1  Workshop Introduction

1.1 Sick burns

It’s been a couple of years since your local mayor proudly opened the new burns ward at your local hospital (Figure 1.1).

Figure 1.1: This is apparently what Bing Image Generator thinks a mayor opening a burns unit looks like.

The unit is a modern, purpose-built 15 bed ward, with 11 side-rooms and two dual-bedded rooms (Figure 15.2). 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.

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 (Mahar et al. (2010), Reynolds and Kollef (2021), Roy et al. (2024), Figure 1.2).

Figure 1.2: Burn wound infection microbes and their effects on burns patients. Reproduced from Roy et al. (2024) (CC-BY-NC-4.0)

1.2 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 (Trautmann, Lepper, and Haller (2005), Breathnach et al. (2012)). Outbreaks transmitted via water have resulted in fatal cases such as at a neonatal critical care unit in Belfast (Wise (2012)).

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.

Figure 1.3: 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

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.

Environment samples

• shower head rosette
• shower drain
• shower chair/trolley
• tap
• bedside table
• patient chair
• instruments

1.3 The samples

During the course of the study, five patients and a number of individual samples were found to be positive for P. aeruginosa (Figure 1.4).

Figure 1.4: 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, Figure 15.2) 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.

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.

Breathnach, A S, M D Cubbon, R N Karunaharan, C F Pope, and T D Planche. 2012. “Multidrug-Resistant Pseudomonas Aeruginosa Outbreaks in Two Hospitals: Association with Contaminated Hospital Waste-Water Systems.” J. Hosp. Infect. 82 (1): 19–24.

Mahar, Patrick, Alexander A Padiglione, Heather Cleland, Eldho Paul, Melissa Hinrichs, and Jason Wasiak. 2010. “Pseudomonas Aeruginosa Bacteraemia in Burns Patients: Risk Factors and Outcomes.” Burns 36 (8): 1228–33.

Reynolds, Dan, and Marin Kollef. 2021. “The Epidemiology and Pathogenesis and Treatment of Pseudomonas Aeruginosa Infections: An Update.” Drugs 81 (18): 2117–31.

Roy, Souvik, Preeti Mukherjee, Sutrisha Kundu, Debashrita Majumder, Vivek Raychaudhuri, and Lopamudra Choudhury. 2024. “Microbial Infections in Burn Patients.” Acute Crit. Care 39 (2): 214–25.

Trautmann, Matthias, Philipp M Lepper, and Mathias Haller. 2005. “Ecology of Pseudomonas Aeruginosa in the Intensive Care Unit and the Evolving Role of Water Outlets as a Reservoir of the Organism.” Am. J. Infect. Control 33 (5 Suppl 1): S41–9.

Wise, Jacqui. 2012. “Three Babies Die in Pseudomonas Outbreak at Belfast Neonatal Unit.” BMJ 344 (jan24 1): e592.