1
|
Fenn D, Abdel-Aziz MI, van Oort PMP, Brinkman P, Ahmed WM, Felton T, Artigas A, Póvoa P, Martin-Loeches I, Schultz MJ, Dark P, Fowler SJ, Bos LDJ, Ahmed WM, Raventos AA, Bannard-Smith J, Bos LDJ, Camprubi M, Coelho L, Dark P, Davie A, Diaz E, Goma G, Felton T, Fowler SJ, Goodacre R, Johnson C, Knobel H, Lawal O, Leopold JH, Martin-Loeches I, Nijsen TME, van Oort PMP, Povoa P, Rattray NJW, Rijnders G, Schultz MJ, Steenwelle R, Sterk PJ, Valles J, Verhoeckx F, Vink A, Weda H, White IR, Winters T, Zakharkina T. Composition and diversity analysis of the lung microbiome in patients with suspected ventilator-associated pneumonia. Crit Care 2022; 26:203. [PMID: 35794610 PMCID: PMC9261066 DOI: 10.1186/s13054-022-04068-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background Ventilator-associated pneumonia (VAP) is associated with high morbidity and health care costs, yet diagnosis remains a challenge. Analysis of airway microbiota by amplicon sequencing provides a possible solution, as pneumonia is characterised by a disruption of the microbiome. However, studies evaluating the diagnostic capabilities of microbiome analysis are limited, with a lack of alignment on possible biomarkers. Using bronchoalveolar lavage fluid (BALF) from ventilated adult patients suspected of VAP, we aimed to explore how key characteristics of the microbiome differ between patients with positive and negative BALF cultures and whether any differences could have a clinically relevant role. Methods BALF from patients suspected of VAP was analysed using 16s rRNA sequencing in order to: (1) differentiate between patients with and without a positive culture; (2) determine if there was any association between microbiome diversity and local inflammatory response; and (3) correctly identify pathogens detected by conventional culture. Results Thirty-seven of 90 ICU patients with suspected VAP had positive cultures. Patients with a positive culture had significant microbiome dysbiosis with reduced alpha diversity. However, gross compositional variance was not strongly associated with culture positivity (AUROCC range 0.66–0.71). Patients with a positive culture had a significantly higher relative abundance of pathogenic bacteria compared to those without [0.45 (IQR 0.10–0.84), 0.02 (IQR 0.004–0.09), respectively], and an increased interleukin (IL)-1β was associated with reduced species evenness (rs = − 0.33, p < 0.01) and increased pathogenic bacteria presence (rs = 0.28, p = 0.013). Untargeted 16s rRNA pathogen detection was limited by false positives, while the use of pathogen-specific relative abundance thresholds showed better diagnostic accuracy (AUROCC range 0.89–0.998). Conclusion Patients with positive BALF culture had increased dysbiosis and genus dominance. An increased caspase-1-dependent IL-1b expression was associated with a reduced species evenness and increased pathogenic bacterial presence, providing a possible causal link between microbiome dysbiosis and lung injury development in VAP. However, measures of diversity were an unreliable predictor of culture positivity and 16s sequencing used agnostically could not usefully identify pathogens; this could be overcome if pathogen-specific relative abundance thresholds are used. Supplementary Information The online version contains supplementary material available at 10.1186/s13054-022-04068-z.
Collapse
|
2
|
van Oort PMP, White IR, Ahmed W, Johnson C, Bannard-Smith J, Felton T, Bos LD, Goodacre R, Dark P, Fowler SJ. Detection and quantification of exhaled volatile organic compounds in mechanically ventilated patients - comparison of two sampling methods. Analyst 2021; 146:222-231. [PMID: 33103170 DOI: 10.1039/c9an01134j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Exhaled breath analysis is a promising new diagnostic tool, but currently no standardised method for sampling is available in mechanically ventilated patients. We compared two breath sampling methods, first using an artificial ventilator circuit, then in "real life" in mechanically ventilated patients on the intensive care unit. In the laboratory circuit, a 24-component synthetic-breath volatile organic compound (VOC) mixture was injected into the system as air was sampled: (A) through a port on the exhalation limb of the circuit and (B) through a closed endo-bronchial suction catheter. Sorbent tubes were used to collect samples for analysis by thermal desorption-gas chromatography-mass spectrometry. Realistic mechanical ventilation rates and breath pressure-volume loops were established and method detection limits (MDLs) were calculated for all VOCs. Higher yields of VOCs were retrieved using the closed suction catheter; however, for several VOCs MDLs were compromised due to the background signal associated with plastic and rubber components in the catheters. Different brands of suction catheter were compared. Exhaled VOC data from 40 patient samples collected at two sites were then used to calculate the proportion of data analysed above the MDL. The relative performance of the two methods differed depending on the VOC under study and both methods showed sensitivity towards different exhaled VOCs. Furthermore, method performance differed depending on recruitment site, as the centres were equipped with different brands of respiratory equipment, an important consideration for the design of multicentre studies investigating exhaled VOCs in mechanically ventilated patients.
Collapse
Affiliation(s)
- Pouline M P van Oort
- Department of Intensive Care, Amsterdam UMC - location Academic Medical Centre (AMC), Amsterdam, the Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
van Oort PMP, de Bruin S, Weda H, Knobel HH, Schultz MJ, Bos LD. Exhaled Breath Metabolomics for the Diagnosis of Pneumonia in Intubated and Mechanically-Ventilated Intensive Care Unit (ICU)-Patients. Int J Mol Sci 2017; 18:ijms18020449. [PMID: 28218729 PMCID: PMC5343983 DOI: 10.3390/ijms18020449] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/03/2017] [Accepted: 02/15/2017] [Indexed: 12/23/2022] Open
Abstract
The diagnosis of hospital-acquired pneumonia remains challenging. We hypothesized that analysis of volatile organic compounds (VOCs) in exhaled breath could be used to diagnose pneumonia or the presence of pathogens in the respiratory tract in intubated and mechanically-ventilated intensive care unit patients. In this prospective, single-centre, cross-sectional cohort study breath from mechanically ventilated patients was analysed using gas chromatography-mass spectrometry. Potentially relevant VOCs were selected with a p-value < 0.05 and an area under the receiver operating characteristics curve (AUROC) above 0.7. These VOCs were used for principal component analysis and partial least square discriminant analysis (PLS-DA). AUROC was used as a measure of accuracy. Ninety-three patients were included in the study. Twelve of 145 identified VOCs were significantly altered in patients with pneumonia compared to controls. In colonized patients, 52 VOCs were significantly different. Partial least square discriminant analysis classified patients with modest accuracy (AUROC: 0.73 (95% confidence interval (CI): 0.57–0.88) after leave-one-out cross-validation). For determining the colonization status of patients, the model had an AUROC of 0.69 (95% CI: 0.57–0.82) after leave-one-out cross-validation. To conclude, exhaled breath analysis can be used to discriminate pneumonia from controls with a modest to good accuracy. Furthermore breath profiling could be used to predict the presence and absence of pathogens in the respiratory tract. These findings need to be validated externally.
Collapse
Affiliation(s)
- Pouline M P van Oort
- Department of Intensive Care, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
| | - Sanne de Bruin
- Department of Intensive Care, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
| | - Hans Weda
- Philips Research, 5656 AE Eindhoven, The Netherlands.
| | - Hugo H Knobel
- Philips Research, 5656 AE Eindhoven, The Netherlands.
| | - Marcus J Schultz
- Department of Intensive Care, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
| | - Lieuwe D Bos
- Department of Intensive Care, Academic Medical Centre, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.
| |
Collapse
|
4
|
van Oort PMP, Nijsen T, Weda H, Knobel H, Dark P, Felton T, Rattray NJW, Lawal O, Ahmed W, Portsmouth C, Sterk PJ, Schultz MJ, Zakharkina T, Artigas A, Povoa P, Martin-Loeches I, Fowler SJ, Bos LDJ. BreathDx - molecular analysis of exhaled breath as a diagnostic test for ventilator-associated pneumonia: protocol for a European multicentre observational study. BMC Pulm Med 2017; 17:1. [PMID: 28049457 PMCID: PMC5210294 DOI: 10.1186/s12890-016-0353-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 12/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The diagnosis of ventilator-associated pneumonia (VAP) remains time-consuming and costly, the clinical tools lack specificity and a bedside test to exclude infection in suspected patients is unavailable. Breath contains hundreds to thousands of volatile organic compounds (VOCs) that result from host and microbial metabolism as well as the environment. The present study aims to use breath VOC analysis to develop a model that can discriminate between patients who have positive cultures and who have negative cultures with a high sensitivity. METHODS/DESIGN The Molecular Analysis of Exhaled Breath as Diagnostic Test for Ventilator-Associated Pneumonia (BreathDx) study is a multicentre observational study. Breath and bronchial lavage samples will be collected from 100 and 53 intubated and ventilated patients suspected of VAP. Breath will be analysed using Thermal Desorption - Gas Chromatography - Mass Spectrometry (TD-GC-MS). The primary endpoint is the accuracy of cross-validated prediction for positive respiratory cultures in patients that are suspected of VAP, with a sensitivity of at least 99% (high negative predictive value). DISCUSSION To our knowledge, BreathDx is the first study powered to investigate whether molecular analysis of breath can be used to classify suspected VAP patients with and without positive microbiological cultures with 99% sensitivity. TRIAL REGISTRATION UKCRN ID number 19086, registered May 2015; as well as registration at www.trialregister.nl under the acronym 'BreathDx' with trial ID number NTR 6114 (retrospectively registered on 28 October 2016).
Collapse
Affiliation(s)
- Pouline M P van Oort
- Institute of Inflammation and Repair, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | | | - Hans Weda
- Philips Research, Eindhoven, The Netherlands
| | - Hugo Knobel
- Philips Research, Eindhoven, The Netherlands
| | - Paul Dark
- Salford Royal NHS Foundation Trust, Greater Manchester, UK
| | - Timothy Felton
- University Hospital of South Manchester NHS Foundation Trust, Manchester, UK
| | - Nicholas J W Rattray
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, Manchester, UK
| | - Oluwasola Lawal
- Institute of Inflammation and Repair, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Waqar Ahmed
- Institute of Inflammation and Repair, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Craig Portsmouth
- Manchester Institute of Biotechnology (MIB), School of Chemistry, University of Manchester, Manchester, UK
| | - Peter J Sterk
- Intensive Care, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Marcus J Schultz
- Intensive Care, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Tetyana Zakharkina
- Intensive Care, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Antonio Artigas
- Critical Care Department, CIBER Enfermedades Respiratorias, Corporacion Sanitaria Universitaria Parc Tauli, Sabadell, Spain
| | - Pedro Povoa
- Hospital de São Fransisco Xavier, Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal
| | - Ignacio Martin-Loeches
- Department of Clinical Medicine, St James's Hospital, Multidisciplinary Intensive Care Research Organization (MICRO), Trinity Centre for Health Sciences, Dublin, Ireland
| | - Stephen J Fowler
- Institute of Inflammation and Repair, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Lieuwe D J Bos
- Intensive Care, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
5
|
Madsen EVE, Elias SG, van Dalen T, van Oort PMP, van Gorp J, Gobardhan PD, Bongers V. Predictive factors of isolated tumor cells and micrometastases in axillary lymph nodes in breast cancer. Breast 2013; 22:748-52. [PMID: 23313060 DOI: 10.1016/j.breast.2012.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 11/24/2012] [Accepted: 12/16/2012] [Indexed: 01/15/2023] Open
Abstract
INTRODUCTION Since the introduction of the sentinel lymph node biopsy (SLNB) in patients with breast cancer, micrometastases and isolated tumor cells are detected frequently in the SLN. As such, they offer an opportunity to study the development of regional metastases in breast cancer. PATIENTS AND METHODS Between June 1999 and November 2010 1418 patients with cT1-2N0 breast cancer underwent SLNB. Primary tumor characteristics and information regarding regional lymph node involvement were collected prospectively. Patients were categorized into four levels of lymph node involvement: pN0, pN0(i+), pN1mi and pN ≥ 1a. An univariate analysis and a binary logistic regression analysis were performed to assess the relation between patient- and tumor characteristics and lymph node involvement. RESULTS Increasing tumor size and younger age were associated with a higher risk of pN1mi and pN ≥ 1a and a lower chance of pN0 and pN0(i+). Triple negative molecular subtype was associated with a decreased risk of pN1mi and pN ≥ 1a. Tumor size was positively related to overall occurrence of regional lymph node metastases in a linear manner. CONCLUSION Patients with larger tumors, no triple negative disease, and younger age showed a decreased chance of both pN0 and pN0(i+) and an increased risk of both pN1mi and pN ≥ 1a. There seems to be a gradual shift in risk pattern from pN0 to pN0(i+) to pN1mi and to pN ≥ 1a-disease. The presence of the smallest metastases remained fairly constant over time when compared to macrometastases. This constant presence suggests that the risk of seeding and outgrowth of metastases remains constant over time.
Collapse
Affiliation(s)
- Eva V E Madsen
- Diakonessenhuis Utrecht, Department of Surgery, Diakonessenhuis, Bosboomstraat 1, 3582 KE Utrecht, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|