Genome-wide mining of diversity and evolutionary signatures revealed selective hotspots in Indian Sahiwal cattle

The Sahiwal cattle breed is the best indigenous dairy cattle breed, and it plays a pivotal role in the Indian dairy industry. This is due to its exceptional milk-producing potential, adaptability to local tropical conditions, and its resilience to ticks and diseases. The study aimed to identify selective sweeps and estimate intrapopulation genetic diversity parameters in Sahiwal cattle using ddRAD sequencing-based genotyping data from 82 individuals. After applying filtering criteria, 78,193 high-quality SNPs remained for further analysis. The population exhibited an average minor allele frequency of 0.221 ± 0.119. Genetic diversity metrics, including observed (0.597 ± 0.196) and expected heterozygosity (0.433 ± 0.096), nucleotide diversity (0.327 ± 0.114), the proportion of polymorphic SNPs (0.726), and allelic richness (1.323 ± 0.134), indicated ample genomic diversity within the breed. Furthermore, an effective population size of 74 was observed in the most recent generation. The overall mean linkage disequilibrium (r2) for pairwise SNPs was 0.269 ± 0.057. Moreover, a greater proportion of short Runs of Homozygosity (ROH) segments were observed suggesting that there may be low levels of recent inbreeding in this population. The genomic inbreeding coefficients, computed using different inbreeding estimates (FHOM, FUNI, FROH, and FGROM), ranged from -0.0289 to 0.0725. Subsequently, we found 146 regions undergoing selective sweeps using five distinct statistical tests: Tajima's D, CLR, |iHS|, |iHH12|, and ROH. These regions, located in non-overlapping 500 kb windows, were mapped and revealed various protein-coding genes associated with enhanced immune systems and disease resistance (IFNL3, IRF8, BLK), as well as production traits (NRXN1, PLCE1, GHR). Notably, we identified interleukin 2 (IL2) on Chr17: 35217075-35223276 as a gene linked to tick resistance and uncovered a cluster of genes (HSPA8, UBASH3B, ADAMTS18, CRTAM) associated with heat stress. These findings indicate the evolutionary impact of natural and artificial selection on the environmental adaptation of the Sahiwal cattle population.

Stable isotope labeling as a promising tool for rapid drug susceptibility testing in Neisseria gonorrhoeae

The world is heading towards an era of intractable and impending untreatable N. gonorrhoeae, thereby underlining the significance of rapid and accurate prediction of drug resistance as an indispensable need of the hour. In the present study, we optimized and evaluated a stable isotope labeling-based approach using the MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry) for rapid and reliable detection of ciprofloxacin and azithromycin resistance in N. gonorrhoeae. All the isolates were cultured under three varied condition setups viz. medium supplemented with normal lysine, heavy lysine (isotope), and heavy lysine along with the antibiotics (ciprofloxacin/azithromycin), respectively. After incubation, spectra were acquired using the MALDI-TOF MS which were further screened for unique patterns (media-specific spectra) to differentiate drug-susceptible and resistant isolates. The results of the stable isotope labeling assay were comparable to the results of phenotypic methods used for susceptibility testing.

P019 A 5-year study on prevalence and molecular determinants of fluconazole -resistance in C. parapsilosis spp. complex

Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM

 

Objectives

Candida parapsilosis species complex is among the leading agents of invasive candidiasis, notably in neonates and transplant recipients. It exhibits intrinsically reduced susceptibility to echinocandins with increasing reports of acquired resistance to fluconazole from many centers. We evaluated antifungal susceptibility and molecular mechanisms of azole resistance in C. parapsilosis species complex, isolated in the last 5 years.

Methods

The isolates of C. parapsilosis species complex causing infections over a 5-year period (2017-2021) were included in the present study. Species identification of the isolates was performed using MALDI-TOF MS and sequencing of Internal Transcribed Spacer, ITS1. Antifungal susceptibility testing was performed by CLSI broth microdilution in accordance with standard operating procedure described in M27-A3 document. For amphotericin B, itraconazole, and posaconazole, the interpretation of the susceptibility data was done using epidemiological cut-off values provided in CLSI M59 document. The entire coding sequence of ERG11 gene in fluconazole-resistant isolates was PCR-amplified in four overlapping fragments. The sequencing of each fragment was performed by Sanger's bidirectional sequencing method using BigDye termination ready-reaction kit, 3.1. The sequences were assembled and proofread using Seqman software (Laser DNA, Applied Biosystems). The nucleotide sequences were translated into ERG11 protein using nucleotide translation tool, https://web.expasy.org/translate. Multiple sequence alignment with C. parapsilosis reference sequence was performed using BioEdit Sequence Alignment editor.

Results

A total of 580 C. parapsilosis complex clinical isolates were evaluated for antifungal susceptibility. C. parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis accounted for 457 (78.8%), 86 (14.8%), and 37 (6.3%), respectively. The isolation distribution revealed an increasing temporal trend over the years. A total of 40 (6.9%) isolates of the species complex exhibited reduced susceptibility to fluconazole, of which 23 were resistant (MIC ≥8 μg/ml) while 17 isolates exhibited susceptible dose-dependent phenotype (MIC, 4 μg/ml). Only two of the fluconazole-resistant isolates were cross-resistant to voriconazole. The resistant isolates were predominantly from adult patients [Median age, IQR; 47 (16-70) years.] The crude mortality rate in resistant cases was 56.5% (13/23). Interestingly, all the fluconazole-resistant isolates were C. parapsilosis sensu stricto, while C. orthopsilosis and C. metapsilosis isolates were susceptible. The fluconazole-resistance rate in the species complex and within the C. parapsilosis sensu stricto was 3.9% (23/599), 4.9% (23/466), respectively. For amphotericin B, the proportion of non-wildtype isolates was 17% (70/411), 25% (9/36), and 0% in C. parapsilosis sensu stricto, C. metapsilosis, and C. orthopsilosis, respectively. For itraconazole, the non-wildtype percentage was 1.7% (7/407), 1.35% (1/74), and 0% in C. parapsilosis sensu stricto, C. orthopsilosis, and C. metapsilosis, respectively. For posaconazole, the non-wildtype percentage was 3.8% (16/413), 2.7% (2/74), and 0% in parapsilosis sensu stricto, C. orthopsilosis and C. metapsilosis, respectively. Sequencing analysis of ERG11 gene revealed two homozygous mutations, Y132F mutation, and R398I in fluconazole-resistant isolates.

Conclusions

C. parapsilosis species complex infections are on the rise. The increasing azole resistance in C. parapsilosis with higher mortality is a great concern in clinical settings.

P017 Echinocandin resistance mechanism in Candida tropicalis and Candida glabrata

Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM

 

Objective

Candida tropicalis and Candida glabrata account for 41.6% and 7.08% of total Candidaemia cases in India. Echinocandins are the first-line treatment option for these infections. Resistance to Echinocandins is rare with Candida sp. However, in recent years, has been noted across many centers. We determined the mechanism of echinocandin resistance in C. tropicalis and C. glabrata.

Methods

C. tropicalis and C. glabrata isolated from Candidaemia patients over a period of 3 years (August 2016-July 2019), identified by MALDI-TOF-MS were used in this study. Antifungal susceptibility testing was done following CLSI broth microdilution reference method (M 27A). FKS1 gene was sequenced using species-specific primers for the presence of any mutation. To determine any changes in the cell wall chitin and glucan contents, expression fold changes of chitin synthase (CHS1, CHS2, and CHS3), and glucan synthase genes upon caspofungin treatment were determined using real-time qPCR. These findings were correlated with cell wall chitin and glucan content determined by flowcytometry.

Results

A total of 3558 Candida species were isolated from patients of all age groups at our hospital. C. tropicalis was the predominant agent (34%), while the prevalence of C. glabrata was 6%. A total of 17 (8.5%) C. glabrata and 3 (0.25%) C. tropicalis exhibited reduced susceptibility to echinocandins. All these isolates carried a wild-type FKS genes.

In C. tropicalis, inducible expression of Chs1, Chs2 and Chs3 genes were comparable among susceptible and resistant isolates1.8 (0.4-2.8) vs. 2.5 (0.9-6.6), P = .247); [0.7 (0.3-1.8) vs. 0.7 (0.2-1.6), P = .793]; [1.3 (0.14-4.8) vs. 1.1(0.48-1.7), P = .522], respectively. In concordance with gene expression, there was no significant difference in cell wall chitin contents among resistant and susceptible [14.37 (6.5-24.8) vs 16.28 (6.0-24.7), P = .114] C. tropicalis isolates. In contrast in resistant isolates of C. glabrata, caspofungin treatment resulted in significantly higher induction of chitin synthase genes compared to susceptible isolates; Chs1 [2.34 (0.24-9.71) vs. 1.56 (0.55-4.5) (P = .007)], CHS2 [1.59 (0.33-8.0) vs. (2.3 (0.69-6.15), P = .0006], and CHS3 gene [3.8 (0.13-12.73) vs. 1.9 (0.56-7.16), P <.0001]. Flowcytometric data in terms of chitin content, correlated well with expression changes as staining index was significantly higher in resistant compared to susceptible isolates [320 (198-535) vs. 164 (5.34-254.10) P = .0001]. Glucan synthase expression was comparable in susceptible and resistant isolates of C. tropicalis [3.47 (1.57-7.63) vs. 4.41 (0.41-17.51), (P = .518)]. However, glucan synthase gene expression was found significantly increased in resistant C. glabrata isolates compared to susceptible isolates; 3.10 (1.02-16.45) vs. 1.61 (0.13-7.67), P <.001.

Conclusion

We evaluated the role of cell wall components in echinocandin resistance in isolates with reduced susceptibility to echinocandins but lacking an FKS1 mutation. While chitin was induced at higher levels in C. glabrata, a similar finding was not observed in C. tropicalis. This warrants further studies to elucidate the role of fungal cell wall polymers in resistance.

P373 Does biofilm forming capacity of Candida tropicalis vary with echinocandin susceptibility?

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM

 

Objectives

Candida tropicalis is a common cause of nosocomial candidemia and candiduria. The role of biofilm formation in virulence and antimicrobial resistance in C. tropicalis remains under-investigated. We aimed to evaluate the biofilm-forming capacity of C. tropicalis isolates exhibiting resistance, borderline resistance, and sensitivity to echinocandins.

Methods

The echinocandin resistant, borderline resistant, and susceptible isolates of C. tropicalis were collected based on their minimum inhibitory concentration (MIC) values according to Clinical and Laboratory Standard Institute (CLSI) broth microdilution guidelines. The isolates were subjected to FKS1 gene sequencing. To estimate biofilm production, echinocandin resistant (n = 2), borderline resistant (n = 5), and susceptible isolates (n = 3) were seeded at the cell concentration of 1 × 10⁶ cells/mL in RPMI-1640 with 0.165 M MOPS in polystyrene 96-well microtiter plates and incubated for 24 and 48 h at 37°C. The biofilm was quantified by crystal violet/safranin-based spectrophotometric method and XTT (2,3-Bis-(2-Methoxy-4-Nitro-5-Sulfophenyl)-2H-Tetrazolium-5-Carboxanilide) reduction assay. Statistical analysis was performed using one-way ANOVA with Bonferroni's post-hoc test for multiple comparisons among the groups.

Results

FKS1 sequencing analysis revealed S654P mutation in HS1 in both resistant isolates while isolates exhibiting borderline MIC to echinocandins carried wild-type FKS1 gene. Biofilm formation in borderline echinocandin-resistant C. tropicalis isolates was significantly (P <.005) higher compared with resistant and susceptible isolates. However, no significant difference in biofilm formation was noted among resistant and susceptible isolates.

Conclusion

This study suggests differential biofilm-formation capacity among C. tropicalis isolates with reduced susceptibility to echinocandins. However, this warrants further studies before any definitive inference can be made.

P115 Reversed-phase high-performance liquid chromatography as rapid and simple method for quantifications of terbinafine drug in human serum from dermatophytosis cases

Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM

 

Objectives

The alarming situation of treatment failure cases in dermatophytosis and resistance to the first-line drug (terbinafine) is a worrisome condition for the management of tinea cases. However, studies also reported non-responders to terbinafine treatment even when the isolates are susceptible to this drug in vitro. Thus, evaluating the pharmacokinetic profile of terbinafine might help better manage dermatophytosis. This study was conducted to standardize and validate a rapid and simple reversed-phase high-performance liquid chromatography (HPLC)-based protocol for terbinafine in serum/plasma of dermatophytosis cases.

Methods

HPLC analysis was standardized for terbinafine drug on an Agilent 1290 infinity system (Agilent Technologies InC., USA). Chromatographic parameters including mobile phase [acetonitrile (A), methanol (M), and water (W)], flow rate (0.7-1.5 ml/min), injection volume (20 μl), and various wavelengths ranging from 220 to 265 nm under isocratic conditions were assessed and optimized. The mobile phase consisted of a filtered and degassed mix of A: W and M: W with various ratios of 85:15, 60:40, 50:50, and M-100%, respectively. Quality control samples were prepared in drug-free serum by spiking with the terbinafine at 0.0312-100 μg/mL concentrations. An equal volume of serum and acetonitrile (A) were mixed. The mixture was vigorously vortexed for 30 s, followed by high-speed centrifugation at 13 000 rpm at 40^°C for 10 min. The supernatant was transferred into the chromatographic vials and placed in the autosampler of HPLC for injection. The standardized method was tested in 6 dermatophytosis patients’ serum/plasma samples collected at 3-time points (first, second, and third week of start of antifungal).

Results

Linearity of calibration standard for terbinafine was optimized at 250C at a flow rate of 1.0 ml/min, injection volume 20 μl, 8 minutes run time with the standardized wavelength at 245 nm under isocratic conditions. The best suitable graph was determined by plotting the area under the curve (AUC) and peak height separately against the drug concentrations measured by reversed-phase- HPLC for terbinafine drugs (Fig. 1a and b). The standardized mobile phase consisted of filtered and degassed Methanol (100, v/v). The chromatographic separation was achieved on an Agilent C18 column, and 4.3 ± 1 time represents the peak for terbinafine drug. Based on the standardized protocol, six tinea cases were included for validation, and the therapeutic range achieved for terbinafine in clinical samples was 0.6 to 1.13 μg/ml.

Conclusions

The standardization of HPLC method was successfully applied to quantify terbinafine in spiked samples with terbinafine drug and showed no observable interferences at the standardized parameter. Further evaluation with larger number of samples is warranted.

Evaluation of environmental Mucorales contamination in and around the residence of COVID-19-associated mucormycosis patients

Introduction

Recently, India witnessed an unprecedented surge of coronavirus disease 2019 (COVID-19)-associated mucormycosis (CAM) cases. In addition to patient management issues, environmental Mucorales contamination possibly contributed to the outbreak. A recent study evaluated environment contamination by Mucorales in the hospital setting. However, a considerable number of CAM patients were never admitted to a hospital before the development of the disease. The present study, therefore, planned to evaluate Mucorales contamination of patients’ residences.

Methods

The residential environment of 25 patients with CAM living in north India was surveyed. Air samples were collected from indoor and immediate outdoor vicinity of the patients’ residence and cultured on Dichloran Rose–Bengal Chloramphenicol (DRBC) agar with benomyl for selective isolation of Mucorales. Surface swab samples were also collected from the air coolers fitted in those residences and cultured on DRBC agar. The isolates were identified by phenotypic and genotypic methods. Amplified fragment length polymorphism (AFLP) was employed to evaluate the genetic relatedness of the environmental and patients’ clinical isolates.

Results

The median spore count (mean ± SD, cfu/m3) of Mucorales in the air of patients’ bedrooms was significantly higher than in the air in other rooms in those residences (3.55 versus 1.5, p = 0.003) or the air collected directly from the front of the air cooler (p &lt; 0.0001). The Mucorales spore count in the environment did not correlate with either ventilation of the room or hygiene level of the patients’ residences. Rhizopus arrhizus was isolated from the environment of all patients’ residences (n = 25); other Mucorales species isolated were Cunninghamella bertholletiae (n = 14), Rhizopus microsporus (n = 6), Rhizopus delemar (n = 6), Syncephalastrum racemosum (n = 1), Lichtheimia corymbifera (n = 1), and Mucor racemosus (n = 1). Genetic relatedness was observed between 11 environmental isolates from the patients’ bedrooms and respective clinical isolates from patients.

Discussion

The study supported the view that the patients might have acquired Mucorales from the home environment during the post-COVID-19 convalescence period. Universal masking at home during patients’ convalescence period and environmental decontamination could minimize exposure in those susceptible patients.

Remote ischaemic conditioning: defining critical criteria for success-report from the 11th Hatter Cardiovascular Workshop

The Hatter Cardiovascular Institute biennial workshop, originally scheduled for April 2020 but postponed for 2 years due to the Covid pandemic, was organised to debate and discuss the future of Remote Ischaemic Conditioning (RIC). This evolved from the large multicentre CONDI-2-ERIC-PPCI outcome study which demonstrated no additional benefit when using RIC in the setting of ST-elevation myocardial infarction (STEMI). The workshop discussed how conditioning has led to a significant and fundamental understanding of the mechanisms preventing cell death following ischaemia and reperfusion, and the key target cyto-protective pathways recruited by protective interventions, such as RIC. However, the obvious need to translate this protection to the clinical setting has not materialised largely due to the disconnect between preclinical and clinical studies. Discussion points included how to adapt preclinical animal studies to mirror the patient presenting with an acute myocardial infarction, as well as how to refine patient selection in clinical studies to account for co-morbidities and ongoing therapy. These latter scenarios can modify cytoprotective signalling and need to be taken into account to allow for a more robust outcome when powered appropriately. The workshop also discussed the potential for RIC in other disease settings including ischaemic stroke, cardio-oncology and COVID-19. The workshop, therefore, put forward specific classifications which could help identify so-called responders vs. non-responders in both the preclinical and clinical settings.

Mechanisms of azole antifungal resistance in clinical isolates of Candida tropicalis

This study was designed to understand the molecular mechanisms of azole resistance in Candida tropicalis using genetic and bioinformatics approaches. Thirty-two azole-resistant and 10 azole-susceptible (S) clinical isolates of C. tropicalis were subjected to mutation analysis of the azole target genes including ERG11. Inducible expression analysis of 17 other genes potentially associated with azole resistance was also evaluated. Homology modeling and molecular docking analysis were performed to study the effect of amino acid alterations in mediating azole resistance. Of the 32 resistant isolates, 12 (37.5%) showed A395T and C461T mutations in the ERG11 gene. The mean overexpression of CDR1, CDR3, TAC1, ERG1, ERG2, ERG3, ERG11, UPC2, and MKC1 in resistant isolates without mutation (R-WTM) was significantly higher (p<0.05) than those with mutation (R-WM) and the sensitive isolates (3.2–11 vs. 0.2–2.5 and 0.3–2.2 folds, respectively). Although the R-WTM and R-WM had higher (p<0.05) CDR2 and MRR1 expression compared to S isolates, noticeable variation was not seen among the other genes. Protein homology modelling and molecular docking revealed that the mutations in the ERG11 gene were responsible for structural alteration and low binding efficiency between ERG11p and ligands. Isolates with ERG11 mutations also presented A220C in ERG1 and together T503C, G751A mutations in UPC2. Nonsynonymous mutations in the ERG11 gene and coordinated overexpression of various genes including different transporters, ergosterol biosynthesis pathway, transcription factors, and stress-responsive genes are associated with azole resistance in clinical isolates of C. tropicalis.

Clinical and mycological profile of fungal keratitis from North and North-East India

Purpose:

To study the clinical presentation, mycological profile, and risk factors of fungal keratitis (FK) cases presenting at two tertiary-care centers, one each at North (Chandigarh) and Northeast (Assam) India, and to compare the spectrum of fungi recovered from the clinical and environmental samples at both locations.

Methods:

All patients with suspected FK were enrolled from both the centers between January 2018 and December 2019. Corneal samples were collected and processed as per standard laboratory protocols. Demographic details and clinical and mycological profiles were noted in all patients. Environmental sampling from the soil, air, and the vegetative matter was performed from both locations and neighboring districts.

Results:

Of the 475 suspected cases, 337 (71%) were diagnosed as FK (median age: 50 years; 77.2% males). The presence of diabetes, hypertension, blurred vision, and corneal discoloration was significantly higher in patients with FK compared to those without FK. Aspergillus sp. (52.1%) and Fusarium sp. (47.61%) were the predominant etiological agents isolated from cases in North and Northeast India, respectively. FK due to melanized fungi was associated with diabetes, trauma with animal tail, and corneal discoloration. A similar spectrum of fungi was seen in environmental and clinical samples in both the regions.

Conclusion:

The difference in etiological agents of FK and environmental fungal isolates in North and Northeast India highlights the need to identify the ecological niche of potential fungal pathogens. Prospective, multicenter studies, systematic environmental sampling, and the evaluation of the differences in causative agents and clinical presentation of FK from different parts of the country can substantially improve our understanding of its region-specific clinico-epidemiological profile.

Fatal cerebral phaeohyphomycosis caused by Cladophialophora bantiana mimicking tuberculous brain abscess

INTRODUCTION

Cladophialophora bantiana, a neurotropic phaeoid fungus, is the primary agent of cerebral phaeohyphomycosis. The disease more commonly affects immunocompetent males and is associated with a high mortality rate.

CASE REPORT

We report a case of brain abscess caused by Cladophialophora bantiana in a 50-year-old immunocompetent male who presented with headache for two months, weakness of both lower limbs for 15 days, and altered sensorium and aphasia for one day. Contrast-enhanced MRI of the brain showed multiple coalescent abscesses in the right basal ganglia and corpus callosum. Based on clinical and radiological suspicion of tuberculoma, treatment with antitubercular drugs was initiated. A month after discharge, the patient was re-admitted with history of loss of consciousness, altered sensorium, respiratory distress and aphasia. Brain CECT revealed multiple ring-enhancing lesions in the right basal ganglia with mass effect and a leftward midline shift. The patient underwent craniotomy and evacuation of abscess. Direct microscopy of pus aspirated from the lesions showed pigmented septate fungal hyphae, which was identified as C. bantiana in fungal culture. The patient was administered intravenous liposomal amphotericin B and voriconazole. However, he died due to multiple organ failure on day 19 after surgery.

CONCLUSIONS

Fungal etiology should be considered in the differential diagnosis of intracranial space occupying lesions, regardless of the host immune status. An early diagnosis, together with aggressive medical and neurosurgical interventions are imperative for improving the survival in such patients.

Expression and Purification along with Evaluation of Serological Response and Diagnostic Potential of Recombinant Sap2 Protein from C. parapsilosis for Use in Systemic Candidiasis

Systemic candidiasis is the fourth most common bloodstream infection in ICU patients worldwide. Although C. albicans is a predominant species causing systemic candidiasis, infections caused by non-albicans Candida (NAC) species are increasingly becoming more prevalent globally along with the emergence of drug resistance. The diagnosis of systemic candidiasis is difficult due to the absence of significant clinical symptoms in patients. We investigated the diagnostic potential of recombinant secreted aspartyl proteinase 2 (rSap2) from C. parapsilosis for the detection of Candida infection. The rSap2 protein was successfully cloned, expressed and purified using Ni-NTA chromatography under denaturing conditions using an E. coli-based prokaryotic expression system, and refolded using a multi-step dialysis procedure. Structural analysis by CD and FTIR spectroscopy revealed the refolded protein to be in its near native conformation. Immunogenicity analysis demonstrated the rSap2 protein to be highly immunogenic as evident from significantly high titers of Sap2-specific antibodies in antigen immunized Balb/c mice, compared to sham-immunized controls. The diagnostic potential of rSap2 protein was evaluated using immunoblotting and ELISA assays using proven candidiasis patient serum and controls. Immunoblotting results indicate that reactivity to rSap2 was specific to candidiasis patient sera with no cross reactivity observed in healthy controls. Increased levels of anti-Sap2-specific Ig, IgG and IgM antibodies were observed in candidiasis patients compared to controls and was similar in sensitivity obtained when whole Candida was used as coating antigen. In summary, the rSap2 protein from C. parapsilosis has the potential to be used in the diagnosis of systemic candidiasis, providing a rapid, convenient, accurate and cost-effective strategy.

Association of ischemic electrocardiographic changes in high-altitude areas with coronary angiography

Background

Soldiers native to lowlands, while sojourning at high altitude (HA), are referred to tertiary care centers with electrocardiographic (ECG) abnormalities. Exposure to HA may precipitate myocardial ischemia in subjects with underlying coronary artery disease (CAD). Conversely, it may produce physiological ECG changes mimicking those of CAD, causing a diagnostic dilemma. This study sought to correlate the presence of CAD on coronary angiography (CAG) with a putative diagnosis of CAD based on clinical findings and ECG.

Methods

A prospective study was conducted on patient's from HA areas, referred for evaluation for CAD to a single center at near-sea-level. Thirty-five minimally symptomatic/asymptomatic soldiers with ECG changes suggestive of CAD, underwent CAG. Correlation was sought between ECG and CAG evidence of CAD.

Results

The association of CAD on CAG with clinical and ECG diagnosis of CAD was not significant, 4 of the 35 soldiers (11.4%) showing CAG evidence of CAD (chi square 3.849, p = 0.697). The association between symptoms and coronary artery lesions was, also, not significant, only four of twenty-three (17.4%) minimally symptomatic subjects having CAD on CAG.

Conclusion

Insignificant numbers of previously healthy persons, who present with minimal symptoms and ECG changes suggestive of CAD while sojourning at HA, have coronary artery involvement on CAG. Those with incidental ECG changes, without symptomatology, do not have CAD on CAG.

Association between overcrowded households, multigenerational households, and COVID-19: a cohort study

OBJECTIVES

The role of overcrowded and multigenerational households as a risk factor for COVID-19 remains unmeasured. The objective of this study is to examine and quantify the association between overcrowded and multigenerational households and COVID-19 in New York City (NYC).

STUDY DESIGN

Cohort study.

METHODS

We conducted a Bayesian ecological time series analysis at the ZIP Code Tabulation Area (ZCTA) level in NYC to assess whether ZCTAs with higher proportions of overcrowded (defined as the proportion of the estimated number of housing units with more than one occupant per room) and multigenerational households (defined as the estimated percentage of residences occupied by a grandparent and a grandchild less than 18 years of age) were independently associated with higher suspected COVID-19 case rates (from NYC Department of Health Syndromic Surveillance data for March 1 to 30, 2020). Our main measure was an adjusted incidence rate ratio (IRR) of suspected COVID-19 cases per 10,000 population. Our final model controlled for ZCTA-level sociodemographic factors (median income, poverty status, White race, essential workers), the prevalence of clinical conditions related to COVID-19 severity (obesity, hypertension, coronary heart disease, diabetes, asthma, smoking status, and chronic obstructive pulmonary disease), and spatial clustering.

RESULTS

39,923 suspected COVID-19 cases were presented to emergency departments across 173 ZCTAs in NYC. Adjusted COVID-19 case rates increased by 67% (IRR 1.67, 95% CI = 1.12, 2.52) in ZCTAs in quartile four (versus one) for percent overcrowdedness and increased by 77% (IRR 1.77, 95% CI = 1.11, 2.79) in quartile four (versus one) for percent living in multigenerational housing. Interaction between both exposures was not significant (β_interaction = 0.99, 95% CI: 0.99-1.00).

CONCLUSIONS

Overcrowdedness and multigenerational housing are independent risk factors for suspected COVID-19. In the early phase of the surge in COVID cases, social distancing measures that increase house-bound populations may inadvertently but temporarily increase SARS-CoV-2 transmission risk and COVID-19 disease in these populations.

Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry: Protocol standardisation, comparison and database expansion for faster and reliable identification of dermatophytes

BACKGROUND

Accurate and early identification of dermatophytes enables prompt antifungal therapy. However, phenotypic and molecular identification methods are time-consuming. MALDI-TOF MS-based identification is rapid, but an optimum protocol is not available.

OBJECTIVES

To develop and validate an optimum protein extraction protocol for the efficient and accurate identification of dermatophytes by MALDI-TOF MS.

MATERIALS/METHODS

Trichophyton mentagrophytes complex (n = 4), T. rubrum (n = 4) and Microsporum gypseum (n = 4) were used for the optimisation of protein extraction protocols. Thirteen different methods were evaluated. A total of 125 DNA sequence confirmed clinical isolates of dermatophytes were used to create and expand the existing database. The accuracy of the created database was checked by visual inspection of MALDI spectra, MSP dendrogram and composite correlation index matrix analysis. The protocol was validated further using 234 isolates.

RESULT

Among 13 protein extraction methods, six correctly identified dermatophytes but with a low log score (≤1.0). The modified extraction protocol developed provided an elevated log score of 1.6. Significant log score difference was observed between the modified protocol and other existing protocols (T. mentagrophytes complex: 1.6 vs. 0.2-1.0, p < .001; T. rubrum: 1.6 vs. 0.4-1.0, p < .001; M. gypseum:1.6 vs. 0.2-1.0, p < .001). Expansion of the database enabled the identification of all 234 isolates (73.5% with log score ≥2.0 and 26.4% with log scores range: 1.75-1.99). The results were comparable to DNA sequence-based identification.

CONCLUSION

MALDI-TOF MS with an updated database and efficient protein extraction protocol developed in this study can identify dermatophytes accurately and also reduce the time for identifying them.

Molecular identification of pathogenic fungi in formalin-fixed and paraffin-embedded tissues

Introduction. Histopathological examination (HPE) of tissue helps in the diagnosis of invasive fungal infections (IFIs) but cannot identify the fungus to the genus/species levelGap Statement Available protocols for the molecular identification of fungi from formalin-fixed and paraffin-embedded (FFPE) tissues have limitations in terms of extraction and target selection, and standardisation.Aim. Development of sequence-based fungal identification protocol after extraction of DNA from formalin-fixed and paraffin-embedded (FFPE) tissues.Methodology. A total of 63 FFPE tissues from histopathology proven IFI cases were used to standardize the DNA extraction (commercial QIAamp kit-based extraction and conventional phenol-chloroform-isoamyl alcohol [PCI] method) and sequence-based fungal identification protocols. The PCR targeted different ribosomal DNA (rDNA) regions including complete internal transcribed spacer (ITS1-5.8S-ITS2), separate ITS1 and ITS2, 18S and D1/D2 of 28S regions. Semi-nested PCR targeting Mucorales-specific 18S rDNA region was performed in tissues having aseptate hyphae. The optimized ITS1-PCR protocol was evaluated in 119 FFPE tissues containing septate hyphae or yeast, and Mucorales-specific semi-nested PCR in 126 FFPE tissues containing aseptate hyphae.Results. The DNA yield by conventional PCI method was significantly higher (P<0.0001) than commercial kit, though the quality of DNA was similar by both protocols. The test accuracy was best while using ITS1 (61.9 %) as the target compared to 7.9, 29.9 and 22.2 % on targeting ITS1-5.8S-ITS2, ITS2, the D1/D2 region of 28S, respectively. The test accuracies of ITS1-PCR in tissues containing septate hyphae, aseptate hyphae and yeasts were 75.5, 18.7 and 100 %, respectively. The amplification (targeting ITS1 region) improved by increasing the thickness of tissue section (up to 50 µm) used for DNA extraction. ITS1-PCR protocol could amplify fungal DNA in 76 (63.8 %) tissues and Mucorales-specific semi-nested PCR in 86 (68.3 %) tissues.Conclusion. Conventional PCI-based DNA extraction from thick tissue (50 µm) may be used until optimal commercial fungal DNA extraction kit is developed. Subsequent ITS1-PCR for septate fungi and yeast, and semi-nested PCR targeting 18S rDNA for Mucorales are recommended to identify the fungus in FFPE tissues.

Rapid detection of ERG11 polymorphism associated azole resistance in Candida tropicalis

Increasing reports of azole resistance in Candida tropicalis, highlight the development of rapid resistance detection techniques. Nonsynonymous mutations in the lanosterol C14 alpha-demethylase (ERG11) gene is one of the predominant mechanisms of azole resistance in C. tropicalis. We evaluated the tetra primer-amplification refractory mutation system-PCR (T-ARMS-PCR), restriction site mutation (RSM), and high-resolution melt (HRM) analysis methods for rapid resistance detection based on ERG11 polymorphism in C. tropicalis. Twelve azole-resistant and 19 susceptible isolates of C. tropicalis were included. DNA sequencing of the isolates was performed to check the ERG11 polymorphism status among resistant and susceptible isolates. Three approaches T-ARMS-PCR, RSM, and HRM were evaluated and validated for the rapid detection of ERG11 mutation. The fluconazole MICs for the 12 resistant and 19 susceptible isolates were 32–256 mg/L and 0.5–1 mg/L, respectively. The resistant isolates showed A339T and C461T mutations in the ERG11 gene. The T-ARMS-PCR and RSM approaches discriminated all the resistant and susceptible isolates, whereas HRM analysis differentiated all except one susceptible isolate. The sensitivity, specificity, analytical sensitivity, time, and cost of analysis suggests that these three methods can be utilized for the rapid detection of ERG11 mutations in C. tropicalis. Additionally, an excellent concordance with DNA sequencing was noted for all three methods. The rapid, sensitive, and inexpensive T-ARMS-PCR, RSM, and HRM approaches are suitable for the detection of azole resistance based on ERG11 polymorphism in C. tropicalis and can be implemented in clinical setups for batter patient management.

Hydrothermal synthesis of gelatin quantum dots for high-performance biological imaging applications

In the present study, we are reporting a one-pot synthesis of gelatin quantum dots (GeQDs) by the hydrothermal process. The synthesized GeQDs were characterized by fourier transform infrared spectroscopy, nuclear magnetic resonance, ultraviolet-visible and photoluminescence spectroscopic techniques, and also by using high-resolution transmission electron microscopy. The GeQDs showed a high level of photoluminescence quantum yield (PLQY) with significantly higher stability for up to 6 months and presented similar fluorescent intensity as the initial PLQY without any precipitation and aggregation at ambient condition. The cell imaging ability of synthesized GeQDs was examined using cells belonging to diverse clinical backgrounds like bacterial cells including Escherichia coli and Staphylococcus aureus, yeast cells including Candida albicans, C. krusei, C. parapsilosis, and C. tropicalis, mycelial fungi including Aspergillus flavus and A. fumigatus cells, cancer cell lines A549, HEK293 and L929. The results demonstrated that the GeQDs illuminates the cells and can be utilized as potential cell labeling non-toxic biomarkers. In conclusion, it can be said that the gelatin stabilized QDs are a promising candidate for stable and long-term fluorescent imaging of different types of cells.

Phenotypic and molecular characterisation of Sporothrix globosa of diverse origin from India

Sporotrichosis is one of the neglected tropical diseases causing subcutaneous chronic granulomatous lesion by thermally dimorphic fungi belonging to Sporothrix species. Sporothrix brasiliensis, Sporothrix mexicana and Sporothrix globosa are the common pathogenic species. In Asian countries, S. globosa constitutes nearly 99.3% of all Sporothrix species. We studied 63 cases of sporotrichosis of geographically diverse origin from India and Sporothrix isolates were characterised for its growth in different media, temperatures, ability to assimilate sugars and antifungal susceptibility profile. Molecular characterization was performed by sequencing of the calmodulin (CAL), beta tubulin (BT) and translational elongation factor 1-alpha (TEF-1α) and typing by fluorescent amplified fragment length polymorphism (FAFLP). In patients who presented with fixed (49.2%), lymphocutaneous lesions (23.8%), in 26.9% the details were not known, none had systemic dissemination. All the isolates tested were Sporothrix globosa and that could grow up to 35 °C and unable to grow at and beyond 37 °C. The assimilation of sucrose, ribitol and raffinose helps in identifying S. globosa. Sequences of CAL or BT or TEF-1α can differentiate S. globosa from other species in the complex. FAFLP results exhibited low genetic diversity. No correlation was noted between genotypes and clinical presentation, or geographic distribution. Itraconazole, terbinafine and posaconazole showed good in vitro antifungal activity against S. globosa whereas fluconazole and micafungin had no activity. S. globosa of Indian origin is relatively less pathogenic than other pathogenic Sporothrix species as it does not cause systemic dissemination and in the diagnostic laboratory, incubation of the cultures below 37 °C is essential for effective isolation.

Roles of Re-entrant cluster glass state and spin-lattice coupling in magneto-dielectric behavior of giant dielectric double perovskite La1.8Pr0.2CoFeO6

La based Co-Fe combined double perovskite (La1.8Pr0.2CoFeO6) was synthesized and the dielectric (zero-field and in-field), magnetic, x-ray absorption and Raman spectroscopy measurements have been investigated for La1.8Pr0.2CoFeO6 double perovskite. The existence of re-entrant cluster glass state is observed. The magneto-dielectric (MD) is found in two temperature regions (25-80 K and 125-275 K). It has been demonstrated that the observed MD at low and high temperatures are respectively due to the spin freezing and the spin-lattice coupling. Furthermore, the very large dielectric constant and the low loss suggest that La1.8Pr0.2CoFeO6 is very important from the application point of view.

Extraordinary magnetic properties of double perovskite Eu2CoMnO6 wide band gap semiconductor

Some novel magnetic behaviours in double perovskite Eu2CoMnO6 (ECMO) have been reported. The x-ray photoemission spectroscopy study shows the presence of mixed valence states of transition metal ions. The UV-visible absorption spectroscopic study suggests that the ECMO has a direct wide band gap. A second-order magnetic phase transition as a sudden jump in the magnetization curve has been observed around 124.5 K. The large bifurcation between the zero field cooling and field cooling, suggests existence of strong spin frustration in the system. The inverse DC susceptibility confirms the presence of the Griffiths like phase. Sharp steps in magnetization have been observed in the M-H curve at 2 K, which vanishes on increasing temperature. The AC susceptibility study demonstrates the Hopkinson like effect as well as the presence of volume spin-glass-like behaviour. The temperature dependent Raman spectrum shows the presence of spin-phonon coupling.

Probing the Griffiths like phase, unconventional dual glassy states, giant exchange bias effects and its correlation with its electronic structure in Pr2-x Sr x CoMnO6

Crystal, electronic structure, dc and ac magnetization properties of the hole substituted (Sr²⁺) and partially B-site disordered double perovskite Pr_2-x Sr _x CoMnO₆ system have been investigated. The XRD pattern analysis showed a systematic decrease in the lattice parameters owing to the enhanced oxidation states of the Co/Mn ions. The electronic structure study by XPS measurements suggested the presence of mixed valence states of the B-site ions (Co²⁺ /Co³⁺ and Mn³⁺ /Mn⁴⁺) with significant enhancement of the average oxidation states due to hole doping. The mere absence of electronic states near the Fermi level in the valence band (VB) spectra for both pure (x  =  0.0) and Sr doped (x  =  0.5) systems indicated the insulating nature of the samples. Sr substitution is observed to increase the spectral weight near the Fermi level suggesting for an enhanced conductivity of the hole doped system. The dc magnetization data divulged a Griffiths like phase above the long-range ordering temperature. A typical re-entrant spin glass like phase driven by the inherent anti-site disorder (ASD) has been recognized by ac susceptibility study for both the pure and doped systems. Most interestingly, the emergence of a new cluster glass like phase (immediately below the magnetic ordering temperature and above the spin-glass transition temperature) solely driven by the Sr substitution has been unravelled by ac magnetization dynamics study. Observation of these dual glassy states in a single system is scarce and hence placed the present system amongst the rare materials. The isothermal magnetization measurements further probed the exhibition of the giant exchange bias effect originated from the interfacial exchange interactions due to existence of low temperature antiferromagnetic clusters embedded in the glassy matrix.

Anomalous Hall effect in Cu doped Bi2Te3 topological insulator

The angle resolved photo-emission spectroscopy (ARPES) study and magneto-transport properties of Bi2Cu x Te3-x have been investigated. ARPES study indicates the clear existence of surface states in the as-prepared samples. The estimated bandgap from ARPES is found to be ∼5 meV and 16 meV respectively for x = 0.03 and x = 0.15 samples. Presence of larger Cu concentration (x = 0.15) introduces magnetic ordering. Observed non-linearity in the Hall data is due to the existence of anomalous Hall effect which can be attributed to the 2D transport. The observed magneto-transport features might be related to the surface carriers which is confirmed by ARPES study.

Selection and evaluation of appropriate reference genes for RT-qPCR based expression analysis in Candida tropicalis following azole treatment

Candida tropicalis arises as one of the predominant non-Candida albicans Candida (NCAC) species causing invasive candidiasis in Asian countries. A rise in reports of C. tropicalis with a parallel increase in fluconazole resistance has also been observed. The genes and underlying pathways associated with azole antifungal resistance in C. tropicalis is still not properly understood. The RT-qPCR is the most promising approach for expression analysis of target genes to understand the mechanisms of resistance. The reliability and reproducibility of this technique depend on the selection of suitable reference genes for the normalization in expression study. The present study investigated the expression stability levels of ten genes including ACT1, EF1, GAPDH, PGK1, RDN5.8, RDN18, RDN28, SDHA, TUB1, and UBC13 for their suitability in fluconazole treated/untreated C. tropicalis. The stability levels of these genes were examined by the ∆∆CT, ΔCT, Pfaffl methods and five independent software including hkgFinder, geNorm, NormFinder, BestKeeper, and RefFinder software. We report, the EF1 and ACT1 were the most stable reference genes for normalization and can be used for the gene expression analysis in C. tropicalis. To the best of our knowledge, our study is the first to select and validate the reference genes in C. tropicalis for RT-qPCR based expression analysis.

P680The clinical value of CMR in the management of Cardio-Oncology patients - a tertiary centre experience

Background

There is increasing awareness of cardiotoxicity arising from cancer treatments. Early diagnosis and treatment is key, to ensure patients receive optimal oncological management. Cardiovascular magnetic resonance (CMR) offers gold standard measurement of cardiac function, alongside tissue characterisation and myocardial perfusion, thereby potentially providing additive value in the context of cardio-oncology.

Purpose

We sought to understand the clinical value of CMR in cardio-oncology at a tertiary cardio-oncology centre.

Methods

We retrospectively reviewed CMR scans requested in cardio-oncology patients at our institution within a ten-month period. We categorised clinical indications and assessed the impact on clinical management using previously-published criteria.

Results

102 CMR studies were requested in 93 cardio-oncology patients (mean age 56 (range 18 to 82), 49% male) between (March to December 2018). 41% of patients had haematological malignancies, 59% solid tumours.

15% of requests were for risk stratification prior to initiation of cancer therapy, 21% for screening for cardio-toxicity in patients currently receiving cardiotoxic agents (3% anthracyclines, 13% HER2 monoclonal antibodies, 4% fluoropyrimidines), 15% for investigation of patients with cardiac complications during cancer treatment, 35% assessment for late effects post cancer treatment, and 14% for cardiac malignancies/ infiltration.

The most common indications for CMR were monitoring of left ventricular ejection fraction (LVEF) in patients where quantification by echocardiography was non-diagnostic or significantly different between imaging studies (39%) and ischaemia assessment including for patients due to receive fluoropyrimidines (26%). Others were aetiology of LV dysfunction/cardiomyopathy (13%) and tissue characterisation (23%), including assessment for cardiac AL amyloid (11 patients), myocarditis (2), cardiac metastases (1), cardiac masses (6), and cardiac iron loading (1).

CMR findings had clinical impact in 61% of patients and assisted in adjudicating a new diagnosis in 29% of patients. 88% of patients were able to continue anthracycline/anti-HER2 therapies based on CMR findings of stable LVEF (93% of whose echocardiograms had suggested reductions). LVEF had reduced significantly in 12% of patients meaning chemotherapy was held/discontinued. 3 patients were recommended to receive non-fluoropyrimidine chemotherapy based on perfusion CMR (pCMR) findings, with one patient permitted to receive capecitabine following normal pCMR.

Conclusion

CMR provides a comprehensive assessment of myocardial structure and function with utility within the context of cardio-oncology for risk stratification pre-chemotherapy, screening for cardiotoxicity during treatment and investigation of cardiac complications of cancer treatment. The additional information derived from CMR generally provides reassurance enabling administration of optimal cancer therapies.

Investigation of multi-mode spin-phonon coupling and local B-site disorder in Pr2CoFeO6 by Raman spectroscopy and correlation with its electronic structure by XPS and XAS studies

Electronic structure of Pr₂CoFeO₆ (at 300 K) was investigated by x-ray photoemission spectroscopy (XPS) and x-ray absorption spectroscopy techniques. All three cations, i.e. Pr, Co and Fe were found to be trivalent in nature. XPS valance band analysis suggested the system to be insulating in nature. The analysis suggested that Co³⁺ ions exist in low spin state in the system. Moreover, Raman spectroscopy study indicated the random distribution of the B-site ions (Co/Fe) triggered by same charge states. In temperature-dependent Raman study, the relative heights of the two observed phonon modes exhibited anomalous behaviour near magnetic transition temperature T _N ~ 270 K, thus indicating towards interplay between spin and phonon degrees of freedom in the system. Furthermore, clear anomalous softening was observed below T _N which confirmed the existence of strong spin-phonon coupling occurring for at least two phonon modes of the system. The line width analysis of the phonon modes essentially ruled out the role of magnetostriction effect in the observed phonon anomaly. The investigation of the lattice parameter variation across T _N (obtained from the temperature-dependent neutron diffraction measurements) further confirmed the existence of the spin-phonon coupling.

Molecular Typing and Antifungal Susceptibility of Candida viswanathii, India

We report invasive candidiasis caused by Candida viswanathii over 2 time periods during 2013–2015 in a tertiary care hospital in Chandigarh, India. Molecular typing revealed multiple clusters of the isolates. We detected high MICs for fluconazole in the second time period.

Rapid detection of fluconazole resistance in Candida tropicalis by MALDI-TOF MS

With the changing epidemiology and emergence of antifungal resistance among Candida species, rapid antifungal susceptibility testing (AFST) is crucial for optimization of antifungal therapy. This study was conducted to standardize a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI -TOF MS) based AFST method (ms-AFST) for susceptibility of Candida tropicalis isolates. Clinical isolates of C. tropicalis were confirmed for fluconazole resistance by the CLSI (M27-A3) method. The incubation period and drug concentration were optimized to determine the minimal profile change concentration (MPCC) by MALDI-TOF MS. The data were analyzed first by direct visual observation of the spectra followed by composite correlation index (CCI) matrix analysis, virtual gel analysis, and cluster analysis for confirmation. Finally, the correlation between minimum inhibitory concentrations (MICs) and MPCCs was evaluated. A total of 15 fluconazole resistant (MICs ranging from 16 to 128 μg/ml) and 19 fluconazole susceptible C. tropicalis isolates (MIC ≤1 μg/ml) were included in this study. All C. tropicalis isolates had significant spectral changes after 4h incubation with fluconazole. Of 34 isolates, MPCCs and MICs were equivalent for 16 isolates, and the MPCC was one dilution lower than the respective MIC in the remaining 18 isolates. This finding was further supported by visual analysis, CCI matrix analysis, virtual gel and principal component analysis dendrogram analysis. The correlation between MPCC and MIC was significant (P < .05). Therefore, a MALDI-TOF MS based AFST assay may be used as a rapid screening technique for fluconazole resistance in C. tropicalis.

Magnitude of Voriconazole Resistance in Clinical and Environmental Isolates of Aspergillus flavus and Investigation into the Role of Multidrug Efflux Pumps

The magnitude of azole resistance in Aspergillus flavus and its underlying mechanism is obscure. We evaluated the frequency of azole resistance in a collection of clinical (n = 121) and environmental isolates (n = 68) of A. flavus by the broth microdilution method. Six (5%) clinical isolates displayed voriconazole MIC greater than the epidemiological cutoff value. Two of these isolates with non-wild-type MIC were isolated from same patient and were genetically distinct, which was confirmed by amplified fragment length polymorphism analysis. Mutations associated with azole resistance were not present in the lanosterol 14-α demethylase coding genes (cyp51A, cyp51B, and cyp51C). Basal and voriconazole-induced expression of cyp51A homologs and various efflux pump genes was analyzed in three each of non-wild-type and wild-type isolates. All of the efflux pump genes screened showed low basal expression irrespective of the azole susceptibility of the isolate. However, the non-wild-type isolates demonstrated heterogeneous overexpression of many efflux pumps and the target enzyme coding genes in response to induction with voriconazole (1 μg/ml). The most distinctive observation was approximately 8- to 9-fold voriconazole-induced overexpression of an ortholog of the Candida albicans ATP binding cassette (ABC) multidrug efflux transporter, Cdr1, in two non-wild-type isolates compared to those in the reference strain A. flavus ATCC 204304 and other wild-type strains. Although the dominant marker of azole resistance in A. flavus is still elusive, the current study proposes the possible role of multidrug efflux pumps, especially that of Cdr1B overexpression, in contributing azole resistance in A. flavus.

MALDI-TOF MS-Based Identification of Melanized Fungi is Faster and Reliable After the Expansion of In-House Database

PURPOSE

Invasive fungal infections caused by melanized fungi are a growing concern. Rapid and reliable identification plays an important role in optimizing therapy. Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)-based identification has emerged as a faster and more accurate diagnostic technique. However, lack of a protein extraction protocol and limited database restricts the identification of melanized fungi by MALDI-TOF MS. The study is designed to standardize protein extraction protocol, to enrich the existing, and to create an in-house database for the rapid identification of melanized fungi.

EXPERIMENTAL DESIGN

In this study, 59 sequence-confirmed, melanized fungi were used to expand and to create an in-house database using a modified protein extraction protocol. A total of 117 clinical isolates are further used to validate the created database.

RESULT

Using existing Bruker database, only 29(24.8%) out of 117 moulds could be identified. However, all the isolates are identified accurately by supplementing the Bruker database with the created in-house database. MALDI-TOF MS takes significantly lesser time for identification compared to DNA sequencing.

CONCLUSION AND CLINICAL RELEVANCE

An expanded database with modified protein extraction protocol can reduce significant time to identify melanized fungi by MALDI-TOF MS.

Local symmetry breaking in SnO2 nanocrystals with cobalt doping and its effect on optical properties

X-ray photoemission spectroscopy (XPS), X-ray diffraction (XRD) and transmission electron microscopy (TEM) have been used to study the structural and morphological characteristics of cobalt doped tin(iv) oxide (Sn1-xCoxO2; 0 ≤ x ≤ 0.04) nanocrystals synthesized by a chemical co-precipitation technique. Electronic structure analysis using X-ray photoemission spectroscopy (XPS) shows the formation of tin interstitials (Sni) and reduction of oxygen vacancies (VO) in the host lattice on Co doping and that the doped Co exists in mixed valence states of +2 and +3. Using XRD, the preferential position of the Sni and doped Co in the unit cell of the nanocrystals have been estimated. Rietveld refinement of XRD data shows that samples are of single phase and variation of lattice constants follows Vegard's law. XRD and TEM measurements show that the crystallite size of the nanocrystals decrease with increase in Co doping concentration. SAED patterns confirm the monocrystalline nature of the samples. The study of the lattice dynamics using Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy shows the existence of many disorder activated forbidden optical phonon modes, along with the corresponding classical modes, signifying Co induced local symmetry breaking in the nanocrystals. UV-Vis spectroscopy shows that the optical band gap has red shifted with increase in doping concentration. The study of Urbach energy confirms the increase in disorder in the nanocrystals with Co doping. Local symmetry breaking induced UV emission along with violet, blue and green luminescence has been observed from the PL study. The spectral contribution of UV emission decreases and green luminescence increases with increase in doping. Using PL, in conjunction with Raman spectroscopy, the type of oxygen vacancy induced in the nanocrystals on Co doping has been confirmed and the position of the defect levels in the forbidden zone (w.r.t. the optical band gap) has been studied.

Identification of Malassezia species by MALDI-TOF MS after expansion of database

The taxonomy of Malassezia species is evolving with introduction of molecular techniques, and difficulty is faced to identify the species by phenotypic methods. Among 15 known Malassezia species, the present Bruker database could identify only 2 species. The present study was aimed to improve Matrix -assisted laser desorption ionization time-flight mass spectrometry (MALDI-TOF MS) based identification of Malassezia species. A total of 88 isolates (DNA sequencing confirmed) for database preparation and, for the validation of database, 190 isolates confirmed by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) were used. The main spectrum profile dendrogram showed the sufficient discrimination between all the species by MALDI-TOF MS. The updated Malassezia database could identify 94.7% and 5.3% strains to the species and genus level, respectively. MALDI-TOF MS is a significantly reliable technique, and results were comparable with PCR-RFLP with kappa value 0.9. In conclusion, MALDI-TOF MS could be a possible alternative tool to other molecular methods for rapid and accurate identification of Malassezia species.

Evaluation of polypropylene/clay nanocomposite foamability based on their morphological and rheological aspects

To identify the effect of rheological influence on the development of microstructure in polypropylene/clay nanocomposites and thereby the influence of the developed microstructure on the foamability of the nanocomposites, a set of nanocomposites was prepared and batch foamed using supercritical CO2. Polypropylene and nanoclay were selected for preparing nanocomposites. During foaming, the nanocomposites were saturated with CO2 gas for three different time periods and subsequently in-situ heating was done to achieve cell growth. The gas saturation was done at subcritical condition followed by the foaming at critical condition of CO2. Thermal studies of the composites were investigated through differential scanning calorimetry, and clay dispersion morphology was investigated and validated using wide-angle X-ray diffraction, transmission electron microscopy, and parallel plate rheology. The improvement in foam morphology (cell size and cell density) and subsequent reduction in foam density was analyzed. The fingerprint characteristics of nanocomposites have an enormous role on foam structure development. With the increase in clay loading, cell density increased; furthermore, with an increase in saturation time, there was a phenomenal decrease in expansion ratio of neat polypropylene due to CO2-induced crystallization which could be mitigated by the incorporation of nanoclay into the polypropylene matrix. Therefore, nanoclay could be exploited as the inhibitor of CO2-induced crystallization.

Matrix-assisted laser desorption/ionization–time of flight mass spectrometry: protocol standardization and database expansion for rapid identification of clinically important molds

Aim: To standardize the matrix-assisted laser desorption ionization–time of flight mass spectrometry protocols and expansion of existing Bruker Biotyper database for mold identification. Materials & methods: Four different sample preparation methods (protocol A, B, C and D) were evaluated. Results: On analyzing each protein extraction method, reliable identification and best log scores were achieved through protocol D. The same protocol was used to identify 153 clinical isolates. Of these 153, 123 (80.3%) were accurately identified by using existing database and remaining 30 (19.7%) were not identified due to unavailability in database. On inclusion of missing main spectrum profile in existing database, all 153 isolates were identified. Conclusion: Matrix-assisted laser desorption ionization–time of flight mass spectrometry can be used for routine identification of clinically important molds.