin-fixed and paraffin-embedded tissue (FFPE) specimens diagnosed in the Department of Pathology of the Eighth Medical Center, Chinese PLA General Hospital were collected. Among 380 cases of MTB, 85 (22.37%) were susceptible to four anti-TB drugs and the remaining 295 (77.63%) were resistant to one or more drugs. The rate of MDR-TB was higher in previously treated cases (52.53%) than in new cases [(36.65%), p < 0.05]. Of previously treated cases, the rate of drug resistance was higher in females than in males (p < 0.05). Among specimens obtained from males, the rate of drug resistance was higher in new cases than in previously treated cases (p < 0.05). Of mutation in drug resistance-related genes, the majority (53/380, 13.95%) of rpoB gene carried the D516V mutation, and 13.42% (51/380) featured mutations in both the katG and inhA genes. Among the total specimens, 18.68% (71/380) carried the 88 M mutation in the rpsL gene, and the embB gene focused on the 306 M2 mutation with a mutation rate of 19.74%. Among the resistant INH, the mutation rate of −15 M was higher in resistance to more than one drug than in monodrug-resistant (p < 0.05). In conclusion, the drug resistance of MTB is still very severe and the timely detection of drug resistance is conducive to the precise treatment of TB.
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