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Leder K, Openshaw JJ, Allotey P, Ansariadi A, Barker SF, Burge K, Clasen TF, Chown SL, Duffy GA, Faber PA, Fleming G, Forbes AB, French M, Greening C, Henry R, Higginson E, Johnston DW, Lappan R, Lin A, Luby SP, McCarthy D, O'Toole JE, Ramirez-Lovering D, Reidpath DD, Simpson JA, Sinharoy SS, Sweeney R, Taruc RR, Tela A, Turagabeci AR, Wardani J, Wong T, Brown R. Study design, rationale and methods of the Revitalising Informal Settlements and their Environments (RISE) study: a cluster randomised controlled trial to evaluate environmental and human health impacts of a water-sensitive intervention in informal settlements in Indonesia and Fiji. BMJ Open 2021; 11:e042850. [PMID: 33419917 PMCID: PMC7798802 DOI: 10.1136/bmjopen-2020-042850] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Increasing urban populations have led to the growth of informal settlements, with contaminated environments linked to poor human health through a range of interlinked pathways. Here, we describe the design and methods for the Revitalising Informal Settlements and their Environments (RISE) study, a transdisciplinary randomised trial evaluating impacts of an intervention to upgrade urban informal settlements in two Asia-Pacific countries. METHODS AND ANALYSIS RISE is a cluster randomised controlled trial among 12 settlements in Makassar, Indonesia, and 12 in Suva, Fiji. Six settlements in each country have been randomised to receive the intervention at the outset; the remainder will serve as controls and be offered intervention delivery after trial completion. The intervention involves a water-sensitive approach, delivering site-specific, modular, decentralised infrastructure primarily aimed at improving health by decreasing exposure to environmental faecal contamination. Consenting households within each informal settlement site have been enrolled, with longitudinal assessment to involve health and well-being surveys, and human and environmental sampling. Primary outcomes will be evaluated in children under 5 years of age and include prevalence and diversity of gastrointestinal pathogens, abundance and diversity of antimicrobial resistance (AMR) genes in gastrointestinal microorganisms and markers of gastrointestinal inflammation. Diverse secondary outcomes include changes in microbial contamination; abundance and diversity of pathogens and AMR genes in environmental samples; impacts on ecological biodiversity and microclimates; mosquito vector abundance; anthropometric assessments, nutrition markers and systemic inflammation in children; caregiver-reported and self-reported health symptoms and healthcare utilisation; and measures of individual and community psychological, emotional and economic well-being. The study aims to provide proof-of-concept evidence to inform policies on upgrading of informal settlements to improve environments and human health and well-being. ETHICS Study protocols have been approved by ethics boards at Monash University, Fiji National University and Hasanuddin University. TRIAL REGISTRATION NUMBER ACTRN12618000633280; Pre-results.
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Affiliation(s)
- Karin Leder
- School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - John J Openshaw
- Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford, California, USA
| | - Pascale Allotey
- International Institute for Global Health, United Nations University, Kuala Lumpur, Malaysia
| | - Ansariadi Ansariadi
- Public Health Faculty, Hasanuddin University, Makassar, Sulawesi Selatan, Indonesia
| | - S Fiona Barker
- School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kerrie Burge
- CRC for Water Sensitive Cities, Monash University, Melbourne, Victoria, Australia
| | - Thomas F Clasen
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Steven L Chown
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Grant A Duffy
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Peter A Faber
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Genie Fleming
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Andrew B Forbes
- School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Matthew French
- Monash Sustainable Development Institute, Monash University, Melbourne, Victoria, Australia
| | - Chris Greening
- Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Rebekah Henry
- Civil Engineering, Monash University, Melbourne, Victoria, Australia
| | - Ellen Higginson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - David W Johnston
- Centre for Health Economics, Monash Business School, Monash University, Melbourne, Victoria, Australia
| | - Rachael Lappan
- Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Audrie Lin
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Stephen P Luby
- Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford, California, USA
| | - David McCarthy
- Civil Engineering, Monash University, Melbourne, Victoria, Australia
| | - Joanne E O'Toole
- School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Daniel D Reidpath
- Monash University - Malaysia Campus, Bandar Sunway, Selangor, Malaysia
| | - Julie A Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Sheela S Sinharoy
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Rohan Sweeney
- Centre for Health Economics, Monash Business School, Monash University, Melbourne, Victoria, Australia
| | - Ruzka R Taruc
- Public Health Faculty, Hasanuddin University, Makassar, Sulawesi Selatan, Indonesia
| | - Autiko Tela
- School of Public Health and Primary Care, Fiji National University, College of Medicine, Nursing and Health Sciences, Tamavua Campus, Suva, Rewa, Fiji
| | - Amelia R Turagabeci
- School of Public Health and Primary Care, Fiji National University, College of Medicine, Nursing and Health Sciences, Tamavua Campus, Suva, Rewa, Fiji
| | - Jane Wardani
- Monash Sustainable Development Institute, Monash University, Melbourne, Victoria, Australia
| | - Tony Wong
- CRC for Water Sensitive Cities, Monash University, Melbourne, Victoria, Australia
| | - Rebekah Brown
- Monash Sustainable Development Institute, Monash University, Melbourne, Victoria, Australia
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Kintz E, Williams NJ, Jones N, van der Es M, Lake IR, O'Brien SJ, Hunter PR. Regional differences in presence of Shiga toxin-producing Escherichia coli virulence-associated genes in the environment in the North West and East Anglian regions of England. Lett Appl Microbiol 2020; 71:179-186. [PMID: 32333799 DOI: 10.1111/lam.13303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/30/2022]
Abstract
Shiga toxin-producing Escherichia coli is carried in the intestine of ruminant animals, and outbreaks have occurred after contact with ruminant animals or their environment. The presence of STEC virulence genes in the environment was investigated along recreational walking paths in the North West and East Anglia regions of England. In all, 720 boot sock samples from walkers' shoes were collected between April 2013 and July 2014. Multiplex PCR was used to detect E. coli based on the amplification of the uidA gene and investigate STEC-associated virulence genes eaeA, stx1 and stx2. The eaeA virulence gene was detected in 45·5% of the samples, where stx1 and/or stx2 was detected in 12·4% of samples. There was a difference between the two regions sampled, with the North West exhibiting a higher proportion of positive boot socks for stx compared to East Anglia. In univariate analysis, ground conditions, river flow and temperature were associated with positive boot socks. The detection of stx genes in the soil samples suggests that STEC is present in the English countryside and individuals may be at risk for infection after outdoor activities even if there is no direct contact with animals. SIGNIFICANCE AND IMPACT OF THE STUDY: Several outbreaks within the UK have highlighted the danger of contracting Shiga toxin-producing Escherichia coli from contact with areas recently vacated by livestock. This is more likely to occur for STEC infections compared to other zoonotic bacteria given the low infectious dose required. While studies have determined the prevalence of STEC within farms and petting zoos, determining the risk to individuals enjoying recreational outdoor activities that occur near where livestock may be present is less researched. This study describes the prevalence with which stx genes, indicative of STEC bacteria, were found in the environment in the English countryside.
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Affiliation(s)
- E Kintz
- Norwich Medical School, University of East Anglia, Norwich, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK
| | - N J Williams
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, Leahurst Campus, University of Liverpool, Liverpool, UK
| | - N Jones
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - M van der Es
- Norwich Medical School, University of East Anglia, Norwich, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK
| | - I R Lake
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK.,School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - S J O'Brien
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK.,Institute of Population Health Sciences, University of Liverpool, Liverpool, UK
| | - P R Hunter
- Norwich Medical School, University of East Anglia, Norwich, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK.,Department of Environmental Health, Tshwane University of Technology, Pretoria, South Africa
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3
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Strain-Specific Differences in Survival of Campylobacter spp. in Naturally Contaminated Turkey Feces and Water. Appl Environ Microbiol 2019; 85:AEM.01579-19. [PMID: 31519663 DOI: 10.1128/aem.01579-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/08/2019] [Indexed: 12/30/2022] Open
Abstract
Campylobacter jejuni and Campylobacter coli are leading causes of human foodborne illness, with poultry as a major vehicle. Turkeys are frequently colonized with Campylobacter, but little is known about Campylobacter survival in turkey feces, even though fecal droppings are major vehicles for Campylobacter within-flock transmission as well as for environmental dissemination. Our objective was to examine survival of Campylobacter, including different strains, in freshly excreted feces from naturally colonized commercial turkey flocks and in suspensions of turkey feces in water from the turkey house. Fecal and water suspensions were stored at 4°C, and Campylobacter populations were enumerated on selective media at 48-h intervals. C. jejuni and C. coli isolates were characterized for resistance to a panel of antibiotics, and a subset was subtyped using multilocus sequence typing. Campylobacter was recovered from feces and water for up to 16 days. Analysis of 548 isolates (218 C. jejuni and 330 C. coli) revealed that C. jejuni survived longer than C. coli in feces (P = 0.0005), while the reverse was observed in water (P < 0.0001). Strain-specific differences in survival were noted. Multidrug-resistant C. jejuni isolates of sequence type 1839 (ST-1839) and the related ST-2935 were among the longest-surviving isolates in feces, being recovered for up to 10 to 16 days, while multidrug-resistant C. coli isolates of ST-1101 were recovered from feces for only up to 4 days. Data on Campylobacter survival upon excretion from the birds can contribute to further understanding of the transmission dynamics of this pathogen in the poultry production ecosystem.IMPORTANCE Campylobacter jejuni and Campylobacter coli are leading foodborne pathogens, with poultry as a major reservoir. Due to their growth requirements, these Campylobacter spp. may be unable to replicate once excreted by their avian hosts, but their survival in feces and the environment is critical for transmission in the farm ecosystem. Reducing the prevalence of Campylobacter-positive flocks can have major impacts in controlling both contamination of poultry products and environmental dissemination of the pathogens. However, understanding the capacity of these pathogens to survive in transmission-relevant vehicles such as feces and farmhouse water remains poorly understood, and little information is available on species- and strain-associated differences in survival. Here, we employed model conditions to investigate the survival of C. jejuni and C. coli from naturally colonized turkey flocks, and with diverse genotypes and antimicrobial resistance profiles, in turkey feces and in farmhouse water.
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Elson R, Davies TM, Jenkins C, Vivancos R, O'Brien SJ, Lake IR. Application of kernel smoothing to estimate the spatio-temporal variation in risk of STEC O157 in England. Spat Spatiotemporal Epidemiol 2019; 32:100305. [PMID: 32007279 DOI: 10.1016/j.sste.2019.100305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 01/27/2023]
Abstract
Identifying geographical areas with significantly higher or lower rates of infectious diseases can provide important aetiological clues to inform the development of public health policy and interventions designed to reduce morbidity. We applied kernel smoothing to estimate the spatial and spatio-temporal variation in risk of STEC O157 infection in England between 2009 and 2015, and to explore differences between the residential locations of cases reporting travel and those not reporting travel. We provide evidence that the distribution of STEC O157 infection in England is non-uniform with respect to the distribution of the at-risk population; that the spatial distribution of the three main genetic lineages infecting humans (I, II and I/II) differs significantly and that the spatio-temporal risk is highly dynamic. Our results also indicate that cases of STEC O157 reporting travel within or outside the UK are more likely to live in the south/south-east of the country, meaning that their residential location may not reflect the location of exposure that led to their infection. We suggest that the observed variation in risk reflects exposure to sources of STEC O157 that are geographically prescribed. These differences may be related to a combination of changes in the strains circulating in the ruminant reservoir, animal movements (livestock, birds or wildlife) or the behavior of individuals prior to infection. Further work to identify the importance of behaviours and exposures reported by cases relative to residential location is needed.
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Affiliation(s)
- Richard Elson
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; School of Environmental Sciences, University of East Anglia, United Kingdom.
| | - Tilman M Davies
- Department of Mathematics & Statistics, University of Otago, Dunedin, New Zealand
| | - Claire Jenkins
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom
| | - Roberto Vivancos
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Emerging and Zoonotic Infections, United Kingdom
| | - Sarah J O'Brien
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; Institute of Population Health Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Iain R Lake
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; School of Environmental Sciences, University of East Anglia, United Kingdom
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Kers JG, Fischer EAJ, Stegeman JA, Smidt H, Velkers FC. Comparison of Different Invasive and Non-Invasive Methods to Characterize Intestinal Microbiota throughout a Production Cycle of Broiler Chickens. Microorganisms 2019; 7:E431. [PMID: 31658673 PMCID: PMC6843853 DOI: 10.3390/microorganisms7100431] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/25/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022] Open
Abstract
In the short life of broiler chickens, their intestinal microbiota undergoes many changes. To study underlying biological mechanisms and factors that influence the intestinal microbiota development, longitudinal data from flocks and individual birds is needed. However, post-mortem collection of samples hampers longitudinal data collection. In this study, invasively collected cecal and ileal content, cloacal swabs collected from the same bird, and boot sock samples and cecal droppings from the litter of the broilers' poultry house, were collected on days 0, 2, 7, 14 and 35 post-hatch. The different sample types were evaluated on their applicability and reliability to characterize the broiler intestinal microbiota. The microbiota of 247 samples was assessed by 16S ribosomal RNA gene amplicon sequencing. Analyses of α and β measures showed a similar development of microbiota composition of cecal droppings compared to cecal content. Furthermore, the composition of cecal content samples was comparable to that of the boot socks until day 14 post-hatch. This study shows that the value of non-invasive sample types varies at different ages and depends on the goal of the microbiota characterization. Specifically, cecal droppings and boot socks may be useful alternatives for cecal samples to determine intestinal microbiota composition longitudinally.
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Affiliation(s)
- Jannigje G Kers
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Department of Farm Animal Health, Utrecht University, 3584 CL Utrecht, The Netherlands.
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Lake IR, Colón-González FJ, Takkinen J, Rossi M, Sudre B, Dias JG, Tavoschi L, Joshi A, Semenza JC, Nichols G. Exploring Campylobacter seasonality across Europe using The European Surveillance System (TESSy), 2008 to 2016. Euro Surveill 2019; 24:1800028. [PMID: 30940318 PMCID: PMC6446507 DOI: 10.2807/1560-7917.es.2019.24.13.180028] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BackgroundCampylobacteriosis is the most commonly reported food-borne infection in the European Union, with an annual number of cases estimated at around 9 million. In many countries, campylobacteriosis has a striking seasonal peak during early/mid-summer. In the early 2000s, several publications reported on campylobacteriosis seasonality across Europe and associations with temperature and precipitation. Subsequently, many European countries have introduced new measures against this food-borne disease.AimTo examine how the seasonality of campylobacteriosis varied across Europe from 2008-16, to explore associations with temperature and precipitation, and to compare these results with previous studies. We also sought to assess the utility of the European Surveillance System TESSy for cross-European seasonal analysis of campylobacteriosis.MethodsWard's Minimum Variance Clustering was used to group countries with similar seasonal patterns of campylobacteriosis. A two-stage multivariate meta-analysis methodology was used to explore associations with temperature and precipitation.ResultsNordic countries had a pronounced seasonal campylobacteriosis peak in mid- to late summer (weeks 29-32), while most other European countries had a less pronounced peak earlier in the year. The United Kingdom, Ireland, Hungary and Slovakia had a slightly earlier peak (week 24). Campylobacteriosis cases were positively associated with temperature and, to a lesser degree, precipitation.ConclusionAcross Europe, the strength and timing of campylobacteriosis peaks have remained similar to those observed previously. In addition, TESSy is a useful resource for cross-European seasonal analysis of infectious diseases such as campylobacteriosis, but its utility depends upon each country's reporting infrastructure.
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Affiliation(s)
- IR Lake
- School of Environmental Sciences, UEA, Norwich, United Kingdom
| | | | - J Takkinen
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - M Rossi
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - B Sudre
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - J Gomes Dias
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - L Tavoschi
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - A Joshi
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - JC Semenza
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - G Nichols
- School of Environmental Sciences, UEA, Norwich, United Kingdom,European Centre for Disease Prevention and Control, Stockholm, Sweden,Centre for Radiation, Chemical and Environmental Hazards, Public Health England, London, United Kingdom,Centre for Infections, Public Health England, London, United Kingdom,University of Exeter, Exeter, United Kingdom
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Rushton SP, Sanderson RA, Diggle PJ, Shirley MDF, Blain AP, Lake I, Maas JA, Reid WDK, Hardstaff J, Williams N, Jones NR, Rigby D, Strachan NJC, Forbes KJ, Hunter PR, Humphrey TJ, O'Brien SJ. Climate, human behaviour or environment: individual-based modelling of Campylobacter seasonality and strategies to reduce disease burden. J Transl Med 2019; 17:34. [PMID: 30665426 PMCID: PMC6341592 DOI: 10.1186/s12967-019-1781-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/11/2019] [Indexed: 11/25/2022] Open
Abstract
Background With over 800 million cases globally, campylobacteriosis is a major cause of food borne disease. In temperate climates incidence is highly seasonal but the underlying mechanisms are poorly understood, making human disease control difficult. We hypothesised that observed disease patterns reflect complex interactions between weather, patterns of human risk behaviour, immune status and level of food contamination. Only by understanding these can we find effective interventions. Methods We analysed trends in human Campylobacter cases in NE England from 2004 to 2009, investigating the associations between different risk factors and disease using time-series models. We then developed an individual-based (IB) model of risk behaviour, human immunological responses to infection and environmental contamination driven by weather and land use. We parameterised the IB model for NE England and compared outputs to observed numbers of reported cases each month in the population in 2004–2009. Finally, we used it to investigate different community level disease reduction strategies. Results Risk behaviours like countryside visits (t = 3.665, P < 0.001 and t = − 2.187, P = 0.029 for temperature and rainfall respectively), and consumption of barbecued food were strongly associated with weather, (t = 3.219, P = 0.002 and t = 2.015, P = 0.045 for weekly average temperature and average maximum temperature respectively) and also rain (t = 2.254, P = 0.02527). This suggests that the effect of weather was indirect, acting through changes in risk behaviour. The seasonal pattern of cases predicted by the IB model was significantly related to observed patterns (r = 0.72, P < 0.001) indicating that simulating risk behaviour could produce the observed seasonal patterns of cases. A vaccination strategy providing short-term immunity was more effective than educational interventions to modify human risk behaviour. Extending immunity to 1 year from 20 days reduced disease burden by an order of magnitude (from 2412–2414 to 203–309 cases per 50,000 person-years). Conclusions This is the first interdisciplinary study to integrate environment, risk behaviour, socio-demographics and immunology to model Campylobacter infection, including pathways to mitigation. We conclude that vaccination is likely to be the best route for intervening against campylobacteriosis despite the technical problems associated with understanding both the underlying human immunology and genetic variation in the pathogen, and the likely cost of vaccine development.
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Affiliation(s)
- Stephen P Rushton
- Modelling, Evidence and Policy Research Group, School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Roy A Sanderson
- Modelling, Evidence and Policy Research Group, School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| | - Peter J Diggle
- Lancaster Medical School, Lancaster University, Lancaster, LA1 4YG, UK
| | - Mark D F Shirley
- Modelling, Evidence and Policy Research Group, School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alasdair P Blain
- Modelling, Evidence and Policy Research Group, School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Iain Lake
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - James A Maas
- Norwich Medical School, University of East Anglia, Norwich 33, NR4 7TJ, UK
| | - William D K Reid
- Ecology Research Group, School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jo Hardstaff
- Institute of Psychology, Health and Society, University of Liverpool, Liverpool, L69 3BX, UK
| | - Nicola Williams
- Institute of Infection and Global Health, Liverpool University, Liverpool, L69 7BE, UK
| | - Natalia R Jones
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Daniel Rigby
- School of Social Sciences, The University of Manchester, Manchester, M13 9PL, UK
| | - Norval J C Strachan
- School of Natural and Computing Sciences/Food Standards Agency Scotland, University of Aberdeen, Aberdeen, AB24 3FX, UK
| | - Ken J Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Paul R Hunter
- Norwich Medical School, University of East Anglia, Norwich 33, NR4 7TJ, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
| | | | - Sarah J O'Brien
- Institute of Infection and Global Health, Liverpool University, Liverpool, L69 7BE, UK.,NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool, UK
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Ryan SF, Adamson NL, Aktipis A, Andersen LK, Austin R, Barnes L, Beasley MR, Bedell KD, Briggs S, Chapman B, Cooper CB, Corn JO, Creamer NG, Delborne JA, Domenico P, Driscoll E, Goodwin J, Hjarding A, Hulbert JM, Isard S, Just MG, Kar Gupta K, López-Uribe MM, O'Sullivan J, Landis EA, Madden AA, McKenney EA, Nichols LM, Reading BJ, Russell S, Sengupta N, Shapiro LR, Shell LK, Sheard JK, Shoemaker DD, Sorger DM, Starling C, Thakur S, Vatsavai RR, Weinstein M, Winfrey P, Dunn RR. The role of citizen science in addressing grand challenges in food and agriculture research. Proc Biol Sci 2018; 285:20181977. [PMID: 30464064 PMCID: PMC6253361 DOI: 10.1098/rspb.2018.1977] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/30/2018] [Indexed: 11/12/2022] Open
Abstract
The power of citizen science to contribute to both science and society is gaining increased recognition, particularly in physics and biology. Although there is a long history of public engagement in agriculture and food science, the term 'citizen science' has rarely been applied to these efforts. Similarly, in the emerging field of citizen science, most new citizen science projects do not focus on food or agriculture. Here, we convened thought leaders from a broad range of fields related to citizen science, agriculture, and food science to highlight key opportunities for bridging these overlapping yet disconnected communities/fields and identify ways to leverage their respective strengths. Specifically, we show that (i) citizen science projects are addressing many grand challenges facing our food systems, as outlined by the United States National Institute of Food and Agriculture, as well as broader Sustainable Development Goals set by the United Nations Development Programme, (ii) there exist emerging opportunities and unique challenges for citizen science in agriculture/food research, and (iii) the greatest opportunities for the development of citizen science projects in agriculture and food science will be gained by using the existing infrastructure and tools of Extension programmes and through the engagement of urban communities. Further, we argue there is no better time to foster greater collaboration between these fields given the trend of shrinking Extension programmes, the increasing need to apply innovative solutions to address rising demands on agricultural systems, and the exponential growth of the field of citizen science.
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Affiliation(s)
- S F Ryan
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - N L Adamson
- Xerces Society for Invertebrate Conservation/USDA NRCS ENTSC, Greensboro, NC, USA
| | - A Aktipis
- Department of Psychology, Arizona State University, Tempe, AZ, USA
| | - L K Andersen
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
| | - R Austin
- Department of Crop and Soil Sciences, NC State Extension, Raleigh, NC, USA
| | - L Barnes
- Lincoln Heights Environmental Connections Magnet Elementary School, Fuquay-Varina, NC, USA
| | - M R Beasley
- Knightdale High School of Collaborative Design, Knightdale, NC, USA
| | - K D Bedell
- School of Education, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S Briggs
- NC Plant Sciences Initiative, College of Agriculture and Life Sciences, NC State Extension, Raleigh, NC, USA
| | - B Chapman
- Department of Agricultural and Human Sciences, NC State Extension, Raleigh, NC, USA
| | - C B Cooper
- Department of Forestry and Environmental Resources, NC State Extension, Raleigh, NC, USA
| | - J O Corn
- William and Ida Friday Institute for Educational Innovation, NC State Extension, Raleigh, NC, USA
| | - N G Creamer
- Department of Horticultural Science, NC State Extension, Raleigh, NC, USA
| | - J A Delborne
- Department of Forestry and Environmental Resources, NC State Extension, Raleigh, NC, USA
| | - P Domenico
- Curriculum Enhancement Programs at Wake County Public School System, Cary, NC, USA
| | - E Driscoll
- Department of Horticultural Science, NC State Extension, Raleigh, NC, USA
| | - J Goodwin
- Department of Communication, NC State Extension, Raleigh, NC, USA
| | - A Hjarding
- North Carolina Wildlife Federation, Charlotte, NC, USA
- The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - J M Hulbert
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - S Isard
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, USA
- Department of Meteorology and Atmospheric Sciences, Pennsylvania State University, State College, PA, USA
| | - M G Just
- Department of Entomology and Plant Pathology, NC State Extension, Raleigh, NC, USA
| | - K Kar Gupta
- Biodiversity Lab, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - M M López-Uribe
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, State College, PA, USA
| | - J O'Sullivan
- Center for Environmental Farming Systems, North Carolina A&T State University, Greensboro, NC, USA
| | - E A Landis
- Department of Biology, Tufts University, Medford, MA, USA
| | - A A Madden
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
| | - E A McKenney
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
- Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - L M Nichols
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
| | - B J Reading
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
| | - S Russell
- Millbrook Environmental Connections Magnet Elementary School, Raleigh, NC, USA
| | - N Sengupta
- Consultant - Biodiversity Conservation & Sustainable Development, Auroville, Tamil Nadu, India
| | - L R Shapiro
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
| | - L K Shell
- Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - J K Sheard
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, Copenhagen University, Copenhagen, Denmark
| | - D D Shoemaker
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - D M Sorger
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
- Research and Collections, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
| | - C Starling
- Heritage High School, Wake Forest, NC, USA
| | - S Thakur
- College of Veterinary Medicine, NC State Extension, Raleigh, NC, USA
| | - R R Vatsavai
- Department of Computer Science, NC State Extension, Raleigh, NC, USA
| | - M Weinstein
- Evaluation and Accountability Coordinator Extension Administration, NC State Extension, Raleigh, NC, USA
| | - P Winfrey
- Arizona State University Biodesign Institute, Tempe, AZ, USA
| | - R R Dunn
- Department of Applied Ecology, NC State Extension, Raleigh, NC, USA
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9
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Carron M, Chang YM, Momanyi K, Akoko J, Kiiru J, Bettridge J, Chaloner G, Rushton J, O’Brien S, Williams N, Fèvre EM, Häsler B. Campylobacter, a zoonotic pathogen of global importance: Prevalence and risk factors in the fast-evolving chicken meat system of Nairobi, Kenya. PLoS Negl Trop Dis 2018; 12:e0006658. [PMID: 30102697 PMCID: PMC6122836 DOI: 10.1371/journal.pntd.0006658] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 09/04/2018] [Accepted: 07/02/2018] [Indexed: 11/18/2022] Open
Abstract
Campylobacteriosis is a leading foodborne zoonosis worldwide, and is frequently associated with handling and consumption of poultry meat. Various studies indicate that Campylobacter causes a substantial human disease burden in low to middle-income countries, but data regarding the organism's epidemiology in countries like Kenya are scarce. In sub-Saharan Africa, 3.8 million deaths of children under-5 years of age are reported annually. Of those, 25% are caused by diarrheal diseases, and Campylobacter is one of the most frequently isolated bacteria from diarrheic children. With the growth of urban conglomerates, such as Kenya's capital, Nairobi, changes in diets, food production systems, and retailing dynamics, it is likely that exposure and susceptibility to this pathogen will change. Therefore, the importance of Campylobacter disease burden in Kenya may increase further. The objectives of this study were: 1) to determine the prevalence of Campylobacter spp. in Nairobi's small-scale chicken farms and meat retailers, and 2) to identify potential risk factors associated with its presence in those sites. The prevalence data provides the first detailed baseline for this pathogen in the urban Kenyan context. The risk factors provide context-specific insights for disease managers. A cross-sectional study of broiler, indigenous chicken farms, and chicken meat retailers, was conducted in a peri-urban, low to middle-income area (Dagoretti), and a very-low income informal settlement (Kibera) of Nairobi. Chicken faeces were collected using one pair of boot socks per farm, and 3 raw chicken meat samples were purchased per retailer. Samples were cultured for viable Campylobacter spp. using mCCDA, followed by blood agar plates in aerobic/microaerobic conditions for prevalence calculations. A questionnaire-based survey on sanitary, sourcing and selling practices was conducted at each site for risk factor identification using logistic regression analyses. A total of 171 farm premises and 53 retailers were sampled and interviewed. The prevalence results for Campylobacter spp. were between 33 to 44% for broiler and indigenous chicken farms, 60% and 64% for retailers, in Dagoretti and Kibera, respectively. Univariable logistic regression showed an association between Campylobacter spp. presence and the easiness of cleaning the display material used by the retailer. Restricting access to the flock was also associated with the pathogen's presence. Multivariable logistic regression identified the selling of defrosted meat as a retailer risk factor (OR: 4.69; 95% CI: 1.31-19.97), calling for more investigation of the reported repetitive freezing-thawing processes and cold chain improvement options. At the farm-level, having a pen floor of material not easy to clean was found to increase the risk (OR: 2.31; 95%CI: 1.06-5.37). The relatively high prevalence of Campylobacter spp. across different areas and value chain nodes indicates a clear human exposure risk. The open nature of both small-scale broiler and indigenous chicken production practices with low biosecurity, hygiene and informal transactions, likely plays a role in this. While gradual improvement of farm biosecurity is recommended, risk factors identified suggest that consumer education and enforcement of basic food safety principles at the retailer end of the food continuum represent key targets for risk reduction in informal settings.
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Affiliation(s)
- Maud Carron
- Royal Veterinary College (RVC), Pathobiology and Population Sciences, Hatfield, United Kingdom
- Leverhulme Centre for Integrative Research on Agriculture and Health (LCIRAH), London, United Kingdom
| | - Yu-Mei Chang
- Royal Veterinary College (RVC), Pathobiology and Population Sciences, Hatfield, United Kingdom
| | - Kelvin Momanyi
- International Livestock Research Institute (ILRI), Animal and Human Health Programme, Nairobi, Kenya
| | - James Akoko
- International Livestock Research Institute (ILRI), Animal and Human Health Programme, Nairobi, Kenya
| | - John Kiiru
- Centre for Microbiology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Judy Bettridge
- International Livestock Research Institute (ILRI), Animal and Human Health Programme, Nairobi, Kenya
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Gemma Chaloner
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Jonathan Rushton
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Sarah O’Brien
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Nicola Williams
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Eric M. Fèvre
- International Livestock Research Institute (ILRI), Animal and Human Health Programme, Nairobi, Kenya
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Neston, United Kingdom
| | - Barbara Häsler
- Royal Veterinary College (RVC), Pathobiology and Population Sciences, Hatfield, United Kingdom
- Leverhulme Centre for Integrative Research on Agriculture and Health (LCIRAH), London, United Kingdom
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10
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Affiliation(s)
- Robert A. Rasmussen
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, USA
| | - Sherry S. Bohn
- University of Maryland at College Park, College Park, MD, USA
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11
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Abstract
This review examined the likely impact of climate change upon food-borne disease in the UK using Campylobacter and Salmonella as example organisms. Campylobacter is an important food-borne disease and an increasing public health threat. There is a reasonable evidence base that the environment and weather play a role in its transmission to humans. However, uncertainty as to the precise mechanisms through which weather affects disease, make it difficult to assess the likely impact of climate change. There are strong positive associations between Salmonella cases and ambient temperature, and a clear understanding of the mechanisms behind this. However, because the incidence of Salmonella disease is declining in the UK, any climate change increases are likely to be small. For both Salmonella and Campylobacter the disease incidence is greatest in older adults and young children. There are many pathways through which climate change may affect food but only a few of these have been rigorously examined. This provides a high degree of uncertainty as to what the impacts of climate change will be. Food is highly controlled at the National and EU level. This provides the UK with resilience to climate change as well as potential to adapt to its consequences but it is unknown whether these are sufficient in the context of a changing climate.
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Affiliation(s)
- Iain R Lake
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
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