1
|
Cocker D, Sammarro M, Chidziwisano K, Elviss N, Jacob ST, Kajumbula H, Mugisha L, Musoke D, Musicha P, Roberts AP, Rowlingson B, Singer AC, Byrne RL, Edwards T, Lester R, Wilson CN, Hollihead B, Thomson NR, Jewell CP, Morse T, Feasey NA. Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs). Wellcome Open Res 2023; 7:55. [PMID: 38817338 PMCID: PMC11137479 DOI: 10.12688/wellcomeopenres.17581.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2023] [Indexed: 06/01/2024] Open
Abstract
In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.
Collapse
Affiliation(s)
- Derek Cocker
- Malawi-Liverpool Wellcome Trust Clinical Research Program, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Melodie Sammarro
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, UK
| | - Kondwani Chidziwisano
- Centre for Water, Sanitation, Health and Appropriate Technology Development (WASHTED), Polytechnic, University of Malawi, Blantyre, Malawi
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK
| | - Nicola Elviss
- Science Group, United Kingdom Health Security Agency, London, UK
| | - Shevin T. Jacob
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Global Health Security Department, Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Henry Kajumbula
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Lawrence Mugisha
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala, Uganda
- Conservation & Ecosystem Health Alliance, Kampala, Uganda
| | - David Musoke
- Department of Disease Control and Environmental Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Patrick Musicha
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Barry Rowlingson
- Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, UK
| | | | - Rachel L. Byrne
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Edwards
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Rebecca Lester
- Malawi-Liverpool Wellcome Trust Clinical Research Program, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Catherine N. Wilson
- Malawi-Liverpool Wellcome Trust Clinical Research Program, Blantyre, Malawi
- Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Beth Hollihead
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Nicholas R. Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Pathogen Molecular Biology, London School of Tropical Medicine and Hygiene, London, UK
| | - Christopher P. Jewell
- Centre for Health Informatics Computing and Statistics, Lancaster University, Lancaster, UK
| | - Tracy Morse
- Centre for Water, Sanitation, Health and Appropriate Technology Development (WASHTED), Polytechnic, University of Malawi, Blantyre, Malawi
- Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, UK
| | - Nicholas A. Feasey
- Malawi-Liverpool Wellcome Trust Clinical Research Program, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| |
Collapse
|
2
|
Barnes K, Levy J, Andersen K, Gauld J, Rigby J, Kanjerwa O, Uzzell C, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana M, Ashton P, Jere K, Meschke J, Diggle P, Cornick J, Jambo K, Kawalazira G, Paterson S, Nyirenda T, Feasey N, Chilima B. Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems. RESEARCH SQUARE 2023:rs.3.rs-2801767. [PMID: 37090541 PMCID: PMC10120776 DOI: 10.21203/rs.3.rs-2801767/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The COVID-19 pandemic continues to impact health systems globally and robust surveillance is critical for pandemic control, however not all countries can sustain community surveillance programs. Wastewater surveillance has proven valuable in high-income settings, but little is known about how river and informal sewage in low-income countries can be used for environmental surveillance of SARS-CoV-2. In Malawi, a country with limited community-based COVID-19 testing capacity, we explored the utility of rivers and wastewater for SARS-CoV-2 surveillance. From May 2020 - January 2022, we collected water from up to 112 river or informal sewage sites/month, detecting SARS-CoV-2 in 8.3% of samples. Peak SARS-CoV-2 detection in water samples predated peaks in clinical cases. Sequencing of water samples identified the Beta, Delta, and Omicron variants, with Delta and Omicron detected well in advance of detection in patients. Our work highlights wastewater can be used for detecting emerging waves, identifying variants of concern and function as an early warning system in settings with no formal sewage systems.
Collapse
Affiliation(s)
| | | | - Kristian Andersen
- Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA USA
| | - Jillian Gauld
- Institute for Disease Modeling, Bill & Melinda Gates Foundation
| | - Jonathan Rigby
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Oscar Kanjerwa
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | - Chisomo Chilupsya
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | | | | | | | - Edward Cairns
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
| | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences
| | - Shannon McSweeney
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | - Marah Chibwana
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences
| | | | | | | | | | - Jennifer Cornick
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool
| | | | | | | | - Tonney Nyirenda
- Department of Pathology, Kamuzu University of Health Sciences
| | | | | |
Collapse
|
3
|
Gibbons E, Tamanna M, Cherayil BJ. The rpoS gene confers resistance to low osmolarity conditions in Salmonella enterica serovar Typhi. PLoS One 2022; 17:e0279372. [PMID: 36525423 PMCID: PMC9757558 DOI: 10.1371/journal.pone.0279372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
Salmonella enterica serovars Typhimurium and Typhi are enteropathogens that differ in host range and the diseases that they cause. We found that exposure to a combination of hypotonicity and the detergent Triton X-100 significantly reduced the viability of the S. Typhi strain Ty2 but had no effect on the S. Typhimurium strain SL1344. Further analysis revealed that hypotonicity was the critical factor: incubation in distilled water alone was sufficient to kill Ty2, while the addition of sodium chloride inhibited killing in a dose-dependent manner. Ty2's loss of viability in water was modified by culture conditions: bacteria grown in well-aerated shaking cultures were more susceptible than bacteria grown under less aerated static conditions. Ty2, like many S. Typhi clinical isolates, has an inactivating mutation in the rpoS gene, a transcriptional regulator of stress responses, whereas most S. Typhimurium strains, including SL1344, have the wild-type gene. Transformation of Ty2 with a plasmid expressing wild-type rpoS, but not the empty vector, significantly increased survival in distilled water. Moreover, an S. Typhi strain with wild-type rpoS had unimpaired survival in water. Inactivation of the wild-type gene in this strain significantly reduced survival, while replacement with an arabinose-inducible allele of rpoS restored viability in water under inducing conditions. Our observations on rpoS-dependent differences in susceptibility to hypotonic conditions may be relevant to the ability of S. Typhi and S. Typhimurium to tolerate the various environments they encounter during the infectious cycle. They also have implications for the handling of these organisms during experimental manipulations.
Collapse
Affiliation(s)
- Eamon Gibbons
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Mehbooba Tamanna
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Medical Sciences Program, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Bobby J. Cherayil
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
4
|
Cocker D, Sammarro M, Chidziwisano K, Elviss N, Jacob ST, Kajumbula H, Mugisha L, Musoke D, Musicha P, Roberts AP, Rowlingson B, Singer AC, Byrne RL, Edwards T, Lester R, Wilson C, Hollihead B, Thomson N, Jewell CP, Morse T, Feasey N. Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs). Wellcome Open Res 2022. [DOI: 10.12688/wellcomeopenres.17581.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In sub-Saharan Africa (sSA), there is high morbidity and mortality from severe bacterial infection and this is compounded by antimicrobial resistance, in particular, resistance to 3rd-generation cephalosporins. This resistance is typically mediated by extended-spectrum beta lactamases (ESBLs). To interrupt ESBL transmission it will be important to investigate how human behaviour, water, sanitation, and hygiene (WASH) practices, environmental contamination, and antibiotic usage in both urban and rural settings interact to contribute to transmission of ESBL E. coli and ESBL K. pneumoniae between humans, animals, and the environment. Here we present the protocol for the Drivers of Resistance in Uganda and Malawi (DRUM) Consortium, in which we will collect demographic, geospatial, clinical, animal husbandry and WASH data from a total of 400 households in Uganda and Malawi. Longitudinal human, animal and environmental sampling at each household will be used to isolate ESBL E. coli and ESBL K. pneumoniae. This will be complimented by a Risks, Attitudes, Norms, Abilities and Self-Regulation (RANAS) survey and structured observations to understand the contextual and psychosocial drivers of regional WASH practices. Bacterial isolates and plate sweeps will be further characterised using a mixture of short-,long-read and metagenomic whole-genome sequencing. These datasets will be integrated into agent-based models to describe the transmission of EBSL resistance in Uganda and Malawi and allow us to inform the design of interventions for interrupting transmission of ESBL-bacteria.
Collapse
|
5
|
Yang X, Xiong W, Huang T, He J. Meteorological and social conditions contribute to infectious diarrhea in China. Sci Rep 2021; 11:23374. [PMID: 34862400 PMCID: PMC8642416 DOI: 10.1038/s41598-021-00932-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
Infectious diarrhea in China showed a significant pattern. Many researchers have tried to reveal the drivers, yet usually only meteorological factors were taken into consideration. Furthermore, the diarrheal data they analyzed were incomplete and the algorithms they exploited were inefficient of adapting realistic relationships. Here, we investigate the impacts of meteorological and social factors on the number of infectious diarrhea cases in China. A machine learning algorithm called the Random Forest is utilized. Our results demonstrate that nearly half of infectious diarrhea occurred among children under 5 years old. Generally speaking, increasing temperature or relative humidity leads to increased cases of infectious diarrhea in China. Nevertheless, people from different age groups or different regions own different sensitivities to meteorological factors. The weight of feces that are harmfully treated could be a possible reason for infectious diarrhea of the elderly as well as children under 5 years old. These findings indicate that infectious diarrhea prevention for children under 5 years old remains a primary task in China. Personalized prevention countermeasures ought to be provided to different age groups and different regions. It is essential to bring the weight of feces that are harmfully treated to the forefront when considering infectious diarrhea prevention.
Collapse
Affiliation(s)
- Xiang Yang
- grid.24695.3c0000 0001 1431 9176Beijing University of Chinese Medicine, No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100029 China
| | - Weifeng Xiong
- grid.24695.3c0000 0001 1431 9176Beijing University of Chinese Medicine, No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100029 China
| | - Tianyao Huang
- grid.12527.330000 0001 0662 3178Tsinghua University, Haidian District, Beijing, 100084 China
| | - Juan He
- Beijing University of Chinese Medicine, No. 11, Bei San Huan Dong Lu, Chaoyang District, Beijing, 100029, China.
| |
Collapse
|
6
|
Giri S, Mohan VR, Srinivasan M, Kumar N, Kumar V, Dhanapal P, Venkatesan J, Gunasekaran A, Abraham D, John J, Kang G. Case-Control Study of Household and Environmental Transmission of Typhoid Fever in India. J Infect Dis 2021; 224:S584-S592. [PMID: 35238355 PMCID: PMC8892545 DOI: 10.1093/infdis/jiab378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background Typhoid fever causes substantial morbidity and mortality in low- and middle-income countries. We conducted a case-control study in Vellore, southern India, to understand risk factors for transmission of typhoid. Methods From April 2018 to October 2019, households of blood culture-confirmed typhoid cases that occurred within a fever surveillance cohort aged 6 months–15 years, and controls matched for age, sex, geographic location, and socioeconomic status, were recruited. Information on risk factors was obtained using standard questionnaires. Household and environmental samples were collected for detection of Salmonella Typhi using real-time polymerase chain reaction. Multivariable analysis was used to evaluate associations between risk factors and typhoid. Results One hundred pairs of cases and controls were recruited. On multivariable regression analysis, mothers eating food from street vendors during the previous week (odds ratio [OR] = 2.04; 95% confidence interval [CI], 1.03–4.12; P = .04) was independently associated with typhoid, whereas treatment of household drinking water (OR = 0.45; 95% CI, 0.25–0.80; P = .007) was protective. There was no significant difference in S Typhi detection between the environmental samples from case and control households. Conclusions Street-vended food is a risk factor for typhoid in densely populated urban communities of Vellore. Improved sanitation facilities and awareness about point-of-use water treatment are likely to contribute to typhoid control.
Collapse
Affiliation(s)
- Sidhartha Giri
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | | | - Nirmal Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Vinoth Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Pavithra Dhanapal
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Annai Gunasekaran
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Dilip Abraham
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jacob John
- Department of Community Health, Christian Medical College, Vellore, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| |
Collapse
|
7
|
Thindwa D, Chipeta MG, Henrion MYR, Gordon MA. Distinct climate influences on the risk of typhoid compared to invasive non-typhoid Salmonella disease in Blantyre, Malawi. Sci Rep 2019; 9:20310. [PMID: 31889080 PMCID: PMC6937328 DOI: 10.1038/s41598-019-56688-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/02/2019] [Indexed: 12/04/2022] Open
Abstract
Invasive Salmonella diseases, both typhoid and invasive non-typhoidal Salmonella (iNTS), are seasonal bloodstream infections causing important morbidity and mortality globally in Africa. The reservoirs and transmission of both are not fully understood. We hypothesised that differences in the time-lagged relationships of rainfall or temperature with typhoid and iNTS incidence might infer differences in epidemiology. We assessed the dynamics of invasive Salmonella incidence over a 16-year period of surveillance, quantifying incidence peaks, seasonal variations, and nonlinear effects of rainfall and temperature exposures on the relative risks of typhoid and iNTS, using monthly lags. An increased relative risk of iNTS incidence was short-lasting but immediate after the onset of the rains, whereas that of typhoid was long-lasting but with a two months delayed start, implying a possible difference in transmission. The relative-risk function of temperature for typhoid was bimodal, with higher risk at both lower (with a 1 month lag) and higher (with a ≥4 months lag) temperatures, possibly reflecting the known patterns of short and long cycle typhoid transmission. In contrast, the relative-risk of iNTS was only increased at lower temperatures, suggesting distinct transmission mechanisms. Environmental and sanitation control strategies may be different for iNTS compared to typhoid disease.
Collapse
Affiliation(s)
- Deus Thindwa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi.
- Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Michael G Chipeta
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Nuffield Department of Medicine, Big Data Institute, Oxford University, Oxford, United Kingdom
- Malawi College of Medicine, University of Malawi, Blantyre, Malawi
| | - Marc Y R Henrion
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- Malawi College of Medicine, University of Malawi, Blantyre, Malawi
| |
Collapse
|