Scenario G

Disaster has struck - hard on the heels of the COVID-19 pandemic, another disease outbreak has hit your fair city, Glenleith. Residents are outraged and worried. There have already been 13 deaths.

The cause of the outbreak appears to be multi-drug resistant Mycobacterium tuberculosis (XDR TB). (Please refer to the CDC Tuberculosis Fact Sheet for more information about the disease.)

Photomicrograph of Ziehl-Nielsen stained Mycobacterium tuberculosis cells. Image credit: [CDC](https://phil.cdc.gov/details.aspx?pid=5789)

Figure 1: Photomicrograph of Ziehl-Nielsen stained Mycobacterium tuberculosis 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 (Riverview)
  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 Glenleith
  9. Epidemiologist from the local university, an expert on Mycobacterium tuberculosis 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, Glenleith. 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 G1

You are the provost of Glenleith, elected in 2016.

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

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

The current population of Glenleith (as of December 2022) is 159025. The demographic data for the city is shown below.

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

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

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

Voting intention by Glenleith residents (Source: YouGov polling)

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

There are currently 36 elected councillors, representing the 5 main political parties in Glenleith as follows:

Political Party Number of Seats
Independent Peace 1
New Progressive 8
Unconditional Green 19
Blue and Gold 6
Conservative Coalition 2



The overall budget (expenditures) for the 2022-2023 financial year was £550791101. A summary of expeditures by category for this financial year is shown below.

Public expenditures by category for the 2202-2023 financial year (Source: Glenleith City Council)

Figure 5: Public expenditures by category for the 2202-2023 financial year (Source: Glenleith City Council)

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

From:
To:
Cc: Subject: This Bloody Pandemic

Dear Provost,

I am so angry to hear about this new pandemic in Glenleith. This seems to be too much to bear on top of COVID, the cost of living crisis, and the war in Ukraine. It is just one tragedy after another.

I hope that your office is going to do something about horrible pandemic very soon.

All the best,
Ailidh

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

Dear Provost,

This new pandemic in Glenleith has the potential to devastate our businesses. I run a toy store on the high street and virtually 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 all of the poor people dying at once, 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.

Best wishes,
Siobhan (Fraser & Co., proprietor)

From:
To:
Cc:
Subject: Government Overreach

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.

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

Best wishes,
Madison (a concerned voter)

From:
To:
Cc:
Subject:

Dear Provost,

I have just learned that my my nephew has passed away due to the new pandemic in Glenleith. The family are all devastated by this loss.

This is especially terrible coming hard on the heels of all of our losses due to COVID-19.

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

Yours truly,
Ailidh

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

Information Packet G2

You are a representative from Public Health Scotland, sent to Glenleith to help with the XDR TB outbreak.

Your briefing packet includes the following documents:

Information Packet G3

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

A team of scientists working together have in a PHS lab have isolated and cultured M. tuberculosis (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 M. tuberculosis 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_000669635.1
2 GCA_000669635.1
3 GCA_000669635.1
4 GCA_000669635.1
5 GCA_000669635.1
6 GCA_000669635.1
7 GCA_000669635.1
8 GCA_000669635.1
9 GCA_000669635.1
10 GCA_000669635.1



Your briefing packet also includes the following documents:

  • Mycobacteria spp. pubMLST

  • Hall, Michael B et al. “Evaluation of Nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis.” The Lancet. Microbe vol. 4,2 (2023): e84-e92. doi:10.1016/S2666-5247(22)00301-9

  • Macedo, Rita et al. “Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences.” International journal of molecular sciences vol. 24,3 2912. 2 Feb. 2023, doi:10.3390/ijms24032912

  • Phelan, Jody et al. “Genome-wide host-pathogen analyses reveal genetic interaction points in tuberculosis disease.” Nature communications vol. 14,1 549. 1 Feb. 2023, doi:10.1038/s41467-023-36282-w

Information Packet G4

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

The Riverview hospital in Glenleith. Image credit: [DALL-E

Figure 6: The Riverview hospital in Glenleith. Image credit: [DALL-E

The annual operating budget for financial year 2202-2023 was £1.5 million, and average expenditures are shown by category in the figure below.

Hospital expenditures by category for financial year 2202-2023 (Source: NHS Scotland)

Figure 7: Hospital expenditures by category for financial year 2202-2023 (Source: NHS Scotland)

The Riverview 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 Riverview in November 2019. Average ICU bed occupancy before and during the COVID-19 pandemic is in the figure below.

ICU bed occupancy for the Glenleith Riverview hospital (Source: NHS Scotland)

Figure 8: ICU bed occupancy for the Glenleith Riverview hospital (Source: NHS Scotland)

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

Admissions to the Glenleith Riverview hospital by category (Source: NHS Scotland)

Figure 9: Admissions to the Glenleith Riverview 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 Glenleith Riverview hospital (Source: NHS Scotland)

Figure 10: ICU waiting times for the Glenleith Riverview hospital (Source: NHS Scotland)

The Riverview 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 Glenleith Riverview hospital (Source: NHS Scotland)

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

There are currently 171 patients in the Riverview with confirmed or suspected XDR TB, 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 G5

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

Community Amenities Details
Schools 3 primary schools, 3 secondary schools, 1 college
Care Homes 2, each with ~30 bed capacity
Restaurants and Cafes 138
Parks and Playgrounds 1
Economic Indicators Details
GDP/capita £46455
Unemployment Rate 6%
Traffic and Transport Details
Traffic fatalities (average/month) 19



Your briefing packet on XDR TB includes the following information.

  • WHO policy on TB infection control in health-care facilities, congregate settings and households

  • Neiderud C. J. (2015). How urbanization affects the epidemiology of emerging infectious diseases. Infection ecology & epidemiology, 5, 27060. https://doi.org/10.3402/iee.v5.27060

  • Prasad, A., Ross, A., Rosenberg, P., & Dye, C. (2016). A world of cities and the end of TB. Transactions of the Royal Society of Tropical Medicine and Hygiene, 110(3), 151–152.

  • Bigio, Jacob et al. “A scoping review on the risk of tuberculosis in specific population groups: can we expand the World Health Organization recommendations?.” European respiratory review : an official journal of the European Respiratory Society vol. 32,167 220127. 11 Jan. 2023, doi:10.1183/16000617.0127-2022

  • Hasan, R., Shakoor, S., Hanefeld, J., & Khan, M. (2018). Integrating tuberculosis and antimicrobial resistance control programmes. Bulletin of the World Health Organization, 96(3), 194–200.

Information Packet G6

You are a microbiologist working in the microbiology department at the Greater Glenleith 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 process1964 samples monthly.

You are familiar with the culture requirements for growth of Mycobacterium tuberculosis, and the range of UK Standards for Microbiology Investigations (UK SMI): Investigation of specimens for Mycobacterium species.

Colony morphology of Mycobacterium tuberculosis grown on an agar plate. Image credit: [CDC](https://phil.cdc.gov/details.aspx?pid=4428)

Figure 12: Colony morphology of Mycobacterium tuberculosis grown on an agar plate. Image credit: CDC

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

  • Taufiq, Saman et al. “Towards portable rapid TB biosensor: Detecting Mycobacterium tuberculosis in raw sputum samples using functionalized screen printed electrodes.” Bioelectrochemistry (Amsterdam, Netherlands) vol. 150 (2023): 108353. doi:10.1016/j.bioelechem.2022.108353

  • Augustin, Linus, and Nisheeth Agarwal. “Designing a Cas9/gRNA-assisted quantitative Real-Time PCR (CARP) assay for identification of point mutations leading to rifampicin resistance in the human pathogen Mycobacterium tuberculosis.” Gene vol. 857 (2023): 147173. doi:10.1016/j.gene.2023.147173

  • Gliddon, Harriet D et al. “A Rapid Drug Resistance Genotyping Workflow for Mycobacterium tuberculosis, Using Targeted Isothermal Amplification and Nanopore Sequencing.” Microbiology spectrum vol. 9,3 (2021): e0061021. doi:10.1128/Spectrum.00610-21

Information Packet G7

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

  • Jackson, A D et al. “Knowledge of tuberculosis transmission among recently infected patients in Glasgow.” Public health vol. 122,10 (2008): 1004-12. doi:10.1016/j.puhe.2008.01.011

  • Gomes, Ricardo Estêvão et al. “Awareness and education in lung diseases: Are we reaching the target?.” Pulmonology vol. 28,5 (2022): 330-332. doi:10.1016/j.pulmoe.2022.02.011

  • Bello-Bravo, Julia et al. “Measuring the impact and reach of informal educational videos on YouTube: The case of Scientific Animations Without Borders.” Heliyon vol. 7,12 e08508. 1 Dec. 2021, doi:10.1016/j.heliyon.2021.e08508

  • WHO World TB Day Resources

Information Packet G8

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

Information Packet G9

You are an epidemiologist working at the University of Glenleith, and have been studying Mycobacterium transmission dynamics for the past 3 years. As such, you are very familiar with the relevant literature, including papers such as:

  • López, Mariana G et al. “Deciphering the Tangible Spatio-Temporal Spread of a 25-Year Tuberculosis Outbreak Boosted by Social Determinants.” Microbiology spectrum, e0282622. 14 Feb. 2023, doi:10.1128/spectrum.02826-22

  • Stucki, David et al. “Tracking a tuberculosis outbreak over 21 years: strain-specific single-nucleotide polymorphism typing combined with targeted whole-genome sequencing.” The Journal of infectious diseases vol. 211,8 (2015): 1306-16. doi:10.1093/infdis/jiu601

  • Roetzer, Andreas et al. “Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.” PLoS medicine vol. 10,2 (2013): e1001387. doi:10.1371/journal.pmed.1001387

  • Arnold, Amber et al. “XDR-TB transmission in London: Case management and contact tracing investigation assisted by early whole genome sequencing.” The Journal of infection vol. 73,3 (2016): 210-8. doi:10.1016/j.jinf.2016.04.037

  • Nikolayevskyy, Vlad et al. “Whole genome sequencing of Mycobacterium tuberculosis for detection of recent transmission and tracing outbreaks: A systematic review.” Tuberculosis (Edinburgh, Scotland) vol. 98 (2016): 77-85. doi:10.1016/j.tube.2016.02.009

  • Napier, Gary et al. “Large-scale genomic analysis of Mycobacterium tuberculosis reveals extent of target and compensatory mutations linked to multi-drug resistant tuberculosis.” Scientific reports vol. 13,1 623. 12 Jan. 2023, doi:10.1038/s41598-023-27516-4

  • Jarchow-MacDonald, Anna et al. “Changing Incidence and Characteristics of Nontuberculous Mycobacterial Infections in Scotland and Comparison With Mycobacterium tuberculosis Complex Incidence (2011 to 2019).” Open forum infectious diseases vol. 10,1 ofac665. 12 Dec. 2022, doi:10.1093/ofid/ofac665