A Nanopore Sequencing-based Pharmacogenomic Panel to Personalize Tuberculosis Drug Dosing

RATIONALE

Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking.

OBJECTIVES

To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing.

MEASUREMENTS AND MAIN RESULTS

We developed a Nanopore sequencing panel targeting 15 single nucleotide polymorphisms (SNP) in 5 genes affecting the metabolism of anti-tuberculous drugs. For validation, we sequenced DNA samples (n=48) from the 1000 genomes project and compared variant calling accuracy with Illumina genome sequencing. We then sequenced DNA samples from patients with active TB (n=100) from South Africa on a MinION Mk1C and evaluated the relationship between genotypes and pharmacokinetic parameters for INH and RIF.

RESULTS

The PGx panel achieved 100% concordance with Illumina sequencing in variant identification for the samples from the 1000 Genomes Project. In the clinical cohort, coverage was >100x for 1498/1500 (99.8%) amplicons across the 100 samples. One third (33%) of participants were identified as slow, 47% were intermediate and 20% were rapid isoniazid acetylators. Isoniazid clearance was 2.2 times higher among intermediate acetylators and 3.8 times higher among rapid acetylators compared with slow acetylators (p<0.0001).. Rifampin clearance was 17.3% (2.50-29.9) lower in individuals with homozygous AADAC rs1803155 G>A substitutions (p=0.0015).

CONCLUSION

Targeted sequencing can enable detection of polymorphisms influencing TB drug metabolism on a low-cost, portable instrument to personalize dosing for TB treatment or prevention. This article is open access and distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).

Natural variability and heritability of root-nodulation traits in chickpea (Cicer arietinum L.) minicore

The existence of large variations for nodulation traits in chickpea minicore was revealed and genetic materials for beneficial biological nitrogen fixation (BNF) traits like early nodulation, high nodulation, and delayed nodule senescence were identified. Early-nodulating genotypes viz. ICC12968, ICC7867, ICC13816, ICC867, ICC15264, ICC15510, and ICC283 produced > 10 nodule number per plant (NNPP) at 15 as well as 30 days after sowing (DAS). Maximum of 36 NNPP at stage 3 i.e., 253% higher than check cultivar were observed in Iran originated ICC6874. Chickpea minicore showed large variations for nodule mass that ranged up to 850 mg/plant at 60 DAS and 2290 mg/plant at 90 DAS. Strong positive correlation was found between nodule fresh weight and specific weight at stage 3 (0.69) and stage 4 (0.76). Besides these, few slight positive significant correlations were also observed viz., nodule number per plant at stage 3 and 4 (0.45), nodule fresh weight at stage 3 and 4 (0.39). Principal component analysis (PCA) indicated that dimensions 1 (21%), 2 (17.6%), and 3 (13%) accounted for a substantial portion of the phenotypic variance, each contributing more than 10%. Accessions viz. ICC1431, ICC13599, ICC13764, and ICC13863 with pink active root nodules and high nodule biomass at later crop growth stages are considered as genetic resources to extend the BNF support in chickpea. High broad-sense heritability values of 76.43 and 90.23 were observed for early nodulation and delayed nodule senescence, respectively. Hence, the identified genotypes for early nodulation and delayed nodule senescence can be used for improving symbiotic efficiency in chickpea.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03908-1.

Is Brucella excreted in cattle faeces? - Evidence from Punjab, India

Brucellosis is a neglected zoonosis that affects animals and people in much of the underdeveloped world. The disease is endemic in cattle in Punjab, India and controlling it is a public health challenge. Dairy farmers and farm labour commonly handle cattle faeces with bare hands and personal protective equipments are not used. No studies have been conducted about the shedding of Brucella species in faeces of sero positive cattle in the state. This study aimed to isolate and identify the Brucella species from faeces of sero positive cattle in Punjab, India. Faecal samples were collected from 350 Brucella sero positive cattle in Ludhiana district of Punjab, India. Isolation was performed using a pre-enriched Brucella selective broth medium as well as Brucella selective medium agar plates containing horse serum and Brucella selective supplements. Isolates were identified using Gram staining technique and rapid slide agglutination test, and then confirmed by using bcsp31 and 16s rRNA genus specific PCR. Isolates were further identified up to species level by using Bruce-Ladder multiplex PCR. Fourteen Brucella species were isolated, all of which showed coccobacilli on gram staining, positive rapid slide agglutination test and amplification of bcsp31 and 16s rRNA genes. Of the 14 isolates, 11 were identified as Brucella abortus and 3 were identified as Brucella melitensis. The study demonstrates that animal faeces could pose a potential risk for animal and human health and faeces of seropositive cattle must be handled with care.

Better among the two for Burn Mortality Prediction in Developing Nations: Revised Baux or Modified Abbreviated Burn Severity Index?

Background

Burns is one of the leading causes of mortality in developing countries like India. Most of the major burns requiring hospital care are not triaged adequately for the use of medical resources. An efficient mortality predicting scale would not only help in better care to those who will benefit the most but also make it easy to explain to patient's attendants. Among the various tools, revised Baux (rBaux) and modified Abbreviated Burn Severity Index (ABSI) are two most commonly used scales in developed nations. We proposed this study to analyze the reliability of these two scoring scales in our burn population.

Aim

This study aimed to retrospectively study the two scoring systems and analyze them for their reliability in predicting mortality compared to actual observed mortality in each case.

Materials and Methods

This study was conducted on all burn patients admitted to the intensive care unit of our hospital. Data on their demographic profile, total burn surface area, thickness of burns, inhalational injury, and other comorbidities were collected from files. rBaux and modified ABSI (mABSI) were calculated. The end result in the form of survival or nonsurvival was also recorded. Appropriate statistical analysis using Mann-Whitney U-test, Chi-square test, and receiver operator characteristic curve was done to look for a better scoring system out of the two.

Results

A total of 504 patients were included in the study, out of which 337 were survivors. Female gender was not a risk factor for mortality in our study. The median rBaux score in the survivor group was 100 (80-110) and in nonsurvivor group was 111 (103-123). The median mABSI score in the survivor group was 8 (7-9) and in nonsurvivor group was 10 (9-11). The area under the receiver operating characteristic curve shows mABSI having better specificity for predicting mortality. rBAUX, though more sensitive, overestimates mortality than actual observed mortality.

Conclusion

mABSI predicts mortality better than rBaux. A multicentric prospective study is recommended for mABSI to be used as a standard mortality predictor in burns in India.

A Nanopore sequencing-based pharmacogenomic panel to personalize tuberculosis drug dosing

Rationale

Standardized dosing of anti-tubercular (TB) drugs leads to variable plasma drug levels, which are associated with adverse drug reactions, delayed treatment response, and relapse. Mutations in genes affecting drug metabolism explain considerable interindividual pharmacokinetic variability; however, pharmacogenomic (PGx) assays that predict metabolism of anti-TB drugs have been lacking.

Objectives

To develop a Nanopore sequencing panel and validate its performance in active TB patients to personalize treatment dosing.

Measurements and Main Results

We developed a Nanopore sequencing panel targeting 15 single nucleotide polymorphisms (SNP) in 5 genes affecting the metabolism of isoniazid (INH), rifampin (RIF), linezolid and bedaquiline. For validation, we sequenced DNA samples (n=48) from the 1000 genomes project and compared variant calling accuracy with Illumina genome sequencing. We then sequenced DNA samples from patients with active TB (n=100) from South Africa on a MinION Mk1C and evaluated the relationship between genotypes and pharmacokinetic parameters for INH and RIF.

Results

The PGx panel achieved 100% concordance with Illumina sequencing in variant identification for the samples from the 1000 Genomes Project. In the clinical cohort, coverage was >100x for 1498/1500 (99.8%) amplicons across the 100 samples. One third (33%) of participants were identified as slow, 47% were intermediate and 20% were rapid isoniazid acetylators. Isoniazid clearance was significantly impacted by acetylator status (p<0.0001) with median (IQR) clearances of 11.2 L/h (9.3-13.4), 27.2 L/h (22.0-31.7), and 45.1 L/h (34.1-51.1) in slow, intermediate, and rapid acetylators. Rifampin clearance was 17.3% (2.50-29.9) lower in individuals with homozygous AADAC rs1803155 G>A substitutions (p=0.0015).

Conclusion

Targeted sequencing can enable detection of polymorphisms influencing TB drug metabolism on a low-cost, portable instrument to personalize dosing for TB treatment or prevention.

Formal mentorship in Canadian radiology residency programmes

AIM

To characterise formal mentorship programmes in Canadian radiology residency programmes, to evaluate residents' perspectives on formal mentorship, and to identify ways to optimise mentorship during radiology training.

MATERIALS AND METHODS

An anonymous survey was distributed to radiology resident representatives of the Canadian Association of Radiologists (CAR) Resident and Fellow Section (RFS). Questions pertained to the presence and structure of formal mentorship programmes at each participant's institution.

RESULTS

The survey was distributed to 33 radiology residents, of which 30 responded. All 16 accredited radiology residency programmes in Canada were represented. Of these programmes, 12 (75%) had formal mentorship programmes and four (25%) did not. The structure of formal mentorship programmes varied among institutions including one-on-one and group mentoring. For 33% of residency programmes, the programme director assigned the mentor and mentee groups. Only 33% of respondents had the option of choosing their mentor. Lack of funding and lack of time were the two main perceived barriers by residents to maintaining mentorship relationships.

CONCLUSION

Although not all radiology residency programmes in Canada have a formal mentorship programme, most have a form of structured mentorship in place. As formal mentorship programmes improve overall mentorship experience during residency, they can lead to improved research productivity, fellowship, and career preparation, as well as work-life balance for Canadian radiology residents.

Reduced graphene Oxide/NiO based nano-composites for the efficient removal of alizarin dye, indigo dye and reduction of nitro aromatic compounds

Removal of alizarin red S (ARS) and Indigo dye from aqueous media and reduction of nitro aromatic compounds are successfully done under mild condition by using reduced Graphene Oxide-Nickel Oxide (rGO-NiO) nanocomposite as catalyst. RGO-NiO is well characterized by different analytical techniques. Morphology, structural, and composition studies done by HRTEM, FESEM, EDX, TGA, FTIR, XPS, Raman spectroscopy, and XRD. RGO-NiO nanocomposite has high stability for the removal of ARS, Indigo dye, reduction reaction nitro aromatic compounds.

Challenges in Harnessing Shared Within-Host Severe Acute Respiratory Syndrome Coronavirus 2 Variation for Transmission Inference

Background

The limited variation observed among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) consensus sequences makes it difficult to reconstruct transmission linkages in outbreak settings. Previous studies have recovered variation within individual SARS-CoV-2 infections but have not yet measured the informativeness of within-host variation for transmission inference.

Methods

We performed tiled amplicon sequencing on 307 SARS-CoV-2 samples, including 130 samples from 32 individuals in 14 households and 47 longitudinally sampled individuals, from 4 prospective studies with household membership data, a proxy for transmission linkage.

Results

Consensus sequences from households had limited diversity (mean pairwise distance, 3.06 single-nucleotide polymorphisms [SNPs]; range, 0-40). Most (83.1%, 255 of 307) samples harbored at least 1 intrahost single-nucleotide variant ([iSNV] median, 117; interquartile range [IQR], 17-208), above a minor allele frequency threshold of 0.2%. Pairs in the same household shared significantly more iSNVs (mean, 1.20 iSNVs; 95% confidence interval [CI], 1.02-1.39) than did pairs in different households infected with the same viral clade (mean, 0.31 iSNVs; 95% CI, .28-.34), a signal that decreases with increasingly stringent minor allele frequency thresholds. The number of shared iSNVs was significantly associated with an increased odds of household membership (adjusted odds ratio, 1.35; 95% CI, 1.23-1.49). However, the poor concordance of iSNVs detected across sequencing replicates (24.8% and 35.0% above a 0.2% and 1% threshold) confirms technical concerns that current sequencing and bioinformatic workflows do not consistently recover low-frequency within-host variants.

Conclusions

Shared within-host variation may augment the information in consensus sequences for predicting transmission linkages. Improving sensitivity and specificity of within-host variant identification will improve the informativeness of within-host variation.

SARS-CoV-2 infection drives an inflammatory response in human adipose tissue through infection of adipocytes and macrophages

Obesity, characterized by chronic low-grade inflammation of the adipose tissue, is associated with adverse coronavirus disease 2019 (COVID-19) outcomes, yet the underlying mechanism is unknown. To explore whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of adipose tissue contributes to pathogenesis, we evaluated COVID-19 autopsy cases and deeply profiled the response of adipose tissue to SARS-CoV-2 infection in vitro. In COVID-19 autopsy cases, we identified SARS-CoV-2 RNA in adipocytes with an associated inflammatory infiltrate. We identified two distinct cellular targets of infection: adipocytes and a subset of inflammatory adipose tissue-resident macrophages. Mature adipocytes were permissive to SARS-CoV-2 infection; although macrophages were abortively infected, SARS-CoV-2 initiated inflammatory responses within both the infected macrophages and bystander preadipocytes. These data suggest that SARS-CoV-2 infection of adipose tissue could contribute to COVID-19 severity through replication of virus within adipocytes and through induction of local and systemic inflammation driven by infection of adipose tissue-resident macrophages.

Detection of M. tuberculosis in the environment as a tool for identifying high-risk locations for tuberculosis transmission

Tuberculosis (TB) remains a leading cause of infectious mortality globally, yet most cases cannot be epidemiologically linked even with extensive contact investigations and whole genome sequencing. Consequently, there remain major gaps in our understanding of where and when M. tuberculosis (Mtb) exposures occur. We aimed to investigate whether Mtb can be detected in environments where TB patients were recently present, which could serve as a tool for characterizing exposure risk. We collected 389 environment surface (ES) swabs from two high TB burden prisons in Brazil, sampling 41 (n = 340) cells occupied by individuals with active TB and 7 (n = 49) cells from individuals without TB. In a subset of pooled swabs (n = 6) and a swab from a cigarette lighter from the cell with active TB patients, we enriched Mtb DNA using RNA-bait hybrid capture assays and performed whole genome sequencing. In prison cells, Mtb DNA was detected in 55/340 (16 %) of ES swabs from cells occupied by active TB patients and none (0/49) from cells in which no active TB patients were present. Mtb was detected in 13/16 (81 %) prison cells occupied by the individuals with high/medium sputum Xpert Mtb load and 8/25 (32 %) with low/very low sputum Mtb load (p = 0.003). Seven hybrid capture samples had a median genomic coverage of 140×. rpoB mutations conferring high-level rifampin resistance were detected in 3/7 ES swabs. Mtb was frequently detectable in environments recently occupied by individuals with active TB. This approach could be applied in congregate environments to identify and characterize high-risk settings for Mtb exposure.

The influence of anastomotic techniques on postoperative anastomotic complications: Results of the Oesophago-Gastric Anastomosis Audit

BACKGROUND

The optimal anastomotic techniques in esophagectomy to minimize rates of anastomotic leakage and conduit necrosis are not known. The aim of this study was to assess whether the anastomotic technique was associated with anastomotic failure after esophagectomy in the international Oesophago-Gastric Anastomosis Audit cohort.

METHODS

This prospective observational multicenter cohort study included patients undergoing esophagectomy for esophageal cancer over 9 months during 2018. The primary exposure was the anastomotic technique, classified as handsewn, linear stapled, or circular stapled. The primary outcome was anastomotic failure, namely a composite of anastomotic leakage and conduit necrosis, as defined by the Esophageal Complications Consensus Group. Multivariable logistic regression modeling was used to identify the association between anastomotic techniques and anastomotic failure, after adjustment for confounders.

RESULTS

Of the 2238 esophagectomies, the anastomosis was handsewn in 27.1%, linear stapled in 21.0%, and circular stapled in 51.9%. Anastomotic techniques differed significantly by the anastomosis sites (P < .001), with the majority of neck anastomoses being handsewn (69.9%), whereas most chest anastomoses were stapled (66.3% circular stapled and 19.3% linear stapled). Rates of anastomotic failure differed significantly among the anastomotic techniques (P < .001), from 19.3% in handsewn anastomoses, to 14.0% in linear stapled anastomoses, and 12.1% in circular stapled anastomoses. This effect remained significant after adjustment for confounding factors on multivariable analysis, with an odds ratio of 0.63 (95% CI, 0.46-0.86; P = .004) for circular stapled versus handsewn anastomosis. However, subgroup analysis by anastomosis site suggested that this effect was predominantly present in neck anastomoses, with anastomotic failure rates of 23.2% versus 14.6% versus 5.9% for handsewn versus linear stapled anastomoses versus circular stapled neck anastomoses, compared with 13.7% versus 13.8% versus 12.2% for chest anastomoses.

CONCLUSIONS

Handsewn anastomoses appear to be independently associated with higher rates of anastomotic failure compared with stapled anastomoses. However, this effect seems to be largely confined to neck anastomoses, with minimal differences between techniques observed for chest anastomoses. Further research into standardization of anastomotic approach and techniques may further improve outcomes.

Stable and Discriminatory Radiomic Features from the Tumor and Its Habitat Associated with Progression-Free Survival in Glioblastoma: A Multi-Institutional Study

BACKGROUND AND PURPOSE

Glioblastoma is an aggressive brain tumor, with no validated prognostic biomarkers for survival before surgical resection. Although recent approaches have demonstrated the prognostic ability of tumor habitat (constituting necrotic core, enhancing lesion, T2/FLAIR hyperintensity subcompartments) derived radiomic features for glioblastoma survival on treatment-naive MR imaging scans, radiomic features are known to be sensitive to MR imaging acquisitions across sites and scanners. In this study, we sought to identify the radiomic features that are both stable across sites and discriminatory of poor and improved progression-free survival in glioblastoma tumors.

MATERIALS AND METHODS

We used 150 treatment-naive glioblastoma MR imaging scans (Gadolinium-T1w, T2w, FLAIR) obtained from 5 sites. For every tumor subcompartment (enhancing tumor, peritumoral FLAIR-hyperintensities, necrosis), a total of 316 three-dimensional radiomic features were extracted. The training cohort constituted studies from 4 sites (n = 93) to select the most stable and discriminatory radiomic features for every tumor subcompartment. These features were used on a hold-out cohort (n = 57) to evaluate their ability to discriminate patients with poor survival from those with improved survival.

RESULTS

Incorporating the most stable and discriminatory features within a linear discriminant analysis classifier yielded areas under the curve of 0.71, 0.73, and 0.76 on the test set for distinguishing poor and improved survival compared with discriminatory features alone (areas under the curve of 0.65, 0.54, 0.62) from the necrotic core, enhancing tumor, and peritumoral T2/FLAIR hyperintensity, respectively.

CONCLUSIONS

Incorporating stable and discriminatory radiomic features extracted from tumors and associated habitats across multisite MR imaging sequences may yield robust prognostic classifiers of patient survival in glioblastoma tumors.

Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery

Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.

Management dilemmas of tracheal paraganglioma: a case report and review of literature

Paragangliomas of the trachea are rare neoplasms and can present to the clinician with acute airway problems. These neoplasms sometimes are misdiagnosed by general practitioners as asthmatic exacerbation. We present the case of a 66-year-old woman who presented to us with a history of dyspnoea at rest in the supine position and on exertion and a productive cough. This was diagnosed as bronchial asthma and she was treated with corticosteroid inhalers for four months by her GP. She was subsequently evaluated by computed tomography of the neck and thorax, which revealed an intratracheal enhancing lesion measuring around 11 mm in the lower cervical trachea. Fibreoptic bronchoscopy showed a mass lesion at the level of mid trachea. A low tracheostomy was followed by telescopic examination and the mass was resected using coablation. Histology of the mass was reported as paraganglioma. Difficulties encountered and literature review of various management options are presented in this report.

Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection

Background

COVID-19 manifests with respiratory, systemic, and gastrointestinal (GI) symptoms.^1, SARS-CoV-2 RNA is detected in respiratory and fecal samples, and recent reports demonstrate viral replication in both the lung and intestinal tissue.2, 3, 4 Although much is known about early fecal RNA shedding, little is known about long-term shedding, especially in those with mild COVID-19. Furthermore, most reports of fecal RNA shedding do not correlate these findings with GI symptoms.⁵.

Methods

We analyzed the dynamics of fecal RNA shedding up to 10 months after COVID-19 diagnosis in 113 individuals with mild to moderate disease. We also correlated shedding with disease symptoms.

Findings

Fecal SARS-CoV-2 RNA is detected in 49.2% [95% confidence interval, 38.2%-60.3%] of participants within the first week after diagnosis. Whereas there was no ongoing oropharyngeal SARS-CoV-2 RNA shedding in subjects at 4 months, 12.7% [8.5%-18.4%] of participants continued to shed SARS-CoV-2 RNA in the feces at 4 months after diagnosis and 3.8% [2.0%-7.3%] shed at 7 months. Finally, we found that GI symptoms (abdominal pain, nausea, vomiting) are associated with fecal shedding of SARS-CoV-2 RNA.

Conclusions

The extended presence of viral RNA in feces, but not in respiratory samples, along with the association of fecal viral RNA shedding with GI symptoms suggest that SARS-CoV-2 infects the GI tract and that this infection can be prolonged in a subset of individuals with COVID-19.

Funding

This research was supported by a Stanford ChemH-IMA grant; fellowships from the AACR and NSF; and NIH R01-AI148623, R01-AI143757, and UL1TR003142.

Textbook outcome following oesophagectomy for cancer: international cohort study

Background

Textbook outcome has been proposed as a tool for the assessment of oncological surgical care. However, an international assessment in patients undergoing oesophagectomy for oesophageal cancer has not been reported. This study aimed to assess textbook outcome in an international setting.

Methods

Patients undergoing curative resection for oesophageal cancer were identified from the international Oesophagogastric Anastomosis Audit (OGAA) from April 2018 to December 2018. Textbook outcome was defined as the percentage of patients who underwent a complete tumour resection with at least 15 lymph nodes in the resected specimen and an uneventful postoperative course, without hospital readmission. A multivariable binary logistic regression model was used to identify factors independently associated with textbook outcome, and results are presented as odds ratio (OR) and 95 per cent confidence intervals (95 per cent c.i.).

Results

Of 2159 patients with oesophageal cancer, 39.7 per cent achieved a textbook outcome. The outcome parameter ‘no major postoperative complication’ had the greatest negative impact on a textbook outcome for patients with oesophageal cancer, compared to other textbook outcome parameters. Multivariable analysis identified male gender and increasing Charlson comorbidity index with a significantly lower likelihood of textbook outcome. Presence of 24-hour on-call rota for oesophageal surgeons (OR 2.05, 95 per cent c.i. 1.30 to 3.22; P = 0.002) and radiology (OR 1.54, 95 per cent c.i. 1.05 to 2.24; P = 0.027), total minimally invasive oesophagectomies (OR 1.63, 95 per cent c.i. 1.27 to 2.08; P &lt; 0.001), and chest anastomosis above azygous (OR 2.17, 95 per cent c.i. 1.58 to 2.98; P &lt; 0.001) were independently associated with a significantly increased likelihood of textbook outcome.

Conclusion

Textbook outcome is achieved in less than 40 per cent of patients having oesophagectomy for cancer. Improvements in centralization, hospital resources, access to minimal access surgery, and adoption of newer techniques for improving lymph node yield could improve textbook outcome.

Textbook outcome following oesophagectomy for cancer: international cohort study

BACKGROUND

Textbook outcome has been proposed as a tool for the assessment of oncological surgical care. However, an international assessment in patients undergoing oesophagectomy for oesophageal cancer has not been reported. This study aimed to assess textbook outcome in an international setting.

METHODS

Patients undergoing curative resection for oesophageal cancer were identified from the international Oesophagogastric Anastomosis Audit (OGAA) from April 2018 to December 2018. Textbook outcome was defined as the percentage of patients who underwent a complete tumour resection with at least 15 lymph nodes in the resected specimen and an uneventful postoperative course, without hospital readmission. A multivariable binary logistic regression model was used to identify factors independently associated with textbook outcome, and results are presented as odds ratio (OR) and 95 per cent confidence intervals (95 per cent c.i.).

RESULTS

Of 2159 patients with oesophageal cancer, 39.7 per cent achieved a textbook outcome. The outcome parameter 'no major postoperative complication' had the greatest negative impact on a textbook outcome for patients with oesophageal cancer, compared to other textbook outcome parameters. Multivariable analysis identified male gender and increasing Charlson comorbidity index with a significantly lower likelihood of textbook outcome. Presence of 24-hour on-call rota for oesophageal surgeons (OR 2.05, 95 per cent c.i. 1.30 to 3.22; P = 0.002) and radiology (OR 1.54, 95 per cent c.i. 1.05 to 2.24; P = 0.027), total minimally invasive oesophagectomies (OR 1.63, 95 per cent c.i. 1.27 to 2.08; P < 0.001), and chest anastomosis above azygous (OR 2.17, 95 per cent c.i. 1.58 to 2.98; P < 0.001) were independently associated with a significantly increased likelihood of textbook outcome.

CONCLUSION

Textbook outcome is achieved in less than 40 per cent of patients having oesophagectomy for cancer. Improvements in centralization, hospital resources, access to minimal access surgery, and adoption of newer techniques for improving lymph node yield could improve textbook outcome.

Assessing impact of ventilation on airborne transmission of SARS-CoV-2: a cross-sectional analysis of naturally ventilated healthcare settings in Bangladesh

OBJECTIVES

To evaluate the risk of exposure to SARS-CoV-2 in naturally ventilated hospital settings by measuring parameters of ventilation and comparing these findings with results of bioaerosol sampling.

STUDY DESIGN

Cross-sectional study.

STUDY SETTING AND STUDY SAMPLE

The study sample included nine hospitals in Dhaka, Bangladesh. Ventilation characteristics and air samples were collected from 86 healthcare spaces during October 2020 to February 2021.

PRIMARY OUTCOME

Risk of cumulative SARS-CoV-2 infection by type of healthcare area.

SECONDARY OUTCOMES

Ventilation rates by healthcare space; risk of airborne detection of SARS-CoV-2 across healthcare spaces; impact of room characteristics on absolute ventilation; SARS-CoV-2 detection by naturally ventilated versus mechanically ventilated spaces.

RESULTS

The majority (78.7%) of naturally ventilated patient care rooms had ventilation rates that fell short of the recommended ventilation rate of 60 L/s/p. Using a modified Wells-Riley equation and local COVID-19 case numbers, we found that over a 40-hour exposure period, outpatient departments posed the highest median risk for infection (7.7%). SARS-CoV-2 RNA was most frequently detected in air samples from non-COVID wards (50.0%) followed by outpatient departments (42.9%). Naturally ventilated spaces (22.6%) had higher rates of SARS-CoV-2 detection compared with mechanically ventilated spaces (8.3%), though the difference was not statistically significant (p=0.128). In multivariable linear regression with calculated elasticity, open door area and cross-ventilation were found to have a significant impact on ventilation.

CONCLUSION

Our findings provide evidence that naturally ventilated healthcare settings may pose a high risk for exposure to SARS-CoV-2, particularly among non-COVID-designated spaces, but improving parameters of ventilation can mitigate this risk.

Thrombocytopenia as a Prognostic Marker in Patients with Acute Encephalitis at a Tertiary Care Centre in Northern India

Encephalitis is challenging to manage given the diversity of clinical and epidemiologic features. Various predictors of outcome have been studied so far including thrombocytopenia, cerebral edema, hypoglycaemia, development of status epilepticus and need for endotracheal intubation. Thrombocytopenia represents one of the potentially modifiable risk factors for poor prognosis in encephalitis. A better understanding of the epidemiology of this devastating disease and identification of predictors of outcome and management of reversible factors will pave the way for better management of the disease.

MATERIAL

A total of 98 Hospitalised patients of Acute Encephalitis were enrolled in the study. Diagnoses were confirmed by CSF and Neuroimaging studies. Platelet count &lt;150,000/cumm was considered as thrombocytopenia. Mild, moderate and severe thrombocytopenia was categorized at platelet count 100,000-150,000, 50,000-100,000 and &lt;50,000/ cumm, respectively. Outcome at discharge was assessed using the Modified Ranking Score, categorized into 3 groups - good (0-2), fair (3-4), and poor (5-6). Chi-square, ANOVA and Independent samples 't'-tests were used to compare the data.

OBSERVATION

Mean age of patients was 34.06±18.76 (range 14-85) years. Majority of patients were males (54.1). Mean GCS at admission was 9.41±1.90. Acute viral encephalitis(unclassified) (n=33; 33.7%), Scrub typhus (n=24; 24.5%) and Japanese encephalitis virus (n=12; 12.2%) were the most common underlying etiologies. A total of 74 (75.5%) patients had thrombocytopenia. Mild, moderate and severe thrombocytopenia was seen in 34 (34.7%), 30 (30.6%) and 10 (10.2%) cases. Thrombocytopenia was significantly higher in Dengue and Scrub as compared to other etiologies. Thrombocytopenia and its severity showed a significant association with lower GCS and higher mRS scores indicating a poor outcome.

CONCLUSION

Thrombocytopenia is associated with a poor clinical status and adverse outcomes in patients with encephalitis of all causes.

Variation in Severe Acute Respiratory Syndrome Coronavirus 2 Bioaerosol Production in Exhaled Breath

We developed a simple, noninvasive mask sampling method to quantify and sequence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from exhaled breath. We found substantial variation between individuals in SARS-CoV-2 copies exhaled over a 15-minute period, which moderately correlated with nasal swab viral load. Talking was associated with a median of 2 log₁₀ greater exhaled viral copies. Exposure varies substantially between individuals but may be risk stratified by nasal swab viral load and whether the exposure involved conversation.

Comprehensive RNAseq analysis for identification of genes expressed under heat stress in lentil

Lentils are highly sensitive to abrupt increases in temperature during the mid to late reproductive stages, leading to severe biomass and seed yield reduction. Therefore, we carried out an RNAseq analysis between IG4258 (heat tolerant) and IG3973 (heat sensitive) lentil genotypes at the reproductive stage under both normal and heat stress conditions in the field. It resulted in 209,549 assembled transcripts and among these 161,809 transcripts had coding regions, of which 94,437 transcripts were annotated. The differential gene expression analysis showed upregulation of 678 transcripts and downregulation of 680 transcripts between the tolerant and sensitive genotypes at the early reproductive stage. While 76 transcripts were upregulated and 47 transcripts were downregulated at the late reproductive stage under heat stress conditions. The validation of 12 up-or downregulated transcripts through RT-PCR corresponded well with the expression analysis data of RNAseq, with a correlation of R²  = 0.89. Among these transcripts, the DN364_c1_g1_i9 and DN2218_c0_g1_i5 transcripts encoded enzymes involved in the tryptophan pathway, indicating that tryptophan biosynthesis plays a role under heat stress in lentil. Moreover, KEGG pathways enrichment analysis identified transcripts associated with genes encoding proteins/regulating factors related to different metabolic pathways including signal transduction, fatty acid biosynthesis, rRNA processing, ribosome biogenesis, gibberellin (GA) biosynthesis, and riboflavin biosynthesis. This analysis also identified 6852 genic-SSRs leading to the development of 4968 SSR primers that are potential genomic resources for molecular mapping of heat-tolerant genes in lentil.

Identification of stage-specific differentially expressed genes and SNPs in gastric cancer employing RNA-Seq based transcriptome profiling

We analysed over 400 million reads obtained from Illumina sequencing of six pairs of libraries representing two each of stage I, II, and III gastric tumors and corresponding normal tissues to identify differentially expressed genes (DEGs), single nucleotide polymorphisms (SNPs), and transcription factors (TFs). In total, 2207 DEGs including 972 upregulated genes and 1235 downregulated genes were detected. Of these, several stage-specific signature genes were identified. The protein-protein interaction networks involving DEGs and TFs were constructed. The KEGG pathway analysis of SNP harbouring genes revealed their involvement in different cancer related pathways like apoptosis, mTOR pathway, and MAPK signaling pathway. The SNP analysis showed implication of host genes in GO categories like immune system process, regulation of signaling, response to stress, and transport. A biased chromosomal distribution of DEGs and SNP harbouring genes was observed. Our study would provide further insights into the complex regulatory mechanisms operating during gastric tumorigenesis.

Postoperative outcomes in oesophagectomy with trainee involvement

BACKGROUND

The complexity of oesophageal surgery and the significant risk of morbidity necessitates that oesophagectomy is predominantly performed by a consultant surgeon, or a senior trainee under their supervision. The aim of this study was to determine the impact of trainee involvement in oesophagectomy on postoperative outcomes in an international multicentre setting.

METHODS

Data from the multicentre Oesophago-Gastric Anastomosis Study Group (OGAA) cohort study were analysed, which comprised prospectively collected data from patients undergoing oesophagectomy for oesophageal cancer between April 2018 and December 2018. Procedures were grouped by the level of trainee involvement, and univariable and multivariable analyses were performed to compare patient outcomes across groups.

RESULTS

Of 2232 oesophagectomies from 137 centres in 41 countries, trainees were involved in 29.1 per cent of them (n = 650), performing only the abdominal phase in 230, only the chest and/or neck phases in 130, and all phases in 315 procedures. For procedures with a chest anastomosis, those with trainee involvement had similar 90-day mortality, complication and reoperation rates to consultant-performed oesophagectomies (P = 0.451, P = 0.318, and P = 0.382, respectively), while anastomotic leak rates were significantly lower in the trainee groups (P = 0.030). Procedures with a neck anastomosis had equivalent complication, anastomotic leak, and reoperation rates (P = 0.150, P = 0.430, and P = 0.632, respectively) in trainee-involved versus consultant-performed oesophagectomies, with significantly lower 90-day mortality in the trainee groups (P = 0.005).

CONCLUSION

Trainee involvement was not found to be associated with significantly inferior postoperative outcomes for selected patients undergoing oesophagectomy. The results support continued supervised trainee involvement in oesophageal cancer surgery.

Paving the way for application of next generation risk assessment to safety decision-making for cosmetic ingredients

Next generation risk assessment (NGRA) is an exposure-led, hypothesis-driven approach that has the potential to support animal-free safety decision-making. However, significant effort is needed to develop and test the in vitro and in silico (computational) approaches that underpin NGRA to enable confident application in a regulatory context. A workshop was held in Montreal in 2019 to discuss where effort needs to be focussed and to agree on the steps needed to ensure safety decisions made on cosmetic ingredients are robust and protective. Workshop participants explored whether NGRA for cosmetic ingredients can be protective of human health, and reviewed examples of NGRA for cosmetic ingredients. From the limited examples available, it is clear that NGRA is still in its infancy, and further case studies are needed to determine whether safety decisions are sufficiently protective and not overly conservative. Seven areas were identified to help progress application of NGRA, including further investments in case studies that elaborate on scenarios frequently encountered by industry and regulators, including those where a ‘high risk’ conclusion would be expected. These will provide confidence that the tools and approaches can reliably discern differing levels of risk. Furthermore, frameworks to guide performance and reporting should be developed.

A Rapid Pharmacogenomic Assay to Detect NAT2 Polymorphisms and Guide Isoniazid Dosing for Tuberculosis Treatment

RATIONALE

Standardized dosing of anti-tubercular drugs contributes to a substantial incidence of toxicities, inadequate treatment response, and relapse, in part due to variable drug levels achieved. Single nucleotide polymorphisms (SNPs) in the N-acetyltransferase-2 (NAT2) gene explain the majority of interindividual pharmacokinetic variability of isoniazid (INH). However, an obstacle to implementing pharmacogenomic-guided dosing is the lack of a point-of-care assay.

OBJECTIVES

To develop and test a NAT2 classification algorithm, validate its performance in predicting isoniazid clearance, and develop a prototype pharmacogenomic assay.

METHODS

We trained random forest models to predict NAT2 acetylation genotype from unphased SNP data using a global collection of 8,561 phased genomes. We enrolled 48 pulmonary TB patients, performed sparse pharmacokinetic sampling, and tested the acetylator prediction algorithm accuracy against estimated INH clearance. We then developed a cartridge-based multiplex qPCR assay on the GeneXpert platform and assessed its analytical sensitivity on whole blood samples from healthy individuals.

MEASUREMENTS AND MAIN RESULTS

With a 5-SNP model trained on two-thirds of the data (n=5,738), out-of-sample acetylation genotype prediction accuracy on the remaining third (n=2,823) was 100%. Among the 48 TB patients, predicted acetylator types were: 27 (56.2%) slow, 16 (33.3%) intermediate and 5 (10.4%) rapid. INH clearance rates were lowest in predicted slow acetylators (median 14.5 L/hr), moderate in intermediate acetylators (median 40.3 L/hr) and highest in fast acetylators (median 53.0 L/hr). The cartridge-based assay accurately detected all allele patterns directly from 25 ul of whole blood.

CONCLUSIONS

An automated pharmacogenomic assay on a platform widely used globally for tuberculosis diagnosis could enable personalized dosing of isoniazid.

SARS-CoV-2 Subgenomic RNA Kinetics in Longitudinal Clinical Samples

BACKGROUND

Given the persistence of viral RNA in clinically recovered coronavirus disease 2019 (COVID-19) patients, subgenomic RNAs (sgRNAs) have been reported as potential molecular viability markers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, few data are available on their longitudinal kinetics, compared with genomic RNA (gRNA), in clinical samples.

METHODS

We analyzed 536 samples from 205 patients with COVID-19 from placebo-controlled, outpatient trials of peginterferon Lambda-1a (Lambda; n = 177) and favipiravir (n = 359). Nasal swabs were collected at 3 time points in the Lambda (days 1, 4, and 6) and favipiravir (days 1, 5, and 10) trials. N-gene gRNA and sgRNA were quantified by quantitative reverse transcription polymerase chain reaction. To investigate the decay kinetics in vitro, we measured gRNA and sgRNA in A549ACE2+ cells infected with SARS-CoV-2, following treatment with remdesivir or dimethylsulfoxide control.

RESULTS

At 6 days in the Lambda trial and 10 days in the favipiravir trial, sgRNA remained detectable in 51.6% (32/62) and 49.5% (51/106) of the samples, respectively. Cycle threshold (Ct) values for gRNA and sgRNA were highly linearly correlated (marginal R 2 = 0.83), and the rate of increase did not differ significantly in the Lambda trial (1.36 cycles/d vs 1.36 cycles/d; P = .97) or the favipiravir trial (1.03 cycles/d vs 0.94 cycles/d; P = .26). From samples collected 15-21 days after symptom onset, sgRNA was detectable in 48.1% (40/83) of participants. In SARS-CoV-2-infected A549ACE2+ cells treated with remdesivir, the rate of Ct increase did not differ between gRNA and sgRNA.

CONCLUSIONS

In clinical samples and in vitro, sgRNA was highly correlated with gRNA and did not demonstrate different decay patterns to support its application as a viability marker.

Mortality from esophagectomy for esophageal cancer across low, middle, and high-income countries: An international cohort study

BACKGROUND

No evidence currently exists characterising global outcomes following major cancer surgery, including esophageal cancer. Therefore, this study aimed to characterise impact of high income countries (HIC) versus low and middle income countries (LMIC) on the outcomes following esophagectomy for esophageal cancer.

METHOD

This international multi-center prospective study across 137 hospitals in 41 countries included patients who underwent an esophagectomy for esophageal cancer, with 90-day follow-up. The main explanatory variable was country income, defined according to the World Bank Data classification. The primary outcome was 90-day postoperative mortality, and secondary outcomes were composite leaks (anastomotic leak or conduit necrosis) and major complications (Clavien-Dindo Grade III - V). Multivariable generalized estimating equation models were used to produce adjusted odds ratios (ORs) and 95% confidence intervals (CI95%).

RESULTS

Between April 2018 to December 2018, 2247 patients were included. Patients from HIC were more significantly older, with higher ASA grade, and more advanced tumors. Patients from LMIC had almost three-fold increase in 90-day mortality, compared to HIC (9.4% vs 3.7%, p < 0.001). On adjusted analysis, LMIC were independently associated with higher 90-day mortality (OR: 2.31, CI95%: 1.17-4.55, p = 0.015). However, LMIC were not independently associated with higher rates of anastomotic leaks (OR: 1.06, CI95%: 0.57-1.99, p = 0.9) or major complications (OR: 0.85, CI95%: 0.54-1.32, p = 0.5), compared to HIC.

CONCLUSION

Resections in LMIC were independently associated with higher 90-day postoperative mortality, likely reflecting a failure to rescue of these patients following esophagectomy, despite similar composite anastomotic leaks and major complication rates to HIC. These findings warrant further research, to identify potential issues and solutions to improve global outcomes following esophagectomy for cancer.

Comparison of short-term outcomes from the International Oesophago-Gastric Anastomosis Audit (OGAA), the Esophagectomy Complications Consensus Group (ECCG), and the Dutch Upper Gastrointestinal Cancer Audit (DUCA)

BACKGROUND

The Esophagectomy Complications Consensus Group (ECCG) and the Dutch Upper Gastrointestinal Cancer Audit (DUCA) have set standards in reporting outcomes after oesophagectomy. Reporting outcomes from selected high-volume centres or centralized national cancer programmes may not, however, be reflective of the true global prevalence of complications. This study aimed to compare complication rates after oesophagectomy from these existing sources with those of an unselected international cohort from the Oesophago-Gastric Anastomosis Audit (OGAA).

METHODS

The OGAA was a prospective multicentre cohort study coordinated by the West Midlands Research Collaborative, and included patients undergoing oesophagectomy for oesophageal cancer between April and December 2018, with 90 days of follow-up.

RESULTS

The OGAA study included 2247 oesophagectomies across 137 hospitals in 41 countries. Comparisons with the ECCG and DUCA found differences in baseline demographics between the three cohorts, including age, ASA grade, and rates of chronic pulmonary disease. The OGAA had the lowest rates of neoadjuvant treatment (OGAA 75.1 per cent, ECCG 78.9 per cent, DUCA 93.5 per cent; P < 0.001). DUCA exhibited the highest rates of minimally invasive surgery (OGAA 57.2 per cent, ECCG 47.9 per cent, DUCA 85.8 per cent; P < 0.001). Overall complication rates were similar in the three cohorts (OGAA 63.6 per cent, ECCG 59.0 per cent, DUCA 62.2 per cent), with no statistically significant difference in Clavien-Dindo grades (P = 0.752). However, a significant difference in 30-day mortality was observed, with DUCA reporting the lowest rate (OGAA 3.2 per cent, ECCG 2.4 per cent, DUCA 1.7 per cent; P = 0.013).

CONCLUSION

Despite differences in rates of co-morbidities, oncological treatment strategies, and access to minimal-access surgery, overall complication rates were similar in the three cohorts.