add introductory text

index.qmd

@@ -6,7 +6,7 @@ This is the first presentation of this material, and we would be very grateful t
 
 ## Overview
 
-This workshop asks you to carry out common bioinformatics analyses to trace the likely source of _Pseudomonas aeruginosa_ infection in a hospital burns unit.
+This workshop asks you to carry out common bioinformatics analyses to trace the likely source of a _Pseudomonas aeruginosa_ infection in a hospital burns unit.
 You will be using online bioinformatics services to do this.
 
 ::: { .callout-warning title="Important Note"}

intro.qmd

@@ -1,21 +1,57 @@
 # Introduction
 
-The Introduction page is intended as a short introduction to the book.
+## Sick burns
 
-Like most Quarto books, this is a book created from markdown and executable code. 
+It's been a couple of years since your local mayor proudly opened the new burns ward at your local hospital (@fig-mayor).
 
-This kind of book is an example of literate programming - the intertwining of nicely-formatted text and images, and executable code. For example, the `R` code cell below executes and produces output when the book is compiled:
+::: {.column-margin}
+![This is apparently what Bing Image Generator thinks a mayor opening a burns unit looks like.](assets/images/mayor_opens_burns_unit.jpg){#fig-mayor}
+:::
 
-```{r}
-1 + 1
-```
+The unit is a modern, purpose-built 15 bed ward, with 11 side-rooms and two dual-bedded rooms (@fig-ward-layout). Any patients requiring mechanical ventilation or organ support are usually treated in two self-contained cubicles, located in the trauma critical care unit. As is typical in the UK, burns patients receive shower cart hydrotherapy as a central part of their treatment.
 
-But the `R` code cell below does not:
+Unfortunately, _Pseudomonas aeruginosa_ is a ubiquitous opportunistic pathogen in healthcare settings, and the ward has rapidly regressed to the mean situation of UK hospitals in which up to one in three burns patients become colonised with _P. aeruginosa_, typically leading to bacteraemia, soft tissue infection or pneumonia (@Mahar2010-xu, @Reynolds2021-zs, @Roy2024-vj, @fig-effects).
 
-```{r}
-#| eval: false
+::: {.column-margin}
+![The 15 bed burns ward layout. Beds 1-4 are located in dual-bedded rooms, and beds 5-15 are located in side-rooms. Water supply pipes are indicated by the blue lines](assets/images/ward_layout.png){#fig-ward-layout .lightbox}
+:::
 
-summary(cars)
-```
+![Burn wound infection microbes and their effects on burns patients. Reproduced from @Roy2024-vj (CC-BY-NC-4.0)](assets/images/acc-2023-01571f1.png){#fig-effects width=80% .lightbox}
 
-See @knuth84 for additional discussion of literate programming.
+## The study
+
+In a nosocomial setting _P. aeruginosa_ especially affects patients with impaired immunity. Outbreaks are frequently reported to be associated with water sources such as taps, showers, mixer valves, sink traps and drains (@Trautmann2005-qp, @Breathnach2012-nn). Outbreaks transmitted _via_ water have resulted in fatal cases such as at a [neonatal critical care unit in Belfast](https://doi.org/10.1136/bmj.e592) (@Wise2012-wb).
+
+You are part of a team conducting an observational, prospective study into the occurrence and spread of _P. aeruginosa_ on this burns ward. Patients were recruited from arrivals presenting with burns injuries covering greater than 7% of of their total body surface area.
+
+All recruited patients were screened for whether they already carried _P. aeruginosa_ in their wounds, urine, or stool. Samples were then taken from each patient during their stay on the ward. If _P. aeruginosa_ was found while the patient was on the ward, then wound swabs and twice-weekly urine samples were taken from the patient.
+
+::: { .callout-important }
+## Patient samples
+
+- wound swabs
+- urine
+- stool
+:::
+
+Samples were also taken from the patient's environment and water from outlets in their bed space, at weekly intervals, during their stay.
+
+::: { .callout-note }
+## Environment samples
+
+- shower head rosette
+- shower drain
+- shower chair/trolley
+- tap
+- bedside table
+- patient chair
+- instruments
+:::
+
+## The samples
+
+During the course of the study, five patients and a number of individual samples were found to be positive for _P. aeruginosa_ (@fig-results).
+
+![A schematic view of samples found to be positive for _P. aeruginosa_ in the study. Time in days is shown along the _x_ axis. The _y_ axis shows bed numbers in the burns unit (upper, @fig-ward-layout) and the critical care unity. Each circular icon indicates a positive isolate of _P. aeruginosa_. The letter in the icon indicates the MLST clade to which the _P. aeruginosa_ sample belongs. The colour of the icon indicates the environment from which it was sampled: red = wound, purple = sputum, yellow = urine, blue = water, green = environment. Patient icons indicate individual patient enrolments in the study, and their locations (arrows indicate movement between beds). Boxes 1-5 indicate patients infected with _P. aeruginosa_.](assets/images/sampling.jpg){#fig-results width=80% .lightbox}
+
+Your role, as the bioinformatician attached to the study, is to investigate the genome sequences of bacteria from these samples, and determine what evidence there is for transmission of _P. aeruginosa_ to patients.

references.bib

@@ -1,19 +1,209 @@
-@article{knuth84,
-  author = {Knuth, Donald E.},
-  title = {Literate Programming},
-  year = {1984},
-  issue_date = {May 1984},
-  publisher = {Oxford University Press, Inc.},
-  address = {USA},
-  volume = {27},
-  number = {2},
-  issn = {0010-4620},
-  url = {https://doi.org/10.1093/comjnl/27.2.97},
-  doi = {10.1093/comjnl/27.2.97},
-  journal = {Comput. J.},
-  month = may,
-  pages = {97–111},
-  numpages = {15}
+@ARTICLE{Mahar2010-xu,
+  title     = "Pseudomonas aeruginosa bacteraemia in burns patients: Risk
+               factors and outcomes",
+  author    = "Mahar, Patrick and Padiglione, Alexander A and Cleland, Heather
+               and Paul, Eldho and Hinrichs, Melissa and Wasiak, Jason",
+  abstract  = "INTRODUCTION: We aimed to identify the risk factors for, and
+               outcomes of Pseudomonas aeruginosa bacteraemia in adult burns
+               patients. METHOD: All adult burns patients who developed a
+               Gram-negative bacteraemia over a period of 7 years were
+               included. Retrospective data analysed included patient
+               demographics, organisms cultured, antibiotic susceptibility
+               patterns, isolation of P. aeruginosa in non-blood isolates,
+               treatment, length of stay and mortality. RESULTS: Forty-three
+               patients developed a Gram-negative bacteraemia over the study
+               period, 12 of whom had Pseudomonas bacteraemia during the course
+               of their admission. In eight patients (18.6\%) P. aeruginosa was
+               the first Gram-negative isolated. The only factor predicting P.
+               aeruginosa bacteraemia as a first episode (compared to another
+               Gram-negative) was prior isolation of Pseudomonas at other sites
+               (wound sites, urine or sputum). Overall length of stay was less
+               in patients who developed P. aeruginosa as a first episode,
+               mainly because of increased mortality in this group. Prior
+               non-blood isolates of P. aeruginosa could have correctly
+               predicted the sensitivity pattern of the strain of P. aeruginosa
+               organism in 75\% of patients who did not receive appropriate
+               initial antibiotics. CONCLUSION: Prior colonisation with P.
+               aeruginosa predicts P. aeruginosa in blood cultures, as opposed
+               to other Gram-negative bacteria. Clinicians should have a high
+               index of suspicion for P. aeruginosa bacteraemia where a septic
+               burns patient has a prior history of non-blood P. aeruginosa
+               cultures. Empirical antibiotic regimes based on the
+               antibiotic-sensitivity patterns of previous non-blood P.
+               aeruginosa isolates in each patient should be given at the time
+               blood cultures are taken.",
+  journal   = "Burns",
+  publisher = "Elsevier BV",
+  volume    =  36,
+  number    =  8,
+  pages     = "1228--1233",
+  month     =  dec,
+  year      =  2010,
+  language  = "en"
 }
 
+@ARTICLE{Reynolds2021-zs,
+  title     = "The epidemiology and pathogenesis and treatment of Pseudomonas
+               aeruginosa infections: An update",
+  author    = "Reynolds, Dan and Kollef, Marin",
+  abstract  = "Pseudomonas aeruginosa is a Gram-negative bacterial pathogen
+               that is a common cause of nosocomial infections, particularly
+               pneumonia, infection in immunocompromised hosts, and in those
+               with structural lung disease such as cystic fibrosis.
+               Epidemiological studies have identified increasing trends of
+               antimicrobial resistance, including multi-drug resistant (MDR)
+               isolates in recent years. P. aeruginosa has several virulence
+               mechanisms that increase its ability to cause severe infections,
+               such as secreted toxins, quorum sensing and biofilm formation.
+               Management of P. aeruginosa infections focuses on prevention
+               when possible, obtaining cultures, and prompt initiation of
+               antimicrobial therapy, occasionally with combination therapy
+               depending on the clinical scenario to ensure activity against P.
+               aeruginosa. Newer anti-pseudomonal antibiotics are available and
+               are increasingly being used in the management of MDR P.
+               aeruginosa.",
+  journal   = "Drugs",
+  publisher = "Springer Science and Business Media LLC",
+  volume    =  81,
+  number    =  18,
+  pages     = "2117--2131",
+  month     =  dec,
+  year      =  2021,
+  language  = "en"
+}
+
+@ARTICLE{Roy2024-vj,
+  title     = "Microbial infections in burn patients",
+  author    = "Roy, Souvik and Mukherjee, Preeti and Kundu, Sutrisha and
+               Majumder, Debashrita and Raychaudhuri, Vivek and Choudhury,
+               Lopamudra",
+  abstract  = "Polymicrobial infections are the leading causes of complications
+               incurred from injuries that burn patients develop. Such patients
+               admitted to the hospital have a high risk of developing
+               hospital-acquired infections, with longer patient stays leading
+               to increased chances of acquiring such drug-resistant
+               infections. Acinetobacter baumannii, Klebsiella pneumoniae,
+               Pseudomonas aeruginosa, and Proteus mirabilis are the most
+               common multidrug-resistant (MDR) Gram-negative bacteria
+               identified in burn wound infections (BWIs). BWIs caused by
+               viruses, like Herpes Simplex and Varicella Zoster, and
+               fungi-like Candida spp. appear to occur occasionally. However,
+               the preponderance of infection by opportunistic pathogens is
+               very high in burn patients. Variations in the causative agents
+               of BWIs are due to differences in geographic location and
+               infection control measures. Overall, burn injuries are
+               characterized by elevated serum cytokine levels, systemic immune
+               response, and immunosuppression. Hence, early detection and
+               treatment can accelerate the wound-healing process and reduce
+               the risk of further infections at the site of injury. A
+               multidisciplinary collaboration between burn surgeons and
+               infectious disease specialists is also needed to properly
+               monitor antibiotic resistance in BWI pathogens, help check the
+               super-spread of MDR pathogens, and improve treatment outcomes as
+               a result.",
+  journal   = "Acute Crit. Care",
+  publisher = "The Korean Society of Critical Care Medicine",
+  volume    =  39,
+  number    =  2,
+  pages     = "214--225",
+  month     =  may,
+  year      =  2024,
+  keywords  = "biofilm; burn wound infections; epidermis; hospital;
+               opportunistic infection",
+  language  = "en"
+}
+
+@ARTICLE{Trautmann2005-qp,
+  title     = "Ecology of Pseudomonas aeruginosa in the intensive care unit and
+               the evolving role of water outlets as a reservoir of the
+               organism",
+  author    = "Trautmann, Matthias and Lepper, Philipp M and Haller, Mathias",
+  abstract  = "In spite of the significant changes in the spectrum of organisms
+               causing intensive care unit (ICU)-associated infections,
+               Pseudomonas aeruginosa has held a nearly unchanged position in
+               the rank order of pathogens causing ICU-related infections
+               during the last 4 decades. Horizontal transmissions between
+               patients have long been considered the most frequent source of P
+               aeruginosa colonizations/infections. The application of
+               molecular typing methods made it possible, during the last
+               approximately 7 years, to identify ICU tap water as a
+               significant source of exogenous P aeruginosa isolates. A review
+               of prospective studies published between 1998 and 2005 showed
+               that between 9.7\% and 68.1\% of randomly taken tap water
+               samples on different types of ICUs were positive for P
+               aeruginosa , and between 14.2\% and 50\% of
+               infection/colonization episodes in patients were due to
+               genotypes found in ICU water. Faucets are easily accessible for
+               preventive measures, and the installation of single-use filters
+               on ICU water outlets appears to be an effective concept to
+               reduce water-to-patient transmissions of this important
+               nosocomial pathogen.",
+  journal   = "Am. J. Infect. Control",
+  publisher = "Elsevier BV",
+  volume    =  33,
+  number    = "5 Suppl 1",
+  pages     = "S41--9",
+  month     =  jun,
+  year      =  2005,
+  language  = "en"
+}
+
+@ARTICLE{Wise2012-wb,
+  title     = "Three babies die in pseudomonas outbreak at Belfast neonatal
+               unit",
+  author    = "Wise, Jacqui",
+  journal   = "BMJ",
+  publisher = "BMJ",
+  volume    =  344,
+  number    = "jan24 1",
+  pages     = "e592",
+  month     =  jan,
+  year      =  2012,
+  language  = "en"
+}
 
+@ARTICLE{Breathnach2012-nn,
+  title     = "Multidrug-resistant Pseudomonas aeruginosa outbreaks in two
+               hospitals: association with contaminated hospital waste-water
+               systems",
+  author    = "Breathnach, A S and Cubbon, M D and Karunaharan, R N and Pope, C
+               F and Planche, T D",
+  abstract  = "BACKGROUND: Multidrug-resistant Pseudomonas aeruginosa (MDR-P)
+               expressing VIM-metallo-beta-lactamase is an emerging infection
+               control problem. The source of many such infections is unclear,
+               though there are reports of hospital outbreaks of P. aeruginosa
+               related to environmental contamination, including tap water.
+               AIM: We describe two outbreaks of MDR-P, sensitive only to
+               colistin, in order to highlight the potential for hospital
+               waste-water systems to harbour this organism. METHODS: The
+               outbreaks were investigated by a combination of descriptive
+               epidemiology, inspection and microbiological sampling of the
+               environment, and molecular strain typing. FINDINGS: The
+               outbreaks occurred in two English hospitals; each involved a
+               distinct genotype of MDR-P. One outbreak was hospital-wide,
+               involving 85 patients, and the other was limited to four cases
+               in one specialized medical unit. Extensive environmental
+               sampling in each outbreak yielded MDR-P only from the
+               waste-water systems. Inspection of the environment and estates
+               records revealed many factors that may have contributed to
+               contamination of clinical areas, including faulty sink, shower
+               and toilet design, clean items stored near sluices, and frequent
+               blockages and leaks from waste pipes. Blockages were due to
+               paper towels, patient wipes, or improper use of bedpan
+               macerators. Control measures included replacing sinks and
+               toilets with easier-to-clean models less prone to splashback,
+               educating staff to reduce blockages and inappropriate storage,
+               reviewing cleaning protocols, and reducing shower flow rates to
+               reduce flooding. These measures were followed by significant
+               reductions in cases. CONCLUSION: The outbreaks highlight the
+               potential of hospital waste systems to act as a reservoir of
+               MDR-P and other nosocomial pathogens.",
+  journal   = "J. Hosp. Infect.",
+  publisher = "Elsevier BV",
+  volume    =  82,
+  number    =  1,
+  pages     = "19--24",
+  month     =  sep,
+  year      =  2012,
+  language  = "en"
+}