Super Bugs Prediction | Detection | Control Mark Tamplin Centre of - - PowerPoint PPT Presentation

Super Bugs Prediction | Detection | Control Mark Tamplin

Centre of Food Safety & Innovation

Outline

Super bugs

• Drivers
• Forecasting and detection
• Management

Outline

Outline

Emerging Infectious Disease

“One that has appeared in the population for the first time, or that may have existed previously but is rapidly increasing in incidence or geographical range.”

World Health Organization

Outline

Emerging Infectious Disease

“Infectious diseases whose incidence in humans has increased in the past 2 decades or threatens to increase in the near future, have been defined as "emerging." ”

US Centers for Disease Control and Prevention

Outline Some major factors that underlie disease emergence and reemergence

Morens DM, Fauci AS (2013) Emerging Infectious Diseases: Threats to Human Health and Global Stability. PLoS Pathog 9(7):

• e1003467. doi:10.1371/journal.ppat.1003467

Hazards

Super bugs

• Antibiotic resistance
• multiple antibiotic resistance
• Virulence factors
• acquisition of single/multiple genes
• Mutations
• increase virulence or change host range

Queenan et al., 2016 Intern. J. Antimicrob. Agents Singh, P. 2017 BJM Robinson et al., 2016 Trans R Soc Trop Med Hyg NCAS, 2016

One Health

Antimicrobial Resistance

Hazards

Antibiotics

Used to Treat, Control and Prevent Microbial Disease Viruses Fungi Parasites Bacteria

Hazards

Natural role of antibiotics

• Provides a competitive advantage for

microbial growth in environmental niches.

• Reduces competition in a space, leading

to a selective advantage for reproduction.

Natural vs anthropogenic

Significant correlation

• tetW - phosphorus buffering index
• ermB - ammonia, chloride and potassium base saturation
• tetW and blaTEM - organic matter, magnesium base saturation

Hazards

Sources of antibiotics

Hazards

Emergence of resistance

• Late 1940s: penicillin-resistant Staphylococcus aureus
• 1940-1950: chloramphenicol, tetracycline and erythromycin resistance
• Late 1970’s: methicillin-resistant S. aureus (MRSA)
• 1997: vancomycin-resistant enterococci (VRE)
• 2002: vancomycin-resistant S. aureus
• Multiple drug-resistant Pseudomonas aeruginosa

Hazards

Antibiotic applications in agri/aqua-culture

Aminoglycosides b,g,p,s,w x x x x Beta-lactams b,d,f,p,s,w x x x x Chloramphenicol b Fluoroquinolones b x x Glycopeptides x Ionophores b,f,g,p,r,s x x x x Macrolides b,p,w x x x x Polypeptides f,p,w x x x x Sulfonamides b,d,f,p,w, fish x x x Tetracyclines b,d,f,bees, p,s,w,fish, lobster x x x x x

Antimicrobial class Animal Disease Disease Growth Plant Human Species Treat. Prev. Prom. Use Use b=beef cattle, g=goats, p=poultry, s=sheep, w=swine, f=fowl, d=dairy cattle

Hazards

Impact of antibiotic resistance

• 2,000,000 infections
• 23,000 deaths
• $20 billion direct medial costs
• $35 billion indirect costs

CDC, 2013

Hazards

Impact of antibiotic resistance

O’Neill, 2016

Hazards Mechanisms of antibiotic resistance

• Cell wall (e.g. gram+ versus gram-)
• Efflux mechanisms (pumps)
• Degradative enzymes (e.g. beta-lactamases)
• Mutations in DNA or RNA (10-6 to 10-9)
• Alteration of receptors
• Membrane permeability changes
• Genetic transfer

Hazards

Plasmids

Extrachromosomal genetic material

Plasmids

Hazards

Transposons

Extrachromosomal genetic material (e.g. bacteriophage-mediated)

Transposons

Drivers of Super Bugs

• Host
• Population densities
• Environment

Categories of persons at risk to serious foodborne disease:

• fetus and infants
• people with chronic

diseases

• elderly
• immuno-compromised
• reduced host defences

Much like how we affect the environment, we also influence our susceptibility. Increasingly, more people have:

• chronic disease
• compromised host defenses

These issues will impact control strategies.

Consumers are also changing

Susceptibility

Mega shock: World population growth

Year 1978 2006 2050 Africa 456 932 2191 Asia 2538 3989 5142 Europe 686 732 719 Latin America1 346 563 750 North America 249 332 446 Oceania 22 34 55 (Australia) (14.3) (20.7) (31.7) World 4300 6583 9306

UN DEMOBASE Extract 2011

1 Includes The Caribbean

Population growth (i.e. density)

millions

• Higher densities of contaminants =

greater probability of genetic transfer (people, agriculture, aquaculture)

• Water (and air) treatment will become

increasingly important.

Higher densities

Climate Change

• ysters
• lobsters
• mussels

Toxic Algal Blooms

0.01 0.1 1 10 100 1000 10000 100000

• 5

5 10 15 20 25 30 35

Water temperature ( C)

• V. parahaemolyticus density

in oyster (Vp/g)

Regression fit of log10 V. parahaemolyticus (Vp) densities in oysters versus water temperature (DePaola et al., 1990). Mean log10 Vp/g or median Vp/g (solid line) and 95% confidence limits (dashed lines).

FDA V. parahaemolyticus Risk Assessment 2005

Modelling pathogens as a function

• f environmental parameters

Vibrio disease

• Example – Vibrio parahaemolyticus
• O3:K6 strain emerged in India in 1996
• Arrival of the Asian O3:K6 serotype in Chile was

facilitated by warm equatorial water displaced from Asia to Americas by two El Niño episodes.

• Example - Vibrio cholerae
• O1 strain emerged in USA Gulf of Mexico in 1980
• O1 strain emerged in Peru in 1991
• O139 emerged in India in 1992

New pathogenic strains

Forecasting and detecting Super Bugs

Foodborne Illness Surveillance

Whole Genome Sequencing

But can we detect them all?

• Creutzfeldt Jakob disease
• Scrapie
• Mad Cow Disease
• bovine spongiform encephalopathy

Real-time monitoring

• Identifying markers (indicators) and the use of

models will become increasingly important.

• Real-time monitoring of microbial

communities.

Log Vp/g=-2.05+ 0.097*tempwater+0.2*sal-0.0055*SAL2

√growth rate = 0.0303 x (temp-13.37)

Managing Super Bugs

One Health

UC Davis, https://www.ucdavis.edu/one-health/collaborations/

• Sep. 18, 2004

Figure 5: Water temperature Figure 6:

• V. vulnificus baseline levels

Figure 7:

• V. vulnificus levels at time of consumption

Figure 8: Log mean risk at consumption

• Sep. 18, 2004

• Sep. 18, 2004

• Sep. 18, 2004

FAO/WHO Working Group 5 Risk Management Exercise 2006

NextGen Antimicrobials

• Bacteriophage
• Bacteriocins
• Quorum factors
• Probiotics/prebiotics

Bacteriophage

Bacteriocins Bacteriocins

Quorum Sensing

Quorum factors

Blocking pathogen signalling

Probiotics and Prebiotics

Manipulating microbial communities

Manipulating species to displace pathogens, prevent disease and improve health.

Managing microbial communities

Manipulating microbial communities PREDICT

http://www.vetmed.ucdavis.edu/ohi/predict/

Thank you!