Utilizing 3D printing to facilitate surgical in-situ paediatric renal artery aneurysm repair for refractory hypertension

Renal artery aneurysmal (RAA) disease is a rare, but potentially life-threatening cause of renovascular disease presenting with hypertension. Conventional management involves aneurysmal excision followed by renal auto-transplantation. We present the management of a 13-year-old girl with complex multiple saccular aneurysmal disease of the left renal artery with hilar extension and symptomatic hypertension. We used 3D printing to print a patient-specific model that was not implanted in the patient but was used for surgical planning and discussion with the patient and their family. Endovascular options were precluded due to anatomical complexities. Following multi-disciplinary review and patient-specific 3D printing, she underwent successful in-situ RAA repair with intraoperative cooling, without the need for auto-transplantation. 3D printing enabled appreciation of aneurysmal spatial configuration and dimensions that also helped plan the interposition graft length needed following aneurysmal excision. The models provided informed multidisciplinary communications and proved valuable during the consent process with the family for this high-risk procedure. To our knowledge, this is the first reported case utilizing 3D printing to facilitate in-situ complex repair of RAA with intra-hilar extension for paediatric renovascular disease.

Adverse events associated with PentaRay Mapping Catheter – MAUDE database analysis

Background

The 20 pole PentaRay Mapping Catheter is a high-definition mapping catheter with five soft, flexible spines providing better and faster acquisition. Despite its design, the catheter is not without glitches.

Objective

We queried the Food and Drug Administration Manufacturer and User Facility Device Experience (MAUDE) database for adverse events related to the use of the PentaRay mapping catheter.

Methods

The Manufacturer and User Facility Device Experience (MAUDE) database was searched for reports received between October 1, 2019, to October 31, 2021, to capture all adverse events associated with PentaRay mapping catheter using the term “PentaRay” in the “brand name” section. The adverse events were adjudicated to various categories based on the review of the event description for each medical device report (MDR).

Results

A total of 159 events were reported in 148 MDRs during the study period. The most common device related issues were: damaged splines 18.2% (n=29), device entrapment 17% (n=27), thrombus on device 15.1% (n=24), foreign material on splines 8.8% (n=14), sensor error 3.8% (n=6). Of the patient related events, 13.8% (n=22) were pericardial effusion, 5% (n=8) cardiac arrest, 1.2% (n=2) coronary vasospasm/STEMI, 0.6% (n=1) heart block, 0.6% (n=1) air embolism, 0.6% (n=1) tear in pulmonary veins. These events lead to procedure abortion 27.7% (n=44) and procedural delay 11.3% (n=18).

Conclusion

Several issues have been reported with the PentaRay mapping catheter leading to to procedure abortion, delay and patients related adverse events. Understanding and troubleshooting may help improve patient outcomes.

Funding Acknowledgement

Type of funding sources: None.

Measuring TB drug levels in the hair in adults and children to monitor drug exposure and outcomes

INTRODUCTION: Testing for anti-TB drugs in small hair samples may serve as a non-invasive tool to measure cumulative drug exposure and/or adherence, as these determine treatment success. We aimed to assess how well hair assays of TB drugs predict TB treatment outcomes.METHODS: A small thatch of hair, ~30 strands, was cut from the occipital region in adults and children from a prospective TB cohort in India. Isoniazid (INH), acetyl-INH and pyrazinamide (PZA) were extracted from the hair samples and quantified using liquid-chromatography-tandem mass spectrometry. The relationship between drug concentrations in hair and time to unfavourable outcomes was assessed using Cox-proportional hazards regression models.RESULTS: A two-fold increase in hair acetyl-INH concentrations in the 264 participants in our cohort with hair assays for TB drugs indicated a lower hazard of unfavourable TB treatment outcomes (aHR 0.67, 95%CI 0.44-1.02) and TB treatment failure (aHR 0.65, 95%CI 0.42-1.01). Higher summed concentrations (a summed measure of INH and acetyl-INH) indicated a lower hazard of treatment failure (aHR 0.69, 95%CI 0.45-1.05)CONCLUSION: Hair levels of INH and its metabolite may predict TB treatment outcomes, indicating the potential utility of this measure to assess and optimise TB treatment outcomes.

Molecular mechanisms in grass-Epichloë interactions: towards endophyte driven farming to improve plant fitness and immunity

All plants harbor many microbial species including bacteria and fungi in their tissues. The interactions between the plant and these microbes could be symbiotic, mutualistic, parasitic or commensalistic. Mutualistic microorganisms are endophytic in nature and are known to play a role in plant growth, development and fitness. Endophytes display complex diversity depending upon the agro-climatic conditions and this diversity could be exploited for crop improvement and sustainable agriculture. Plant-endophyte partnerships are highly specific, several genetic and molecular cascades play a key role in colonization of endophytes in host plants leading to rapid changes in host and endophyte metabolism. This results in the accumulation of secondary metabolites, which play an important role in plant defense against biotic and abiotic stress conditions. Alkaloids are one of the important class of metabolites produced by Epichloë genus and other related classes of endophytes and confer protection against insect and mammalian herbivory. In this context, this review discusses the evolutionary aspects of the Epichloë genus along with key molecular mechanisms determining the lifestyle of Epichloë endophytes in host system. Novel hypothesis is proposed to outline the initial cellular signaling events during colonization of Epichloë in cool season grasses. Complex clustering of alkaloid biosynthetic genes and molecular mechanisms involved in the production of alkaloids have been elaborated in detail. The natural defense and advantages of the endophyte derived metabolites have also been extensively discussed. Finally, this review highlights the importance of endophyte-arbitrated plant immunity to develop novel approaches for eco-friendly agriculture.

Assessment of the Xpert assay among adult pulmonary tuberculosis suspects with and without diabetes mellitus

SETTING: Pune and Pimpri-Chinchwad Municipal Corporation area, Maharashtra State, India.OBJECTIVE: To assess the sensitivity and specificity of the Xpert® MTB/RIF assay among adults with suspected pulmonary tuberculosis (PTB) and with or without diabetes (DM).DESIGN: As part of a prospective cohort study, we screened 2359 adults presumed to have PTB with no history of TB. All individuals underwent testing for two sputum smears, culture, Xpert, glycated haemoglobin and fasting blood sugar. We calculated sensitivity and specificity of Xpert by comparing it with TB sputum culture result as a gold standard.RESULTS: Among screened individuals, 483 (20%) were diagnosed with DM and 1153 (49%) with pre-DM; 723 (31%) had no DM. Overall sensitivity of Xpert was 96% (95%CI 95–97) and specificity was 91% (95%CI 89–93). Xpert sensitivity was significantly higher among DM group (98%) than in the ‘No DM' (95%; P < 0.01) and pre-DM (96%; P < 0.05) groups. Among sputum smear-negative individuals, Xpert sensitivity was higher in the DM group than in the No DM (92% vs. 82%; P = 0.054) and pre-DM group (92% vs. 82%; P = 0.037).CONCLUSION: High sensitivity and specificity of Xpert underscores the need for its rapid scale up for the early detection of TB in settings with a high dual burden of TB and DM.

Trends in HbA1c levels and implications for diabetes screening in tuberculosis cases undergoing treatment in India

SETTING

The optimal timing of screening for diabetes mellitus (DM) among tuberculosis (TB) cases is unclear due to the possibility of stress hyperglycemia.

DESIGN

We evaluated adult (18 years) pulmonary TB cases at treatment initiation as well as at 3 months, 6 months and 12 months. DM was identified by self-report (known DM) or glycated hemoglobin (HbA1c)  6.5% (new DM). Trends in HbA1c levels during treatment were assessed using non-parametric tests.

RESULTS

Of the 392 participants enrolled, 75 (19%) had DM, 30 (40%) of whom had new DM. Of the 45 participants with known DM, respectively 37 (82%) and 40 (89%) received medication to lower glucose levels at treatment initiation and completion; one participant with new DM initiated glucose-lowering medication during follow-up. The median HbA1c level in participants with known, new and no DM was respectively 10.1% (interquartile range [IQR] 8.3-11.6), 8.5% (IQR 6.7-11.5) and 5.6% (IQR 5.3-5.9) at treatment initiation, and 8.7% (IQR 6.8-11.3), 7.1% (IQR 5.8-9.5) and 5.3% (IQR 5.1-5.6) at treatment completion (P < 0.001). Overall, 5 (12%) with known and 13 (43%) with new DM at treatment initiation had reverted to HbA1c < 6.5% by treatment completion (P = 0.003); the majority of reversions occurred during the first 3 months, with no significant reversions beyond 6 months.

CONCLUSION

HbA1c levels declined with anti-tuberculosis treatment. Repeat HbA1c testing at treatment completion could reduce the risk of misdiagnosis of DM.

Resolving the full spectrum of human genome variation using Linked-Reads

Large-scale population analyses coupled with advances in technology have demonstrated that the human genome is more diverse than originally thought. To date, this diversity has largely been uncovered using short-read whole-genome sequencing. However, these short-read approaches fail to give a complete picture of a genome. They struggle to identify structural events, cannot access repetitive regions, and fail to resolve the human genome into haplotypes. Here, we describe an approach that retains long range information while maintaining the advantages of short reads. Starting from ∼1 ng of high molecular weight DNA, we produce barcoded short-read libraries. Novel informatic approaches allow for the barcoded short reads to be associated with their original long molecules producing a novel data type known as "Linked-Reads". This approach allows for simultaneous detection of small and large variants from a single library. In this manuscript, we show the advantages of Linked-Reads over standard short-read approaches for reference-based analysis. Linked-Reads allow mapping to 38 Mb of sequence not accessible to short reads, adding sequence in 423 difficult-to-sequence genes including disease-relevant genes STRC, SMN1, and SMN2 Both Linked-Read whole-genome and whole-exome sequencing identify complex structural variations, including balanced events and single exon deletions and duplications. Further, Linked-Reads extend the region of high-confidence calls by 68.9 Mb. The data presented here show that Linked-Reads provide a scalable approach for comprehensive genome analysis that is not possible using short reads alone.

Prevalence of dysglycemia and clinical presentation of pulmonary tuberculosis in Western India

SETTING

Pune, India.

OBJECTIVES

To estimate the prevalence and risk factors of pre-diabetes mellitus (DM) and DM, and its associations with the clinical presentation of tuberculosis (TB).

DESIGN

Screening for DM was conducted among adults (age  18 years) with confirmed TB between December 2013 and January 2017. We used multinomial regression to evaluate the risk factors for pre-DM (glycated hemoglobin [HbA1c]  5.7-6.5% or fasting glucose 100-125 mg/dl) and DM (HbA1c  6.5% or fasting glucose  126 mg/dl or random blood glucose > 200 mg/dl or self-reported DM history/treatment) and the association of dysglycemia with the severity of TB disease.

RESULTS

Among 1793 participants screened, 890 (50%) had microbiologically confirmed TB. Of these, 33% had pre-DM and 18% had DM; 41% were newly diagnosed. The median HbA1c level among newly diagnosed DM was 7.0% vs. 10.3% among known DM (P < 0.001). DM (adjusted OR [aOR] 4.94, 95%CI 2.33-10.48) and each per cent increase in HbA1c (aOR 1.42, 95%CI 1.01-2.01) was associated with >1+ smear grade or 9 days to TB detection.

CONCLUSION

Over half of newly diagnosed TB patients had DM or pre-DM. DM and increasing dysglycemia was associated with higher bacterial burden at TB diagnosis, potentially indicating a higher risk of TB transmission to close contacts.

Abstract 281: Identifying genetic variation and cellular heterogeneity with a comprehensive cancer analysis toolkit

Understanding disease development, progression and response to treatment remains elusive for most types of cancer. This is due both to the genetic complexity seen in tumors as well as differences in how the surrounding cells and immune system respond to the developing tumor. To fully understand all aspects of disease progression and response to treatment, a systems level approach is needed. We have developed a platform that allows for high resolution multi-omics analysis of the tumor and its microenvironment. This platform is built upon a microfluidic system that enables the production of hundreds of thousands to millions of partitioned barcoded reactions. On this platform we generate Linked-Reads that allow for the detailed resolution of complex structural variant events. To obtain more detailed information about tumor heterogeneity and clonal structure, we also perform single cell DNA analysis that allows for the detection of sub-megabase copy number variants at the single cell level.The platform also provides detailed resolution of the cells occupying the microenvironment surrounding the tumor. Using a combination of single cell gene expression and enriched V(D)J B and T cell repertoire analysis, we identify cells constituting a tumor, as well as the immune and nonimmune cells surrounding the tumor. We also provide single cell profiling of the paired antigen receptor chains for both B and T cells. As a demonstration, we have performed this analysis on three types of tumor samples: metastatic melanoma (MM), primary colorectal cancer (CRC) and primary clear cell renal carcinoma (CCRC). We are able to identify a clonal expansion in the CCRC sample and determine there is no expansion in the CRC sample. The combination of these approaches allows for unparalleled characterization of disease development, progression and response.

Citation Format: Sarah Garcia, Rajiv Bharadwaj, Stéphane Boutet, Claudia Catalanotti, Valeria Giangerra, Josephine Lee, Jessica Terry, Stephen Williams, Grace X. Zheng, Tarjei Mikkelsen, Michael Schnall-Levin, Ben Hindson, Deanna M. Church. Identifying genetic variation and cellular heterogeneity with a comprehensive cancer analysis toolkit [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 281.

Abstract 3395: A scalable microfluidic platform for determining cellular heterogeneity by copy number detection

The ability to sequence entire genomes at the level of single cells (SCs) is an essential tool for mapping heterogeneity in cancer. Knowledge of this variability provides insight into cancer dynamics and the efficacy of therapeutics. Copy number variant (CNV) analysis requires only sparse coverage creating an affordable means for measuring cellular differences genome-wide. However, current approaches to SC DNA sequencing suffer from low throughput, cumbersome workflows and remain accessible to only a few select laboratories. We have developed a microfluidic, partitioning-based solution that allows sensitive CNV detection of thousands of SCs concomitantly. Isolated cells or nuclei are treated to gain complete accessibility to genomic DNA then co-partitioned along with gel beads supporting oligonucleotide barcodes. Barcoded fragments, representing genomic abundance, are generated and converted into Illumina-compatible libraries. The workflow supports various sample types including primary cells, cultured cells, tissue-dissociated cells and nuclei extracted from flash-frozen tissues. Accompanying this platform we have also developed a scalable bioinformatics pipeline for genome alignment, normalization, copy-number detection, and clustering of SC profiles. Using clusters for CNV analysis we can reliably detect 100 kb scale events and, in large clones, identify CNV events down to tens of kilobases with high confidence. Analysis of our SC whole-genome sequencing data shows excellent coverage uniformity, comparable to leading plate-based SC amplification techniques. To validate the accuracy of CNV detection, calls are measured against orthogonal data from well-characterized cell lines including RPMI8226, HCC1954, and HCC1143 and high concordance is observed. Furthermore, we are able to observe multiple clones including CNVs in normal cell lines GM12878 and BJ suggesting absolute cell line validation requires whole-genome SC sequencing. Evaluating nuclei extracted from stage 1 breast carcinoma and stage 1 renal cell carcinoma we find clones exhibiting common somatic mutations. Furthermore, many cells exhibit extensive genomic heterogeneity, effects we attribute to DNA replication, with the frequency of such events elevated in fast growing samples such as tumors or fresh cell cultures.

In conclusion, we demonstrate a novel droplet-based system that permits scalable CNV calling at the SC level enabling high resolution characterization of intra-tumor heterogeneity. It is our intention that a reliable and cost-effective system will encourage widespread adoption of SC analysis as a means of characterizing the progression of cancer, lead to more effective treatments and unveil genomic diversity in other genetically heterogenous systems such as neuronal cells, high-passage cell lines and samples from aging populations.

Citation Format: Andrew Price, Jon Sorenson, Kamila Belhocine, Claudia Catalanotti, Zeljko Dzakula, Susana Jett, Viajy Kumar, Bill Lin, Tony Makarewicz, Alaina Puleo, Mohammad Rahimi, Sanjam Sawhney, Joe Shuga, Maengseok Song, Katie Sullivan-Bibee, Tobias Wheeler, Yifeng Yin, Michael Schnall-Levin, Rajiv Bharadwaj. A scalable microfluidic platform for determining cellular heterogeneity by copy number detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3395.

Abstract 3400: Characterizing genomic variation and tumor heterogeneity in cancer

Cancer genomes are highly unstable with new genetic variations emerging even within a single metastatic site, making it difficult to track the causal changes that drive metastasis and treatment resistance. Here we present a two-pronged approach for analyzing the full spectrum of genetic variations present in cancer samples. The first approach allows for comprehensive and high-resolution characterization of a broad range of variant types on bulk tumor sample. While the second approach characterizes structural variation at the level of the single cell, allowing for the exploration of tumor clonality and heterogeneity. At the core of our approaches is a microfluidics platform that enables the production of hundreds of thousands to millions of partitioned barcoded reactions. This platform can partition high-molecular weight DNA or single cells. Together, these complementary approaches provide a more complete picture of the genomic variation and clonal structure present in a tumor.

For bulk tumor analysis, we obtained high molecular weight DNA from known cancer cell lines and used the 10x Chromium Genome solution to produce Illumina-ready sequencing libraries. In this workflow, partitioning of a limited amount of genomic DNA allows for haplotype-level dilution of genome equivalents, which are then barcoded to create a novel data type referred to as “Linked-Reads”. These molecular barcodes are used to identify reads originating from the same input molecule providing long range information on highly accurate short reads. In addition to highly accurate SNP calling, this further enables identification of complex structural rearrangements in tumor genomes. To gain insight into tumor heterogeneity and clonal structure, we performed single cell DNA sequencing and analysis using 10x Chromium scDNA solution. This platform integrates single cell encapsulation, cell lysis and DNA barcoding into a streamlined workflow. Molecular barcodes are used to associate reads with individual cells allowing for copy number variant (CNV) detection. We applied our scDNA sequencing method to a variety of cancer cell lines revealing their clonal structure, as identified by CNVs, with the capability to identify as few as 10 cells in a sample size of one thousand cells. Using cluster analyses we were able to detect 100kb scale events and by aggregating reads in large clones we were able to confidently identify smaller CNV events down to tens of kilobases. Using whole genome bulk sequencing we identified more than 500 large structural variants in HCC1954, including balanced and unbalanced events. In this presentation, we will integrate this Linked-Read data with single cell genome analysis on the same samples, and compare the genetic variation revealed by these two approaches. We will further explore the power of combining these data types for a more complete picture of tumor genome dynamic

Citation Format: Claudia Catalanotti, Sarah Garcia, Kamila Belhocine, Vijay Kumar, Zeljko Dzakula, Andrew Price, Shamoni Maheshwar, Yifeng Yin, Michael Schnall-Levin, Rajiv Bharadwaj, Sara Agee Le, Deanna M. Church. Characterizing genomic variation and tumor heterogeneity in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3400.

Novel interferon-gamma assays for diagnosing tuberculosis in young children in India

SETTING

The tuberculin skin test (TST) and interferon-gamma release assays (IGRAs) are used as supportive evidence to diagnose active tuberculosis (TB). Novel IGRAs could improve diagnosis, but data are lacking in young children.

DESIGN

Children (age 5 years) with suspected TB were prospectively screened at a tertiary hospital in Pune, India; the children underwent TST, and standard (early secretory antigenic target 6 and culture filtrate protein 10) and enhanced (five additional novel antigens) enzyme-linked immunospot (ELISpot) assays.

RESULTS

Of 313 children (median age 30 months) enrolled, 92% had received bacille Calmette-Guérin vaccination, 53% were malnourished and 9% were coinfected with the human immunodeficiency virus (HIV); 48 (15%) had TB, 128 (41%) did not, and TB could not be ruled out in 137 (44%). The sensitivity of enhanced (45%) and standard (42%) ELISpot assays for diagnosing TB was better than that of TST (20%) (P  0.03); however, enhanced ELISpot was not more sensitive than the standard ELISpot assay (P = 0.50). The specificity of enhanced ELISpot, standard ELISpot and TST was respectively 82% (95%CI 74-89), 88% (95%CI 81-94) and 98% (95%CI 93-100). Rv3879c and Rv3615c, previously reported to be promising antigens, failed to improve the diagnostic performance of the ELISpot assay.

CONCLUSION

The TST and the standard and novel ELISpot assays performed poorly in diagnosing active TB among young children in India.

Isoniazid hair concentrations in children with tuberculosis: a proof of concept study

Assessing treatment adherence and quantifying exposure to anti-tuberculosis drugs among children is challenging. We undertook a 'proof of concept' study to assess the drug concentrations of isoniazid (INH) in hair as a therapeutic drug monitoring tool. Children aged <12 years initiated on a thrice-weekly treatment regimen including INH (10 mg/kg) for newly diagnosed tuberculosis were enrolled. INH concentrations in hair were measured using liquid chromatography-tandem mass spectrometry at 1, 2, 4 and 6 months after initiating anti-tuberculosis treatment. We found that INH hair concentrations in all children on thrice-weekly INH were detectable and displayed variability across a dynamic range.

Massively parallel digital transcriptional profiling of single cells

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.

Vitamin D deficiency and risk of postpartum tuberculosis among HIV-infected breastfeeding mothers in India

Some studies have associated low vitamin D levels with the risk of tuberculosis (TB), but its association in human immunodeficiency virus (HIV) infected mothers in a TB-endemic region has not been well studied. We conducted a nested 1:2 case-control study among HIV-infected mothers in western India to evaluate the association between maternal vitamin D levels and the risk of postpartum TB. Vitamin D insufficiency, moderate deficiency and severe deficiency were observed in a high proportion of HIV-infected mothers, but were not associated with the risk of postpartum TB.

The Exeter technique can lead to a lower incidence of leg-length discrepancy after total hip arthroplasty

We evaluated an operative technique, described by the Exeter Hip Unit, to assist accurate introduction of the femoral component. We assessed whether it led to a reduction in the rate of leg-length discrepancy after total hip arthroplasty (THA). A total of 100 patients undergoing THA were studied retrospectively; 50 were undertaken using the test method and 50 using conventional methods as a control group. The groups were matched with respect to patient demographics and the grade of surgeon. Three observers measured the depth of placement of the femoral component on post-operative radiographs and measured the length of the legs. There was a strong correlation between the depth of insertion of the femoral component and the templated depth in the test group (R = 0.92), suggesting accuracy of the technique. The mean leg-length discrepancy was 5.1 mm (0.6 to 21.4) pre-operatively and 1.3 mm (0.2 to 9.3) post-operatively. There was no difference between Consultants and Registrars as primary surgeons. Agreement between the templated and post-operative depth of insertion was associated with reduced post-operative leg-length discrepancy. The intra-class coefficient was R ≥ 0.88 for all measurements, indicating high observer agreement. The post-operative leg-length discrepancy was significantly lower in the test group (1.3 mm) compared with the control group (6.3 mm, p < 0.001). The Exeter technique is reproducible and leads to a lower incidence of leg-length discrepancy after THA.

Pasteurella multocida infected total knee arthroplasty: a case report and review of the literature

Pasteurella multocida is a rare cause of prosthetic joint infection. This infection generally follows significant animal contact, usually licks and scratches. We report a case of P multocida infection that was treated with linezolid with salvage of the implant. Linezolid is generally active against Gram-positive organisms only with the exception of Pasteurella, which is Gram-negative. We extensively review the previous reported cases of implant infection with P multocida.

Modifiable risk factors associated with tuberculosis disease in children in Pune, India

SETTING

India accounts for the largest burden of tuberculosis (TB) worldwide, with 26% of the world's cases.

OBJECTIVE

To assess the association between novel modifiable risk factors and TB in Indian children.

DESIGN

Cases were children aged ≤ 5 years with confirmed/probable TB based on World Health Organization definitions (definition 1). Controls were healthy children aged ≤ 5 years. Logistic regression was performed to estimate the adjusted odds ratio (aOR) of being a TB case given exposure, including indoor air pollution (IAP; exposure to tobacco smoke and/or biomass fuels) and vitamin D deficiency. Cases were re-analyzed according to a new consensus research definition of pediatric TB (definition 2).

RESULTS

Sixty cases and 118 controls were enrolled. Both groups had high levels of vitamin D deficiency (55% vs. 50%, P = 0.53). In multivariable analysis, TB was associated with household TB exposure (aOR 25.41, 95%CI 7.03-91.81), household food insecurity (aOR 11.55, 95%CI 3.33-40.15) and IAP exposure (aOR 2.67, 95%CI 1.02-6.97), but not vitamin D deficiency (aOR 1.00, 95%CI 0.38-2.66). Use of definition 2 reduced the number of cases to 25. In multivariate analysis, TB exposure, household food insecurity and IAP remained associated with TB.

CONCLUSIONS

Household TB exposure, exposure to IAP and household food insecurity were independently associated with pediatric TB.

Impact of maternal hepatitis B virus coinfection on mother-to-child transmission of HIV

OBJECTIVES

Despite high hepatitis B virus (HBV) endemicity in various resource-limited settings (RLSs), the impact of maternal HIV/HBV coinfection on infant health outcomes has not been defined. We aimed to assess the prevalence of HBV coinfection among HIV-infected pregnant women and its impact on HIV transmission and infant mortality.

METHODS

In this study, the seroprevalence of HBV coinfection was determined among HIV-infected pregnant women enrolled in the Six-Week Extended-Dose Nevirapine (SWEN) India trial. The impact of maternal HIV/HBV coinfection on mother-to-child transmission (MTCT) of HIV and infant mortality was assessed using univariate and multivariate logistic regression analysis.

RESULTS

Among 689 HIV-infected pregnant Indian women, 32 (4.6%) had HBV coinfection [95% confidence interval (CI) 3.4%, 5.3%]. HBV DNA was detectable in 18 (64%) of 28 HIV/HBV-coinfected women; the median HBV viral load was 155 copies/mL [interquartile range (IQR) < 51-6741 copies/mL]. Maternal HIV/HBV coinfection did not increase HIV transmission risk [adjusted odds ratio (aOR) 1.06; 95% CI 0.30, 3.66; P = 0.93]. Increased odds of all-cause infant mortality was noted (aOR 3.12; 95% CI 0.67, 14.57; P = 0.15), but was not statistically significant.

CONCLUSIONS

The prevalence of active maternal HBV coinfection in HIV-infected pregnant women in India was 4.6%. HIV/HBV coinfection was not independently associated with HIV transmission.

Clinicoradiologic correlation in adult patients diagnosed with novel influenza A (H1N1)

BACKGROUND

Influenza A(H1N1) infection affected Indian population in 2009. Patients needed ICU admission and monitoring.

OBJECTIVES

To describe and correlate clinical and radiographic features of Influenza A(H1N1) infection in patients hospitalised in Intensive care unit.

MATERIAL AND METHODS

Retrospective study of records of 100 RT-PCR confirmed patients with Influenza A(H1N1) infection from August 2009 to March 2010 was done. Each patient underwent an evaluation to determine clinical and radiographic features.

RESULTS

Mean age of the patients was 33.43 years (+/- 12.152) with maximum patients between 18-40 years, with 53% males and 43% females. Cough (96%), Fever (95%), breathlessness (83%), throat pain (34%), crepitations (69%), Tachypnoea (59%)were the prominent symptoms and signs. 61% (n = 63) had comorbid condition like pregnancy (n = 13,20.63%), Diabetes Mellitus (DM) (n = 12,19.05%), HT (n = 11,17.60%), Obesity (n = 10, 15.87%) and Rheumatic Valvular Heart Disease (RVHD) (n = 6,09.52%). Chest X ray was abnormal in 91% patients and normal in 09% pts. Bilateral findings were seen in 61.53% cases. Most common zones affected were lower zones (77.46%), then middle zones (71.42%), followed by upper zones (42.7%). Most common patterns were consolidation (64.83%), reticulonodular (24.17%) and nodular (10.98%). 27.47% had two, 21.97% had four, 19.78% had three,12.08% had six, 7.69% had five and 10.98% had single zone involvement. Fever, cough and tachypnoea were present in all 100% pts with nodular pattern while crepitations were observed in 79.66% cases of consolidation. Patchy consolidation was seen in comorbidities like pregnancy (n = 10) and obesity (n = 06), while reticulonodular pattern was observed in hypertensive patients (n = 06). Maximum number of deaths were between 21 and 30 years of age (60.71%). Total number of deaths were 28 with 60.71% (n = 17) deaths between 21 and 30 years of age. Deaths were more in presence of comorbidities like Pregnancy (n = 5, 17.85%), Hypertension (n = 4,14.28%), Diabetes (n = 3 10.21%) and RVHD (n = 3,10.71%), in presence of RLZ involvement (92.85%), RMZ (89.28%), LMZ (85.21%) and RUZ involvement (71.42%), with consolidation pattern (57.14%) followed by reticulonodular pattern (21.42%) and in presence of six zone involvement (36.37%) followed by four zone (35%) and then by three(33%) and two (32%) zone involvement. Mean duration of hospital stay was 9.1 days. 23% patients stayed for less than 5 days, 41% stayed between 9 and 14 days while only 7% required to stay for more than 15 days. 37% pts showed normal Xray at the time of discharge or death. 38% patients showed persistence of radiological lesion at discharge or death.

CONCLUSIONS

Young to middle age patients were commonly affected. Common comorbidities were Pregnancy, Diabetes, Hypertension, and Obesity and patients had fever, cough, breathlessness, tachypnoea, crepitations as common clinical features. Radiologically it was multizonal, bilateral disease with predominant lower zone involvement and common patterns were consolidation followed by reticulonodular and nodular. Patchy consolidation was more common in pregnancy and obesity while reticulonodular pattern was more in hypertensive patients. Fever, cough and tachypnoea were present in all 100% pts with nodular pattern. Crepitations were common in pts with consolidation. Clinical recovery preceded radiological recovery. Young to middle aged individuals died more. Deaths were more in presence of comorbidities like Pregnancy, HT, DM and RVHD, also with RLZ, RMZ, LMZ involvement and with consolidation pattern and with six zone involvement.

Droplet-based microfluidic platform for heterogeneous enzymatic assays

Heterogeneous enzymatic reactions are used in many industrial processes including pulp and paper, food, and biofuel production. Industrially-relevant optimization of the enzymes used in these processes requires assaying them with insoluble substrates. However, platforms for high throughput heterogeneous assays do not exist thereby severely increasing the cost and time of enzyme optimization, or leading to the use of assays with soluble substrates for convenient, but non-ideal, optimization. We present an innovative approach to perform heterogeneous reactions in a high throughput fashion using droplet microfluidics. Droplets provide a facile platform for heterogeneous reactions as internal recirculation allows rapid mixing of insoluble substrates with soluble enzymes. Moreover, it is easy to generate hundreds or thousands of picoliter droplets in a small footprint chip allowing many parallel reactions. We validate our approach by screening combinations of cellulases with real-world insoluble substrates, and demonstrate that the chip-based screening is in excellent agreement with the conventional screening methods, while offering advantages of throughput, speed and lower reagent consumption. We believe that our approach, while demonstrated for a biofuel application, provides a generic platform for high throughput monitoring of heterogeneous reactions.

Clinical impact of the use of 16S rRNA sequencing method for the identification of "difficult-to-identify" bacteria in immunocompromised hosts

Molecular method of 16S rRNA sequencing is reported to be helpful in the accurate identification of organisms with ambiguous phenotypic profiles. We analyzed the use of 16S rRNA sequencing method to identify clinically significant, "difficult-to-identify" bacteria recovered from clinical specimens, and evaluated its role in patient management and consequent clinical outcome. Among the 172 "difficult-to-identify" bacteria recovered over a 4-year period, 140 were gram-positive cocci or gram-negative bacilli; identification by 16S rRNA did not play a role in the management of patients infected with these bacteria. From 32 patients, 33 "difficult-to-identify" gram-positive bacilli were identified; the organisms were mycobacteria, Nocardia, Tsukamurella, Rhodococcus, and Gordonia. In 24 patients for whom clinical data were available, results from the 16S rRNA sequencing method led to treatment change in 14 immunocompromised patients (including 7 hematopoietic stem cell recipients and 1 liver transplant recipient). Therapy was modified in 9 patients, initiated in 3 patients, and discontinued in 2 patients. Most patients' therapy was switched to oral antibiotics with discontinuation of intravascular catheters, facilitating early hospital discharge. All 14 patients were alive 30 days after infection onset. The present study demonstrates the clinical application of 16S rRNA sequencing method to identify "difficult-to-identify" mycobacteria and other gram-positive bacilli in clinical specimens, particularly in immunocompromised hosts.

Retrospective analysis of necropsy findings in patients of H1N1 and their correlation to clinical features

India reported its first case of H1N1 in July 2009 in Pune and since then, the number of reported cases and deaths exploded in India. Since very little data is available about histopathological findings in patients of H1N1 fatal cases in India, a retrospective chart analysis of necropsy findings of 15 cases of 2009 H1N1 fatal cases was performed. Common clinical features were fever, cough, and breathlessness followed by sore throat and rhinorrhea. Common lung findings were mononuclear cell infiltration, thick alveolar septae, intraalveolar hemorrhage. The other findings were congested pulmonary blood vessels, pulmonary edema, cytomegaly, fibrin accumulation and formation of eosinophilic membrane. These findings are suggestive of diffuse alveolar damage (DAD) and DAD with hemorrhage. All patients who underwent necropsy had radiographic findings suggestive of unilobar or multilobar pneumonia. This clinical finding can be correlated pathologically in these patients as all of them had either polymorphonuclear or mononuclear infiltrate. Furthermore, necrotizing pneumonitis pattern seen on these patients is the likely cause of mortality in these patients. Although clinical ARDS pattern was noted in all these patients, it was well correlated in lung pathology in all these cases.

Immunophenotypic Characterization of Benign and Malignant Prostatic Lesions

BACKGROUND

Biopsy diagnosis is the gold standard for differentiating benign and malignant prostatic enlargements. This study was aimed at supplementing biopsy diagnosis with immunophenotypic characters of prostatic lesions.

METHODS

Twenty five cases each of nodular hyperplasia and adenocarcinoma prostate were compared for their morphologic appearances and immunophenotyping, by studying antibodies to prostate specific antigen (PSA), transglutaminase, chromogranin and high molecular weight keratin, proliferating cell nuclear antigen, cell death (apoptosis) and neovascularisation (CD 34).

RESULTS

Markers of differentiation (PSA and transglutaminase) aided recognition of higher-grade tumours. PSA negativity avoided metaplasia being overcalled as carcinoma. Loss of basal cells around malignant prostatic acini as determined by high molecular weight keratin (HMWK), was useful in foci of atypical small acinar proliferation and in prostatic intraepithelial neoplasia. Assessment of proliferation indices identified subsets of tumours, within conventional morphologic Gleason's grades, with a higher growth fraction. Cell death determination and study of tumour vessels did not offer any improvement on morphology.

CONCLUSION

Immunophenotypic assessment helps in refining morphologic diagnosis of prostatic lesions. Differentiation and proliferation markers objectively assess tumour characteristics with their biologic growth potential and are recommended for diagnostic use. They also help in assessement of response to therapy.

Laparoscopic kidney transplantation: an initial experience

Laparoscopic donor nephrectomy has the advantages of less pain, early ambulation and shorter hospitalization compared to open donor nephrectomy. Kidney recipient surgery is, however, traditionally performed by open surgery. Our aim was to study feasibility and safety of laparoscopic kidney transplantation (LKT). After permission from Internal Review Board, LKT was performed in four patients. All kidneys were procured from deceased donors. Left kidney was used for LKT and transplanted in left iliac fossa while right kidney was used for standard open kidney transplantation (OKT). All transplantation procedures were performed successfully. Cold ischemia time varied between 4 h and 14 h. For LKT, mean time for anastomosis was 65 (range 62-72) min, mean operative time was 3.97 (range 3.5-5) h, mean blood loss was 131.25 mL (range 45-350) mL. Mean wound length was 7 cm in LKT group and 18.4 cm in OKT group. Delayed graft function was observed in one patient in each group. One patient was lost in OKT group due to posttransplant bacterial meningitis. At 6 months, both groups have comparable value of serum creatinine. In conclusion, LKT is technically feasible and safe. Long term outcome needs to be evaluated in a larger study.

Utility of in vitro proton magnetic resonance spectroscopy in aetiological characterisation of brain abscesses

PURPOSE

Brain abscesses often present an aetiological dilemma. Microscopy is insensitive and culture techniques are time consuming. Hence, a new rapid technique in vitro Proton Magnetic Resonance Spectroscopy (1HMRS) was evaluated for its usefulness in the identification of aetiology of brain abscesses.

MATERIALS AND METHODS

A total of 39 pus specimens from brain abscesses were subjected to in vitro 1HMRS. These pus specimens were also processed by conventional culture methods. The spectral patterns generated by in vitro 1HMRS were further correlated with culture results.

RESULTS

Pus specimens which showed the presence of anaerobes on culture revealed the presence of multiplet at 0.9 ppm (100%), lactate-lipid at 1.3 ppm (100%), acetate at 1.92 ppm (100%) and succinate at 2.4 ppm (75%). Pus specimens that revealed the presence of facultative anaerobes on culture showed a pattern B, i.e., the presence of lactate-lipid at 1.3 ppm (100%), acetate at 1.92 ppm (88.88%) along with the multiplet at 0.9 ppm (100%). Pattern C was seen in aerobic infection which showed the presence of lactate-lipid at 1.3 ppm (100%) along with the multiplet at 0.9 ppm. Pus from two tuberculous abscesses showed the complete absence of multiplet at 0.9 ppm.

CONCLUSIONS

We observed in this study that it was possible to differentiate bacterial and tuberculous brain abscesses using in vitro 1HMRS. Further, it was also possible to distinguish between aerobic and anaerobic brain abscesses on the basis of spectral patterns. In vitro 1HMRS of fungal and actinomycotic brain abscess are also presented for its unusual spectra.

High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration

The high cost of lignocellulolytic enzymes is one of the main barriers towards the development of economically competitive biorefineries. Enzyme engineering can be used to significantly increase the production rate as well as specific activity of enzymes. However, the success of enzyme optimization efforts is currently limited by a lack of robust high-throughput (HTP) cellulase screening platforms for insoluble pretreated lignocellulosic substrates. We have developed a cost-effective microplate based HTP enzyme-screening platform for ionic liquid (IL) pretreated lignocellulose. By performing in-situ biomass regeneration in micro-volumes, we can volumetrically meter biomass (sub-mg loading) and also precisely control the amount of residual IL for engineering novel IL-tolerant cellulases. Our platform only requires straightforward liquid-handling steps and allows the integration of biomass regeneration, washing, saccharification, and imaging steps in a single microtiter plate. The proposed method can be used to screen individual cellulases as well as to develop novel cellulase cocktails.

Weissella confusa: an unexpected cause of vancomycin-resistant gram-positive bacteremia in immunocompromised hosts

We report the first case of Weissella confusa bacteremia in an allogeneic hematopoietic stem cell transplant patient. After engraftment and discharge, the patient returned with fever and graft failure and was started on an empiric regimen of aztreonam and vancomycin. A blood culture grew an alpha-hemolytic, gram-positive coccus forming pairs and chains, originally thought to be a viridans Streptococcus and a skin contaminant. The isolation of the organism from multiple blood cultures, and the presence of vancomycin resistance prompted identification and additional susceptibility testing. The RapID(™) Str panel, which has W. confusa in its database, provided multiple incorrect identifications. The MicroScan WalkAway 96 SI, using PC-20 or -29 panels, also did not identify this bacterium, because it is not in their database. The organism was identified as W. confusa by 16S rDNA sequencing. Antibiotic susceptibility determination by Etest revealed vancomycin resistance and daptomycin susceptibility. Therapy was changed to daptomycin, and the infection resolved. Additionally, W. confusa sepsis, with multiple positive blood cultures, developed in a patient in the burn unit at our medical center. The patient's blood cultures remained positive until vancomycin was discontinued and daptomycin therapy initiated. Infections with vancomycin-resistant, gram-positive cocci are emerging among immuno compromised hosts. Under appropriate circumstances, clinicians need to request that the laboratory perform susceptibility testing and accurate identification, by nucleic acid sequencing if necessary. Sequencing of 16S rDNA is an important tool in the accurate identification of unusual pathogens.

Rapid identification of non-sporing anaerobes using nuclear magnetic resonance spectroscopy and an identification strategy

PURPOSE

The non-sporing anaerobes cause a wide spectrum of infections. They are difficult to culture and their identification is tedious and time-consuming. Rapid identification of anaerobes is highly desirable. Towards this end, the potential of nuclear magnetic resonance (NMR) spectroscopy for providing a fingerprint within the proton spectrum of six genera belonging to anaerobes reflecting their characteristic metabolites has been investigated.

METHODS

NMR analysis was carried out using Mercury plus Varian 300 MHz (7.05 T) NMR spectrophotometer on six different anaerobes. These included Bacteroides fragilis, Prevotella melaninogenica, Prevotella denticola, Fusobacterium necrophorum, Peptococcus niger and Peptostreptococcus spp. After the NMR analysis (256/512 scans), the different peaks were noted. The eight pus specimens, which yielded pure culture of anaerobe, also were analysed similarly.

RESULTS

The major resonances of multiplex of amino acids/lipid at 0.9 ppm along with lactate/lipid at 1.3 ppm, acetate at 1.92 ppm and multiplex of lysine at 3.0 ppm remained constant to label the organism as an anaerobe. There was a difference found in the MR spectra of different genera and species. A simple algorithm was developed for the identification of the six different anaerobes studied. The MR spectra of the pure culture of the organism matched the MR spectra of pus from which the organism was isolated.

CONCLUSIONS

MR-based identification was of value in the identification of anaerobes. However, a larger database of the peaks produced by anaerobes needs to be created for identification of all genera and species. It could then have the potential of diagnosing an anaerobic infection in vivo and thus expedite management of deep-seated abscesses.

Cytomorphologic findings of hemangiopericytoma of the meninges: a case report

Hemangiopericytomas (HPCs) are tumors, constituting 2.5%, of soft tissue neoplasms. Meningeal hemangiopericytomas are rare non meningothelial mesenchymal tumors of the dura. They were classified as angioblastic meningiomas because of their similarity to meningiomas. However, these tumors are now regarded as distinct entities, akin to hemangiopericytoma elsewhere in the body. Few reports have addressed the fine needle aspiration (FNA) cytology of HPC. We present the cytological findings of one such rare case ofprimary meningeal hemangiopericytoma which metastasized to the lymph node. A 47 years male presented with cervical lymphadenopathy of 2 months duration. He was operated twice in the last 4 years and diagnosed atypical meningioma both times. The patient now also had spinal metastasis producing nerve root compression. Aspiration cytology of the node revealed cellular aspirate demonstrating round to oval cells with ample cytoplasm, round nuclei and inconspicuous nuclei. They showed a characteristic ferning out of blood vessels. Occasional mitosis was present. A diagnosis of malignant tumor of vascular origin was offered. Lymph node biopsy showed a characteristic histological picture of hemangiopericytoma described in other soft tissues. The cytology of this tumor is characteristic, but the rarity of the lesion, especially in metastatic sites makes diagnosis difficult unless a high index of suspicion is present. The recognition of the distinct cytological findings makes this possible. The case documents the role of FNA cytology in confirming HPC.

Parathyroid Neoplasms: The Army Hospital (Research & Referral) Experience

BACKGROUND

Neoplasms of the parathyroid are common but parathyroid carcinoma is exceptionally rare. In contrast to most other malignant endocrine tumours that are usually less hormonally active, malignant parathyroid tumours are hyper functional. Malignant parathyroid tumours pose a diagnostic dilemma for the pathologist.

OBJECTIVE

To study the clinicopathological profile of a case series of parathyroid neoplasms and determine features which facilitate a malignant diagnosis.

METHODS

A retrospective analysis of seven cases of surgically treated parathyroid tumours over a three-year period at a single centre was done. Clinical, haematological, biochemical, and radiological data was accrued from medical records. The histopathology slides were reviewed along with the clinicopathological profile in an attempt to delineate markers of malignancy.

RESULTS

Patients ranged from 30 to 58 years of age. Males and females were approximately equal. Weakness and bone pain were the commonest presenting symptoms. Over 50% had significant hypercalcaemia and all had elevated serum parathormone. Clinically apparent mass was seen in only one. All tumours were successfully localised using CT scan and MRI. Thick fibrous capsule and broad septal fibrosis was seen in both the carcinomas; these were thin in the adenomas. Mitotic counts of 1-3 per high power field (HPF), capsular invasion and nodal metastasis were noted in the malignant tumours.

CONCLUSION

Elevated serum calcium and parathormone values point to a parathyroid neoplasm. Current imaging modalities are successful in localising the tumour preoperatively. Markedly elevated serum calcium, broad fibrous bands, mitotic counts and capsular invasion are indicators of malignancy.

On-Chip Millionfold Sample Stacking Using Transient Isotachophoresis

We present a simple and robust isotachophoresis (ITP) method that can be integrated with microchip-based capillary electrophoresis (CE) devices to achieve millionfold sample stacking. We performed an experimental parametric study to show the effects of initial sample ion concentration, leading ion concentration, and trailing ion concentration on ITP stacking. We also discuss the usefulness and limitations of a simple one-dimensional nondispersive model and a scaling analysis for dispersion rate. We found that a single-column ITP configuration together with electroosmotic flow suppression and high leading ion concentration provide high-performance ITP and can be integrated readily with CE separation. We demonstrated detection of trace of 100 fM Alexa Fluor 488 (signal-to-noise ratio of 11) with a concentration increase of a factor of 2 x 10(6). Application of our ITP/CE protocol to the stacking and separation of negatively charged fluorescent tracers (Alexa Fluor 488 and bodipy) resulted in a concentration increase of 6.4 x 10(4) and a signal increase of 4.5 x 10(5). The ITP/CE protocol can be performed with a standard microchannel cross design or simple flow control. The method can be implemented with available off-the-shelf chip systems using off-the-shelf voltage control systems and buffer chemistries.