Scenario C

Disaster has struck - hard on the heels of the COVID-19 pandemic, another disease outbreak has hit your fair city, Malleith. Residents are outraged and worried. There have already been 10 deaths.

The cause of the outbreak appears to be methicillin-resistant Staphylococcus aureus (MRSA). (Please refer to the CDC MRSA Fact Sheet for more information about the pathogen.)

False-coloured scanning electron microscopy (SEM) image of MRSA cells. Image credit: [CDC](https://phil.cdc.gov/Details.aspx?pid=18127)

Figure 1: False-coloured scanning electron microscopy (SEM) image of MRSA cells. 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 (Central Highland)
  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 Malleith
  9. Epidemiologist from the local university, an expert on S. aureus 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, Malleith. 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 C1

You are the provost of Malleith, elected in 2019.

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

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

The current population of Malleith (as of December 2022) is 163339. The demographic data for the city is shown below.

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

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

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

Voting intention by Malleith residents (Source: YouGov polling)

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

There are currently 41 elected councillors, representing the 5 main political parties in Malleith as follows:

Political Party Number of Seats
New Progress 3
Social Change 11
Freedom and Green 18
Purple 8
Thistle 1



The overall budget (expenditures) for the 2022-2023 financial year was £565122758. A summary of expenditures by category for this financial year is shown below.

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

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

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

From:
To:
Cc: Subject: This Horrible Pandemic

Dear Provost,

I am outraged to hear about this new pandemic in Malleith. Too many people have died and it is such a tragedy.

I wish that your office is going to do something about all of the poor people dying at once.

Yours sincerely,
Rodrigo

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

Dear Provost,

This new pandemic in Malleith has the potential to ruin our businesses. I run a restaurant on the high street and almost had to close because of all the draconian lockdowns due to COVID.

Things are bad enough already with the cost of living crisis, war in Ukraine, and Brexit, we can’t afford another pandemic.

I hope that your office is going to do something about tragedy immediately, keeping in mind the economic interests of businesses in our city and the fact that we cannot afford the draconian lockdowns you imposed during COVID.

Sincerely,
Eleanor (Around the Corner, proprietor)

From:
To:
Cc:
Subject: Government Overstep

Dear Provost,

I dread that you and your office are going to use this new pandemic as yet another excuse for government overreach into citizens’ lives. The mental health consequences of the last pandemic were underappreciated, but very real - people suffered due to the lockdowns and children’s development was affected by the wearing of face masks and the closing of schools.

Facemasks are just the tyranny of the minority over the majority, I hope that you will not permit them again on your watch.

Yours sincerely,
Anika (a concerned voter)

From:
To:
Cc:
Subject:

Dear Provost,

I have just learned that my my auntie has passed away due to the new pandemic in Malleith. This is an unspeakable loss.

The family are all devastated by this loss.

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

Respectfully,
Ailidh

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

Information Packet C2

You are a representative from Public Health Scotland, sent to Malleith to help with the MRSA outbreak.

Your briefing packet includes the following documents:

  • Staphylococcus aureus bacteraemia (NHS)

  • Staphylococcus aureus epidemiology (UKHSA)

  • Tong SY, Davis JS, Eichenberger E, Holland TL, Fowler VG Jr. Staphylococcus aureus infections: epidemiology, pathophysiology, clinical manifestations, and management. Clin Microbiol Rev. 2015 Jul;28(3):603-61.

  • Lawes T, Edwards B, López-Lozano JM, Gould I. Trends in Staphylococcus aureus bacteraemia and impacts of infection control practices including universal MRSA admission screening in a hospital in Scotland, 2006-2010: retrospective cohort study and time-series intervention analysis. BMJ Open. 2012 Jun 8;2(3):e000797.

Information Packet C3

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

A team of scientists working together have in a PHS lab have isolated and cultured MRSA from a number of patient samples taken during this outbreak; isolated genomic DNA from cultures of these isolates; sequenced this DNA using an Illumina MiSeq platform; assembled the short paired-end reads; and compared these assemblies to the extant Staphylococcus aureus 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_003595405.1
2 GCA_003595465.1
3 GCA_002000805.1
4 GCA_003595405.1
5 GCA_002000805.1
6 GCA_002000805.1
7 GCA_013836525.1
8 GCA_003595405.1
9 GCA_003595465.1
10 GCA_003595465.1



Your briefing packet also includes the following documents:

  • Staphylococcus aureus pubMLST

  • Reuter, Sandra et al. “Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland.” Genome research vol. 26,2 (2016): 263-70.

  • Mollerup, Sarah et al. “spa Typing of Methicillin-Resistant Staphylococcus aureus Based on Whole-Genome Sequencing: the Impact of the Assembler.” Microbiology spectrum vol. 10,6 (2022): e0218922. doi:10.1128/spectrum.02189-22

  • Cunningham, Scott A et al. “Comparison of Whole-Genome Sequencing Methods for Analysis of Three Methicillin-Resistant Staphylococcus aureus Outbreaks.” Journal of clinical microbiology vol. 55,6 (2017): 1946-1953. doi:10.1128/JCM.00029-17

Information Packet C4

You are the director of Malleith’s main hospital, the Central Highland, which has 500 beds across 10 different wards and 10 operating theatres.

The Central Highland hospital in Malleith. Image credit: [DALL-E

Figure 6: The Central Highland hospital in Malleith. Image credit: [DALL-E

The annual operating budget for financial year 2022-2023 was £1.7 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 Central Highland has units specialising in maternity care; dermatology; paediatrics; an ear, nose, and throat clinic; an eye clinic; and an orthopedic unit.

There are currently 23 ICU beds (with ventilators) available, an increase from the 18 ICU beds in the Central Highland in November 2019. Average ICU bed occupancy before and during the COVID-19 pandemic is in the figure below.

ICU bed occupancy for the Malleith Central Highland hospital (Source: NHS Scotland)

Figure 8: ICU bed occupancy for the Malleith Central Highland hospital (Source: NHS Scotland)

There are approximately 1.5m admissions to the Central Highland hospital annually, the majority of these being to the emergency (A&E) department.

Admissions to the Malleith Central Highland hospital by category (Source: NHS Scotland)

Figure 9: Admissions to the Malleith Central Highland hospital by category (Source: NHS Scotland)

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

ICU waiting times for the Malleith Central Highland hospital (Source: NHS Scotland)

Figure 10: ICU waiting times for the Malleith Central Highland hospital (Source: NHS Scotland)

The Central Highland 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 Malleith Central Highland hospital (Source: NHS Scotland)

Figure 11: Key Performance Indicators (KPIs) related to infectious diseases for the Malleith Central Highland hospital (Source: NHS Scotland)

There are currently 145 patients in the Central Highland with confirmed or suspected MRSA, 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 C5

You are a civil servant working in Malleith, 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 Malleith facts and figures at a glance are summarized in the table below.

Community Amenities Details
Schools 4 primary schools, 3 secondary schools, 1 college
Care Homes 1, each with ~50 bed capacity
Restaurants and Cafes 85
Parks and Playgrounds 11
Economic Indicators Details
GDP/capita £40089
Unemployment Rate 4%
Traffic and Transport Details
Traffic fatalities (average/month) 13



Your briefing packet on MRSA includes the following information.

Information Packet C6

You are a microbiologist working in the virology department at the Greater Malleith 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 process1582 samples monthly.

You are familiar with the culture requirements for growth of MRSA in the laboratory, and the UK Standards for Microbiology Investigations (SMI) for identification of Staphylococcus.

MRSA grown on Mannitol Salt Agar (MSA). Image credit: [CDC](https://phil.cdc.gov/Details.aspx?pid=16810)

Figure 12: MRSA grown on Mannitol Salt Agar (MSA). Image credit: CDC

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

  • Methicillin-resistant Staphylococcus aureus (MRSA): Laboratory Testing (CDC)

  • Hunt AC, Edwards B, Girvan EK, Cosgrove B, Edwards GF, Gould IM. Methicillin-resistant Staphylococcus aureus in Northeastern Scotland in 2003 to 2007: evolving strain distribution and resistance patterns. J Clin Microbiol. 2011 May;49(5):1975-8.

  • Giulieri SG, Tong SYC, Williamson DA. Using genomics to understand meticillin- and vancomycin-resistant Staphylococcus aureus infections. Microb Genom. 2020 Jan;6(1):e000324.

Information Packet C7

You are a public communications expert, often employed by the Malleith 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:

  • Dickmann P, Keeping S, Döring N, Schmidt AE, Binder C, Ariño-Blasco S, Gil J. Communicating the Risk of MRSA: The Role of Clinical Practice, Regulation and Other Policies in Five European Countries. Front Public Health. 2017 Mar 17;5:44.

  • Mason, Thuy et al. “Knowledge and awareness of the general public and perception of pharmacists about antibiotic resistance.” BMC public health vol. 18,1 711. 8 Jun. 2018.

  • Djerf-Pierre, Monika, and Mia Lindgren. “Making sense of”superbugs” on YouTube: A storytelling approach.” Public understanding of science (Bristol, England) vol. 30,5 (2021): 535-551.

Information Packet C8

You are one of the doctors at the largest surgery in Malleith. In the past fortnight, 69 of your patients have recently presented to the surgery with symptoms consistent with MRSA. You have therefore recently been familiarising yourself with the relevant literature:

Information Packet C9

You are an epidemiologist working at the University of Malleith, and have been studying S. aureus transmission dynamics for the past 5 years. As such, you are very familiar with the relevant literature, including papers such as:

  • Dung TTN, Phat VV, Vinh C, et al. Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes. BMC Infect Dis. 2024;24(1):164. Published 2024 Feb 7. doi:10.1186/s12879-024-09028-2

  • Benvenga V, Cuénod A, Purushothaman S, et al. Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection. Genome Med. 2024;16(1):23. Published 2024 Feb 5. doi:10.1186/s13073-024-01292-w

  • Aung MS, Urushibara N, Kawaguchiya M, et al. Molecular Epidemiological Characterization of Methicillin-Resistant Staphylococcus aureus from Bloodstream Infections in Northern Japan: Increasing Trend of CC1 and Identification of ST8-SCCmec IVa USA300-Like Isolate Lacking Arginine Catabolic Mobile Element. Microb Drug Resist. 2024;30(2):63-72. doi:10.1089/mdr.2023.0203

  • Jiang J-H, Cameron DR, Nethercott C, Aires-de-Sousa M, Peleg AY. Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages. Clin Microbiol Rev. 2023;36(4):e0014822. doi:10.1128/cmr.00148-22

  • Zaghen F, Sora VM, Meroni G, et al. Epidemiology of Antimicrobial Resistance Genes in Staphylococcus aureus Isolates from a Public Database from a One Health Perspective-Sample Origin and Geographical Distribution of Isolates. Antibiotics (Basel). 2023;12(12):1654. Published 2023 Nov 24. doi:10.3390/antibiotics12121654

  • Wendel AF, Otchwemah R, Layer-Nicolaou F, et al. Investigating a possible link between antiseptic treatment and the increased occurrence of daptomycin-resistant Staphylococcus aureus. Clin Microbiol Infect. 2023;29(10):1334.e1-1334.e6. doi:10.1016/j.cmi.2023.06.007

  • Giulieri SG, Guérillot R, Holmes NE, et al. A statistical genomics framework to trace bacterial genomic predictors of clinical outcomes in Staphylococcus aureus bacteremia. Cell Rep. 2023;42(9):113069. doi:10.1016/j.celrep.2023.113069

  • Sato T, Yamaguchi T, Aoki K, et al. Whole-genome sequencing analysis of molecular epidemiology and silent transmissions causing meticillin-resistant Staphylococcus aureus bloodstream infections in a university hospital. J Hosp Infect. 2023;139:141-149. doi:10.1016/j.jhin.2023.05.014

  • Zhang Z, Wang J, Wang H, et al. Molecular Surveillance of MRSA in Raw Milk Provides Insight into MRSA Cross Species Evolution. Microbiol Spectr. 2023;11(4):e0031123. doi:10.1128/spectrum.00311-23