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Biosecurity Surveillance: Quantitative Approaches. CABI Invasives Series. 6

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This book is a source of information on practical and innovative approaches to biosecurity surveillance. It explains the foundation and concepts behind surveillance design, with examples of methods and tools created to deal with surveillance challenges. With supporting case studies and including current directions in research, it covers evidence-based approaches to surveillance, statistics, detectability, single and multi-species detection, risk assessment, diagnostics, data-basing, modelling of invasion and spread, optimisation, and future climate challenges.

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1 Introduction to Biosecurity Surveillance: Quantitative Approaches

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1

Introduction to Biosecurity

Surveillance: Quantitative

Approaches

Frith Jarrad*

The University of Melbourne, Parkville, Australia

1.1 Purpose and Scope of this Book

Biosecurity is a general term that means the measures put in place to secure against unwanted biological invasions. Here, ‘measures’ includes a wide range of actions and processes relevant to different biosecurity problems and different components of the biosecurity domain; the term ‘secure’ includes protection against an act, threat or risk of an invasion, arrival or spread, or in some cases of the removal or misuse of biological items; and the term ‘biological’ also embraces a range of definitions, including humans, plants, animals, viruses and so on.

In this book, we focus on plant and animal biosecurity. As discussed in Chapter

2, this is a very wide arena in itself, encompassing many definitions of the term

‘biosecurity’ and its constitutent definitions of measures, security and biology. Within this arena, we focus even more closely on one aspect of the biosecurity domain: surveillance.

 

2 Biosecurity Surveillance in Agriculture and Environment: a Review

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2

Biosecurity Surveillance in

Agriculture and Environment: a Review

Megan Quinlan,1* Mark Stanaway2 and Kerrie

Mengersen2

1Centre

for Environmental Policy, Imperial College London, UK;

University of Technology, Brisbane, Australia

2Queensland

2.1 Introduction: the Concept of

Biosecurity

The term biosecurity has many definitions.

It is frequently perceived as a new, more coordinated approach, generally led by a particular governmental authority or network of authorities, to understand and manage natural and human-caused threats to a range of biological resources. The approach includes an ‘increasing reliance on systematic risk analysis’ (FAO, 2007) and integration of existing sectoral capacities, which consequentially highlights any gaps in authority or coverage of risk management measures. The holistic, almost organic nature of the concept (for which the specific objective or desired outcome may not always be clear) is balanced against a pragmatic insistence on cost-effective, efficient steps towards protection of valued resources.

 

3 Getting the Story Straight: Laying the Foundations for Statistical Evaluation of the Performance of Surveillance

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3

Getting the Story Straight: Laying the Foundations for Statistical

Evaluation of the Performance of

Surveillance

Samantha Low-Choy*

Queensland University of Technology, Brisbane, Australia

Abstract

This chapter describes the foundations for statistical evaluation of the performance of surveillance. A ‘story’, about a conversation between biosecurity and quantitative participants, helps weave together these concepts and make them less abstract.

The chapter begins with an overview of the biosecurity questions applicable to quantitative analysis, by defining the types of response variables. This provides a basis for introducing the different statistical modelling paradigms that might be adopted for analysis, such as classical or frequentist hypothesis testing, Bayesian approaches and deterministic modelling. Regardless of paradigm, various objectives of the surveillance programme can be identified, and characterized, as ‘seek and destroy’, ‘maintaining the status quo’ or hybrids. The chapter proceeds by addressing the elements of statistical design, requiring a more detailed view of the spatio-temporal context of surveillance: identifying the unit of surveillance, the role of randomization, and issues of extent, scale and sampling effort.

 

4 Hierarchical Models for Evaluating Surveillance Strategies: Diversity Within a Common Modular Structure

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4

Hierarchical Models for Evaluating

Surveillance Strategies: Diversity

Within a Common Modular

Structure

Samantha Low-Choy*

Queensland University of Technology, Brisbane, Australia

Abstract

4.1 Introduction

This chapter introduces a hierarchical modelling approach to biosecurity surveillance, arguing that this provides a common structure for representing many different existing models, ostensibly proposed within different quantitative paradigms. A Bayesian formulation is demonstrated to provide a natural framework for analysing such hierarchical models. The chapter commences with a description of Bayesian models for estimation and prediction of pest prevalence as well as detectability, and uses this as motivation for describing the concept of

Bayesian learning. The role of prior distributions in facilitating estimation with uncertainty is then discussed in detail.

Attention then turns to the process of constructing hierarchical Bayesian models for surveillance, including how to model search effort, detectability, prevalence and other important features. The generality of the approach is illustrated through a commentary on stochastic scenario trees, via three-stage Bayesian hierarchical models, three-stage cluster sampling and four-stage multi-scale detection. The chapter concludes with comments on how to choose among quantitative methods, and a comparative discussion of features in the modular modelbased view described here.

 

5 The Relationship Between Biosecurity Surveillance and Risk Analysis

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5

The Relationship Between

Biosecurity Surveillance and Risk

Analysis

Alan MacLeod*

Food and Environment Research Agency, York, UK

Abstract

National authorities that seek to protect plant and animal health and welfare follow international agreements and guidelines designed to inhibit the introduction and spread of pests and diseases harmful to animals and plants by conducting formal risk analyses. Analyses are generally initiated by: (i) new information about a pest or disease; (ii) discovery of a pathway for pest or disease introduction (e.g. through preborder, border and post-border biosecurity surveillance); or (iii) review of a relevant pest or disease management policy.

Quantitative and qualitative techniques are used in risk analyses whose conclusions can form the basis of sanitary and phytosanitary regulations and inform biosecurity surveillance strategies generating data that helps narrow uncertainties within risk analyses.

5.1 Introduction

In seeking to implement a biosecurity regime that protects a nation’s plant and animal resources, organizations with lead responsibility should recognize that there is a dynamic relationship between biosecurity surveillance and the analysis of risks that threaten biotic resources though biological invasions. Risk analyses to inform decision

 

6 Designing Surveillance for Emergency Response

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6

Designing Surveillance for

Emergency Response

Zoé van Havre* and Peter Whittle

Queensland University of Technology, Brisbane, Australia

Abstract

This chapter concerns designing surveillance measures for responding to a detected incursion of non-indigenous species (NIS) in an area. The context may be agricultural, urban or natural landscapes – or combinations of these. The NIS may be a plant pest, or an animal disease, or an environmental pest or weed. This is a very broad sphere and so there are relevant extensive literature and policy frameworks covering NIS, especially for plant pests

(International Plant Protection Convention) and animal diseases (World Organisation for

Animal Health). Our intention is to contribute to this large body of work, rather than to review it, with a focus on surveillance in an emergency response. We discuss concepts, tools and guidelines for the development of both contingency plans for likely or high-risk invasive species, as well as the information required to mount a response for an unanticipated threat. We include strategic advice for planning proofof-absence studies following an NIS incursion response. We also discuss strategies for dealing with large and heterogeneous landscapes.

 

7 The Role of Surveillance in Evaluating and Comparing International Quarantine Systems

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The Role of Surveillance in

Evaluating and Comparing

International Quarantine Systems

Murthy Mittinty,1* Peter Whittle,2 Mark Burgman3 and

Kerrie Mengersen2

1The

University of Adelaide, Adelaide, Australia; 2Queensland

University of Technology, Brisbane, Australia; 3Centre of Excellence for Biosecurity Risk Analysis, The University of Melbourne,

Parkville, Australia

Abstract

The two major aims of this chapter are to understand the role of surveillance in quarantine and to develop a checklist that facilitates the evaluation of international quarantine systems. Despite the global similarity of intention regarding quarantine, there still exist dissimilarities between countries in specific aspects of quarantine practice, that impact on the role that surveillance plays in different quarantine systems and on corresponding risk assessment frameworks.

In order to create the checklist, we define the concept of risk in the context of biosecurity and quarantine. The six principles that we used in the comparisons are: (i) harmonization; (ii) appropriate level of protection; (iii) consistency; (iv) equivalence; (v) transparency; and (vi) uncertainty. The checklist is intended to provide a structured platform for evaluating a country’s risk analysis methodology, making international comparisons of risk analysis systems, promoting good practice and identifying areas for further improvement. Based on these six principles, surveillance was observed to be an enabler and evidence base for many of the checklist indicators. Surveillance outputs and out-

 

8 Estimating Detection Rates and Probabilities

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Estimating Detection Rates and

Probabilities

Cindy E. Hauser,1* Georgia E. Garrard2 and

Joslin L. Moore3

1University

of Melbourne, Parkville, Australia; 2RMIT University,

Melbourne, Australia; 3Monash University, Clayton, Australia

Abstract

Surveillance activities provide only imperfect detection of biosecurity threats, and so quantifying detection rates and probabilities is important for making reliable inferences from survey data.

Furthermore, an understanding of detection rates and probabilities allows for effective survey design and resource allocation to address biosecurity threats. Detection rates and probabilities can be estimated directly via experiments or indirectly during routine surveillance activities. In this chapter we introduce basic presence/absence detection models and provide guidelines for designing a detection experiment. We also summarize other methods available for estimating detection rates and probabilities when pest abundance, as well as presence/absence, affects management.

 

9 Ad hoc Solutions to Estimating Pathway Non-compliance Rates Using Imperfect and Incomplete Information

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Ad hoc Solutions to Estimating

Pathway Non-compliance Rates

Using Imperfect and Incomplete

Information

Andrew P. Robinson,1* Matthew Chisholm,1 Robert

Mudford2 and Robert Maillardet1

1The

University of Melbourne, Parkville, Australia; 2Australian

Government Department of Agriculture, Canberra, Australia

Abstract

This chapter provides ad hoc tools to assist in estimating the non-compliance rate of biosecurity risk material (BRM) in a given pathway when certain data are unavailable.

We use the inspection of international mail as a case study. Estimating the noncompliance rate of a pathway is essential in order to assess the risk of the environment, and to make defensible decisions about the allocation of inspection effort. Counts of articles inspected and articles found to have

BRM are necessary for estimating the pathway non-compliance rate, and inspection counts by cohort (sub-pathway) are needed in order to perform profiling within a pathway, for example, identifying and prioritizing high-risk countries of origin for mail articles. Detailed information is usually kept on non-compliant mail articles that have been intercepted, but sometimes not on the articles that were inspected and passed, which is needed to report the inspection effort undertaken. Hence, the inspection effort by cohort may be unknown.

 

10 Surveillance for Soilborne Microbial Biocontrol Agents and Plant Pathogens

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10

Surveillance for Soilborne

Microbial Biocontrol Agents and

Plant Pathogens

Peter Whittle,1* Ingvar Sundh2 and Stephen

Neate3

1Queensland

University of Technology, Brisbane, Australia;

University of Agricultural Sciences, Uppsala, Sweden;

3Department of Agriculture, Fisheries and Forestry,

Queensland, Toowoomba, Australia

2Swedish

Abstract

10.1 Introduction

Soilborne microbes are well known in agriculture as biological control agents and plant pathogens. Methods for their detection or diagnosis have been studied extensively over decades in order to identify the organisms, elucidate their biology, detect their presence and estimate their prevalence in environments, manipulate and control their populations, and answer questions about risk. The high importance of microbial biocontrol agents and soilborne plant pathogens in agriculture and the environment has given rise to needs to undertake surveillance on them. The appropriate design of surveillance (the deployment of detection methods in practice in order to create surveillance information) is driven by the questions that need to be answered, which depend on the context. This chapter will discuss the reasons for surveillance for these two groups of soilborne microbes and the methods used for their detection, to see whether there are opportunities, or needs, to improve the design of soilborne microbe surveillance.

 

11 Design of a Surveillance System for Non-indigenous Species on Barrow Island: Plants Case Study

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Design of a Surveillance System for Non-indigenous Species on

Barrow Island: Plants Case

Study

Justine Murray,1* Peter Whittle,2 Frith Jarrad,3

Susan Barrett,4 Richard Stoklosa5 and Kerrie

Mengersen2

1CSIRO

Biosecurity Flagship, Brisbane, Australia; 2Queensland

University of Technology, Brisbane, Australia; 3The University of

Melbourne, Parkville, Australia; 4National Plant Biosecurity

Cooperative Research Centre, Bruce, Australia; 5E-Systems Pty

Limited, Hobart, Tasmania

Abstract

Complex surveillance problems are common in biosecurity, such as prioritizing detection among multiple invasive species, specifying risk over a heterogeneous landscape and combining multiple sources of surveillance data in surveillance design.

Programmes for surveillance generally do not incorporate power but instead are heavily influenced by budgetary constraints.

However, when designing biosecurity programmes for surveillance, monitoring and eradication, it is logical and desirable to design to a statistical standard to detect invaders and then demonstrate that standard was achieved in implementation.

 

12 Towards Reliable Mapping of Biosecurity Risk: Incorporating Uncertainty and Decision Makers’ Risk Aversion

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12

Towards Reliable Mapping of

Biosecurity Risk: Incorporating

Uncertainty and Decision

Makers’ Risk Aversion

Denys Yemshanov,1* Frank H. Koch,2 Mark Ducey3 and Robert A. Haack4

1Natural

Resources Canada, Canadian Forest Service, Sault

Ste Marie, Canada; 2USDA Forest Service, Southern Research

Station, North Carolina, USA; 3University of New Hampshire,

Durham, USA; 4USDA Forest Service, Northern Research

Station, Michigan, USA

Abstract

Pest risk maps are an important source of decision support when devising strategies to minimize introductions of invasive organisms and mitigate their impacts. When possible management responses to an invader include costly or socially sensitive activities, decision makers tend to follow a more certain (i.e. risk-averse) course of action. We present a new mapping technique that assesses pest invasion risk from the perspective of a risk-averse decision maker.

We demonstrate the approach by evaluating the likelihood that an invasive forest pest will be transported to one of the continental

 

13 Detection Survey Design for Decision Making During Biosecurity Incursions

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13

Detection Survey Design for

Decision Making During

Biosecurity Incursions

John M. Kean,1* Graham M. Burnip2 and

Amin Pathan2

1AgResearch

Ltd, Hamilton, New Zealand; 2Ministry for Primary

Industries, Christchurch, New Zealand

Abstract

13.1 Introduction

Biosecurity surveillance involves special challenges, in particular dealing with the fact that the target organism is usually absent from the surveyed area. In this context, surveys must be designed to detect small target populations and to estimate the likelihood that failing to detect the population means it is really not there. We summarize the basic formulae used to design simple detection surveys and show how they can be combined to create multilevel sample plans that are quick and easy to formulate, parameterize and optimize during a biosecurity incursion response. In particular, incursion investigators often need to assess the spatial extent of populations to evaluate whether eradication is a viable management option, but strict delimitation of the occupied area requires substantial sampling effort. Instead, we advocate a pragmatic approach whereby detection surveys are designed to address a particular data need, such as whether the population is present too widely to be eradicated. In this way key decisions, such as whether or not to attempt eradication, may be informed in the most rapid and costefficient way. This approach was used during the investigation of an incursion of an

 

14 Inference and Prediction with Individual-based Stochastic Models of Epidemics

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14

Inference and Prediction with

Individual-based Stochastic

Models of Epidemics

Gavin Gibson1* and Christopher A. Gilligan2

1Maxwell Institute for Mathematical Sciences, Heriot-Watt

University, Edinburgh, UK; 2University of Cambridge,

Cambridge, UK

Abstract

Stochastic models for the spread of epidemics in space and time are increasingly being used as predictive tools to help in the control of emergent pests and pathogens and as tools for the interpretation of observations of epidemics as they occur.

This chapter provides an introduction to a particular class of stochastic model – the individual-based, spatio-temporal compartment model – that is frequently applied in this context. An overview of the techniques used to implement these models and to fit them to observations is provided. The main implications of different model formulations for biosecurity and the design of control strategies are given. The chapter aims to provide the reader, who already has some knowledge of mathematical and statistical approaches to modelling infectious diseases, with a technical overview of the Bayesian computational approach.

 

15 Evidence of Absence for Invasive Species: Roles for Hierarchical Bayesian Approaches in Regulation

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15

Evidence of Absence for

Invasive Species: Roles for

Hierarchical Bayesian

Approaches in Regulation

Mark Stanaway*

Queensland University of Technology, Brisbane, Australia

Abstract

Regulatory agencies responsible for managing pest incursions rely upon an adequate knowledge of the distribution of the pest. Spatio-temporal estimates of distribution for an actively invading pest require ecological and surveillance information to be assimilated, a task which is well suited to hierarchical Bayesian inference.

The process of developing a pest observation model and a pest status model to evaluate the evidence for absence is explained in relation to existing simple models used for biosecurity surveillance. A case study to estimate the probability of exotic fruit fly absence in a district illustrates how simple invasion process models can be incorporated into the analysis of surveillance programmes.

Trapping information from a previous incursion of Bactrocera papayae in Queensland in 1995 is brought into the detection model. The economic value of maintaining or altering the surveillance programme is assessed in terms of the putative costs of incursion management given different surveillance regimes.

 

16 Using Bayesian Networks to Model Surveillance in Complex Plant and Animal Health Systems

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16

Using Bayesian Networks to

Model Surveillance in Complex

Plant and Animal Health

Systems

Sandra Johnson,1* Kerrie Mengersen,1 Michael

Ormsby2 and Peter Whittle1

1Queensland

2Ministry

University of Technology, Brisbane, Australia; for Primary Industries, Wellington, New Zealand

Abstract

In this chapter we consider biosecurity surveillance as part of a complex system comprising many different biological, environmental and human factors and their interactions. Modelling and analysis of surveillance strategies should take into account these complexities, and also facilitate the use and integration of the many types of different information that can provide insight into the system as a whole. After a brief discussion of a range of options, we focus on Bayesian networks for representing such complex systems. We summarize the features of Bayesian networks and describe these in the context of surveillance.

16.1 Introduction

Surveillance for pests or diseases (hereafter we refer to these jointly as ‘pests’) under the

 

17 Statistical Emulators of Simulation Models to Inform Surveillance and Response to New Biological Invasions

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17

Statistical Emulators of

Simulation Models to Inform

Surveillance and Response to

New Biological Invasions

Michael Renton* and David Savage

The University of Western Australia, Crawley, Australia

Abstract

When a new biosecurity incursion is detected, rapid response is critical to maximize the chance of containment and eradication and minimize the threat to important industries. However, inappropriate response can be extremely costly. For example, we might waste resources on trying to eradicate a pest that has already spread too far to be contained, or use a management strategy that has a lower chance of success than another possibility, and thus allow the pest to escape and establish permanently. Simulation modelling is a tool that can be used to evaluate different management options in the light of available knowledge about the pest’s dispersal and population dynamics and its new environment, but simulation models typically take a long time to develop, parameterize, test, run and analyse. How can modelling be used to provide valuable predictions when rapid response is critical?

 

18 Animal, Vegetable, or … ? A Case Study in Using Animal-health Monitoring Design Tools to Solve a Plant-health Surveillance Problem

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Animal, Vegetable, or …? A Case

Study in Using Animal-health

Monitoring Design Tools to Solve a Plant-health Surveillance

Problem

Susan Hester,1,2* Evan Sergeant,3 Andrew P.

Robinson2,4 and Graham Schultz5

1University

of New England, Armidale, Australia; 2Centre of

Excellence for Biosecurity Risk Analysis, The University of

Melbourne, Melbourne, Australia; 3Ausvet Animal Health

Services, Orange, Australia; 4The University of Melbourne,

Parkville, Australia; 5Department of Primary Industry and

Fisheries, Darwin, Australia

Abstract

Biosecurity managers are often responsible for designing the surveys that are used to demonstrate pest absence from a region or country. This design process involves determining the number of locations to measure and choosing the locations from which survey information is collected (the sampling plan) as well as the number of units within each location that will be sampled (sample size). The choice of sampling plan may be influenced by prior information about the locations and by their spatial distribution. Sample size is influenced by the effectiveness of the testing method, the confidence interval required and the available budget. Biosecurity managers who do not have the time or skills to design appropriate surveys would benefit from applying pre-existing tools or templates to determine the sampling plan, the sample size and the level of resources needed to meet the survey requirements to ensure market access. Unfortunately such tools have not been developed specifically for

 

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