Scenario H

Disaster has struck - hard on the heels of the COVID-19 pandemic, another disease outbreak has hit your fair city, Dalessie. Residents are outraged and worried. There have already been 26 deaths.

The cause of the outbreak appears to be Group A Streptococcus (Streptococcus pyogenes). (Please refer to the CDC Group A Streptococcus resources for more information about the pathogen and the diseases it causes.)

Scanning electron micrograph of Group A Streptococcus cells on a human neutrophil. Image credit: [CDC](https://phil.cdc.gov/Details.aspx?pid=18257)

Figure 1: Scanning electron micrograph of Group A Streptococcus cells on a human neutrophil. Image credit: CDC

Each member of your group will play one of the following roles as you attempt to tackle the disease outbreak and save your city:

  1. Provost (head of the city council)
  2. Representative from a national public health org. (Public Health Scotland)
  3. Epidemiologist (on secondment from Public Health Scotland)
  4. Director of the city’s main hospital (Fairview)
  5. City planner/civil servant
  6. Microbiologist (working in one of the NHS Scotland clinical labs)
  7. Public communications expert (past and current sci comm campaigns)
  8. Doctor at a major surgery in Dalessie
  9. Epidemiologist from the local university, an expert on Streptococcus pyogenes transmission

You must work together, using the information that has been provided for you in the attached information packets, and decide what action(s) should be taken to control the outbreak currently plaguing your city, Dalessie. Your actions should be evidence-based – use the peer-reviewed literature to decide on measures that will stop the pandemic in your scenario.

Your action points may include directives to gather more information (e.g., contact tracing of current cases, microbiological testing of food/water, etc.), or specific directives (e.g. public health measures, non-pharmaceutical interventions, etc.). Use the data/expertise of all group members. Be clear, concise, and specific.

You may choose to include mathematical modeling as part of your decision making (for example, using an epidemic calculator or other models); if you do so, you should provide details of your modelling and predictions when you submit your group’s pro forma.

You should submit 3-5 specific actions to control the pandemic, using the workshop 3 pro forma (also available on MyPlace). Submit this by noon, Friday March 1st, via the submission link on MyPlace.

Information Packet H1

You are the provost of Dalessie, elected in 2016.

Photograph of Dalessie city centre. Image credit: DALL-E

Figure 2: Photograph of Dalessie city centre. Image credit: DALL-E

The current population of Dalessie (as of December 2022) is 150816. The demographic data for the city is shown below.

Dalessie demographics (Source: Office for National Statistics)Dalessie demographics (Source: Office for National Statistics)

Figure 3: Dalessie demographics (Source: Office for National Statistics)

You were elected as a member of the popular “Unity First” party and made a number of election promises regarding a “Green New Deal” for Dalessie.

Voting intention by Dalessie residents (Source: YouGov polling)

Figure 4: Voting intention by Dalessie residents (Source: YouGov polling)

There are currently 39 elected councillors, representing the 5 main political parties in Dalessie as follows:

Political Party Number of Seats
National Renovation 3
Progressive Rights 8
Unity First 20
Maroon 6
United Future 2



The overall budget (expenditures) for the 2022-2023 financial year was £442209121. A summary of expeditures by category for this financial year is shown below.

Public expenditures by category for the 2022-2023 financial year (Source: Dalessie City Council)

Figure 5: Public expenditures by category for the 2022-2023 financial year (Source: Dalessie City Council)

Your office has recently received a great deal of correspondence regarding the pandemic in Dalessie. A representative sample of these e-mails is shown below.

From:
To:
Cc: Subject: This Disgraceful Pandemic

Dear Provost,

I am so angry to hear about this new pandemic in Dalessie. There seems to be no end to the suffering that pandemics inflict on our city in these days.

I hope that your office is going to do something about tragedy as soon as possible.

Yours truly,
Su

From:
To:
Cc:
Subject: Pandemic Disaster for Businesses

Dear Provost,

This new pandemic in Dalessie has the potential to destroy our businesses. I run a sweet shop on the high street and nearly had to shut our doors during COVID due to COVID.

I hope you realise how costly the last pandemic was for millions of people across the country, and that we can’t afford another one.

I hope that your office is going to do something about dreadful state of affairs very soon, keeping in mind the economic interests of businesses in our city and the fact that we cannot afford face masks and gallons of hand sanitizer.

All the best,
Graham (The Dalessie Shop, proprietor)

From:
To:
Cc:
Subject: New Pandemic Measures

Dear Provost,

I hate the idea that you and your office are going to use this new pandemic as yet another excuse for government overreach into citizens’ lives. This last pandemic was just a typical example of what governments do when given a little too much power.

You must not allow the city to suffer through another round of lockdowns, face-masks, and other punitive restrictions that destroy people’s lives.

Respectfully,
Anna (a concerned voter)

From:
To:
Cc:
Subject:

Dear Provost,

I have just learned that my my sister-in-law has passed away due to the new pandemic in Dalessie. The family are all devastated as you can surely imagine.

You cannot begin to imagine the grief that we are feeling.

I hope that you will do everything you can to stop this pandemic so that no other families need to suffer this pain.

Sincerely,
Su

As Provost of Dalessie, you are of course familiar with the work of the Standing Committee on Pandemic Preparedness. You are also familiar with:

Information Packet H2

You are a representative from Public Health Scotland, sent to Dalessie to help with the Group A Streptococcus outbreak.

Your briefing packet includes the following documents:

Information Packet H3

You are an epidemiologist working for Public Health Scotland, sent to Dalessie to help with the measles outbreak.

A team of scientists working together have in a PHS lab have isolated and cultured Group A Streptococcus species (following standard protocols) from a number of patient samples taken during this outbreak; isolated DNA from these cultures; sequenced this DNA using an Illumina MiSeq platform; assembled the short paired-end reads; and compared these assemblies to the extant Group A Streptococcus sequences available in the NCBI databases. The results of these experiments are summarised in the table below.

Patient NCBI accession of closest database match
1 GCA_028370295.1
2 GCA_028370295.1
3 GCA_028370195.1
4 GCA_028370195.1
5 GCA_028370295.1
6 GCA_028370295.1
7 GCA_028370295.1
8 GCA_028370195.1
9 GCA_028370195.1
10 GCA_028370195.1



Your briefing packet also includes the following documents:

  • Chochua, Sopio et al. “Population and Whole Genome Sequence Based Characterization of Invasive Group A Streptococci Recovered in the United States during 2015.” mBio vol. 8,5 e01422-17. 19 Sep. 2017, doi:10.1128/mBio.01422-17

  • Streptococcus pyogenes pubMLST

  • Cordery, Rebecca et al. “Frequency of transmission, asymptomatic shedding, and airborne spread of Streptococcus pyogenes in schoolchildren exposed to scarlet fever: a prospective, longitudinal, multicohort, molecular epidemiological, contact-tracing study in England, UK.” The Lancet. Microbe vol. 3,5 (2022): e366-e375. doi:10.1016/S2666-5247(21)00332-3

  • Pagnossin, Davide et al. “Complete Genome Sequences of Three Invasive Strains of Streptococcus pyogenes Subtype emm5.23 Isolated in Scotland.” Microbiology resource announcements vol. 10,15 e00101-21. 15 Apr. 2021, doi:10.1128/MRA.00101-21

Information Packet H4

You are the director of Dalessie’s main hospital, the Fairview, which has 550 beds across 9 different wards and 10 operating theatres.

The Fairview hospital in Dalessie. Image credit: [DALL-E

Figure 6: The Fairview hospital in Dalessie. Image credit: [DALL-E

The annual operating budget for financial year 2022-2023 was £1.5 million, and average expenditures are shown by category in the figure below.

Hospital expenditures by category for financial year 2022-2023 (Source: NHS Scotland)

Figure 7: Hospital expenditures by category for financial year 2022-2023 (Source: NHS Scotland)

The Fairview has units specialising in coronary care; maternity care; dermatology; gastroenterology; an ear, nose, and throat clinic; an eye clinic; and an orthopedic unit.

There are currently 25 ICU beds (with ventilators) available, an increase from the 14 ICU beds in the Fairview in November 2019. Average ICU bed occupancy before and during the COVID-19 pandemic is in the figure below.

ICU bed occupancy for the Dalessie Fairview hospital (Source: NHS Scotland)

Figure 8: ICU bed occupancy for the Dalessie Fairview hospital (Source: NHS Scotland)

There are approximately 1.3m admissions to the Fairview hospital annually, the majority of these being to the emergency (A&E) department.

Admissions to the Dalessie Fairview hospital by category (Source: NHS Scotland)

Figure 9: Admissions to the Dalessie Fairview hospital by category (Source: NHS Scotland)

A&E waiting times have been called “disastrously high” in recent months, both by the press and by tthe hospital ombudsman.

ICU waiting times for the Dalessie Fairview hospital (Source: NHS Scotland)

Figure 10: ICU waiting times for the Dalessie Fairview hospital (Source: NHS Scotland)

The Fairview has been set a goal of 25% reduction in sepsis mortality (compared to past years)and 50% reduction in the nosocomial transmission of superbugs such as methicillin-resistant Staphylococcus aureus (MRSA), Clostridiodes difficile (C. diff), and Candida auris (C. auris).

Key Performance Indicators (KPIs) related to infectious diseases for the Dalessie Fairview hospital (Source: NHS Scotland)

Figure 11: Key Performance Indicators (KPIs) related to infectious diseases for the Dalessie Fairview hospital (Source: NHS Scotland)

There are currently 148 patients in the Fairview with confirmed or suspected Group A Streptococcus infections, with 15 of these patients currently in the ICU.

The hospital follows the guidelines set out in the National Infection Prevention and Control Manual.

As a hospital director, you are familiar with the literature surrounding hospital pandemic preparedness, and regularly read papers such as:

  • Mer, Mervyn et al. “Critical Care Pandemic Preparation: Considerations and Lessons Learned from COVID-19.” Critical care clinics vol. 38,4 (2022): 761-774.

  • Tacconelli, Evelina et al. “Challenges of data sharing in European Covid-19 projects: A learning opportunity for advancing pandemic preparedness and response.” The Lancet regional health. Europe vol. 21 (2022): 100467.

  • Adelaja, I., Sayma, M., Walton, H., McLachlan, G., de Boisanger, J., Bartlett-Pestell, S., Roche, E., Gandhi, V., Wilson, G. J., Brookes, Z., Yeen Fung, C., Macfarlane, H., Navaratnam, A., James, C., Scolding, P., & Sara, H. (2020). A comprehensive hospital agile preparedness (CHAPs) tool for pandemic preparedness, based on the COVID-19 experience. Future healthcare journal, 7(2), 165–168.

Information Packet H5

You are a civil servant working in Dalessie, working closely with the provost, city council and various agencies including the NHS, the UK Health Security Agency (UKHSA), and the Scottish Environment Protection Agency (SEPA).

Some of the key Dalessie facts and figures at a glance are summarized in the table below.

Community Amenities Details
Schools 5 primary schools, 4 secondary schools, 1 college
Care Homes 4, each with ~40 bed capacity
Restaurants and Cafes 64
Parks and Playgrounds 11
Economic Indicators Details
GDP/capita £38959
Unemployment Rate 3%
Traffic and Transport Details
Traffic fatalities (average/month) 15



Your briefing packet on Group A Streptococcus includes the following information.

Information Packet H6

You are a microbiologist working in the virology department at the Greater Dalessie Clinical Laboratory. Your laboratory is equipped to handle a range of culture samples (including anaerobic and microaerobic bacteria, as well as viruses), and you routinely process1989 samples monthly.

You are familiar with the culture requirements for growth of Group A Streptococci, and the UK Standards for Microbiology Investigations (UK SMI): Identification of Streptococcus species, Enterococcus species and morphologically similar organisms.

Group A Streptococci grown on sheep's blood agar. Image credit: [CDC](https://phil.cdc.gov/details.aspx?pid=8170)

Figure 12: Group A Streptococci grown on sheep’s blood agar. Image credit: CDC

You are also familiar with the literature surrounding Streptococcus pyogenes identification, and often read papers such as:

  • Robberts, F J Lourens et al. “Rapid, Low-Complexity, Simultaneous Bacterial Group Identification and Antimicrobial Susceptibility Testing Performed Directly on Positive Blood Culture Bottles Using Chromogenic Agar.” The American journal of tropical medicine and hygiene vol. 107,6 1302-1307. 14 Nov. 2022, doi:10.4269/ajtmh.22-0278

  • Velusamy, Srinivasan et al. “Sequential Quadriplex Real-Time PCR for Identifying 20 Common emm Types of Group A Streptococcus.” Journal of clinical microbiology vol. 59,1 e01764-20. 17 Dec. 2020, doi:10.1128/JCM.01764-20

  • Wang, Jie et al. “Identification and cluster analysis of Streptococcus pyogenes by MALDI-TOF mass spectrometry.” PloS one vol. 7,11 (2012): e47152. doi:10.1371/journal.pone.0047152

Information Packet H7

You are a public communications expert, often employed by the Dalessie city council to manage the PR response to different initiatives or crises.

As a public communications expert, you are familiar with the literature surrounding science communication in a pandemic, including papers such as:

  • Matta, G. Science communication as a preventative tool in the COVID19 pandemic. Humanit Soc Sci Commun 7, 159 (2020).

  • Abdool Karim, Salim S. “Public understanding of science: Communicating in the midst of a pandemic.” Public understanding of science (Bristol, England) vol. 31,3 (2022): 282-287.

  • Royan, Regina et al. “Use of Twitter Amplifiers by Medical Professionals to Combat Misinformation During the COVID-19 Pandemic.” Journal of medical Internet research vol. 24,7 e38324. 22 Jul. 2022, doi:10.2196/38324

  • Tait, Margaret E et al. “Serving the public? A content analysis of COVID-19 public service announcements airing from March - December of 2020 in the U.S.” Preventive medicine reports vol. 29 (2022): 101971.

You have assembled the following information/resources for this meeting:

  • UKHSA Group A streptococcus Communications Support Pack

  • Huttner, Benedikt et al. “Characteristics and outcomes of public campaigns aimed at improving the use of antibiotics in outpatients in high-income countries.” The Lancet. Infectious diseases vol. 10,1 (2010): 17-31. doi:10.1016/S1473-3099(09)70305-6

  • Veys, Koen et al. “The effect of hand hygiene promotion programs during epidemics and pandemics of respiratory droplet-transmissible infections on health outcomes: a rapid systematic review.” BMC public health vol. 21,1 1745. 25 Sep. 2021, doi:10.1186/s12889-021-11815-4

  • Hay, Alastair D. “The group A strep crisis: can we do better?.” BMJ (Clinical research ed.) vol. 380 58. 10 Jan. 2023, doi:10.1136/bmj.p58

Information Packet H8

You are one of the doctors at the largest surgery in Dalessie. In the past fortnight, 81 of your patients have recently presented to the surgery with symptoms consistent with Group A Streptococcus infections. You have therefore recently been familiarising yourself with the relevant literature:

Information Packet H9

You are an epidemiologist working at the University of Dalessie, and have been studying Streptococcus pyogenes transmission dynamics for the past 9 years. As such, you are very familiar with the relevant literature, including papers such as:

  • Friães, A et al. “Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes.” Journal of clinical microbiology vol. 60,6 (2022): e0031522. doi:10.1128/jcm.00315-22

  • Jespersen, Magnus G et al. “Global genomic epidemiology of Streptococcus pyogenes.” Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases vol. 86 (2020): 104609. doi:10.1016/j.meegid.2020.104609

  • Latronico, Francesca et al. “Genomic Characteristics Behind the Spread of Bacteremic Group A Streptococcus Type emm89 in Finland, 2004-2014.” The Journal of infectious diseases vol. 214,12 (2016): 1987-1995. doi:10.1093/infdis/jiw468

  • Hayes, Andrew et al. “Restricted Sequence Variation in Streptococcus pyogenes Penicillin Binding Proteins.” mSphere vol. 5,2 e00090-20. 29 Apr. 2020, doi:10.1128/mSphere.00090-20

  • Tagini, F et al. “Importance of whole genome sequencing for the assessment of outbreaks in diagnostic laboratories: analysis of a case series of invasive Streptococcus pyogenes infections.” European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology vol. 36,7 (2017): 1173-1180. doi:10.1007/s10096-017-2905-z

  • Turner, Claire E et al. “Community outbreaks of group A Streptococcus revealed by genome sequencing.” Scientific reports vol. 7,1 8554. 17 Aug. 2017, doi:10.1038/s41598-017-08914-x

  • Smeesters PR, de Crombrugghe G, Tsoi SK, et al. Global Streptococcus pyogenes strain diversity, disease associations, and implications for vaccine development: a systematic review. Lancet Microbe. 2024;5(2):e181-e193. doi:10.1016/S2666-5247(23)00318-X

  • Maldonado-Barrueco A, Bloise I, Cendejas-Bueno E, López-Rodrigo F, García-Rodríguez J, Lázaro-Perona F. Epidemiological changes in invasive Streptococcus pyogenes infection during the UK alert period: A molecular comparative analysis from a tertiary Spanish hospital in 2023. Enferm Infecc Microbiol Clin (Engl Ed). 2024;42(1):34-37. doi:10.1016/j.eimce.2023.09.003

  • Toorop MMA, Kraakman MEM, Hoogendijk IV, et al. A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters. J Clin Microbiol. 2023;61(11):e0055823. doi:10.1128/jcm.00558-23