Idiopathic Pulmonary Fibrosis Is Associated with Common Genetic Variants and Limited Rare Variants.

Rationale: Idiopathic pulmonary fibrosis (IPF) is a rare, irreversible, and progressive disease of the lungs. Common genetic variants, in addition to nongenetic factors, have been consistently associated with IPF. Rare variants identified by candidate gene, family-based, and exome studies have also been reported to associate with IPF. However, the extent to which rare variants, genome-wide, may contribute to the risk of IPF remains unknown. Objectives: We used whole-genome sequencing to investigate the role of rare variants, genome-wide, on IPF risk. Methods: As part of the Trans-Omics for Precision Medicine Program, we sequenced 2,180 cases of IPF. Association testing focused on the aggregated effect of rare variants (minor allele frequency ⩽0.01) within genes or regions. We also identified individual rare variants that are influential within genes and estimated the heritability of IPF on the basis of rare and common variants. Measurements and Main Results: Rare variants in both TERT and RTEL1 were significantly associated with IPF. A single rare variant in each of the TERT and RTEL1 genes was found to consistently influence the aggregated test statistics. There was no significant evidence of association with other previously reported rare variants. The SNP heritability of IPF was estimated to be 32% (SE = 3%). Conclusions: Rare variants within the TERT and RTEL1 genes and well-established common variants have the largest contribution to IPF risk overall. Efforts in risk profiling or the development of therapies for IPF that focus on TERT, RTEL1, common variants, and environmental risk factors are likely to have the largest impact on this complex disease.

Meta-Analysis on Utility of Bronchoscopy in Addition to Computed Tomography Thorax in the Investigation of Lung Cancer in Patients with Haemoptysis.

BACKGROUND: In patients with haemoptysis, many healthcare systems support bronchoscopy regardless of computed tomography (CT) findings. OBJECTIVE: This meta-analysis aimed to address whether a normal CT alone is sufficient to out-rule lung cancer in patients with haemoptysis. METHODS: A search was performed of the following databases: EBSCO (Medline), PubMed, Academic Search Complete, CINAHL, Cochrane Library, and Embase. Meta-Disc 1.4 and RevMan software were used to test for heterogeneity, risk of bias, and to summarize the test performance characteristics using forest plots and summary receiver operating characteristic (SROC) curves. SPSS was used to compare the diagnostic accuracy of CT and bronchoscopy. RESULTS: A total of 14 studies (2,960 patients) were included. The pooled sensitivities for detection of lung cancer using CT scan and bronchoscopy were 0.99 (95% CI: 0.97-1.00) and 0.84 (95% CI: 0.78-0.88), respectively. The sensitivity of CT was higher than that of bronchoscopy (p < 0.001). The pooled specificities for CT scan and bronchoscopy were 0.99 (95% CI: 0.99-1.00) and 1.00 (95% CI: 0.99-1.00), respectively. Of 2,960 patients, 257 had lung cancer (8.7%) at initial investigation. 254 of these had a CT thorax, and the CT scan was false negative in 4/255 (1.6%), with bronchoscopy only identifying one cancer with a normal CT (0.4%). CONCLUSION: CT scan showed a higher diagnostic accuracy than bronchoscopy. This study indicated that bronchoscopy offers an insignificant additional value in the investigation of lung cancer in patients with haemoptysis and a negative CT scan.

Single-Use or Disposable Flexible Bronchoscopy in Advanced Bronchoscopy Procedures: Experience in a Quaternary Referral Centre.

BACKGROUND: The development of single-use flexible or disposable bronchoscopes (SUFBs) has accelerated in recent years, with the reduced risk of infectious transmission and reduced need for endoscopy staffing particularly advantageous in the COVID-19 pandemic era. OBJECTIVE: The objective of this study was to assess the performance of a novel single-use bronchoscope in an academic quaternary referral centre with on-site interventional pulmonology programme. METHODS: With ethical approval in a quaternary referral centre, we prospectively collected data on sequential bronchoscopy procedures using The Surgical Company Broncoflex© range of SUFBs. Data collected included demographic, procedural, scope performance, user satisfaction, and complication parameters in a tertiary bronchoscopy service. RESULTS: 139 procedures were performed by five pulmonology faculty from January to July 2021. The majority were carried out for infection (45%) and malignancy (32%). Most were performed in the endoscopy suite and 8% were COVID positive or suspected. Most procedures reported the highest score in satisfaction (85%) with technical limitations reported in 15% (predominately related to scope suction or inadequate image quality) reverting to a reusable scope in 2.8 %. CONCLUSION: In our subset of patients in a bronchoscopy unit, SUFBs are safe, and both routine and advanced bronchoscopy procedures can be performed with high satisfaction reported.

Endobronchial Balloon Blockers: A Retrospective Analysis of Their Implementation for Use in Transbronchial Cryobiopsy Under Conscious Sedation.

INTRODUCTION: Transbronchial lung cryobiopsy (TBLC) is a promising technique that is evolving as a standard diagnostic procedure in the diagnosis of interstitial lung disease. However, there are a variety of non-standardised techniques adopted for this procedure. We aim to describe our approach to TBLC with balloon blockade under conscious sedation (CS). METHODS: We performed a retrospective analysis of patients undergoing TBLC using flexible bronchoscopy under CS in our institution over the calendar years 2017-2018; before and after a transition to the use of endobronchial balloon blockers (EBB) in 2017. RESULTS: 25 patients underwent transbronchial cryobiopsy during the study period. Of these; 12 procedures used EBB. EBB subjects had significantly less moderate or severe airway bleeding (8.3% vs 38.5%) despite higher biopsy rates in the EBB group, 2.9 (2-4) vs 2.4 (1-4) in the non-EBB group. No severe airway bleeding occurred in the EBB group. A multidisciplinary meeting (MDM) confirmed diagnosis was achieved in 88% of patients. 10/12 subjects (83%) in the EBB group and 12/13 subjects (92%) in the non-EBB group (p = 0.5). CONCLUSION: Our institution is novel in using EBB as standard during TBLC specifically under CS with flexible bronchoscopy in the bronchoscopy suite. This retrospective analysis demonstrates that EBB enhances the safety profile of performing TBLC under CS and did not appear to impact diagnostic yield or patient safety.

Peripheral tumour targeting using open-source virtual bronchoscopy with electromagnetic tracking: a multi-user pre-clinical study.

Objectives: The goal was to demonstrate the utility of open-source tracking and visualisation tools in the targeting of lung cancer.Material and methods: The study demonstrates the first deployment of the Anser electromagnetic (EM) tracking system with the CustusX image-guided interventional research platform to navigate using an endobronchial catheter to injected tumour targets. Live animal investigations validated the deployment and targeting of peripheral tumour models using an innovative tumour marking routine.Results: Novel tumour model deployment was successfully achieved at all eight target sites across two live animal investigations without pneumothorax. Virtual bronchoscopy with tracking successfully guided the tracked catheter to 2-12 mm from the target tumour site. Deployment of a novel marker was achieved at all eight sites providing a reliable measure of targeting accuracy. Targeting accuracy within 10 mm was achieved in 7/8 sites and in all cases, the virtual target distance at marker deployment was within the range subsequently measured with x-ray.Conclusions: Endobronchial targeting of peripheral airway targets is feasible using existing open-source technology. Notwithstanding the shortcomings of current commercial platforms, technological improvements in EM tracking and registration accuracy fostered by open-source technology may provide the impetus for widespread clinical uptake of electromagnetic navigation in bronchoscopy.

Optimizing parameters of an open-source airway segmentation algorithm using different CT images.

BACKGROUND: Computed tomography (CT) helps physicians locate and diagnose pathological conditions. In some conditions, having an airway segmentation method which facilitates reconstruction of the airway from chest CT images can help hugely in the assessment of lung diseases. Many efforts have been made to develop airway segmentation algorithms, but methods are usually not optimized to be reliable across different CT scan parameters. METHODS: In this paper, we present a simple and reliable semi-automatic algorithm which can segment tracheal and bronchial anatomy using the open-source 3D Slicer platform. The method is based on a region growing approach where trachea, right and left bronchi are cropped and segmented independently using three different thresholds. The algorithm and its parameters have been optimized to be efficient across different CT scan acquisition parameters. The performance of the proposed method has been evaluated on EXACT'09 cases and local clinical cases as well as on a breathing pig lung phantom using multiple scans and changing parameters. In particular, to investigate multiple scan parameters reconstruction kernel, radiation dose and slice thickness have been considered. Volume, branch count, branch length and leakage presence have been evaluated. A new method for leakage evaluation has been developed and correlation between segmentation metrics and CT acquisition parameters has been considered. RESULTS: All the considered cases have been segmented successfully with good results in terms of leakage presence. Results on clinical data are comparable to other teams' methods, as obtained by evaluation against the EXACT09 challenge, whereas results obtained from the phantom prove the reliability of the method across multiple CT platforms and acquisition parameters. As expected, slice thickness is the parameter affecting the results the most, whereas reconstruction kernel and radiation dose seem not to particularly affect airway segmentation. CONCLUSION: The system represents the first open-source airway segmentation platform. The quantitative evaluation approach presented represents the first repeatable system evaluation tool for like-for-like comparison between different airway segmentation platforms. Results suggest that the algorithm can be considered stable across multiple CT platforms and acquisition parameters and can be considered as a starting point for the development of a complete airway segmentation algorithm.

Impact of the introduction of an integrated adult retrieval service on major trauma outcomes.

OBJECTIVES: The primary aim of this study was to examine the impact of the introduction of an integrated adult critical care patient retrieval system in Victoria, Australia, on early clinical outcomes for major trauma patients who undergo interhospital transfer. The secondary aims were to examine the impact on quality and process measures for interhospital transfers in this population, and on longer-term patient-reported outcomes. METHODS: This is a cohort study using data contained in the Victorian State Trauma Registry (VSTR) for major trauma patients >18 years of age between 2009 and 2013 who had undergone interhospital transfer. For eligible patients, data items were extracted from the VSTR for analysis: demographics, injury details, hospital details, transfer details, Adult Retrieval Victoria (ARV) coordination indicator and transfer indicator, key clinical observations and outcomes. RESULTS: There were 3009 major trauma interhospital transfers in the state with a transfer time less than 24 h. ARV was contacted for 1174 (39.0%) transfers. ARV-coordinated metropolitan transfers demonstrated lower adjusted odds of inhospital mortality compared with metropolitan transfers occurring without ARV coordination (OR 0.39, 0.15 to 0.97). Adjusting for destination hospital type demonstrates that this impact was principally due to ARV facilitation of a Major Trauma Service as the destination for transferred patients (OR 0.41, 0.16 to 1.02). The median time spent at the referral hospital was lower for ARV-coordinated transfers (5.4 h (3.8 to 7.5) vs 6.1 (4.2 to 9.2), p<0.0001). CONCLUSIONS: In a mature trauma system, an effective retrieval service can further reduce mortality and improve long-term outcomes.

Transbronchial lung cryobiopsy (TBLC) in the diagnosis of interstitial lung disease: experience of first 100 cases performed under conscious sedation with flexible bronchoscope.

BACKGROUND: Diagnosing the aetiology of interstitial lung disease (ILD) may require histology via a surgical lung biopsy (SLB). SLB is associated with significant complications. Transbronchial lung cryobiopsy (TBLC) can provide large, adequate biopsies with fewer complications offering a potential alternative to SLB. AIMS: This study evaluated the safety, diagnostic yield and impact of TBLC on diagnostic certainty in the multidisciplinary diagnosis (MDD) of ILD within routine clinical practice. METHODS: A retrospective study of all TBLC performed in a tertiary institute from March 2014 to December 2016 was performed. Procedures were performed using a flexible bronchoscope and cryoprobe without fluoroscopic guidance. RESULTS: One hundred procedures were performed on 85 patients. A total of 272 cryobiopsies were obtained with a mean biopsy diameter of 5.9 ± 3.2 mm. Ninety-seven percent contained alveolated lung tissue. Diagnosis based against MDD gold standard was confirmed using TBLC in 67.1% of patients and in 72/100 procedures. Three patients proceeded to SLB. The addition of histological information changed the clinic-radiological diagnosis in twelve patients. The most common diagnosis based on clinical-radiologic-pathologic correlation at MDD was idiopathic pulmonary fibrosis (IPF) (51.2%) and hypersensitivity pneumonitis (15.9%). Moderate bleeding occurred in 18% of cases and five patients (5%) developed pneumothorax requiring intervention. Eleven patients required admission, with a mean length of stay of 1.3 ± 0.9 days. CONCLUSION: TBLC aids the diagnosis of ILD in the appropriate patient and may be an acceptable alternative to SLB with fewer complications. Further work on standardizing the procedure is required.

Evaluation of the impact of implementation of a Medical Assessment and Planning Unit on length of stay.

OBJECTIVE: The Medical Assessment and Planning Unit (MAPU) model provides a multidisciplinary and 'front end loading' approach to acute medical care. The objective of this study was to evaluate the impact of a 10-bed MAPU in Royal Melbourne Hospital (RMH) on hospital length of stay. METHODS: A pre-post study design was used. Cases were defined as all general medical patients admitted to the RMH between 1 August 2003 and 31 January 2004. MAPU patients were defined as general medical patients who had been discharged from RMH MAPU unit as part of their RMH inpatient admission. Historical controls were defined as all general medical patients admitted to the RMH between 1 August 2002 and 31 January 2003. RESULTS: There was a reduction in median length of stay that did not reach statistical significance. During the study period, median emergency department length of stay for MAPU patients was 10.3 h compared with 13.2 h for non-MAPU patients who were admitted directly to general wards. CONCLUSIONS: The reductions in length of stay are likely to be of clinical significance at the emergency department (ED) level. The MAPU model also contributes to providing care appropriate care for older admitted patients.

Single-Use (Disposable) Flexible Bronchoscopes: The Future of Bronchoscopy?

The coronavirus disease (COVID-19) pandemic has highlighted the importance of reducing occupational exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reprocessing procedure for reusable flexible bronchoscopes (RFBs) involves multiple episodes of handling of equipment that has been used during an aerosol-generating procedure and thus is a potential source of transmission. Single-use flexible bronchoscopes (SUFBs) eliminate this source. Additionally, RFBs pose a risk of nosocomial infection transmission between patients with the identification of human proteins, deoxyribonucleic acid (DNA) and pathogenic organisms on fully reprocessed bronchoscopes despite full adherence to the guidelines. Bronchoscopy units have been hugely impacted by the pandemic with restructuring of pre- and post-operative areas, altered patient protocols and the reassessment of air exchange and cleaning procedures. SUFBs can be incorporated into these protocols as a means of improving occupational safety. Most studies on the efficacy of SUFBs have occurred in an anaesthetic setting so it remains to be seen whether they will perform to an acceptable standard in complex respiratory procedures such as transbronchial biopsies and cryotherapy. Here, we outline their potential uses in a respiratory setting, both during and after the current pandemic.

Hyponatremia and hypercalcemia: a study of a large cohort of patients with lung cancer.

BACKGROUND: Hyponatremia and hypercalcemia are reported to be associated with poorer prognosis in lung cancer. Our study assessed the incidence of hyponatremia and hypercalcemia in a recent large cohort of patients diagnosed with lung cancer in an academic institution and correlated incidence with patient and tumour parameters. METHODS: All patients presented at our regional lung cancer multidisciplinary team meeting between January 2011 and December 2016 were included. The incidence of hyponatremia (serum sodium ≤135 mEq/L) and hypercalcemia (serum calcium >2.62 mmol/L), including severity (mild, moderate or severe) was evaluated and stratified by tumour subtype and stage, and correlated with patient parameters. RESULTS: A total of 624 patients (mean age, 67.4 years; 59.3% male) diagnosed with tissue-proven lung cancer were included. Hyponatremia and hypercalcemia were present in 31.6% (n=197) and 7.1% (n=44) at time of diagnosis. Hyponatremia occurred most commonly in patients with small cell lung carcinoma (SCLC) (n=42; 41.2%; P=0.001). Hypercalcemia occurred most commonly in patients with non-small cell lung carcinoma (NSCLC) squamous subtype (n=27; 12.2%; P=0.003). The incidence of hyponatremia and hypercalcemia were significantly higher in the advanced stages (P<0.041), except in SCLC where no difference in hypercalcemia incidence across the stages was observed (P=0.573). The Eastern Cooperative Oncology Group Performance Status (ECOG-PS) score was positively correlated with severity of hyponatremia at the early stage of NSCLC (Spearman correlation coefficient =0.325; P=0.003). CONCLUSIONS: Hyponatremia is a common association in lung cancer, especially in SCLC. Hypercalcemia is an uncommon but significant association in the NSCLC squamous subtype. Hyponatremia might contribute to poorer ECOG-PS scores at the early stage of NSCLC.

Lung cancer in young patients: tumour characteristics and treatment in an Irish population.

BACKGROUND: Lung cancer is the leading cause of cancer death in both sexes in Ireland. Studies suggest that lung cancer in younger patients has distinct characteristics. The aim of this study is to define the characteristics of lung cancer in patients 55-year-old or younger in an Irish population. METHODS: Data was collected retrospectively from local medical records and the hospital electronic database regarding all patients diagnosed with lung cancer aged 55-year-old and younger, from 2010-2016. Information regarding patient demographics, smoking status, tumour histology, molecular analysis, stage and location, diagnostic modality and initial treatment choice was collected. In all cases the diagnosis of lung cancer was confirmed at the regional lung cancer multidisciplinary team (MDT) meeting. RESULTS: In total, 8% (n=130) of all cases of lung cancer diagnosed from 2010 to 2016 in our center occurred in patients aged 55 years old or younger; 83% (n=108) were 45 to 55-year-old, 15% (n=19) were 35 to 44-year-old and 2% (n=3) were younger than 35-year-old; 88% (n=115) of patients reported a smoking history. There was a female preponderance (58%, n=76), higher rates of NSCLC non-squamous subtype (53%, n=69) and an upper lobe predominance (42%, n=54); 53% (n=68) of patients had IV or extensive disease at presentation. Epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK) and Kirsten rat sarcoma oncogene (KRAS) mutation rates were 9% (n=4) and 3% (n=1) and 80% (n=4) respectively. CONCLUSIONS: Lung cancer in younger patients has distinct characteristics. This study suggests a female preponderance, high smoking rates and a predilection for the upper lobes. Further large-scale multicenter studies are required to verify these results and to clarify the responsible mechanisms.

Congenital heart disease and other heterotaxic defects in a large cohort of patients with primary ciliary dyskinesia.

BACKGROUND: Primary ciliary dyskinesia (PCD) is a recessive genetic disorder that is characterized by sinopulmonary disease and reflects abnormal ciliary structure and function. Situs inversus totalis occurs in approximately 50% of PCD patients (Kartagener's syndrome in PCD), and there are a few reports of PCD with heterotaxy (situs ambiguus), such as cardiovascular anomalies. Advances in diagnosis of PCD, such as genetic testing, allow the systematic investigation of this association. METHODS AND RESULTS: The prevalence of heterotaxic defects was determined in 337 PCD patients by retrospective review of radiographic and ultrasound data. Situs solitus (normal situs) and situs inversus totalis were identified in 46.0% and 47.7% of patients, respectively, and 6.3% (21 patients) had heterotaxy. As compared with patients with situs solitus, those with situs abnormalities had more ciliary outer dynein arm defects, fewer inner dynein arm and central apparatus defects (P<0.001), and more mutations in ciliary outer dynein arm genes (DNAI1 and DNAH5; P=0.022). Seven of 12 patients with heterotaxy who were genotyped had mutations in DNAI1 or DNAH5. Twelve patients with heterotaxy had cardiac and/or vascular abnormalities, and most (8 of 12 patients) had complex congenital heart disease. CONCLUSIONS: At least 6.3% of patients with PCD have heterotaxy, and most of those have cardiovascular abnormalities. The prevalence of congenital heart disease with heterotaxy is 200-fold higher in PCD than in the general population (1:50 versus 1:10 000); thus, patients with PCD should have cardiac evaluation. Conversely, mutations in genes that adversely affect both respiratory and embryological nodal cilia are a significant cause of heterotaxy and congenital heart disease, and screening for PCD is indicated in those patients.

Prehospital noninvasive ventilation: a viable treatment option in the urban setting.

OBJECTIVE: To determine the viability of prehospital noninvasive ventilation (NIV) as a prelude to a definitive clinical trial. METHODS: This was a retrospective observational study of patients (aged > 55 years, severe shortness of breath) transported to a tertiary emergency department (10/5/03-12/28/04). Data were extracted from paramedic and hospital medical records. The primary outcome measure was the number of patients who could potentially benefit from prehospital NIV. They were defined as "conscious upon paramedic arrival and who required ventilatory support (bag/valve/mask ventilation [BVM], NIV or endotracheal intubation) during transport or within 30 minutes of arrival at the emergency department (ED)." The secondary outcome measures were the effectiveness of existing paramedic treatment regimens and paramedic management times. RESULTS: Two hundred sixty-four patients were enrolled (mean age 75.5 +/- 8.7 years, 59.1% male). Sixty-seven patients (25.4%, 95% CI: 20.3-31.2) met the primary outcome measure: 31 (11.7%, 95% CI: 8.2-16.4) received prehospital BVM, an additional 35 (13.3%, 95% CI: 9.5-18.1) received NIV in the ED and one (0.4%, 95% CI: 0.0-2.4) was intubated in the ED. Prehospital treatment resulted in significant (p < 0.001) improvements in systolic blood pressure (151.2 dropping to 144.2 mmHg), respiratory rate (29.4 dropping to 26.3 breaths/minute), and oxygen saturation (92.3% rising to 96.2%). Median paramedic management time was 33 minutes (IQR 29-40). CONCLUSION: Prehospital treatment significantly improved patient vital signs. However, a considerable proportion of patients still required ventilatory support either prehospital or early in their ED course. Further research is indicated to determine if these patients would benefit from prehospital NIV.

Improving antibiotic prescribing for adults with community acquired pneumonia: Does a computerised decision support system achieve more than academic detailing alone?--A time series analysis.

BACKGROUND: The ideal method to encourage uptake of clinical guidelines in hospitals is not known. Several strategies have been suggested. This study evaluates the impact of academic detailing and a computerised decision support system (CDSS) on clinicians' prescribing behaviour for patients with community acquired pneumonia (CAP). METHODS: The management of all patients presenting to the emergency department over three successive time periods was evaluated; the baseline, academic detailing and CDSS periods. The rate of empiric antibiotic prescribing that was concordant with recommendations was studied over time comparing pre and post periods and using an interrupted time series analysis. RESULTS: The odds ratio for concordant therapy in the academic detailing period, after adjustment for age, illness severity and suspicion of aspiration, compared with the baseline period was OR = 2.79 [1.88, 4.14], p < 0.01, and for the computerised decision support period compared to the academic detailing period was OR = 1.99 [1.07, 3.69], p = 0.02. During the first months of the computerised decision support period an improvement in the appropriateness of antibiotic prescribing was demonstrated, which was greater than that expected to have occurred with time and academic detailing alone, based on predictions from a binary logistic model. CONCLUSION: Deployment of a computerised decision support system was associated with an early improvement in antibiotic prescribing practices which was greater than the changes seen with academic detailing. The sustainability of this intervention requires further evaluation.

A case study of centralised monitoring of hospital access performance.

Access to care for patients remains a concern for all parties in the provision of hospital services. It is the subject of patient complaints, large investments of funds and vigorous debate in the community, hospitals and the political arena. This is a common problem in developed nations. There has been little achievement in information technology solutions to this significant problem in Australia. This paper presents a case study of the development and implementation of an organisational access display system intended to provide real-time, or near to real-time information and feedback on access for staff on the floor. This is believed to be one of the first times such a development has been reported in the Australian literature, albeit limited to the context of a single organisation.