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---
title: 'BM424 workshop: infectious disease outbreak control'
author: "Morgan Feeney"
date: "24/02/2023"
output:
bookdown::html_document2:
toc: true
toc_float:
toc_collapsed: false
number_sections: false
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
library(knitr)
outbreak_deaths <- floor(runif(1, min = 10, max = 30))
city_name <- "Inverkeld"
hospital_name <- "Queen Rose"
```
## Scenario A
Disaster has struck - hard on the heels of the COVID-19 pandemic, another disease outbreak has hit your fair city, `r city_name`. Residents are outraged and worried. There have already been `r outbreak_deaths` deaths.
The cause of the outbreak appears to be <i>Legionella pneumophila</i>. (Please refer to the [Legionnaire's Disease Fact Sheet](https://www.cdc.gov/legionella/downloads/fs-legionnaires.pdf) for more information about the pathogen.)
```{r Legionella, out.width="50%", out.height="50%", echo=FALSE, fig.cap="False-coloured scanning electron microscopy (SEM) image of a group of Legionella pneumophila cells. Image credit: [CDC](https://phil.cdc.gov/details.aspx?pid=11152)"}
knitr::include_graphics(rep("images/Legionella.jpg"))
```
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 (`r hospital_name`)
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 `r city_name`
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 <i>Legionella</i> outbreak currently plaguing your city, `r city_name`. 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 should submit 3-5 specific actions to control the pandemic, using the [workshop 3 pro forma](/proformas/BM424_workshop3_proforma.docx) (also available on MyPlace). Submit this by noon, Friday March 10th, via the submission link on MyPlace.
***
## Information Packet A1
You are the provost of `r city_name`, elected in `r sample(2012:2021, size=1)`.
```{r city, echo=FALSE, fig.cap="Photograph of Inverkeld city centre. Image credit: DALL-E"}
knitr::include_graphics(rep("images/Inverkeld.png"))
```
The current population of `r city_name` (as of December 2022) is `r sample(150000:170000, size=1)`. The demographic data for the city is shown below.
```{r A1, fig.show="hold", out.width="50%", echo=FALSE, fig.cap="Inverkeld demographics (Source: Office for National Statistics)"}
Pop <- c(sample(150000:170000, size=3, replace=TRUE), sample(170000:180000, size=3, replace=TRUE), sample(190000:170000, size=2, replace=TRUE), sample(150000:170000, size=2, replace=TRUE))
PopYears <- c(2012:2021)
population <- data.frame(Pop, PopYears)
ggplot(data = population, aes(x=PopYears, y=Pop)) +
geom_point() +
geom_line() +
labs(y = "Number of Inverkeld residents (estimated)", x = "Year") +
scale_y_continuous(limits=c(0, 200000)) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
Demog <- c((rep("Births", 10)), (rep("Deaths", 10)))
Num <- c(sample(1000:2000, size=10, replace=TRUE), sample(500:1500, size=8, replace=TRUE), sample(3000:5500, size=2, replace=TRUE))
DemogYears <- c(rep(2012:2021, 2))
birthdeath <- data.frame(Demog, Num, DemogYears)
ggplot(data = birthdeath, aes(x=DemogYears, y=Num, group=Demog, colour=Demog)) +
geom_point() +
geom_line() +
labs(y = "Number of births and deaths in Inverkeld (estimated)", x = "Year", colour = "Demographics") +
scale_y_continuous(limits=c(0, 5500)) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +
scale_color_discrete(name="")
```
You were elected as a member of the popular "Environment First" party and made a number of election promises regarding a "Green New Deal" for `r city_name`. This is your first full year in office.
```{r A2, fig.cap="Voting intention by Inverkeld residents (Source: YouGov polling)", echo=FALSE}
Party <- c((rep("Revolutionary", 10)), (rep("Social Capital", 10)), (rep("Environment First", 10)), (rep("Wind Power", 10)), (rep("Social Redistribution", 10)))
Polls <- c(sample(1:3, size=10, replace=TRUE), sample(8:14, size=10, replace=TRUE), sample(15:20, size=10, replace=TRUE), sample(5:10, size=10, replace=TRUE), sample(1:2, size=10, replace=TRUE))
PolYears <- c(rep(2012:2021, 5))
politics <- data.frame(Party, Polls, PolYears)
ggplot(data = politics, aes(x=PolYears, y=Polls, color=Party)) +
geom_point() +
geom_line() +
labs(y = "Voting Intention", x = "Year") +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
Councillors <- sum(politics[politics$PolYears>2020, 2])
```
There are currently `r Councillors` elected councillors, representing the 5 main political parties in `r city_name` as follows:
```{r A3, echo=FALSE}
pol2021 <- (politics[politics$PolYears>2020, 2])
Parties <- c("Revolutionary", "Social Capital", "Environment First", "Wind Power", "Social Redistribution")
Councillors <- data.frame(Parties, pol2021)
kable(x = Councillors,
format = "html",
col.names = c("Political Party", "Number of Seats"))
```
<br><br>
The overall budget (expenditures) for the 2021-2022 financial year is £`r sample(400000000:600000000, size=1)`. A summary of expeditures by category for this financial year is shown below.
```{r A4, fig.cap="Public expenditures by category for the 2021-2022 financial year (Source: Inverkeld City Council)", echo=FALSE}
expenses <- data.frame(
Category=c("Education", "Industry and Agriculture", "Social Care", "Transport", "Public order and safety", "Healthcare", "Housing", "Other"),
value=c(13,7,9,5,7,21,8,2)
)
ggplot(expenses, aes(x="", y=value, fill=Category)) +
geom_bar(stat="identity", width=1, color="white") +
coord_polar("y", start=0) +
theme_void()
```
```{r emails, echo=FALSE}
clos1 <- c("Yours sincerely,", "Best wishes,", "Kind regards,", "All the best,", "Sincerely,", "Yours truly,", "Respectfully,")
email1 <- c("gldk", "aptr", "bhr", "tgh", "pbr", "js", "lucy", "amd", "oirl", "jim", "ygg", "oli", "end", "lulu", "rye", "att")
adj1 <- c("Disgraceful", "Terrible", "Horrible", "Devastating", "Sad", "Bloody")
emotion1 <- c("outraged", "upset", "extremely vexed", "so angry", "devastated")
sent1 <- c("As if COVID wasn't enough! Has this city not suffered enough, I ask you.", "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.", "Too many people have already died from COVID and it seems completely cruel to have another pandemic strike our city again so soon.", "There seems to be no end to the suffering that pandemics inflict on our city in these days.", "It seems almost like the apocalypse must be upon us, with this pandemic following so close upon the heels of COVID19.", "Too many people have died and it is such a tragedy.")
wish1 <- c("hope", "hope very much", "wish", "expect", "sincerely hope")
state1 <- c("dreadful state of affairs", "horrible pandemic", "all of the poor people dying", "tragedy")
time1 <- c("immediately", "very soon", "at once", "as soon as possible")
name1 <- c("Anna", "Luke", "Siobhan", "Su", "Ailidh", "Fiona", "Graham", "Madison", "Eleanor", "Rodrigo", "Kieran", "Wilson", "Anika", "Rosemary", "Alise", "Gordon", "Roman", "Karen")
verb1 <- c("devastate", "obliterate", "ruin", "destroy", "crush")
business1 <- c("small coffee shop", "coffee shop", "cafe", "restaurant", "bookshop", "boutique clothing store", "records shop", "used bookstore", "toy store", "sweet shop")
business2 <- c("The Inverkeld Shop", "Fraser & Co.", "Bella's", "Around the Corner", "Jewels")
adj2 <- c("nearly", "almost", "virtually", "almost literally", "practically")
conseq1 <- c("lost my business due to those pandemic lockdowns", "had to close because of all the draconian lockdowns", "went out of business", "went bankrupt", "had to shut our doors during COVID")
sent2 <- c("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.", "You should be ashamed to think of all the businesses that have had to close because of the coronavirus measures this city took, and all of the people who lost their jobs.", "Businesses must be free to operate, not prosecuted by some nanny state.", "Things are bad enough already with the cost of living crisis, war in Ukraine, and Brexit, we can't afford another pandemic.", "I hope you realise that you need to put businesses first now - we were unfairly forced to bear the costs of the last pandemic.", "I hope you realise how much business we have all lost in recent years, and how much businesses in this city are struggling financially.")
subj1 <- c("Government Overreach", "Government Overstep", "Stop This Madness", "New Pandemic Measures")
state2 <- c("awful pandemic", "terrible pandemic", "new crisis", "new pandemic", "new disease")
conseq2 <- c("another lockdown", "a return to COVID rules", "face masks and gallons of hand sanitizer", "the draconian lockdowns you imposed during COVID", "restrictions that cripple our businesses")
wish2 <- c("fear", "dread", "abhor the idea", "hate the idea", "am afraid")
sent3 <- c("This last pandemic was just a typical example of what governments do when given a little too much power.", "Machiavelli said that power corrupts absolutely, and he was absolutely right - look at what happened during the last pandemic.", "I am sick and tired of government interference with my life, I have the right to go about my life without some do-gooder from a public health agency telling me that I need to wear a mask and can't visit my grandmother.", "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.")
sent4 <- c("Please do not use this disaster as another opportunity for oppressive lockdowns and government control of our lives.", "You must not allow the city to suffer through another round of lockdowns, face-masks, and other punitive restrictions that destroy people's lives.", "I hope that you will do the right thing in this time of crisis and that I will be able to vote for you again in the coming elections with a clean conscience.", "Facemasks are just the tyranny of the minority over the majority, I hope that you will not permit them again on your watch.")
subj2 <- c("This Terrible Tragedy", "Another Terrible Loss")
rel1 <- c("my mother-in-law", "my aunt", "my auntie", "my niece", "my nephew", "my husband's best friend", "my wife's best friend", "my sister-in-law", "my brother-in-law", "my uncle", "my granddad", "my gran", "my nana", "my nana's best friend")
sent5 <- c("The family are all devastated as you can surely imagine.", "Words cannot begin to describe our loss.", "This is truly a tragedy.", "This is an unspeakable loss.", "The family are all devastated by this loss.", "You cannot begin to imagine the grief that we are feeling.", "This is especially terrible coming hard on the heels of all of our losses due to COVID-19.")
sent6 <- c("I don't understand why we haven't learned how to deal with pandemics better, after all our experiences with COVID-19, I don't understand how this could have happened.", "I really wish that our government had better learned its lessons from the COVID-19 pandemic and could have prevented this terrible tragedy.", "I hope that, considering how many other families have also lost loved ones, that you and your office will be doing everything in their power to halt this pandemic and prevent more needless deaths.", "I hope that you will do everything you can to stop this pandemic so that no other families need to suffer this pain.", "I hope that you will do everything you can to stop this pandemic so that no more lives will be lost.", "I am sure that you and your office are doing your best, but I hope that in the fullness of time, there will be a public inquiry into how this pandemic was handled and why so many families have lost loved ones. Especially coming so soon after the lessons that we learned during the COVID-19 pandemic, I would have thought that this tragedy could have been prevented.")
```
Your office has recently received a great deal of correspondence regarding the pandemic in `r city_name`. A representative sample of these e-mails is shown below.
***
<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b>
<b>Subject:</b> This `r sample(adj1, 1)` Pandemic
Dear Provost,
I am `r sample(emotion1, 1)` to hear about this new pandemic in `r city_name`. `r sample(sent1, 1)`
I `r sample(wish1, 1)` that your office is going to do something about `r sample(state1, 1)` `r sample(time1, 1)`.
`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)`
***
<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b> city-council@`r city_name`.co.uk <br>
<b>Subject:</b> Pandemic Disaster for Businesses
Dear Provost,
This new pandemic in `r city_name` has the potential to `r sample(verb1, 1)` our businesses. I run a `r sample(business1, 1)` on the high street and `r sample(adj2, 1)` `r sample(conseq1, 1)` due to COVID.
`r sample(sent2, 1)`
I `r sample(wish1, 1)` that your office is going to do something about `r sample(state1, 1)` `r sample(time1, 1)`, keeping in mind the economic interests of businesses in our city and the fact that we cannot afford `r sample(conseq2, 1)`.<br>
`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)` (`r sample(business2, 1)`, proprietor)
***
<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b> city-council@`r city_name`.co.uk <br>
<b>Subject:</b> `r sample(subj1, 1)`
Dear Provost,
I `r sample(wish2, 1)` that you and your office are going to use this new pandemic as yet another excuse for government overreach into citizens' lives. `r sample(sent3, 1)`
`r sample(sent4, 1)`
`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)` (a concerned voter)
***
<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b> city-council@`r city_name`.co.uk <br>
<b>Subject:</b>
Dear Provost,
I have just learned that my `r sample(rel1, 1)` has passed away due to the new pandemic in `r city_name`. `r sample(sent5, 1)`
`r sample(sent5, 1)`
`r sample(sent6, 1)`
`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)`
***
As Provost of `r city_name`, you are of course familiar with the work of the [Standing Committee on Pandemic Preparedness](https://www.gov.scot/groups/standing-committee-on-pandemic-preparedness/). You are also familiar with:
* The [UK Pandemic Preparedness plan](https://www.gov.uk/government/publications/uk-pandemic-preparedness/uk-pandemic-preparedness)
* The latest [COVID-19 health protection guidance](https://publichealthscotland.scot/our-areas-of-work/conditions-and-diseases/covid-19/covid-19-health-protection-guidance/#section-1) released by Public Health Scotland
* [Tackling antimicrobial resistance 2019–2024: The UK’s five-year national action plan](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1070263/UK_AMR_5_year_national_action_plan.pdf)
* The [UK One Health Report - Joint report on antibiotic use and antibiotic resistance, 2013–2017 ](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/921039/Ted_Final_version__1318703-v45-One_Health_Report_2019_FINAL-accessible.pdf)
* [Communicating risk in public health emergencies: A WHO guideline for emergency risk communication (ERC) policy and practice](https://apps.who.int/iris/bitstream/handle/10665/259807/9789241550208-eng.pdf?sequence=2&isAllowed=y)
***
## Information Packet A2
You are a representative from Public Health Scotland, sent to `r city_name` to help with the <i>Legionella</i> outbreak.
Your briefing packet includes the following documents:
* [Guideline on the management of <i>Legionella</i> cases, incidents,outbreaks and clusters in the community: Health Protection Network Scottish Guidance](https://hpspubsrepo.blob.core.windows.net/hps-website/nss/2070/documents/1_legionella-guidelines-2014-2.pdf)
* [Cluster of <i>Legionella longbeachae</i> cases in Scotland in September/October 2013: Report from a national Incident Management Team](https://hpspubsrepo.blob.core.windows.net/hps-website/nss/1918/documents/1_legionella-outbreak-report-2014.pdf)
* Kawasaki, Takeshi et al. “Diagnostic accuracy of urinary antigen tests for legionellosis: A systematic review and meta-analysis.” Respiratory investigation vol. 60,2 (2022): 205-214.
* Nisar, Muhammad Atif et al. “<i>Legionella pneumophila</i> and Protozoan Hosts: Implications for the Control of Hospital and Potable Water Systems.” Pathogens (Basel, Switzerland) vol. 9,4 286. 15 Apr. 2020,
***
## Information Packet A3
You are an epidemiologist working for Public Health Scotland, sent to `r city_name` to help with the <i>Legionella</i> outbreak.
A team of scientists working together have cultured <i>Legionella pneumophila</i> from a number of patient sputum samples; isolated genomic DNA from these strains; sequenced this genomic DNA using an Illumina MiSeq platform; assembled the short paired-end reads; and compared these assemblies to the extant <i>Legionella pneumophila</i> sequences available in the NCBI databases. The results of these experiments are summarised in the table below.
<table>
<table border="1">
<tr>
<th>Patient </th>
<th>NCBI accession of closest database match</th>
</tr>
<tr>
<td>1</td>
<td>GCA_022577225.1</td>
</tr>
<tr>
<td>2</td>
<td>GCA_022577275.1</td>
</tr>
<tr>
<td>3</td>
<td>GCA_022577345.1</td>
</tr>
<tr>
<td>4</td>
<td>GCA_022576795.1 </td>
</tr>
<tr>
<td>5</td>
<td>GCA_022577275.1</td>
</tr>
<tr>
<td>6</td>
<td>GCA_022577225.1</td>
</tr>
<tr>
<td>7</td>
<td>GCA_022577345.1</td>
</tr>
<tr>
<td>8</td>
<td>GCA_022577345.1</td>
</tr>
<tr>
<td>9</td>
<td>GCA_022577225.1</td>
</tr>
<tr>
<td>10</td>
<td>GCA_022577345.1</td>
</tr>
</table>
<br><br>
Your briefing packet also includes the following documents:
* Gorzynski, Jamie et al. “Epidemiological analysis of Legionnaires' disease in Scotland: a genomic study.” The Lancet. Microbe vol. 3,11 (2022): e835-e845.
* Cameron, R L et al. “Comparison of <i>Legionella longbeachae</i> and <i>Legionella pneumophila</i> cases in Scotland; implications for diagnosis, treatment and public health response.” Journal of medical microbiology vol. 65,2 (2016): 142-146.
* Khodr, A et al. “Molecular epidemiology, phylogeny and evolution of Legionella.” Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases vol. 43 (2016): 108-22. doi:10.1016/j.meegid.2016.04.033
* Buultjens, Andrew H et al. “A Supervised Statistical Learning Approach for Accurate Legionella pneumophila Source Attribution during Outbreaks.” Applied and environmental microbiology vol. 83,21 e01482-17. 17 Oct. 2017, doi:10.1128/AEM.01482-17
***
## Information Packet A4
You are the director of `r city_name`'s main hospital, the `r hospital_name`, which has 500 beds across 8 different wards and 10 operating theatres.
```{r hospital, echo=FALSE, fig.cap="The Queen Rose hospital in Inverkeld. Image credit: [DALL-E"}
knitr::include_graphics(rep("images/Queen-Rose.png"))
```
The annual operating budget for financial year 2021-2022 was £1.3 million, and average expenditures are shown by category in the figure below.
```{r A5, fig.cap="Hospital expenditures by category for financial year 2021-2022 (Source: NHS Scotland)", echo=FALSE}
expenses <- data.frame(
Category=c("Staff costs", "Healthcare expenditures (drugs, supplies, etc.)", "Other supplies", "Other running costs (procurement, IT, HR, etc.)"),
value=c(25,17,9,12)
)
ggplot(expenses, aes(x="", y=value, fill=Category)) +
geom_bar(stat="identity", width=1, color="white") +
coord_polar("y", start=0) +
theme_void()
```
The `r hospital_name` has units specialising in coronary care; maternity care; paediatic care; 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 17 ICU beds in the `r hospital_name` in September 2019. Average ICU bed occupancy before and during the COVID-19 pandemic is in Figure 8.
```{r A6, fig.cap="ICU bed occupancy for the Inverkeld Queen Rose hospital (Source: NHS Scotland)", echo=FALSE}
ICU <- c(sample(10:15, size=16, replace=TRUE), sample(23:25, size=4, replace=TRUE), sample(17:20, size=4, replace=TRUE), sample(22:25, size=4, replace=TRUE), sample(15:20, size=5, replace=TRUE), sample(22:25, size=3, replace=TRUE), sample(15:20, size=4, replace=TRUE), sample(22:25, size=4, replace=TRUE), sample(17:21, size=4, replace=TRUE))
ICUdates <- c("1/2019", "2/2019", "3/2019", "4/2019", "5/2019", "6/2019", "7/2019", "8/2019", "9/2019", "10/2019", "11/2019", "12/2019", "1/2020", "2/2020", "3/2020", "4/2020", "5/2020", "6/2020", "7/2020", "8/2020", "9/2020", "10/2020", "11/2020", "12/2020", "1/2021", "2/2021", "3/2021", "4/2021", "5/2021", "6/2021", "7/2021", "8/2021", "9/2021", "10/2021", "11/2021", "12/2021","1/2022", "2/2022", "3/2022", "4/2022", "5/2022", "6/2022", "7/2022", "8/2022", "9/2022", "10/2022", "11/2022", "12/2022")
ICUdates <- factor(ICUdates, levels = ICUdates)
ICUstats <- data.frame(ICU, ICUdates)
ggplot(data = ICUstats, aes(x=ICUdates, y=ICU, group = 1)) +
geom_point() +
geom_line() +
labs(y = "Average Queen Rose ICU bed occupancy/month", x = "Month") +
scale_y_continuous(limits=c(0, 25)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
```
There are approximately 1.1m admissions to the `r hospital_name` hospital annually, the majority of these being to the emergency (A&E) department.
```{r A7, fig.cap="Admissions to the Inverkeld Queen Rose hospital by category (Source: NHS Scotland)", echo=FALSE}
admissions <- data.frame(
Category=c("Elective Inpatient", "A&E", "Day case"),
value=c(16,55,22)
)
ggplot(admissions, aes(x="", y=value, fill=Category)) +
geom_bar(stat="identity", width=1, color="white") +
coord_polar("y", start=0) +
theme_void()
```
A&E waiting times have been called "unacceptably high" in recent months, both by the press and by tthe hospital ombudsman.
```{r A8, fig.cap="ICU waiting times for the Inverkeld Queen Rose hospital (Source: NHS Scotland)", echo=FALSE}
WaitTimes <- c(sample(1:2, size=16, replace=TRUE), sample(1:2, size=4, replace=TRUE), sample(2:4, size=4, replace=TRUE), sample(2:5, size=4, replace=TRUE), sample(1:5, size=5, replace=TRUE), sample(2:5, size=3, replace=TRUE), sample(3:5, size=4, replace=TRUE), sample(2:5, size=4, replace=TRUE), sample(5:6, size=4, replace=TRUE))
AEdates <- c("1/2019", "2/2019", "3/2019", "4/2019", "5/2019", "6/2019", "7/2019", "8/2019", "9/2019", "10/2019", "11/2019", "12/2019", "1/2020", "2/2020", "3/2020", "4/2020", "5/2020", "6/2020", "7/2020", "8/2020", "9/2020", "10/2020", "11/2020", "12/2020", "1/2021", "2/2021", "3/2021", "4/2021", "5/2021", "6/2021", "7/2021", "8/2021", "9/2021", "10/2021", "11/2021", "12/2021","1/2022", "2/2022", "3/2022", "4/2022", "5/2022", "6/2022", "7/2022", "8/2022", "9/2022", "10/2022", "11/2022", "12/2022")
AEdates <- factor(AEdates, levels = AEdates)
AEwaits <- data.frame(WaitTimes, AEdates)
ggplot(data = AEwaits, aes(x=AEdates, y=WaitTimes, group = 1)) +
geom_point() +
geom_line() +
labs(y = "Percentage of A&E patients with a wait time > 4 hours", x = "Month") +
scale_y_continuous(limits=c(0, 15)) +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
```
The `r hospital_name` 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 <i>Staphylococcus aureus</i> (MRSA), <i>Clostridiodes difficile</i> (C. diff), and <i>Candida auris</i> (C. auris).
```{r A9, fig.cap="Key Performance Indicators (KPIs) related to infectious diseases for the Inverkeld Queen Rose hospital (Source: NHS Scotland)", echo=FALSE}
hosKPIs <- data.frame(
KPI=c("Reduction in MRSA cases", "Reduction in C diff cases", "Reduction in sepsis mortality", "Reduction in C auris cases"),
percent=c(62, 54, 12, 43)
)
ggplot(hosKPIs, aes(x = KPI, y = percent)) +
geom_col() +
coord_flip() +
scale_y_continuous(limits=c(0, 100)) +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
```
There are currently `r sample(43:80, size=1)` patients in the `r hospital_name` with confirmed or suspected Legionnaire's disease, with `r sample(5:17, size=1)` of these patients currently in the ICU.
The hospital follows the guidelines set out in the [National Infection Prevention and Control Manual](https://www.nipcm.hps.scot.nhs.uk/).
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 A5
You are a civil servant working in `r city_name`, working closely with the provost, city council and various agencies including the NHS and and SEPA (Scottish Environment Protection Agency).
Some of the key `r city_name` facts and figures at a glance are summarized in the table below.
<table>
<table border="1">
<tr>
<th>Community Amenities</th>
<th>Details</th>
</tr>
<tr>
<td>Schools</td>
<td>`r sample(4:10, size=1)` primary schools, `r sample(2:6, size=1)` secondary schools, 1 college</td>
</tr>
<tr>
<td>Care Homes</td>
<td>`r sample(2:6, size=1)`, each with ~50 bed capacity</td>
</tr>
<tr>
<td>Restaurants and Cafes</td>
<td>`r sample(50:150, size=1)`</td>
</tr>
<tr>
<td>Parks and Playgrounds</td>
<td>`r sample(1:15, size=1)`</td>
</tr>
<tr>
<th>Economic Indicators</th>
<th>Details</th>
</tr>
<tr>
<td>GDP/capita</td>
<td>£`r sample(36000:50000, size=1)`</td>
</tr>
<tr>
<td>Unemployment Rate</td>
<td>`r sample(3:8, size=1)`%</td>
</tr>
<tr>
<th>Traffic and Transport</th>
<th>Details</th>
</tr>
<tr>
<td>Traffic fatalities (average/month)</td>
<td>`r sample(5:15, size=1)`</td>
</tr>
</table>
<br><br>
Most of the `r city_name` water supply comes from nearby Loch Cairnavar. There are two wastewater treatment plants serving `r city_name`, employing a total of `r sample(75:150, size=1)` people.
```{r A10, fig.cap="Inverkeld water usage for 2021-2022 (Source: SEPA)", echo=FALSE}
water <- data.frame(
Category=c("Residential", "Business", "Industrial", "Agricultural"),
value=c(57,17,9,12)
)
ggplot(water, aes(x="", y=value, fill=Category)) +
geom_bar(stat="identity", width=1, color="white") +
coord_polar("y", start=0) +
theme_void()
```
Your briefing packet on Legionnaires' Disease includes the following information.
* [Legionnaires’ Disease: Use water management programs in buildings to help prevent outbreaks](https://www.cdc.gov/vitalsigns/pdf/2016-06-vitalsigns.pdf) CDC fact-sheet.
* Currie, S L et al. “<i>Legionella</i> spp. in UK composts--a potential public health issue?.” Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases vol. 20,4 (2014): O224-9.
* McCormick, D et al. “Public health response to an outbreak of Legionnaires' disease in Edinburgh, United Kingdom, June 2012.” Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin vol. 17,28 20216. 12 Jul. 2012, doi:10.2807/ese.17.28.20216-en
* Hyland, J M et al. “Outbreak of Legionnaires' disease in West Fife: review of environmental guidelines needed.” Public health vol. 122,1 (2008): 79-83.
***
## Information Packet A6
You are a microbiologist working in the bacteriology department at the Greater `r city_name` Clinical Laboratory. Your laboratory is equipped to handle a range of culture samples (including anaerobic and microaerobic organisms), and you routinely process `r sample(1500:2000, size=1)` samples monthly.
You are familiar with the culture requirements for growth of <i>Legionella pneumophila</i>, and [UK Standards for Microbiology Investigations (UK SMI): Identification of <i>Legionella</i> species](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/422702/ID_18i3.pdf).
```{r Legionella-agar, out.width="50%", out.height="50%", echo=FALSE, fig.cap="Legionella grown on BCYE agar. Image credit: [CDC](https://www.cdc.gov/legionella/resources/materials.html)"}
knitr::include_graphics(rep("images/Legionella-BCYE.jpg"))
```
You are also familiar with the literature surrounding <i>Legionella</i> identification, and often read papers such as:
* [CDC guidance on processing environmental samples](https://www.cdc.gov/legionella/labs/procedures-manual.html)
* Benitez, Alvaro J, and Jonas M Winchell. “Clinical application of a multiplex real-time PCR assay for simultaneous detection of <i>Legionella</i> species, <i>Legionella pneumophila</i>, and <i>Legionella pneumophila</i> serogroup 1.” Journal of clinical microbiology vol. 51,1 (2013): 348-51.
* Pascale, Maria Rosaria et al. “Use of Fourier-Transform Infrared Spectroscopy With IR Biotyper® System for Legionella pneumophila Serogroups Identification.” Frontiers in microbiology vol. 13 866426. 26 Apr. 2022, doi:10.3389/fmicb.2022.866426
***
## Information Packet A7
You are a public communications expert, often employed by the `r city_name` 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:
* [CDC <i>Legionella</i> Communications Resources](https://www.cdc.gov/legionella/health-depts/communications-resources.html)
* [Legionnaires' disease outbreak investigation toolbox: Developing Communications](https://legionnaires.ecdc.europa.eu/?pid=600)
* [<i>Legionella</i> awareness campaign highlights deadly <i>Legionella</i> hotspots](https://hydrochemgroup.co.uk/2021/09/22/legionella-awareness-campaign-highlights-deadly-legionella-hotspots/)
***
## Information Packet A8
You are one of the doctors at the largest surgery in `r city_name`. In the past fortnight, `r sample(15:50, size=1)` of your patients have recently presented to the surgery with symptoms consistent with Legionnaire's disease. You have therefore recently been familiarising yourself with the relevant literature:
* [Clinician Factsheet: Legionnaire's Disease](https://www.cdc.gov/legionella/downloads/fs-legionella-clinicians.pdf)
*
[Clinical features of Legionnaire's Disease and Pontiac Fever](https://www.cdc.gov/legionella/clinicians/clinical-features.html)
* [Diagnosis, Treatment, and Prevention - CDC guidelines](https://www.cdc.gov/legionella/clinicians/diagnostic-testing.html)
* [National Enhanced <i>Legionella</i> Surveillance Scotland](https://publichealthscotland.scot/media/8072/2021-01-surveillance-form-legionella.pdf)
* Mandell, Lionel A et al. “Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults.” Clinical infectious diseases : an official publication of the Infectious Diseases Society of America vol. 44 Suppl 2,Suppl 2 (2007): S27-72. doi:10.1086/511159
* Kalil, Andre C et al. “Management of Adults With Hospital-acquired and Ventilator-associated Pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society.” Clinical infectious diseases : an official publication of the Infectious Diseases Society of America vol. 63,5 (2016): e61-e111. doi:10.1093/cid/ciw353
* Viasus, Diego et al. “Legionnaires' Disease: Update on Diagnosis and Treatment.” Infectious diseases and therapy vol. 11,3 (2022): 973-986. doi:10.1007/s40121-022-00635-7