Environmental Engineering for Pathogen Control
1st Edition
Will be published approx. on 18. November 2026
Book
Hardback
704 pages
978-1-394-25338-8 (ISBN)
Description
Control pathogen exposure through unified environmental engineering interventions
Environmental engineers and public health professionals require systematic approaches to pathogen control across air, water, dust, and soil. Environmental Engineering for Pathogen Control delivers a unified framework for mitigating infectious diseases through environmental interventions. Written by Charles N. Haas, a National Academy of Engineering member and distinguished fellow of the International Water Association, this book grounds the emerging intersection of environmental engineering and public health.
The text covers dispersion and transmission of environmental pathogens, disinfection interventions, drinking water contamination, aerosol transmission of disease, and bioterrorist attack response. Detailed coverage addresses air transmission and movement in indoor environments, viability and growth-decay dynamics of microbes in environmental media, and quantitative microbial risk assessment methodologies. Case studies demonstrate practical risk assessment applications across diverse contamination scenarios.
Readers will also find:
Systematic methods for analyzing pathogen dispersion across environmental media including air, water, dust, and soil transmission pathways
Quantitative frameworks for assessing microbial viability, growth rates, and decay patterns in diverse environmental conditions and media
Engineering approaches to disinfection interventions with detailed coverage of drinking water treatment and contamination response protocols
Indoor air quality analysis techniques addressing aerosol transmission mechanics and ventilation strategies for pathogen control measures
Risk assessment case studies with step-by-step guidance for evaluating exposure scenarios and determining appropriate intervention strategies
Environmental Engineering for Pathogen Control serves advanced environmental engineering students, public health professionals, and practitioners in environmental health and industrial hygiene. This authoritative resource equips readers with the quantitative tools and engineering frameworks needed to reduce human exposure to pathogens and control associated health risks.
Environmental engineers and public health professionals require systematic approaches to pathogen control across air, water, dust, and soil. Environmental Engineering for Pathogen Control delivers a unified framework for mitigating infectious diseases through environmental interventions. Written by Charles N. Haas, a National Academy of Engineering member and distinguished fellow of the International Water Association, this book grounds the emerging intersection of environmental engineering and public health.
The text covers dispersion and transmission of environmental pathogens, disinfection interventions, drinking water contamination, aerosol transmission of disease, and bioterrorist attack response. Detailed coverage addresses air transmission and movement in indoor environments, viability and growth-decay dynamics of microbes in environmental media, and quantitative microbial risk assessment methodologies. Case studies demonstrate practical risk assessment applications across diverse contamination scenarios.
Readers will also find:
Systematic methods for analyzing pathogen dispersion across environmental media including air, water, dust, and soil transmission pathways
Quantitative frameworks for assessing microbial viability, growth rates, and decay patterns in diverse environmental conditions and media
Engineering approaches to disinfection interventions with detailed coverage of drinking water treatment and contamination response protocols
Indoor air quality analysis techniques addressing aerosol transmission mechanics and ventilation strategies for pathogen control measures
Risk assessment case studies with step-by-step guidance for evaluating exposure scenarios and determining appropriate intervention strategies
Environmental Engineering for Pathogen Control serves advanced environmental engineering students, public health professionals, and practitioners in environmental health and industrial hygiene. This authoritative resource equips readers with the quantitative tools and engineering frameworks needed to reduce human exposure to pathogens and control associated health risks.
More details
Language
English
Place of publication
New York
United States
Target group
Professional and scholarly
ISBN-13
978-1-394-25338-8 (9781394253388)
Copyright in bibliographic data and cover images is held by Nielsen Book Services Limited or by the publishers or by their respective licensors: all rights reserved.
Schweitzer Classification
Person
Charles N. Haas, PhD, is the L.D. Betz Professor of Environmental Engineering amd Distinguished Professor at Drexel University and a member of the National Academy of Engineering. He co-directed the USEPA/DHS Center for Advancing Microbial Risk Assessment and holds is a fellow in multiple societies, including fellowships in the International Water Association, American Academy for the Advancement of Science, Society for Risk Analysis, Association of Environmental Engineering and Science Professors, and American Academy of Microbiology. His honors include the Dr. John Leal Award, AP Black Award, and Clarke Water Prize from the American Water Works Association. He is a Board Certified Environmental Engineering Member by eminence of the American Academy of Environmental Engineers and Scientists.
Content
Contents i
List of Figures ix
List of Tables xiv
1 Introduction 1
1.1 Scope of Coverage 2
1.2 Instructor Notes 3
1.3 Bibliography 3
I Environmental Engineering and Pathogen Basics 5
2 Who, How, Where 7
2.1 Pathogens of Concern 8
2.1.1 Sub-Viral Agents 9
2.1.2 Viruses 9
2.1.3 Bacteria 14
Classification by Metabolic Strategy 15
Other Important Characteristics 18
Formal Taxonomy and Classification 19
2.1.4 Protozoa 22
2.1.5 Fungi 26
Zoosporic Fungi 28
Zygomycetous Fungi 28
Dikarya 29
2.1.6 Other Agents of Concern 30
2.2 Portals of Entry 30
2.3 Venues of Concern 32
2.3.1 Indoor Environments 32
2.3.2 Outdoor Environments 34
2.3.3 In Vehicles 35
2.4 Discussion Questions and Problems 35
2.5 Bibliography 35
3 Key Paradigms of Environmental Engineering 45
3.1 Risk Framework 45
3.1.1 Problem Definition 48
3.1.2 Risk Assessment 48
Hazard Characterization 48
Dose Response Assessment 49
Exposure Assessment 49
Risk Characterization 50
3.1.3 Risk Management 51
3.1.4 Risk Communication 53
3.2 Source, Fate, Transport, Receptor 54
3.3 Uncertainty & Variability 57
3.4 Discussion Questions and Problems 60
3.5 Bibliography 60
4 Unique Features of Pathogens 63
4.1 Stochastic Variability and Low concentrations 63
4.2 Growth as well as Decay 66
4.3 Humans as Sources and Receptors 69
4.4 Dose Response 71
4.5 Contagiousness and Population Spread 72
4.6 Key Takeaways 73
4.7 Discussion Questions and Problems 73
4.8 Bibliography 74
5 Pathogen Sampling 77
5.1 Workflow 77
5.2 Taking the Sample 79
5.2.1 Wastewater 79
5.2.2 DrinkingWater, Other Liquids 85
Backflow and Cross Connections 88
Groundwater 89
Rainwater Collection 90
Premise (Building) Plumbing 91
5.2.3 RecreationalWaters 93
5.2.4 Air 94
Ambient Air Sampling 94
Passive Air Samplers 99
5.2.5 Dusts, Surfaces, Fomites 100
5.2.6 Solids and Semisolids 102
5.3 Decontamination and Biosafety 103
5.4 Isolation, Concentration, and Separation 105
5.5 Discussion Questions and Problems 107
5.6 Bibliography 108
6 How Pathogens Are Quantified 117
6.1 Selection of Targets 117
6.1.1 Indicator Organisms 117
6.1.2 Microbial Source Tracking 119
6.1.3 Direct Measurement of Pathogens . 120
6.2 Count, Quantal, and Time to Response Methods 120
6.2.1 Count Methods 120
Statistics of Count Methods 122
6.2.2 Quantal Methods 136
Statistics of Quantal Methods 138
6.2.3 Time to Response Methods 141
6.3 Direct Microscopy 142
6.3.1 Optical Microscopy 142
Quantification by Optical Microscopy 147
6.3.2 Electron Microscopy 148
6.4 Flow Cytometry 151
6.5 Culture Methods 154
6.5.1 Pre-enrichment or Pre-selection 154
6.5.2 Culture Media Types, Selection, Incubation 154
6.5.3 Whole Organism, Organ or Cell Culture 155
6.6 Molecular Methods 158
6.6.1 Microbial Nucleic Acids 158
Molecules of Interest 158
Extraction, Separation and Concentration of Nucleic Acids 160
6.6.2 Polymerase Chain Reaction Based Methods 160
6.6.3 Sequencing Approaches 165
Amplicon Based Sequencing 166
Shotgun sequencing methods 168
6.6.4 Use for Quantitative Exposure Estimation 171
Relationship to Viability and Infectiousness 171
6.7 Implications for Exposure 173
6.8 Discussion Questions and Problems 173
6.9 Bibliography 175
II Quantifying Exposure 189
7 Sources of Pathogens 191
7.1 Generic Approach 191
7.2 Human Excreta 192
7.3 Exhalation 195
7.4 Other Bodily Discharges 198
7.5 Skin Associated Pathogens 200
7.6 Our biological cohabitants 202
7.6.1 Plants 202
7.6.2 Pets 203
7.6.3 Agricultural Animals 205
7.6.4 Wild Animals 207
7.7 Waste Management Practices 210
7.7.1 Sanitary Landfills 210
7.7.2 Biosolids Application to Land 211
7.7.3 Wastewater Treatment 213
7.8 Other Sources via Aerosolization of Water . 216
7.9 Discussion Questions and Problems 216
7.10 Bibliography 217
8 Transport, Growth and Decay in the Environment 231
8.1 Chapter Overview 231
8.2 Taxonomy of Models . 232
8.2.1 Batch and Simple Flow Systems 234
8.2.2 Modeling Approaches for Complex Flow Systems 242
8.3 Quantitative description of Transport 243
8.3.1 Box Models 243
8.3.2 Box Models with Particle Tracking 246
8.3.3 Advection Reaction Processes -Eulerian-Eulerian Approach 250
Brief Outline of Fluid Flow Modeling 250
Contaminants in a Flowing System 252
8.3.4 A Priori Estimation of Dispersion 257
8.3.5 Advection Reaction Processes - Eulerian-Lagrangian Approach 261
8.4 Quantitative Description of Rate Processes 264
8.4.1 Physical 264
Processes Unique to Air 265
Generally Applicable Processes 267
8.4.2 Decay 271
Reaction Rate Approach 274
Hazard Rate Approach 276
Phenomenological and Empirical Models 278
Fitting Decay Rate Models to Data 279
Modulators of Decay Rates and Data Sources 287
8.4.3 Growth 292
8.4.4 Stochastic Treatment of Growth and Decay 299
8.4.5 Predator-Prey and Other Biotic Interactions 301
8.5 Quantitative Description of Other Flux Processes 305
8.5.1 External Fields 305
Gravitational Force 305
Electrical Force 309
Magnetic Force 312
8.5.2 Interphase Transfer Processes 313
Indoor Environments 313
Outdoor Land Air Exchange 314
Water Sediment Exchange 315
Liquid Air Exchange 315
8.6 Longer range and more complex models 317
8.6.1 Atmospheric Dispersion Models 317
8.6.2 Indoor Air Models 320
8.6.3 Water Quality Models 321
8.7 Discussion Questions and Problems 325
8.8 Bibliography 326
III Mitigating Exposure 343
9 Characterizing Interventions 345
9.1 Multiple Barriers . 345
9.2 Typology of Interventions 348
9.3 Quantifying Performance 349
9.4 Incorporating Variability and Uncertainty 352
9.5 Estimating Performance of Multiple Barriers with Variability and Uncertainty 360
9.6 Discussion Questions and Problems 366
9.7 Bibliography 367
10 Physical Removal and Reduction 369
10.1 Removal by Action of Gravitational Forces 369
10.1.1 Water Applications 370
10.1.2 Air Applications 374
10.1.3 Cyclonic Separators 374
10.2 Removal by Virtue of Size 377
10.2.1 Depth Filters . 378
Air Filtration . 378
Water Filtration 383
Depth Filter Removal Efficiency 384
Depth Filter Pressure Drop 391
Depth Filter Regeneration 395
10.2.2 Membranes 395
10.3 Removal by Virtue of Charge 397
10.4 Surface Cleaning . 398
10.5 Discussion Questions and Problems 400
10.6 Bibliography 401
11 Inactivation Fundamentals 407
11.1 Disinfecting Agents 408
11.1.1 Chemical Disinfectants 408
Halogens 409
Hydrogen Peroxide 414
Ozone 415
Peracetic and Other Peroxy Acids 418
Ethylene Dioxide 419
Organic Disinfecting Compounds 420
11.1.2 Physical Disinfectants 422
Heat 422
Light 422
Ionizing Radiation 424
11.1.3 Advanced Oxidation - Combinations of Processes 424
11.2 Kinetics of Disinfection 425
11.2.1 General Inactivation Models 425
11.2.2 Chemical Disinfection 435
11.2.3 Thermal Inactivation 451
11.2.4 UV and Radiation Disinfection 457
11.3 Discussion Questions and Problems 470
11.4 Bibliography 471
12 Inactivation Applications 483
12.1 Fitting Performance Models to Data 483
12.1.1 Basic Count Data 486
12.1.2 Basic Quantal Data 491
12.1.3 Basic Continuous Data 494
12.1.4 Continuous Data With Censoring 497
12.1.5 Complex Models 498
12.1.6 Comparing Models 505
12.2 Byproducts 509
12.2.1 Chlorine and Halogen Compounds 509
12.2.2 Non Halogen Oxidants 510
12.2.3 UV and Other Radiation Systems 510
12.3 Coincidental Inactivation by Other Processes 511
12.4 Applications 511
12.4.1 Liquids 511
Chlorine 512
Ozone 516
Peracetic Acid 518
UV and Light 518
12.4.2 Air 519
Chemical Agents 520
UV 527
12.4.3 Solids and Semi-Solids 528
12.4.4 Surface Disinfection 530
12.5 Questions and Problems 531
12.6 Bibliography 533
13 Exposure Assessment 543
13.1 Microorganism Distributions 545
13.1.1 Direct Measurement 545
13.1.2 From Source to Receptor Models 546
13.1.3 Uncertainty of Distributions 548
13.2 Medium Contact 548
13.2.1 Ingestion 548
13.2.2 Inhalation 549
13.2.3 Fomites 550
13.2.4 Miscellaneous Other Routes 550
13.3 Formal Computation of Uncertainty and Variability 551
13.3.1 Determining Best Distributional Forms 551
13.3.2 Parametric Uncertainty of Distributional Parameters 552
13.3.3 Combining Multiple Distributions 561
13.3.4 Advanced Concepts 564
Correlated Variables 564
Copulas 568
Sampling Methods 572
13.4 Discussion Questions and Problems 576
13.5 Bibliography 577
IV Balancing and Deciding 583
14 From Dose Response to Risk Characterization 585
14.1 Dose Response 585
14.1.1 Dose Response Models 588
Generation 0 588
Generation 1 Dose Response 589
Generation 2 Dose Response with Modulating Factors 596
Generation 3 Dose Response Models with Dynamics 599
Beyond Generation 3 602
14.1.2 Fitting Dose Response Models 604
14.1.3 Multiple Exposures 611
14.1.4 Uncertainty in Dose Response Models 614
14.2 Combining with Exposure 616
14.2.1 Example Risk Characterization 616
14.3 Integrating to Populations 621
14.4 Risk Characterization Applications 627
14.5 Research Needs for Risk Assessment 629
14.6 Discussion Questions and Problems 630
14.7 Bibliography 631
15 Balancing Interventions and Risk 641
15.1 Introduction 641
15.2 Implementation of Strategies 642
15.3 Concept of Acceptable Risk 644
15.3.1 Historical 644
15.3.2 HALY, QALY, DALY Concept 645
Critiques of HALY 648
15.4 Balancing Interventions with Benefits 649
15.4.1 Direct economic valuation 649
Direct Adverse Effects 650
Healthcare Costs 650
Indirect Factors 651
Propagation of Uncertainties 653
Secondary and Indirect costs and Benefits 653
Future Costs and Benefits 653
15.4.2 Cost-Effectiveness Analysis 655
15.4.3 Formal Cost Benefit Analysis 657
History 657
Methodology 658
Critiques 660
15.4.4 Formal Multicriteria Decision Analysis 661
15.5 Discussion Questions and Problems 667
15.6 Bibliography 669
List of Figures
2.1 The Disease Triad 8
2.2 Various Shapes and Sizes of Pathogenic Viruses 10
2.3 Schematic Definition of Baltimore Virus Groups 11
2.4 Depiction of Poliovirus Type 3 13
2.5 Structure of the Encapsulated Influenza A Virus 14
2.6 Different Bacterial Shapes 16
2.7 GC Ratio of Various Bacterial Groups 21
2.8 Microscopic Image of Endamoeba histolytica 24
2.9 Microscopic Image of Giardia muris 25
2.10 Microscopic Image of Balantidium coli 25
2.11 Life Cycle of Giardia 27
2.12 Photomicrograph of Fungus Showing Hyphae and Spores 29
2.13 Chain of Infection 31
2.14 Time Indoors vs Outdoors based on Average U.S. Lifespan 33
3.1 Risk Analysis Framework 47
3.2 Conceptual Dose Response for a Single Exposure 49
3.3 Ratings of Different Risks by Experts and Members of the League of Women Voters 54
3.4 Source Transport Receptor Framework 56
3.5 Taxonomy of forms of Epistemic Uncertainty 58
3.6 Effect of Subdividing Populations on Distribution 59
4.1 Poisson Distribution for Different Values of _ 65
4.2 Impact of Subsampling from EnvironmentWith Few Organisms 66
4.3 Relative Standard Deviation based on Poisson Distribution 67
4.4 Effect of Overdispersion and Underspersion Relative to Poisson at Constant Mean 68
4.5 Exhaled Liquid Volume Produced During Certain Activities 70
4.6 January/February 2020 COVID-19 Cluster in Guangzhou Restaurant associated with a Lunch on January 24 72
5.1 ConceptualWorkflow Pipeline for Methods 78
5.2 Schematic of an Idealized Sewer Network 80
5.3 Sampling from a Sewer Maintenance Hole 82
5.4 SimplifiedWater Distribution System 87
5.5 A Simple ResidentialWell 89
5.6 Residential Rainwater Harvesting System 91
5.7 Schematic of a Residential Water System 92
5.8 Classification of Types of RecreationalWaters 94
5.9 Schematic of Impinger Used for Bioaserosol Sampling 96
5.10 Cascade Impoctor Sampler 98
5.11 Cyclone Sampler 99
5.12 Petri dish culture plate left on a rooftop for a period of 30 minutes, then incubated at a temperature of 25oC 100
5.13 Technician Swabbing Mockup of Indoor Surface of NASA International Space Station 101
5.14 Filter that has been used to sample water showing captured solid material 105
6.1 Effect of Amount Cultured on Recovery 123
6.2 Effect of Negative Binomial k on Probability for Fixed Mean=5 128
6.3 Fermentation Tube Design of Durham 137
6.4 Bacterial Growth Curve 141
6.5 Relationship Between Sizes of Microorganisms and Use of Types of Microscopy. 143
6.6 Parts of a Basic Optical Microscope 144
6.7 Micrograph of Candida albicans with Bright Field and Phase Contrast illumination.146
6.8 Hemocytometer Top View and Side View 147
6.9 Hemocytometer Slide Grid 148
6.10 Transmission Electron Micrograph of Adenovirus 150
6.11 SEM of Vibrio vulnificus 152
6.12 Structure of DNA and Nucleotides 159
6.13 Basics of Conventional Quantitative PCR Calibration 162
6.14 Cost of DNA Sequencing 166
6.15 Simple Example Illustrating Sequence Assembly from Fragments 170
7.1 Particle Size Distribution of Emitted Aerosols vs. Activity198
7.2 Activated Sludge Aeration Tank 214
7.3 Photograph of a Trickling Filter 215
8.1 Output of Solution to Example 7-2 238
8.2 Dimensionless Concentration versus Dimensionless Time for a CSTR Washout Tracer Experiment 239
8.3 Output of Complete Mix Flow System with First Order Reaction and Time-Varying Inputs and Source Term 241
8.4 Analogy of a Plug Flow System as a Conveyor Belt of Discrete Closed Volumes 242
8.5 Schematic of TwoWell Mixed Volumes in Series 244
8.6 E Curves for Multiple Well Mixed Systems in Series with Mean Residence Time=10 245
8.7 Trajectories of 10 Runs for a Complete Mix Volume Initialized with 20 Particles 248
8.8 Trajectories of 10 Runs for a Complete Mix Volume Initialized with 20 Particles, with Growth Rate and Internal Source 250
8.9 Laminar vs Turbulent Flow 252
8.10 Comparison of Axial Dispersion to Compartment in Series Model for Mean Residence Time of 1.0 and Variance Equal to Three Compartment Model . 255
8.11 Dispersion of Particles from an Infector in a Room for Various Scenarios 263
8.12 Types of Rate Processes Considered 264
8.13 Schematic of Exponential and More Complex Decay Relationships in Closed Batch Systems 273
8.14 Electron Micrograph (left) of Aggregate of Delta Variant of SARS-CoV-2 Grown on Cell Culture, and Histogram of Aggregate Size (right) 276
8.15 Comparison of Different Decay Models with Similar Values for t90 and t99 280
8.16 Fit of Decay Data to the Log-Normal Model 288
8.17 Comparison of Gompertz vs Logistic Curves 294
8.18 Model Output of Growth with Lag and Inhibitor Excretion 298
8.19 Williams Birth Death Model Output 301
8.20 Conceptual Model of Legionella Colonization of Biofilm on the Side of a Pipe Wall.303
8.21 Force Balance on Particle Moving in Gravitational Field 307
8.22 Electrical Environment of Particles Moving in a Fluid 310
8.23 Microbial and Chemical Interactions in Surface Microlayer 316
8.24 Production of Aerosols Immediately After Toilet Flushing, visualized using Fluorescent Dyes 320
8.25 Conceptual Model of Some Processes in Modeling Fate and Transport in a Single Mixed Room 321
8.26 Schematic of an Aquifer 324
8.27 Processes Included in EPANET-C Model 325
9.1 Swiss Cheese Model of Multiple Barriers 346
9.2 Relationship Between k_ and Survival Ratio for Weibull Decay in a CSTR for Different Values of the Exponent "m" 352
9.3 Schematic of Input and Output Time Series from a Process 353
9.4 Cumulative Distribution Function for Giardia Data in Table 9.2 356
9.5 Time Series Plot for Giardia Data from Table 9.2 357
9.6 Correlation Plots and Histograms of Natural Log Transformed Giardia Concentrations for Data in Table 9.2 358
9.7 Histogram of LRVs For Secondary and Tertiary Giardia Removal and Correlations.359
9.8 Schematic of Three Process Cascade with Probabilistic Approach 361
9.9 Logic Flow for Monte Carlo Analysis 361
9.10 Scatter Plot of Points in 2 Dimensional Space Generated by Pseudorandom vs Sobol Quasirandom Algorithms 363
9.11 Comparison of Simulation Standard Deviations For Mean, Median, and First Decile of the Giardia Example as a Function of Number of Monte Carlo Replications 365
10.1 Types of Settling 370
10.2 Rectangular Sedimentation Tank 371
10.3 Cyclone Separator for Air Treatment 375
10.4 Flat Air Filter Module . 379
10.5 Corsi-Rosenthal Box 381
10.6 Depth Versus Surface Filtration 384
10.7 Mechanisms of Filtration . 386
10.8 Evolution of Head Loss and Effluent Quality During Filtration 393
10.9 Categorization of Membrane Types 396
11.1 Classification of Chemical Disinfectants 408
11.2 Combinations of Hydrogen Ion and Chloride at which [Cl2(aq)]=[HOCl] 411
11.3 Idealized Chlorine Breakpoint Curve 412
11.4 Structure of Trichloroisocyanuric Aci 413
11.5 Structure of Peracetic Acid 419
11.6 Structure of Ethylene Oxide 420
11.7 Structure of Quaternary Ammonium Ion 420
11.8 The Electromagnetic Spectrum 423
11.9 Plots of ChickWatson Kinetics in a Batch System with no Decay 426
11.10 Examples of the Hom Power Law Model with Different Parameter values 429
11.11 Effect of _0 on Power Law Kinetics (k0Cn = 1) 429
11.12 Comparison of Series Event, Multitarget and Hom Models 431
11.13 Inactivation Curves for Two Population Mixtures of Chick-Watson and Hom-Chick-Watson 434
11.14 Uniform Decay vs Biphasic Decay of a Chemical Disinfectant in a BatchWell Mixed System 436
11.15 Time Course of Disinfectant Residual and Survival for the Example of Hom Inactivation with Second Order Decay Kinetics 438
11.16 Illustration of a CSTR and a PFR Connected in Series in Two Different Manners. 442
11.17 Idealized Conceptual Diagram of a Water Heater 456
11.18 Schematic of Batch UV Collimated Beam Apparatus 462
11.19 Comparison of Batch UV Systems for the Mixed versus Stratified Models at Ad = 0:5 466
12.1 Flowchart for Parameter Estimation of Models 485
12.2 Observed versus Predicted Colonies for Hom fit to Anotai Data 490
12.3 Plot of Hom Fitted Model versus Observations 497
12.4 Comparison of Predicted Hom Fit to Anotai Data Analyzed Using the Censored Regression Method 501
12.5 Conceptual Subsetting of Data 507
12.6 Schematic of a Vacuum Chlorinator 512
12.7 Schematic of a Submerged Diffuser Downstream of a Weir 514
12.8 One Type of Static Mixer Insert 515
12.9 Common Geometric Configurations for Contact Tank 517
12.10Schematic of Three Chamber Ozone Contactor 518
12.11Upper Air UV Wall Mounted Fixture 527
13.1 Fit of Sylvestre Cryptosporidium data to Inverse Gaussian Distribution 553
13.2 Parameter Pairs for the Inverse Gaussian that are in the 90 Percentile Confidence Region of the Fit to Sylvestre Data 555
13.3 Schematic of Simple Bootstrap Method 555
13.4 Bootstrapped Parameters (1000 replicates) for Inverse Gaussian Fit to Sylvestre Data 559
13.5 Pairs Plot for Bootstrapping Regression Residuals of Hom Model Fit to Data of B. subtilis Inactivation 562
13.6 Scatter Plot of Five Years of Fecal and Coliform Organisms Measured at Peoria, IL.565
13.7 Examples of Associations Between Random Variables with Misleading Correlations 569
13.8 Beta and Gamma Correlated Random Deviates with a Spearman Correlation of 0.7 576
14.1 Exponential vs. Beta-Poisson Dose-Response on Semilog and Log-Log Scales 594
14.2 Deposition Fraction of Particles in Different Portions of the Human Respiratory Tract from Nasal Inhaled Exposures 598
14.3 Effect of Incubation Time Distribution on the Case Distribution 600
14.4 Plot of Fitted Dose Response Time Model to 2.1_ Franciscella tularensis Model 602
14.5 Observed Proportion of Positives Compared to Exact Beta-Poisson Best Fit 607
14.6 Effect of Dose Splitting on Approximate Beta Poisson Risk 613
14.7 Schematic of Construction of Bootstrap Pseudosamples from a Dose-Response Experiment 614
14.8 Bootstrap Parameters for Exact Beta-Poisson Fit to Rotavirus Data 615
14.9 Distribution of Log10 Risk from 10,000 Simulations 619
14.10Tornado Plot of Spearman Rank Correlation Coefficients for Inputs to Rotavirus Risk Characterization from 10,000 Monte Carlo Simulations 620
14.11Basic SIR ModelWith Possibility of Incomplete Immunity 622
14.12Basic SEIR ModelWith Possibility of Incomplete Immunity 622
14.13Environmental Mediated Infectious Disease Model. From [10], CC-By-4 License 624
15.1 Hypothetical Time Course of Disability Weights for Three Circumstances 646
15.2 Schematic Cost-Effectiveness Curve with a Continuum of Alternatives 657
15.3 Cost Effectiveness Curve with Countervailing Risk 658
15.4 Hierarchy of Criteria, Attributes and Sub-attributes 663
15.5 Example Sub-Attribute Utility Functions for Cost 666
List of Tables
2.1 Example Pathogens in Each Baltimore Group 12
2.2 Viral Realms and Example Human Pathogens 13
2.3 Examples of Gram Negative and Gram Positive Genera with Pathogenic Bacteria. 17
2.4 Bacterial Phyla with no Currently Known Human Pathogens 23
2.5 Bacterial Phyla with Known Pathogens 23
2.6 Some Important Pathogenic Protozoa Genera 26
3.1 Attributes of Two Factors Associated with Risk Amplification or Attenuation 55
3.2 Stages in Risk Communication 55
4.1 Measurement of Influenza Virus - Infectious Particles and RNA - in Symptomatic Individuals 71
5.1 Some Significant Requirements of Different Biosafety Levels 104
6.1 Plaque counts for Poliovirus after 4 Days of Incubation as a Function of Sample Dilution 126
6.2 Data on Secondary Effluent Coliform Measured by Membrane Filter . 135
6.3 Some QA/QC Considerations for Each Step in Flow of a qPCR Assay 164
7.1 Bacterial, Viral, Protozoal and Helminth Pathogens in Human Excreta 193
7.2 Emission Rate (nL/h) of Aerosols from Individuals Engaged in Different Activities 195
7.3 Emission Rate (ng/h) of Aerosols from Individuals Engaged in Different Activities 195
7.4 PCR gene copies of SARS-CoV-2 detected in respiratory aerosols of patients during different activities 196
7.5 Pet Ownership Statistics in the US (2024) 203
7.6 Example Pet Related Infectious Diseases 204
7.7 Inventory of Major Animal Groups in Agriculture 205
7.8 Fecal Output of Different Livestock 206
7.9 Bacterial Pathogens in Dairy Manure 206
7.10 Protozoans in Animal Fecal Samples in Sydney, Australia Watershed 209
7.11 Pathogen Percent Positivity in Biosolids Receiving Various Treatments (determined by PCR) 213
7.12 Partition Factors (air/water) for Microbial Groups in Biological Wastewater Treatment 215
8.1 Examples of Simple Reaction Rates for Decay 235
8.2 Example Reactions and Rates for a Viable to Injured to Killed Process 236
8.3 Definition of Variables in Lighthart Evaporation Model 266
8.4 Condition for Perikinetic and Orthokinetic Rates to be Equal at 20oC 270
8.5 Common Two Parameter Survival Distributions and Hazard Functions 277
8.6 Empirical Survival Functions 279
8.7 Burr Type XII and III Complementary Cumulative Distributions Expressed as Survival Functions 279
8.8 Schema of Decay Experiment Using Count Data Presented in "Tidy" Form 281
8.9 Data for a Hypothetical Decay Experiment with Count Data 282
8.10 Results of Fitting Data in Equation 8.4.2 to Candidate Survival Distributions 284
8.11 AIC and BIC for Different Models Fitting Data in Equation 8.4.2 to Candidate Survival Distributions 285
8.12 Upper Percentiles of the _2 Distribution 285
8.13 Survival of E. coli O157:H7 in Creek Water 286
8.14 Fit of Data in Table 8.13 To Candidate Decay Models 287
8.15 AIC and BIC Criteria for Analysis of Concentration Decay Experiment of Eaton et al 287
8.16 Generalizations of the Logistic Growth Rate Expressions 293
8.17 Coefficients in Two Population Model Describing Two Population Interactions 304
8.18 Isoelectric Points for Selected Minerals in Water 312
8.19 Stability Classes based on Meterological Conditions[129] 318
8.20 Coefficients for Atmospheric Dispersion Correlations as a Function of Stability Class 319
9.1 Removal Expressions ((E = N Nin in PFR and CSTR Reactors for Different Orders of Removal 350
9.2 Giardia Concentrations in a Pilot Wastewater Treatment System (#/L) in Raw,
Secondary Effluent and Tertiary Effluent 355
9.3 Mean and Median Concentrations of the Giardia data from Table 9.2 355
9.4 Shapiro Wilk Test of Normality of Giardia LRVs 357
9.5 Summary Statistics for Fit of log10 Giardia Reduction Values to Alternative Distributions 359
9.6 Goodness of Fit Statistics for fit of LRVs from Data in Table 9.5 and Best Fit Parameters of the Weibull Distribution 360
10.1 Geometric Ratios and Euler and Stokes Numbers for Two Common Cyclone Designs 377
10.2 Particle Removal Efficiency by MERV Category 380
10.3 Porosity and Ergun Equation Parameters for Some Water and Air Filter Media. 392
10.4 Size Cutoffs, Pressure Drop, and Permeability of Various Membrane Types Used in Water Systems 396
11.1 Inactivation Expressions for Batch Systems with First Order Demand 437
11.2 Levels of Elaboration of CFD Models for Inactivation Processes 449
11.3 Antoine Equation Parameters for Water Vapor Pressures 455
11.4 Rates for UV Inactivation of Selected Microorganisms in Water 461
11.5 Rates for UV Inactivation of Selected Microorganisms on Surfaces 463
12.1 Batch Inactivation of E. coli by Free Chlorine at pH 10, 25oC 487
12.2 Initial E. coli Concentrations in Anotai Experiments 487
12.3 Survival of Giardia muris After Chlorination at pH 7 and 5oC 493
12.4 Survival of Bacillus subtilis Spores on Paper in Presence of Gas Phase Chlorine Dioxide 496
12.5 Anotai data Presented as Censored Concentration Data 499
12.6 Survival of spores of Bacillus subtilis Exposed to Ozone in Water in a CSTR at 15oC and pH 8 503
12.7 Comparison of Models Fit to Hibler Data on Giardia muris Inactivation 506
12.8 Correlation Parameters for Number of Mixing Modules to Get to 5% Coefficient of Variation Under Turbulent Conditions 515
12.9 Comparison of Textile Damage from Vaporized Hydrogen Peroxide (VHP)Exposure 525
12.10 Comparison of Pathogen Reduction Processes: PSRP vs. PFRP 529
13.1 qPCR Abundance of Campylobacter jejuni in Water Column at a State Park Recreational Area 545
13.2 Key Chapters of the US EPA Exposure Factors Handbook 549
13.3 Short Term Inhalation Rates Versus Activity Level, Individuals 6 years and older 549
13.4 Oocyst Concentration in Raw Water of Utility C1 552
13.5 Fit of Two Parameter Distributions to Data of Sylvestre et al 552
13.6 Bootstrap Replicates for Campylobacter data 556
13.7 Best Principles for Monte Carlo Methods in Risk Assessment 563
13.8 Measurements of Enterococcus in Wastewater and Environmental Waters by Culture and qPCR 567
14.1 Modifications of Dose Response Models for Time to Effect (_ ) 601
14.2 Human Response to Rotavirus 605
14.3 Model Fit and Dose-Response Parameter estimates forWard Rotavirus Data 606
14.4 Test of Pooling Multiple Strains 610
14.5 Dose-Response Data for Rhesus Monkey Exposure to Aerosolized Franciscella tularensis of Different Particle Sizes 611
14.6 Response of Mice to Interperitoneal Injection of Yersinia pestis 612
14.7 Model variables and parameters for an environmentally mediated infectious disease transmission model with dose-response and a latency period 625
14.8 Selected Recreational Water QMRA Examples 628
15.1 Ratio between Disability Adjusted Life Years and Infections for Selected Pathogens
Transmissible by Ingestion or Inhalation. Based on Data from The Netherlands. 647
15.2 Value of Statistical Life by Several US Agencies 650
15.3 Medical and Productivity Costs for 1993 Milwaukee Cryptosporidium Outbreak Per Case 651
15.4 Estimated Costs for Cryptosporidium Outbreak in Galway, Ireland 652
15.5 Weighting Factors for Criteria and Sub-attributes for Nanomaterial Risk Assessment.
List of Figures ix
List of Tables xiv
1 Introduction 1
1.1 Scope of Coverage 2
1.2 Instructor Notes 3
1.3 Bibliography 3
I Environmental Engineering and Pathogen Basics 5
2 Who, How, Where 7
2.1 Pathogens of Concern 8
2.1.1 Sub-Viral Agents 9
2.1.2 Viruses 9
2.1.3 Bacteria 14
Classification by Metabolic Strategy 15
Other Important Characteristics 18
Formal Taxonomy and Classification 19
2.1.4 Protozoa 22
2.1.5 Fungi 26
Zoosporic Fungi 28
Zygomycetous Fungi 28
Dikarya 29
2.1.6 Other Agents of Concern 30
2.2 Portals of Entry 30
2.3 Venues of Concern 32
2.3.1 Indoor Environments 32
2.3.2 Outdoor Environments 34
2.3.3 In Vehicles 35
2.4 Discussion Questions and Problems 35
2.5 Bibliography 35
3 Key Paradigms of Environmental Engineering 45
3.1 Risk Framework 45
3.1.1 Problem Definition 48
3.1.2 Risk Assessment 48
Hazard Characterization 48
Dose Response Assessment 49
Exposure Assessment 49
Risk Characterization 50
3.1.3 Risk Management 51
3.1.4 Risk Communication 53
3.2 Source, Fate, Transport, Receptor 54
3.3 Uncertainty & Variability 57
3.4 Discussion Questions and Problems 60
3.5 Bibliography 60
4 Unique Features of Pathogens 63
4.1 Stochastic Variability and Low concentrations 63
4.2 Growth as well as Decay 66
4.3 Humans as Sources and Receptors 69
4.4 Dose Response 71
4.5 Contagiousness and Population Spread 72
4.6 Key Takeaways 73
4.7 Discussion Questions and Problems 73
4.8 Bibliography 74
5 Pathogen Sampling 77
5.1 Workflow 77
5.2 Taking the Sample 79
5.2.1 Wastewater 79
5.2.2 DrinkingWater, Other Liquids 85
Backflow and Cross Connections 88
Groundwater 89
Rainwater Collection 90
Premise (Building) Plumbing 91
5.2.3 RecreationalWaters 93
5.2.4 Air 94
Ambient Air Sampling 94
Passive Air Samplers 99
5.2.5 Dusts, Surfaces, Fomites 100
5.2.6 Solids and Semisolids 102
5.3 Decontamination and Biosafety 103
5.4 Isolation, Concentration, and Separation 105
5.5 Discussion Questions and Problems 107
5.6 Bibliography 108
6 How Pathogens Are Quantified 117
6.1 Selection of Targets 117
6.1.1 Indicator Organisms 117
6.1.2 Microbial Source Tracking 119
6.1.3 Direct Measurement of Pathogens . 120
6.2 Count, Quantal, and Time to Response Methods 120
6.2.1 Count Methods 120
Statistics of Count Methods 122
6.2.2 Quantal Methods 136
Statistics of Quantal Methods 138
6.2.3 Time to Response Methods 141
6.3 Direct Microscopy 142
6.3.1 Optical Microscopy 142
Quantification by Optical Microscopy 147
6.3.2 Electron Microscopy 148
6.4 Flow Cytometry 151
6.5 Culture Methods 154
6.5.1 Pre-enrichment or Pre-selection 154
6.5.2 Culture Media Types, Selection, Incubation 154
6.5.3 Whole Organism, Organ or Cell Culture 155
6.6 Molecular Methods 158
6.6.1 Microbial Nucleic Acids 158
Molecules of Interest 158
Extraction, Separation and Concentration of Nucleic Acids 160
6.6.2 Polymerase Chain Reaction Based Methods 160
6.6.3 Sequencing Approaches 165
Amplicon Based Sequencing 166
Shotgun sequencing methods 168
6.6.4 Use for Quantitative Exposure Estimation 171
Relationship to Viability and Infectiousness 171
6.7 Implications for Exposure 173
6.8 Discussion Questions and Problems 173
6.9 Bibliography 175
II Quantifying Exposure 189
7 Sources of Pathogens 191
7.1 Generic Approach 191
7.2 Human Excreta 192
7.3 Exhalation 195
7.4 Other Bodily Discharges 198
7.5 Skin Associated Pathogens 200
7.6 Our biological cohabitants 202
7.6.1 Plants 202
7.6.2 Pets 203
7.6.3 Agricultural Animals 205
7.6.4 Wild Animals 207
7.7 Waste Management Practices 210
7.7.1 Sanitary Landfills 210
7.7.2 Biosolids Application to Land 211
7.7.3 Wastewater Treatment 213
7.8 Other Sources via Aerosolization of Water . 216
7.9 Discussion Questions and Problems 216
7.10 Bibliography 217
8 Transport, Growth and Decay in the Environment 231
8.1 Chapter Overview 231
8.2 Taxonomy of Models . 232
8.2.1 Batch and Simple Flow Systems 234
8.2.2 Modeling Approaches for Complex Flow Systems 242
8.3 Quantitative description of Transport 243
8.3.1 Box Models 243
8.3.2 Box Models with Particle Tracking 246
8.3.3 Advection Reaction Processes -Eulerian-Eulerian Approach 250
Brief Outline of Fluid Flow Modeling 250
Contaminants in a Flowing System 252
8.3.4 A Priori Estimation of Dispersion 257
8.3.5 Advection Reaction Processes - Eulerian-Lagrangian Approach 261
8.4 Quantitative Description of Rate Processes 264
8.4.1 Physical 264
Processes Unique to Air 265
Generally Applicable Processes 267
8.4.2 Decay 271
Reaction Rate Approach 274
Hazard Rate Approach 276
Phenomenological and Empirical Models 278
Fitting Decay Rate Models to Data 279
Modulators of Decay Rates and Data Sources 287
8.4.3 Growth 292
8.4.4 Stochastic Treatment of Growth and Decay 299
8.4.5 Predator-Prey and Other Biotic Interactions 301
8.5 Quantitative Description of Other Flux Processes 305
8.5.1 External Fields 305
Gravitational Force 305
Electrical Force 309
Magnetic Force 312
8.5.2 Interphase Transfer Processes 313
Indoor Environments 313
Outdoor Land Air Exchange 314
Water Sediment Exchange 315
Liquid Air Exchange 315
8.6 Longer range and more complex models 317
8.6.1 Atmospheric Dispersion Models 317
8.6.2 Indoor Air Models 320
8.6.3 Water Quality Models 321
8.7 Discussion Questions and Problems 325
8.8 Bibliography 326
III Mitigating Exposure 343
9 Characterizing Interventions 345
9.1 Multiple Barriers . 345
9.2 Typology of Interventions 348
9.3 Quantifying Performance 349
9.4 Incorporating Variability and Uncertainty 352
9.5 Estimating Performance of Multiple Barriers with Variability and Uncertainty 360
9.6 Discussion Questions and Problems 366
9.7 Bibliography 367
10 Physical Removal and Reduction 369
10.1 Removal by Action of Gravitational Forces 369
10.1.1 Water Applications 370
10.1.2 Air Applications 374
10.1.3 Cyclonic Separators 374
10.2 Removal by Virtue of Size 377
10.2.1 Depth Filters . 378
Air Filtration . 378
Water Filtration 383
Depth Filter Removal Efficiency 384
Depth Filter Pressure Drop 391
Depth Filter Regeneration 395
10.2.2 Membranes 395
10.3 Removal by Virtue of Charge 397
10.4 Surface Cleaning . 398
10.5 Discussion Questions and Problems 400
10.6 Bibliography 401
11 Inactivation Fundamentals 407
11.1 Disinfecting Agents 408
11.1.1 Chemical Disinfectants 408
Halogens 409
Hydrogen Peroxide 414
Ozone 415
Peracetic and Other Peroxy Acids 418
Ethylene Dioxide 419
Organic Disinfecting Compounds 420
11.1.2 Physical Disinfectants 422
Heat 422
Light 422
Ionizing Radiation 424
11.1.3 Advanced Oxidation - Combinations of Processes 424
11.2 Kinetics of Disinfection 425
11.2.1 General Inactivation Models 425
11.2.2 Chemical Disinfection 435
11.2.3 Thermal Inactivation 451
11.2.4 UV and Radiation Disinfection 457
11.3 Discussion Questions and Problems 470
11.4 Bibliography 471
12 Inactivation Applications 483
12.1 Fitting Performance Models to Data 483
12.1.1 Basic Count Data 486
12.1.2 Basic Quantal Data 491
12.1.3 Basic Continuous Data 494
12.1.4 Continuous Data With Censoring 497
12.1.5 Complex Models 498
12.1.6 Comparing Models 505
12.2 Byproducts 509
12.2.1 Chlorine and Halogen Compounds 509
12.2.2 Non Halogen Oxidants 510
12.2.3 UV and Other Radiation Systems 510
12.3 Coincidental Inactivation by Other Processes 511
12.4 Applications 511
12.4.1 Liquids 511
Chlorine 512
Ozone 516
Peracetic Acid 518
UV and Light 518
12.4.2 Air 519
Chemical Agents 520
UV 527
12.4.3 Solids and Semi-Solids 528
12.4.4 Surface Disinfection 530
12.5 Questions and Problems 531
12.6 Bibliography 533
13 Exposure Assessment 543
13.1 Microorganism Distributions 545
13.1.1 Direct Measurement 545
13.1.2 From Source to Receptor Models 546
13.1.3 Uncertainty of Distributions 548
13.2 Medium Contact 548
13.2.1 Ingestion 548
13.2.2 Inhalation 549
13.2.3 Fomites 550
13.2.4 Miscellaneous Other Routes 550
13.3 Formal Computation of Uncertainty and Variability 551
13.3.1 Determining Best Distributional Forms 551
13.3.2 Parametric Uncertainty of Distributional Parameters 552
13.3.3 Combining Multiple Distributions 561
13.3.4 Advanced Concepts 564
Correlated Variables 564
Copulas 568
Sampling Methods 572
13.4 Discussion Questions and Problems 576
13.5 Bibliography 577
IV Balancing and Deciding 583
14 From Dose Response to Risk Characterization 585
14.1 Dose Response 585
14.1.1 Dose Response Models 588
Generation 0 588
Generation 1 Dose Response 589
Generation 2 Dose Response with Modulating Factors 596
Generation 3 Dose Response Models with Dynamics 599
Beyond Generation 3 602
14.1.2 Fitting Dose Response Models 604
14.1.3 Multiple Exposures 611
14.1.4 Uncertainty in Dose Response Models 614
14.2 Combining with Exposure 616
14.2.1 Example Risk Characterization 616
14.3 Integrating to Populations 621
14.4 Risk Characterization Applications 627
14.5 Research Needs for Risk Assessment 629
14.6 Discussion Questions and Problems 630
14.7 Bibliography 631
15 Balancing Interventions and Risk 641
15.1 Introduction 641
15.2 Implementation of Strategies 642
15.3 Concept of Acceptable Risk 644
15.3.1 Historical 644
15.3.2 HALY, QALY, DALY Concept 645
Critiques of HALY 648
15.4 Balancing Interventions with Benefits 649
15.4.1 Direct economic valuation 649
Direct Adverse Effects 650
Healthcare Costs 650
Indirect Factors 651
Propagation of Uncertainties 653
Secondary and Indirect costs and Benefits 653
Future Costs and Benefits 653
15.4.2 Cost-Effectiveness Analysis 655
15.4.3 Formal Cost Benefit Analysis 657
History 657
Methodology 658
Critiques 660
15.4.4 Formal Multicriteria Decision Analysis 661
15.5 Discussion Questions and Problems 667
15.6 Bibliography 669
List of Figures
2.1 The Disease Triad 8
2.2 Various Shapes and Sizes of Pathogenic Viruses 10
2.3 Schematic Definition of Baltimore Virus Groups 11
2.4 Depiction of Poliovirus Type 3 13
2.5 Structure of the Encapsulated Influenza A Virus 14
2.6 Different Bacterial Shapes 16
2.7 GC Ratio of Various Bacterial Groups 21
2.8 Microscopic Image of Endamoeba histolytica 24
2.9 Microscopic Image of Giardia muris 25
2.10 Microscopic Image of Balantidium coli 25
2.11 Life Cycle of Giardia 27
2.12 Photomicrograph of Fungus Showing Hyphae and Spores 29
2.13 Chain of Infection 31
2.14 Time Indoors vs Outdoors based on Average U.S. Lifespan 33
3.1 Risk Analysis Framework 47
3.2 Conceptual Dose Response for a Single Exposure 49
3.3 Ratings of Different Risks by Experts and Members of the League of Women Voters 54
3.4 Source Transport Receptor Framework 56
3.5 Taxonomy of forms of Epistemic Uncertainty 58
3.6 Effect of Subdividing Populations on Distribution 59
4.1 Poisson Distribution for Different Values of _ 65
4.2 Impact of Subsampling from EnvironmentWith Few Organisms 66
4.3 Relative Standard Deviation based on Poisson Distribution 67
4.4 Effect of Overdispersion and Underspersion Relative to Poisson at Constant Mean 68
4.5 Exhaled Liquid Volume Produced During Certain Activities 70
4.6 January/February 2020 COVID-19 Cluster in Guangzhou Restaurant associated with a Lunch on January 24 72
5.1 ConceptualWorkflow Pipeline for Methods 78
5.2 Schematic of an Idealized Sewer Network 80
5.3 Sampling from a Sewer Maintenance Hole 82
5.4 SimplifiedWater Distribution System 87
5.5 A Simple ResidentialWell 89
5.6 Residential Rainwater Harvesting System 91
5.7 Schematic of a Residential Water System 92
5.8 Classification of Types of RecreationalWaters 94
5.9 Schematic of Impinger Used for Bioaserosol Sampling 96
5.10 Cascade Impoctor Sampler 98
5.11 Cyclone Sampler 99
5.12 Petri dish culture plate left on a rooftop for a period of 30 minutes, then incubated at a temperature of 25oC 100
5.13 Technician Swabbing Mockup of Indoor Surface of NASA International Space Station 101
5.14 Filter that has been used to sample water showing captured solid material 105
6.1 Effect of Amount Cultured on Recovery 123
6.2 Effect of Negative Binomial k on Probability for Fixed Mean=5 128
6.3 Fermentation Tube Design of Durham 137
6.4 Bacterial Growth Curve 141
6.5 Relationship Between Sizes of Microorganisms and Use of Types of Microscopy. 143
6.6 Parts of a Basic Optical Microscope 144
6.7 Micrograph of Candida albicans with Bright Field and Phase Contrast illumination.146
6.8 Hemocytometer Top View and Side View 147
6.9 Hemocytometer Slide Grid 148
6.10 Transmission Electron Micrograph of Adenovirus 150
6.11 SEM of Vibrio vulnificus 152
6.12 Structure of DNA and Nucleotides 159
6.13 Basics of Conventional Quantitative PCR Calibration 162
6.14 Cost of DNA Sequencing 166
6.15 Simple Example Illustrating Sequence Assembly from Fragments 170
7.1 Particle Size Distribution of Emitted Aerosols vs. Activity198
7.2 Activated Sludge Aeration Tank 214
7.3 Photograph of a Trickling Filter 215
8.1 Output of Solution to Example 7-2 238
8.2 Dimensionless Concentration versus Dimensionless Time for a CSTR Washout Tracer Experiment 239
8.3 Output of Complete Mix Flow System with First Order Reaction and Time-Varying Inputs and Source Term 241
8.4 Analogy of a Plug Flow System as a Conveyor Belt of Discrete Closed Volumes 242
8.5 Schematic of TwoWell Mixed Volumes in Series 244
8.6 E Curves for Multiple Well Mixed Systems in Series with Mean Residence Time=10 245
8.7 Trajectories of 10 Runs for a Complete Mix Volume Initialized with 20 Particles 248
8.8 Trajectories of 10 Runs for a Complete Mix Volume Initialized with 20 Particles, with Growth Rate and Internal Source 250
8.9 Laminar vs Turbulent Flow 252
8.10 Comparison of Axial Dispersion to Compartment in Series Model for Mean Residence Time of 1.0 and Variance Equal to Three Compartment Model . 255
8.11 Dispersion of Particles from an Infector in a Room for Various Scenarios 263
8.12 Types of Rate Processes Considered 264
8.13 Schematic of Exponential and More Complex Decay Relationships in Closed Batch Systems 273
8.14 Electron Micrograph (left) of Aggregate of Delta Variant of SARS-CoV-2 Grown on Cell Culture, and Histogram of Aggregate Size (right) 276
8.15 Comparison of Different Decay Models with Similar Values for t90 and t99 280
8.16 Fit of Decay Data to the Log-Normal Model 288
8.17 Comparison of Gompertz vs Logistic Curves 294
8.18 Model Output of Growth with Lag and Inhibitor Excretion 298
8.19 Williams Birth Death Model Output 301
8.20 Conceptual Model of Legionella Colonization of Biofilm on the Side of a Pipe Wall.303
8.21 Force Balance on Particle Moving in Gravitational Field 307
8.22 Electrical Environment of Particles Moving in a Fluid 310
8.23 Microbial and Chemical Interactions in Surface Microlayer 316
8.24 Production of Aerosols Immediately After Toilet Flushing, visualized using Fluorescent Dyes 320
8.25 Conceptual Model of Some Processes in Modeling Fate and Transport in a Single Mixed Room 321
8.26 Schematic of an Aquifer 324
8.27 Processes Included in EPANET-C Model 325
9.1 Swiss Cheese Model of Multiple Barriers 346
9.2 Relationship Between k_ and Survival Ratio for Weibull Decay in a CSTR for Different Values of the Exponent "m" 352
9.3 Schematic of Input and Output Time Series from a Process 353
9.4 Cumulative Distribution Function for Giardia Data in Table 9.2 356
9.5 Time Series Plot for Giardia Data from Table 9.2 357
9.6 Correlation Plots and Histograms of Natural Log Transformed Giardia Concentrations for Data in Table 9.2 358
9.7 Histogram of LRVs For Secondary and Tertiary Giardia Removal and Correlations.359
9.8 Schematic of Three Process Cascade with Probabilistic Approach 361
9.9 Logic Flow for Monte Carlo Analysis 361
9.10 Scatter Plot of Points in 2 Dimensional Space Generated by Pseudorandom vs Sobol Quasirandom Algorithms 363
9.11 Comparison of Simulation Standard Deviations For Mean, Median, and First Decile of the Giardia Example as a Function of Number of Monte Carlo Replications 365
10.1 Types of Settling 370
10.2 Rectangular Sedimentation Tank 371
10.3 Cyclone Separator for Air Treatment 375
10.4 Flat Air Filter Module . 379
10.5 Corsi-Rosenthal Box 381
10.6 Depth Versus Surface Filtration 384
10.7 Mechanisms of Filtration . 386
10.8 Evolution of Head Loss and Effluent Quality During Filtration 393
10.9 Categorization of Membrane Types 396
11.1 Classification of Chemical Disinfectants 408
11.2 Combinations of Hydrogen Ion and Chloride at which [Cl2(aq)]=[HOCl] 411
11.3 Idealized Chlorine Breakpoint Curve 412
11.4 Structure of Trichloroisocyanuric Aci 413
11.5 Structure of Peracetic Acid 419
11.6 Structure of Ethylene Oxide 420
11.7 Structure of Quaternary Ammonium Ion 420
11.8 The Electromagnetic Spectrum 423
11.9 Plots of ChickWatson Kinetics in a Batch System with no Decay 426
11.10 Examples of the Hom Power Law Model with Different Parameter values 429
11.11 Effect of _0 on Power Law Kinetics (k0Cn = 1) 429
11.12 Comparison of Series Event, Multitarget and Hom Models 431
11.13 Inactivation Curves for Two Population Mixtures of Chick-Watson and Hom-Chick-Watson 434
11.14 Uniform Decay vs Biphasic Decay of a Chemical Disinfectant in a BatchWell Mixed System 436
11.15 Time Course of Disinfectant Residual and Survival for the Example of Hom Inactivation with Second Order Decay Kinetics 438
11.16 Illustration of a CSTR and a PFR Connected in Series in Two Different Manners. 442
11.17 Idealized Conceptual Diagram of a Water Heater 456
11.18 Schematic of Batch UV Collimated Beam Apparatus 462
11.19 Comparison of Batch UV Systems for the Mixed versus Stratified Models at Ad = 0:5 466
12.1 Flowchart for Parameter Estimation of Models 485
12.2 Observed versus Predicted Colonies for Hom fit to Anotai Data 490
12.3 Plot of Hom Fitted Model versus Observations 497
12.4 Comparison of Predicted Hom Fit to Anotai Data Analyzed Using the Censored Regression Method 501
12.5 Conceptual Subsetting of Data 507
12.6 Schematic of a Vacuum Chlorinator 512
12.7 Schematic of a Submerged Diffuser Downstream of a Weir 514
12.8 One Type of Static Mixer Insert 515
12.9 Common Geometric Configurations for Contact Tank 517
12.10Schematic of Three Chamber Ozone Contactor 518
12.11Upper Air UV Wall Mounted Fixture 527
13.1 Fit of Sylvestre Cryptosporidium data to Inverse Gaussian Distribution 553
13.2 Parameter Pairs for the Inverse Gaussian that are in the 90 Percentile Confidence Region of the Fit to Sylvestre Data 555
13.3 Schematic of Simple Bootstrap Method 555
13.4 Bootstrapped Parameters (1000 replicates) for Inverse Gaussian Fit to Sylvestre Data 559
13.5 Pairs Plot for Bootstrapping Regression Residuals of Hom Model Fit to Data of B. subtilis Inactivation 562
13.6 Scatter Plot of Five Years of Fecal and Coliform Organisms Measured at Peoria, IL.565
13.7 Examples of Associations Between Random Variables with Misleading Correlations 569
13.8 Beta and Gamma Correlated Random Deviates with a Spearman Correlation of 0.7 576
14.1 Exponential vs. Beta-Poisson Dose-Response on Semilog and Log-Log Scales 594
14.2 Deposition Fraction of Particles in Different Portions of the Human Respiratory Tract from Nasal Inhaled Exposures 598
14.3 Effect of Incubation Time Distribution on the Case Distribution 600
14.4 Plot of Fitted Dose Response Time Model to 2.1_ Franciscella tularensis Model 602
14.5 Observed Proportion of Positives Compared to Exact Beta-Poisson Best Fit 607
14.6 Effect of Dose Splitting on Approximate Beta Poisson Risk 613
14.7 Schematic of Construction of Bootstrap Pseudosamples from a Dose-Response Experiment 614
14.8 Bootstrap Parameters for Exact Beta-Poisson Fit to Rotavirus Data 615
14.9 Distribution of Log10 Risk from 10,000 Simulations 619
14.10Tornado Plot of Spearman Rank Correlation Coefficients for Inputs to Rotavirus Risk Characterization from 10,000 Monte Carlo Simulations 620
14.11Basic SIR ModelWith Possibility of Incomplete Immunity 622
14.12Basic SEIR ModelWith Possibility of Incomplete Immunity 622
14.13Environmental Mediated Infectious Disease Model. From [10], CC-By-4 License 624
15.1 Hypothetical Time Course of Disability Weights for Three Circumstances 646
15.2 Schematic Cost-Effectiveness Curve with a Continuum of Alternatives 657
15.3 Cost Effectiveness Curve with Countervailing Risk 658
15.4 Hierarchy of Criteria, Attributes and Sub-attributes 663
15.5 Example Sub-Attribute Utility Functions for Cost 666
List of Tables
2.1 Example Pathogens in Each Baltimore Group 12
2.2 Viral Realms and Example Human Pathogens 13
2.3 Examples of Gram Negative and Gram Positive Genera with Pathogenic Bacteria. 17
2.4 Bacterial Phyla with no Currently Known Human Pathogens 23
2.5 Bacterial Phyla with Known Pathogens 23
2.6 Some Important Pathogenic Protozoa Genera 26
3.1 Attributes of Two Factors Associated with Risk Amplification or Attenuation 55
3.2 Stages in Risk Communication 55
4.1 Measurement of Influenza Virus - Infectious Particles and RNA - in Symptomatic Individuals 71
5.1 Some Significant Requirements of Different Biosafety Levels 104
6.1 Plaque counts for Poliovirus after 4 Days of Incubation as a Function of Sample Dilution 126
6.2 Data on Secondary Effluent Coliform Measured by Membrane Filter . 135
6.3 Some QA/QC Considerations for Each Step in Flow of a qPCR Assay 164
7.1 Bacterial, Viral, Protozoal and Helminth Pathogens in Human Excreta 193
7.2 Emission Rate (nL/h) of Aerosols from Individuals Engaged in Different Activities 195
7.3 Emission Rate (ng/h) of Aerosols from Individuals Engaged in Different Activities 195
7.4 PCR gene copies of SARS-CoV-2 detected in respiratory aerosols of patients during different activities 196
7.5 Pet Ownership Statistics in the US (2024) 203
7.6 Example Pet Related Infectious Diseases 204
7.7 Inventory of Major Animal Groups in Agriculture 205
7.8 Fecal Output of Different Livestock 206
7.9 Bacterial Pathogens in Dairy Manure 206
7.10 Protozoans in Animal Fecal Samples in Sydney, Australia Watershed 209
7.11 Pathogen Percent Positivity in Biosolids Receiving Various Treatments (determined by PCR) 213
7.12 Partition Factors (air/water) for Microbial Groups in Biological Wastewater Treatment 215
8.1 Examples of Simple Reaction Rates for Decay 235
8.2 Example Reactions and Rates for a Viable to Injured to Killed Process 236
8.3 Definition of Variables in Lighthart Evaporation Model 266
8.4 Condition for Perikinetic and Orthokinetic Rates to be Equal at 20oC 270
8.5 Common Two Parameter Survival Distributions and Hazard Functions 277
8.6 Empirical Survival Functions 279
8.7 Burr Type XII and III Complementary Cumulative Distributions Expressed as Survival Functions 279
8.8 Schema of Decay Experiment Using Count Data Presented in "Tidy" Form 281
8.9 Data for a Hypothetical Decay Experiment with Count Data 282
8.10 Results of Fitting Data in Equation 8.4.2 to Candidate Survival Distributions 284
8.11 AIC and BIC for Different Models Fitting Data in Equation 8.4.2 to Candidate Survival Distributions 285
8.12 Upper Percentiles of the _2 Distribution 285
8.13 Survival of E. coli O157:H7 in Creek Water 286
8.14 Fit of Data in Table 8.13 To Candidate Decay Models 287
8.15 AIC and BIC Criteria for Analysis of Concentration Decay Experiment of Eaton et al 287
8.16 Generalizations of the Logistic Growth Rate Expressions 293
8.17 Coefficients in Two Population Model Describing Two Population Interactions 304
8.18 Isoelectric Points for Selected Minerals in Water 312
8.19 Stability Classes based on Meterological Conditions[129] 318
8.20 Coefficients for Atmospheric Dispersion Correlations as a Function of Stability Class 319
9.1 Removal Expressions ((E = N Nin in PFR and CSTR Reactors for Different Orders of Removal 350
9.2 Giardia Concentrations in a Pilot Wastewater Treatment System (#/L) in Raw,
Secondary Effluent and Tertiary Effluent 355
9.3 Mean and Median Concentrations of the Giardia data from Table 9.2 355
9.4 Shapiro Wilk Test of Normality of Giardia LRVs 357
9.5 Summary Statistics for Fit of log10 Giardia Reduction Values to Alternative Distributions 359
9.6 Goodness of Fit Statistics for fit of LRVs from Data in Table 9.5 and Best Fit Parameters of the Weibull Distribution 360
10.1 Geometric Ratios and Euler and Stokes Numbers for Two Common Cyclone Designs 377
10.2 Particle Removal Efficiency by MERV Category 380
10.3 Porosity and Ergun Equation Parameters for Some Water and Air Filter Media. 392
10.4 Size Cutoffs, Pressure Drop, and Permeability of Various Membrane Types Used in Water Systems 396
11.1 Inactivation Expressions for Batch Systems with First Order Demand 437
11.2 Levels of Elaboration of CFD Models for Inactivation Processes 449
11.3 Antoine Equation Parameters for Water Vapor Pressures 455
11.4 Rates for UV Inactivation of Selected Microorganisms in Water 461
11.5 Rates for UV Inactivation of Selected Microorganisms on Surfaces 463
12.1 Batch Inactivation of E. coli by Free Chlorine at pH 10, 25oC 487
12.2 Initial E. coli Concentrations in Anotai Experiments 487
12.3 Survival of Giardia muris After Chlorination at pH 7 and 5oC 493
12.4 Survival of Bacillus subtilis Spores on Paper in Presence of Gas Phase Chlorine Dioxide 496
12.5 Anotai data Presented as Censored Concentration Data 499
12.6 Survival of spores of Bacillus subtilis Exposed to Ozone in Water in a CSTR at 15oC and pH 8 503
12.7 Comparison of Models Fit to Hibler Data on Giardia muris Inactivation 506
12.8 Correlation Parameters for Number of Mixing Modules to Get to 5% Coefficient of Variation Under Turbulent Conditions 515
12.9 Comparison of Textile Damage from Vaporized Hydrogen Peroxide (VHP)Exposure 525
12.10 Comparison of Pathogen Reduction Processes: PSRP vs. PFRP 529
13.1 qPCR Abundance of Campylobacter jejuni in Water Column at a State Park Recreational Area 545
13.2 Key Chapters of the US EPA Exposure Factors Handbook 549
13.3 Short Term Inhalation Rates Versus Activity Level, Individuals 6 years and older 549
13.4 Oocyst Concentration in Raw Water of Utility C1 552
13.5 Fit of Two Parameter Distributions to Data of Sylvestre et al 552
13.6 Bootstrap Replicates for Campylobacter data 556
13.7 Best Principles for Monte Carlo Methods in Risk Assessment 563
13.8 Measurements of Enterococcus in Wastewater and Environmental Waters by Culture and qPCR 567
14.1 Modifications of Dose Response Models for Time to Effect (_ ) 601
14.2 Human Response to Rotavirus 605
14.3 Model Fit and Dose-Response Parameter estimates forWard Rotavirus Data 606
14.4 Test of Pooling Multiple Strains 610
14.5 Dose-Response Data for Rhesus Monkey Exposure to Aerosolized Franciscella tularensis of Different Particle Sizes 611
14.6 Response of Mice to Interperitoneal Injection of Yersinia pestis 612
14.7 Model variables and parameters for an environmentally mediated infectious disease transmission model with dose-response and a latency period 625
14.8 Selected Recreational Water QMRA Examples 628
15.1 Ratio between Disability Adjusted Life Years and Infections for Selected Pathogens
Transmissible by Ingestion or Inhalation. Based on Data from The Netherlands. 647
15.2 Value of Statistical Life by Several US Agencies 650
15.3 Medical and Productivity Costs for 1993 Milwaukee Cryptosporidium Outbreak Per Case 651
15.4 Estimated Costs for Cryptosporidium Outbreak in Galway, Ireland 652
15.5 Weighting Factors for Criteria and Sub-attributes for Nanomaterial Risk Assessment.