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Mtetwa HN, Amoah ID, Kumari S, Bux F, Reddy P. Exploring the role of wastewater-based epidemiology in understanding tuberculosis burdens in Africa. ENVIRONMENTAL RESEARCH 2023; 231:115911. [PMID: 37105295 PMCID: PMC10318412 DOI: 10.1016/j.envres.2023.115911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023]
Abstract
Tuberculosis (TB) remains a persistent challenge to public health and presents a substantial menace, especially in developing nations of sub-Saharan Africa. It exerts a considerable strain on healthcare systems in these regions. Effective control requires reliable surveillance, which can be improved by incorporating environmental data alongside clinical data. Molecular advances have led to the development of alternative surveillance methods, such as wastewater-based epidemiology. This studyinvestigated the presence, concentration, and diversity of Mycobacterium tuberculosis complex, the cause of TB, in from six African countries: Ghana, Nigeria, Kenya, Uganda, Cameroon, and South Africa. Samples were collected from wastewater treatment plants. All samples were found to contain Mycobacterium species that have been linked to TB in both humans and animals, including Mycobacterium tuberculosis complex, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium caprae, at varying concentrations. The highest median concentration was found in Ghana, reaching up to 4.7 Log copies/ml for MTBC, 4.6 Log copies/ml for M. bovis, and 3.4 Log copies/ml for M. africanum. The presence of M. africanum outside of West Africa was found in South Africa, Kenya, and Uganda and could indicate the spread of the pathogen. The study underscores the usefulness of wastewater-based epidemiology for tracking TB and shows that even treated wastewater may contain these pathogens, posing potential public health risks.
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Affiliation(s)
- Hlengiwe N Mtetwa
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa; Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Isaac D Amoah
- Department of Environmental Science, University of Arizona, Tuscon, USA
| | - Sheena Kumari
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Poovendhree Reddy
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa; Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa.
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Loganathachetti DS, Alhashmi F, Chandran S, Mundra S. Irrigation water salinity structures the bacterial communities of date palm ( Phoenix dactylifera)-associated bulk soil. FRONTIERS IN PLANT SCIENCE 2022; 13:944637. [PMID: 35991423 PMCID: PMC9388049 DOI: 10.3389/fpls.2022.944637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
The irrigation of date palms (Phoenix dactylifera) with saline groundwater is routinely practiced in the agroecosystems of arid environments because of freshwater scarcity. This leads to salts deposition in topsoil layers and increases soil salinization. However, how different irrigation sources affect soil microbiota is poorly understood. Bulk soil samples were collected from date farms receiving non-saline water and saline groundwater to examine bacterial communities using metabarcoding. Overall, bacterial diversity measures (Shannon diversity index, richness, and evenness) did not vary between irrigation sources. Bacterial communities were structured based on irrigation water sources and were significantly associated with their electrical conductivity. Of 5,155 operational taxonomic units (OTUs), 21.3% were unique to soil irrigated with saline groundwater, 31.5% received non-saline water irrigation, and 47.2% were shared. The Proteobacteria abundance was higher in soil under saline groundwater irrigation while Actinobacteriota abundance was lower. A compositional shift at the genera level was also evident; the abundance of Subgroup_10 and Mycobacterium was higher under saline groundwater irrigation. Mycobacterium was a key indicator of OTU under saline groundwater irrigation while Solirubrobacter was an indicator of non-saline water irrigation. Functional gene analyses showed enrichment of fatty acid, cell wall, and starch biosynthesis pathways in soil under saline groundwater irrigation. These findings provide insights into how "salinity filtering" influences bacterial communities, key taxa, and the potential metabolic function in soil under increasing irrigation water salinities, and have broad implications for arid agroecosystems.
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Affiliation(s)
| | - Fardous Alhashmi
- Department of Biology, College of Science, United Arab Emirate University, Al Ain, United Arab Emirates
| | - Subha Chandran
- Department of Biology, College of Science, United Arab Emirate University, Al Ain, United Arab Emirates
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirate University, Al Ain, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
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Rebollo-Ramirez S, Larrouy-Maumus G. NaCl triggers the CRP-dependent increase of cAMP in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2019; 116:8-16. [PMID: 31153521 DOI: 10.1016/j.tube.2019.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 11/19/2022]
Abstract
The second messenger 3',5'-cyclic adenosine monophosphate (3',5'-cAMP) has been shown to be involved in the regulation of many biological processes ranging from carbon catabolite repression in bacteria to cell signalling in eukaryotes. In mycobacteria, the role of cAMP and the mechanisms utilized by the bacterium to adapt to and resist immune and pharmacological sterilization remain poorly understood. Among the stresses encountered by bacteria, ionic and non-ionic osmotic stresses are among the best studied. However, in mycobacteria, the link between ionic osmotic stress, particularly sodium chloride, and cAMP has been relatively unexplored. Using a targeted metabolic analysis combined with stable isotope tracing, we show that the pathogenic Mycobacterium tuberculosis but not the opportunistic pathogen Mycobacterium marinum nor the non-pathogenic Mycobacterium smegmatis responds to NaCl stress via an increase in intracellular cAMP levels. We further showed that this increase in cAMP is dependent on the cAMP receptor protein and in part on the threonine/serine kinase PnkD, which has previously been associated with the NaCl stress response in mycobacteria.
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Affiliation(s)
- Sonia Rebollo-Ramirez
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.
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4
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Bouzid F, Osman DA, Baptiste E, Delerce J, Hassan MO, Arreh WI, Levasseur A, Garnotel E, Drancourt M. Pulmonary Isolation of Multidrug resistant "Mycobacterium simulans" and Mycobacterium tuberculosis from a patient in the Horn of Africa. Sci Rep 2018; 8:15341. [PMID: 30367075 PMCID: PMC6203708 DOI: 10.1038/s41598-018-33737-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 07/30/2018] [Indexed: 11/22/2022] Open
Abstract
In low-income countries of the Horn of Africa, pulmonary infections are usually considered as tuberculosis, which diagnosis relies on clinical data and positive microscopic observation. This strategy allows non-tuberculous mycobacteria to escape detection, facilitating their emergence in populations. A non-tuberculous mycobacterium strain FB-527 was unexpectedly cultured from the sputum of a Djiboutian patient otherwise diagnosed with multi-drug resistant (MDR) tuberculosis. The sequencing of the rpoB and 16S rRNA genes showed that the isolate was identical to strain FI-09026 previously named "Mycobacterium simulans" and reported only once from a Somali patient. Strain FB-527 mimicked Mycobacterium tuberculosis colonies and enzymatic profile using API ZYM strip and was in vitro resistant to rifampicin and isoniazid. Isolation of two MDR mycobacteria complicated the diagnosis and therapeutic management of the patient. We here report on the complete description of strain FB-527 and strain FI-09026 including genome sequencing, finalizing the description of the proposed new species "Mycobacterium simulans".
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Affiliation(s)
- Fériel Bouzid
- Aix Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Djaltou Aboubaker Osman
- Centre d'Études et de Recherche de Djibouti (CERD), Institut de Recherche Médicinale (IRM), Djibouti, Djibouti
| | - Emeline Baptiste
- Aix Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jeremy Delerce
- Aix Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | | | | | - Anthony Levasseur
- Aix Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Eric Garnotel
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Michel Drancourt
- Aix Marseille Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France.
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Surmik D, Szczygielski T, Janiszewska K, Rothschild BM. Tuberculosis-like respiratory infection in 245-million-year-old marine reptile suggested by bone pathologies. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180225. [PMID: 30110474 PMCID: PMC6030318 DOI: 10.1098/rsos.180225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/24/2018] [Indexed: 05/05/2023]
Abstract
An absence of ancient archaeological and palaeontological evidence of pneumonia contrasts with its recognition in the more recent archaeological record. We document an apparent infection-mediated periosteal reaction affecting the dorsal ribs in a Middle Triassic eosauropterygian historically referred to as 'Proneusticosaurus' silesiacus. High-resolution X-ray microtomography and histological studies of the pathologically altered ribs revealed the presence of a continuous solid periosteal reaction with multiple superficial blebs (protrusions) on the visceral surfaces of several ribs. Increased vascularization and uneven lines of arrested growth document that the pathology was the result of a multi-seasonal disease. While visceral surface localization of this periosteal reaction represents the earliest identified evidence for pneumonia, the blebs may have an additional implication: they have only been previously recognized in humans with tuberculosis (TB). Along with this diagnosis is the presence of focal vertebral erosions, parsimoniously compared to vertebral manifestation of TB in humans.
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Affiliation(s)
- Dawid Surmik
- Faculty of Earth Sciences, University of Silesia, Będzińska 60, 41-200 Sosnowiec, Poland
- Park of Science and Human Evolution, 1 Maja 10, 46-040 Krasiejów, Poland
- Author for correspondence: Dawid Surmik e-mail:
| | - Tomasz Szczygielski
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland
| | - Katarzyna Janiszewska
- Institute of Paleobiology, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland
| | - Bruce M. Rothschild
- Carnegie Museum, 4400 Forbes Avenue, Pittsburgh, PA 15213, USA
- West Virginia University School of Medicine, Morgantown, WV 26506, USA
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Buruli Ulcer, a Prototype for Ecosystem-Related Infection, Caused by Mycobacterium ulcerans. Clin Microbiol Rev 2017; 31:31/1/e00045-17. [PMID: 29237707 DOI: 10.1128/cmr.00045-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Buruli ulcer is a noncontagious disabling cutaneous and subcutaneous mycobacteriosis reported by 33 countries in Africa, Asia, Oceania, and South America. The causative agent, Mycobacterium ulcerans, derives from Mycobacterium marinum by genomic reduction and acquisition of a plasmid-borne, nonribosomal cytotoxin mycolactone, the major virulence factor. M. ulcerans-specific sequences have been readily detected in aquatic environments in food chains involving small mammals. Skin contamination combined with any type of puncture, including insect bites, is the most plausible route of transmission, and skin temperature of <30°C significantly correlates with the topography of lesions. After 30 years of emergence and increasing prevalence between 1970 and 2010, mainly in Africa, factors related to ongoing decreasing prevalence in the same countries remain unexplained. Rapid diagnosis, including laboratory confirmation at the point of care, is mandatory in order to reduce delays in effective treatment. Parenteral and potentially toxic streptomycin-rifampin is to be replaced by oral clarithromycin or fluoroquinolone combined with rifampin. In the absence of proven effective primary prevention, avoiding skin contamination by means of clothing can be implemented in areas of endemicity. Buruli ulcer is a prototype of ecosystem pathology, illustrating the impact of human activities on the environment as a source for emerging tropical infectious diseases.
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Drancourt M. Please, No More Gastric Aspirate to Diagnose Pulmonary Tuberculosis in Children. Clin Infect Dis 2017; 65:2158. [PMID: 29020229 DOI: 10.1093/cid/cix712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Michel Drancourt
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD198, Inserm 1095, IHU Méditerranée Infection, Marseille, France
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Bouam A, Ghigo E, Drancourt M. Intra-amoebal killing of Mycobacterium ulcerans by Acanthamoeba griffini: A co-culture model. Microb Pathog 2017; 114:1-7. [PMID: 29155010 DOI: 10.1016/j.micpath.2017.11.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
Abstract
Mycobacterium ulcerans, a decaying Mycobacterium marinum derivative is responsible for Buruli ulcer, a notifiable non-contagious disabling infection highly prevalent in some West African countries. Aquatic environments are suspected to host M. ulcerans, however, the exact reservoirs remain unknown. While M. marinum was found to resist amoebal microbicidal activities, this remains unknown for M. ulcerans. In this study M. ulcerans was co-cultured with the moderately halophile Acanthamoeba griffini at 30 °C to probe this tropical amoeba as a potential reservoir for M. ulcerans. In triplicate experiments, we observed engulfment of M. ulcerans by A. griffini trophozoites, followed by an unexpected significant difference of 98.4% (day 1), 99.5% (day 2), 99.5% (day 3) and 99.9% (day 7) between the number of intra-amoebal mycobacteria detected by PCR and the number of viable intra-amoebal mycobacteria measured by 10-week culture. Further encystment revealed only one Mycobacterium organism for 150 A. griffini cysts observed by electron microscopy and the culture of excysted amoebae remained sterile. In conclusion, these data install M. ulcerans as susceptible to A. griffini microbicidal activities rendering this amoeba species an unlikely host of M. ulcerans in natural environments.
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Affiliation(s)
- Amar Bouam
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille 13005, France
| | - Eric Ghigo
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille 13005, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille 13005, France.
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Grandjean Lapierre S, Phelippeau M, Hakimi C, Didier Q, Reynaud-Gaubert M, Dubus JC, Drancourt M. Cystic fibrosis respiratory tract salt concentration: An Exploratory Cohort Study. Medicine (Baltimore) 2017; 96:e8423. [PMID: 29381919 PMCID: PMC5708918 DOI: 10.1097/md.0000000000008423] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In cystic fibrosis patients, electrolytic and osmolality imbalance secondary to cystic fibrosis transmembrane conductance regulator mutations may impact on mucoid secretion accumulation and secondary colonization by opportunistic pathogens such as nontuberculous mycobacteria.We performed a noninvasive exploratory prospective controlled clinical study comparing sputum salinity and acid-base characteristics of cystic fibrosis and noncystic fibrosis control patients. A total of 57 patients and 62 controls were included.Sputum salt concentrations were 10.5 g/L (95% CI: 7.7-13.3) in patients and 7.4 g/L (95% CI: 5.9-8.9) in aged-matched controls, a difference that was found to be statistically significant (P < .05). No difference in pH was observed between patients and controls.These differences in respiratory secretions salt concentrations could influence host-pathogen interactions in the context of cystic fibrosis respiratory infections. We propose to include respiratory secretion salt measurement as a routine analysis on cystic fibrosis patients' sputum submitted for bacterial culture.
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Affiliation(s)
| | | | - Cyrine Hakimi
- Aix-Marseille Université, URMITE Méditerranée Infection
| | | | - Martine Reynaud-Gaubert
- Center de Resource et de Compétences de la Mucoviscidose adulte; équipe de Transplantation pulmonaire, CHU Hôpital Nord, URMITE Aix-Marseille Université
| | - Jean-Christophe Dubus
- Center de Resource et de Compétences de la Mucoviscidose pédiatrique CHU Hôpital la Timone, Marseille, France
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Lapierre SG, Fellag M, Magan C, Drancourt M. Mycobacterium malmoense pulmonary infection in France: a case report. BMC Res Notes 2017; 10:436. [PMID: 28859675 PMCID: PMC5580279 DOI: 10.1186/s13104-017-2753-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium malmoense infections have frequently been reported in northern Europe since the late 1970s. Factors accounting for this geographically localized epidemiology remain poorly understood. CASE PRESENTATION We report the case of a 54-year old man concomitantly diagnosed with non-small cell lung carcinoma and M. malmoense pulmonary infection. We present detailed clinical, microbiological and radiological elements strongly arguing for M. malmoense true pathogenicity. Since M. malmoense infection has rarely been reported in France, we also provide elements of the epidemiological investigation and a literature review of potential acquisition and transmission pathways of M. malmoense. We detail therapeutic interventions and subsequent favorable evolution. CONCLUSION Mycobacterium malmoense is a recognized respiratory pathogen for which routes of infection need to be better investigated.
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Affiliation(s)
- Simon Grandjean Lapierre
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095-IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Mustapha Fellag
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095-IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Célia Magan
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095-IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Michel Drancourt
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095-IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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Zingue D, Flaudrops C, Drancourt M. Direct matrix-assisted laser desorption ionisation time-of-flight mass spectrometry identification of mycobacteria from colonies. Eur J Clin Microbiol Infect Dis 2016; 35:1983-1987. [PMID: 27549109 DOI: 10.1007/s10096-016-2750-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/03/2016] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) identification of mycobacteria requires a standard acetonitrile/formic acid pre-MALDI-TOF-MS. We prospectively compared this standard protocol with direct deposit with matrix for the identification of mycobacteria cultured on solid media. We first verified that Mycobacterium tuberculosis was killed after it was mixed with matrix. Then, 111 Mycobacterium isolates previously identified by partial rpoB gene sequencing were tested in parallel by the two protocols. An identification score >1.7 was obtained in 86/111 (77.5 %) isolates after protein extraction versus 97/111 (87.4 %) isolates after direct deposit (p = 0.039, Chi-squared test). In a third step, we determined that direct deposit achieved identification for as few as 2.104 M. tuberculosis organisms. In a fourth step, we evaluated direct deposit of one colony for 116 solid medium-cultured clinical isolates finally identified as representative of 12 species (63.8 % M. tuberculosis). For 114/116 (98.3 %) isolates with an identification score >1.2, the MALDI-TOF-MS identification was in complete agreement with the reference rpoB gene sequencing identification. One isolate with a MALDI-TOF-MS identification score of 1.22 for M. fortuitum was identified as M. avium by partial rpoB gene sequencing. One other isolate with a MALDI-TOF-MS identification score of 1.22 for M. tuberculosis was identified as M. tuberculosis by genotyping. All the original MALDI-TOF-MS spectra reported here have been deposited in a public database. Direct deposit of one colony on a MALDI-TOF-MS plate allows for an accurate identification of mycobacteria for an identification score >1.3.
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Affiliation(s)
- D Zingue
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - C Flaudrops
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France
| | - M Drancourt
- Aix-Marseille Université, INSERM, CNRS, IRD, URMITE, Marseille, France.
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