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. 2022 Mar 9;13:1231. doi: 10.1038/s41467-022-28188-w

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Prospective study design describing the enrollment strategy of mechanically ventilated patients in the ICU. Of 87 patients screened, 49 eligible patients were identified, from which 31 consented to enrollment. We focused on 2 pilot patients sampled at only day 1, and 7 patients sampled serially across 4–11 days that exhibited predominant P. aeruginosa growth in both samples. b Sampling sputum and stool across patients (y-axis) over time (x-axis) from the onset of symptoms. Day 1 sputum sample (teal box) were collected in all patients, and a follow-up sputum (dark blue box) were collected in 7 patients between day 5 and day 12, i.e. 4–11 days after day 1. Stool samples (brown box) with confirmed P. aeruginosa growth were collected in 2 patients. Asterisk: patients with prior P. aeruginosa infection. Treatment with anti-pseudomonal antibiotics are indicated by horizontal lines: piperacillin/tazobactam (weighted black), cefepime (thin black), ceftazidime (dotted black), ciprofloxacin (dotted blue), meropenem (weighted pink). c Samples (sputum or stool) were cultured on cetrimide agar in serial dilutions. A single isolate from day 1 sputum of each patient was used to construct a patient-specific reference genome using long-read sequencing. From each sample, 24 isolates were randomly selected for short-read whole-genome sequencing and phenotyping.