Polymorphisms in Innate and Adaptive Immune Genes in Subjects with Allergic Bronchopulmonary Aspergillosis Complicating Asthma.

Innate and adaptive immunity play a crucial role in allergic bronchopulmonary aspergillosis (ABPA) pathogenesis. We performed next-generation sequencing using the Illumina TruSight One panel (4,811 human disease-associated genes, at least 20 × coverage) and selected 22 known immune genes (toll-like receptors (TLRs), C-type lectin, interleukin-4 receptor, and others). We included ABPA (n = 18), asthma without ABPA (n = 12), and healthy controls (n = 8). We analyzed 3011 SNPs from 22 genes and identified 145 SNPs (13 genes) that were present only in the disease groups and absent in controls. The SNP frequency overall was significantly higher in ABPA than in asthmatics (89/145 [61.4%] vs. 56/145 [38.6%], p = 0.0001). The SNP frequency in the TLR10 gene was also significantly higher in ABPA than in asthma (p = 0.017). Association analysis further revealed three genes having significant associations. Of these, NOS3 and HLA-DQB1 are associated with antimicrobial activity and adaptive immunity. More extensive studies are required to confirm our findings.

Whole genome sequencing for the prediction of resistant tuberculosis strains from northern India.

PURPOSE: Tuberculosis is an important public health problem among infectious diseases. The problem becomes more concerning with the emergence of MDR-TB and pre-XDR-TB. Whole genome sequencing (WGS) detection of resistance has recently gained popularity as it has advantages over other commercial techniques. METHODS: We performed in-house WGS followed by detailed analysis by an in-house pipeline to identify the resistance markers. This was accompanied by Phenotypic DST, and Sanger sequencing on all the 12 XDR, 06 pre-XDR, and 06 susceptible M. tb isolates. These results were collated with online M. tb WGS pipelines (TB profiler, PhyResSE, Mykrobe predictor) for comparative analysis. RESULTS: Following our in-house analysis, we observed 64 non-synonymous SNPs, fifteen synonymous SNPs, and five INDELs in 25 drug resistance-associated genes/intergenic regions (IGRs) in M. tb isolates. Sensitivity for detecting XDR is 33%, 58%, 83%, and 83%, respectively, using Mykrobe predictor, PhyResSE, TB-profiler, and in-house pipeline for WGS analysis, respectively. TB-profiler detected a rare mutation H70R in the gyrA gene in one pre-XDR isolate. Lineage 2.2.1 East-Asian (Beijing sublineage type) predominated (60%) in WGS data analysis of the XDR isolates. CONCLUSIONS: Our findings suggest that in-house analysis of WGS data and TB-profiler sensitivity was better for the detection of second-line resistance as compared to other automated tested tools. Frequent upgradation of newer mutations associated with resistance needs to be updated, as it potentiates tailored treatment for patients.

Molecular characterization of Orientia tsutsugamushi causing fatal scrub typhus in a young male affected by so-called "mystery fever" in North India.

Scrub typhus is a zoonotic disease caused by Orientia tsutsugamushi. Although the presence of eschar is considered pathognomic, diagnosis of scrub typhus is challenging due to overlapping presentation. The diagnosis is based on the serological and molecular assay. Here, we describe a case of a young male patient who was diagnosed with scrub typhus and developed complications in the course of the disease. We also performed molecular characterization of the strain which revealed a close relatedness to Karp-like Linh.DT strains were previously reported from Vietnam.

Microbial cell-free DNA detection: Minimally invasive diagnosis of infectious diseases.

BACKGROUND: Detection of infectious diseases, especially among immunocompromised and patients on prolonged anti-microbial treatment, remains challenging, limited by conventional techniques with low sensitivity and long-turnaround time. Molecular detection by polymerase chain reaction (PCR) also has limited utility as it requires a targeted approach with prior suspicion of the infecting organism. Advancements in sequencing methodologies, specifically next-generation sequencing (NGS), have presented a promising opportunity to identify pathogens in cases where conventional techniques may be inadequate. However, the direct application of these techniques for diagnosing invasive infections is still limited by the need for invasive sampling, highlighting the pressing need to develop and implement non-invasive or minimally invasive approaches to improve the diagnosis of invasive infections. OBJECTIVES: The objectives of this article are to explore the notable features, clinical utility, and constraints associated with the detection of microbial circulating cell-free DNA (mcfDNA) as a minimally invasive diagnostic tool for infectious diseases. CONTENT: The mcfDNA detection provides an opportunity to identify micro-organisms in the blood of a patient. It is especially beneficial in immunocompromised patients where invasive sampling is not possible or where repeated cultures are negative. This review will discuss the applications and constraints of detecting mcfDNA for diagnosing infections and the various platforms available for its detection.

Association of intermediate Nugent Score and bacterial vaginosis with sexually transmitted infections and vulvovaginal candidiasis.

Background Bacterial vaginosis is a common vaginal syndrome among females, which leads to significant morbidity and complications, if left untreated. The association of bacterial vaginosis with various sexually transmitted infections has been mentioned in previous literature. However, studies on the intermediate Nugent Score are lacking. This study was planned to examine the association of sexually transmitted infections with the intermediate Nugent Score. Materials and Methods The study included was conducted to include females presenting with vaginal discharge, burning micturition, itching, lower abdominal pain and infertility. The Nugent scoring was used to categorize patients into those having normal flora, intermediate or bacterial vaginosis. Conventional and molecular techniques targeting Trichomonas vaginalis, Chlamydia trachomatis, Ureaplasma urealyticum, Mycoplasma hominis, Syphilis, Neisseria gonorrhoeae and vulvovaginal candidiasis were performed. Results A total of 3,531 clinical samples were collected from females with a median age of 28.0 years. The number of patients with bacterial vaginosis and intermediate Nugent Score and positive cases were significantly higher in the 21-35 years age group (P < 0.0001). We observed that the likelihood of test results being positive for Trichomonas vaginalis was higher (P < 0.05), as the abnormality of the vaginal flora increased. Mycoplasma hominis was observed to be significantly higher in the intermediate Nugent Score group than the BV-positive patients (0.6 vs 0.2, P = 0.002). The number of vulvovaginal candidiasis cases in both the bacterial vaginosis-negative and bacterial vaginosis-positive groups were nearly the same (9.3 vs 9.8%). Limitation Individual follow-up couldn't be performed on the patients. Conclusion We observed that the dysbiosis in vaginal microbiota, with an increase in Nugent scoring, was significantly associated with an increased risk for the acquisition of sexually transmitted infections and vulvovaginal candidiasis.

Prevalence of Trichomonas vaginalis by polymerase chain reaction-based molecular method among symptomatic women from Northern India.

Introduction: Trichomoniasis remains one of the most common sexually transmitted infections, which is curable. To prevent complications and transmission, prompt and correct diagnosis is essential to treat Trichomonas vaginalis. The present study was done to evaluate polymerase chain reaction (PCR) with other conventional techniques for the diagnosis of T. vaginalis infection and determine the prevalence of T. vaginalis in women with vaginal discharge based on PCR assay. Methods: Vaginal swabs were collected by the trained health-care professional using FLOQSwabs™ (Copan, Italy) during routine pelvic examinations among 1974 symptomatic females. The wet microscopy, culture, and PCR were performed. Results: The sensitivity of wet mount and culture in comparison to PCR was 60.87% and 56.52%, respectively. The kappa inter-rater agreement of T. vaginalis PCR showed substantial agreement with wet mount microscopy (κ = 0.742) and culture (κ = 0.707). The PCR detected an additional 17 cases that were missed by conventional techniques. Discussion: The study highlights the importance of PCR for T. vaginalis screening among symptomatic females.

Extra-intestinal complications of Ascaris lumbricoides infections in India: A systematic review and meta-analysis.

The aberrant migration of Ascaris lumbricoides may cause extra-intestinal ascariasis (EIA) involving hepato-biliary-pancreatic (HBP) or other extra-gastro-intestinal (EGI) organs. We performed a systematic review and meta-analysis to study the risk factors and clinical presentations of EIA, and differences in HBP and EGI ascariasis. Medline, Web of Science and Embase were searched for cases of EIA in the English language from India. From 1204 articles, 86 studies (105 cases) were included. The majority of the cases involved the HBP system (78%). Among HBP ascariasis, the most commonly involved site was the bile duct (53.6%). Females had 11.3 times higher odds (95% CI 2.852 to 44.856; p=0.001) of HBP ascariasis, while the pediatric population had lower odds (OR=0.323). Previous gallbladder disease was significantly associated with HBP ascariasis in adults (p=0.046), while a significantly higher number of cases of EGI ascariasis were observed among pediatric patients (p=0.003). Ocular symptoms occurred exclusively in the pediatric population (p=0.017). Overall, death was reported in 3.8% of patients (n=4). This review emphasizes the importance of the complications of EIA. It encourages future research into issues such as the reasons of higher gall bladder ascariasis in females and the implications of Ascaris-related complications following biliary tract interventions. It also suggests considering Ascaris as a differential diagnosis for airway obstuction in intubated critically ill patients.

Aspergillosis: an Update on Clinical Spectrum, Diagnostic Schemes, and Management.

Purpose of Review: This review gives an overview of the diseases caused by Aspergillus, including a description of the species involved and the infected clinical systems. We provide insight into the various diagnostic methods available for diagnosing aspergillosis, particularly invasive aspergillosis (IA), including the role of radiology, bronchoscopy, culture, and non-culture-based microbiological methods. We also discuss the available diagnostic algorithms for the different disease conditions. This review also summarizes the main aspects of managing infections due to Aspergillus spp., such as antifungal resistance, choice of antifungals, therapeutic drug monitoring, and new antifungal alternatives. Recent Findings: The risk factors for this infection continue to evolve with the development of many biological agents that target the immune system and the increase of viral illnesses such as coronavirus disease. Due to the limitations of present mycological test methods, establishing a fast diagnosis is frequently difficult, and reports of developing antifungal resistance further complicate the management of aspergillosis. Many commercial assays, like AsperGenius®, MycAssay Aspergillus®, and MycoGENIE®, have the advantage of better species-level identification and concomitant resistance-associated mutations. Fosmanogepix, ibrexafungerp, rezafungin, and olorofim are newer antifungal agents in the pipeline exhibiting remarkable activity against Aspergillus spp. Summary: The fungus Aspergillus is found ubiquitously around the world and can cause various infections, from harmless saprophytic colonization to severe IA. Understanding the diagnostic criteria to be used in different patient groups and the local epidemiological data and antifungal susceptibility profile is critical for optimal patient management.

Clinical and Mycologic Characteristics of Emerging Mucormycosis Agent Rhizopus homothallicus.

We retrospectively reviewed consecutive cases of mucormycosis reported from a tertiary-care center in India to determine the clinical and mycologic characteristics of emerging Rhizopus homothallicus fungus. The objectives were ascertaining the proportion of R. homothallicus infection and the 30-day mortality rate in rhino-orbital mucormycosis attributable to R. homothallicus compared with R. arrhizus. R. homothallicus accounted for 43 (6.8%) of the 631 cases of mucormycosis. R. homothallicus infection was independently associated with better survival (odds ratio [OR] 0.08 [95% CI 0.02-0.36]; p = 0.001) than for R. arrhizus infection (4/41 [9.8%] vs. 104/266 [39.1%]) after adjusting for age, intracranial involvement, and surgery. We also performed antifungal-susceptibility testing, which indicated a low range of MICs for R. homothallicus against the commonly used antifungals (amphotericin B [0.03-16], itraconazole [0.03-16], posaconazole [0.03-8], and isavuconazole [0.03-16]). 18S gene sequencing and amplified length polymorphism analysis revealed distinct clustering of R. homothallicus.

Saksenaea vasiformis infection: Extensive abdominal wall necrotizing fasciitis with systematic review and analysis of 65 cases.

INTRODUCTION: Saksenaea vasiformis is a rarely reported Mucorales causing mucormycosis in both immunocompromised and immunocompetent individuals. Due to few reported cases, the clinical characteristics and optimal management strategy for this rare agent are not clearly described. METHODS: We systematically reviewed Medline, EmBase and CINHAL for studies on S. vasiformis infections reported until 1 January 2022 and 57 studies (63 patients) were retrieved. Additionally, one more case of extensive abdominal wall necrotizing fasciitis managed by our team was also included. The clinical and demographic characteristics and outcomes were extracted and analysed. RESULTS: Out of the 65 included cases, the majority were reported from India (26.6%). The most common risk factors for infection were accidental trauma wounds (31.3%), health-care-related wounds (14.1%) and animal/insect bites (12.5%). Most common clinical presentation was subcutaneous mucormycosis (60.9%) followed by rhino-orbito cerebral mucormycosis (14%), necrotizing fasciitis (10%), disseminated infection (9.3%), pulmonary mucormycosis (3.2%) and osteomyelitis (1.6%). Mortality was observed in 24 (37.5%) patients and health care related injuries were significantly associated with higher mortality (p = .001). The use of posaconazole (p = .019) and the use of surgical management (p = .032) was associated with significantly better survival. DISCUSSION: In this study, we describe the largest compendium of mucormycosis due to S. vasiformis, which can be useful in increasing awareness regarding this rare Mucorales and guiding patient management.

Comparative evaluation of phenotypic and genotypic methods for the rapid and cost-effective detection of carbapenemases in extensively drug resistant Klebsiella pneumoniae.

PURPOSE: Carbapenemases are the enzymes that can hydrolyze carbapenems and other ß-lactam antibiotics. These enzymes confer resistance to multiple antibiotics and act as a stumbling block in the treatment of infections caused by gram-negative bacteria. Therefore, rapid and specific detection of these enzymes is crucial for deciding the course of treatment and better clinical outcomes. MATERIAL AND METHODS: This study was conducted to compare various phenotypic and PCR based methods for the detection of carbapenemases in carbapenem- and colistin-resistant Klebsiella pneumoniae. One hundred clinical isolates of extensively resistant Klebsiella pneumoniae were included in the study. Phenotypic detection for carbapenemases was performed by Rapidec® Carba NP (Biomerieux), modified carbapenem inactivation method (mCIM), imipenem-ethylenediaminetetraacetic acid disk synergy (EDS), double disk synergy test using mercaptopropionic acid (DDST-MPA), and combined disk method (CD) and for colistin by microbroth dilution method. Genotypic detection for carbapenemases and colistin resistance was performed by targeted PCR. RESULTS: The sensitivity of Carba NP test and mCIM were positive in 95% and 96% respectively and specificity was 100% for both methods. The sensitivity of EDS, DDST-MPA, and CD were 55.6%, 88.9% and 54.5% respectively. Among the carbapenem resistance genes, blaOXA-48 (82%) genes were the most prevalent. Among metallo-beta lactamases, blaVIM (56%) was most common followed by blaNDM (54%) and blaIMP (20%). The mcr-1 gene for colistin resistance was not detected in any isolate. CONCLUSION: Among the five phenotypic assays analyzed, the mCIM is the most simple, inexpensive, accurate and reproducible method for carbapenemase detection in Klebsiella pneumoniae. The DDST-MPA test provides the best sensitivity for the detection of carbapenemases, although specificity is low. These tests, when applied in a clinical laboratory and assessed by the microbiologist, can help in guiding the course of treatment.

Clinical utility of time to positivity of blood cultures in cases of fungaemia: A prospective study.

PURPOSE: Fungaemia due to yeast is a major cause of morbidity and mortality in critically ill patients. Although, automated blood cultures have improved the time to diagnosis, very few studies have systematically evaluated the utility of blood culture time to positivity (TTP) of fungaemia in the clinical scenario. In this study, we evaluated the TTP for different yeast species to determine its clinical utility. MATERIAL AND METHODS: A prospective study including 244 consecutive patients admitted to the adult (n â€‹= â€‹76) and paediatric (n â€‹= â€‹168) intensive care units (ICUs) was conducted between December 2017 through March 2019. The clinical and demographic characteristics, BACTEC blood culture results and TTP for yeast positive blood cultures were recorded for analysis. RESULTS: A total of 244 patients with 357 episodes of candidaemia were enrolled during the study period. The TTP (mean â€‹± â€‹SD) for all yeast species was 26.8 â€‹± â€‹23.6 â€‹h while it was significantly longer in paediatric than adult patients (30.5 ± 24.7 vs. 25.2 â€‹± â€‹22.9 â€‹h; p â€‹= â€‹<0.0001). Wickerhamomyces anomalus and Cyberlindnera jadinii (previously C. utilis) were exclusively isolated from paediatric population where W. anomalus demonstrated significantly longer TTP than C. jadinii. Among adult cases, C. albicans exhibited significantly longer TTP than C. tropicalis. In paediatric cases, >80% of C. tropicalis and C. utilis flagged positive in blood culture before 24 â€‹h while majority (65.9%) of W. anomalus isolates flagged positive later than 24 â€‹h. Similarly in adult samples, 63% of C. tropicalis isolates beeped positive before 24 â€‹h. CONCLUSION: TTP for yeast may provide insight regarding the responsible yeast species before final identification among critical patients with candidaemia. Larger studies are warranted for evaluating clinical utility of TTP considering other complex factors like yeast burden, generation time, virulence and host factors, which may affect TTP.

Avian influenza revisited: concerns and constraints.

Avian influenza (AVI) is being known for its pandemic potential and devastating effects on poultry and birds. The AVI outbreaks in domesticated birds are of concern because the Low pathogenic avian influenza virus (LPAI) tends to evolve into a High pathogenic avian influenza virus (HPAI) resulting in the rapid spread and significant outbreak in poultries. The containment should be rapid and stringent precautions should be taken in handling the infected poultry cases or infected materials. In general, AVI viruses do not replicate efficiently in humans, indicating that transmitting these viruses to humans directly is a very rare preference. However, the HPAI ability to the cross-species barrier and infect humans has been known for H5N1 and H7N9. Recently, the world's first human case of transmission of the H5N8 strain from the avian species to humans has been documented. In this recent scenario, it is worth discussing the strain variations, disease severity, economic loss, and effective controlling strategies for controlling avian influenza.

Epidemiological, clinical and genetic characterization of scrub typhus in patients presenting with acute febrile illness in New Delhi.

PURPOSE: Scrub typhus (ST) is a zoonotic disease, caused by O. tsutsugamushi is a major cause of acute febrile illness (AFI) in India. There is a need to study the prevalence and risk factors in various regions of India. METHODS: A study to estimate the prevalence and study the risk factors of ST in patients presenting with acute febrile illness (AFI) was performed. All patients underwent serology for IgM antibodies to Orientia tsutsugamushi (In Bios International Inc, Seattle, WA) as per the manufacturers' protocol. Following this, Polymerase Chain reaction (PCR) (real time SYBR green based targeting groEL gene and conventional PCR targeting 56 â€‹kDa type specific antigen gene) was performed from stored serum samples. RESULTS: During the study period, 473 patients were admitted. Of these 56 (11.8%) patients were ST positive by IgM serology. The conventional PCR targeting 56 â€‹kDa type specific antigen gene of O. tsutsugamushi was positive in six patients while Ot groEL SYBR green based PCR) was positive in five. PCR was positive in patients who had demonstrated a higher OD value in ELISA. Conventional PCR positive amplicons were sent for Sanger sequencing and confirmed to be O. tsutsugamushi. The mean age of the patients was 49 â€‹± â€‹18.3 years and males constituted a higher number of patients (67.9%, n â€‹= â€‹38). The pathognomonic eschar was present in 7 (12.5%) patients. Phylogenetic analysis revealed that sequences clustered close to Kato-like Hualein-20 strain and Karp-like Linh DT strains. All patients were administered doxycycline in our study. Mortality was recorded in 8.9% of the patients. CONCLUSIONS: In patients presenting with acute febrile illness, ST should be considered as a differential diagnosis, especially in post-monsoon season. Along with serology, serum can also be used as sample for PCR in an intracellular bacterium like O. tsutsugamushi.

Occurrence of Cystic Fibrosis Transmembrane Conductance Regulator Gene Mutations in Patients with Allergic Bronchopulmonary Aspergillosis Complicating Asthma.

BACKGROUND: Whether cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations contribute to the high prevalence of allergic bronchopulmonary aspergillosis (ABPA) in India remains unknown. We aimed to evaluate the occurrence of CFTR mutations in subjects with ABPA complicating asthma. METHODS: We sequenced the CFTR gene using genomic DNA from blood on the Illumina NextSeq500 platform. Before undertaking zygosity analysis by genome analysis toolkit, the known or novel single nucleotide polymorphisms (SNPs) and indels were called. For rigorous analysis, we included only high-quality SNPs (scores > 500) and coverage ranging from 30 × 150x. RESULTS: We included 18, 12, and eight adult participants of ABPA, asthma, and healthy controls, respectively. The frequency of SNPs was higher in asthmatic subjects than ABPA or healthy controls, albeit not statistically significant (9/12 [75%] vs. 11/18 [61.1%] vs. 3/8 [37.5%], p = 0.24). Of the 38 subjects, 23 yielded 50 variants (healthy controls [n = 5], ABPA [n = 22], asthma [n = 23]) corresponding to six SNPs not previously linked with ABPA. Of these, four SNPs (rs213950, rs200735475, rs1800113, and rs1800136) were catalogued in the NCBI database. We identified two novel SNPs (chr7:117250703, chr7:117282655) in four (ABPA [n = 1], asthma [n = 3]) subjects without corresponding reference SNP. Most SNPs (85.5%) were heterozygous. The frequency of SNPs was higher in ABPA subjects with high-attenuation mucus (52.2%) and bronchiectasis (39.1%) than serological ABPA (8.7%). CONCLUSIONS: Our study suggests the role of CFTR mutations in the pathogenesis of ABPA. The SNPs in the CFTR gene may contribute to disease severity in ABPA. Larger studies are required to confirm our findings.

Budding yeast in a child with acute leukemia: Nothing CRYPT(O)IC about it.

A 13-year-old girl child with B-cell precursor acute lymphoblastic leukemia presented with complaints of fever, fatigue and left-sided iliac mass of 20 days duration. Preliminary blood culture from the peripherally inserted central catheter (PICC) demonstrated the presence of budding yeast cells. This is a rare form of "Disseminated cryptococcosis". Budding yeast cells emphasizes the significance of various differentials of yeast in positive blood cultures bottles, as identifying Cryptococcus from gram stain can be complicated. This manuscript also highlights the presence of crystalloid geometric appearance like "Buckminsterfullerene", which is derived from the mucopolysaccharide capsule in Cryptococcus. These structures are rarely observed, and in this case, are exceptionally remarkable.

Diagnostic accuracy of the metagenomic next-generation sequencing (mNGS) for detection of bacterial meningoencephalitis: a systematic review and meta-analysis.

The early diagnosis of bacterial meningoencephalitis (BM/E) is difficult, and delay in diagnosis can cause complications leading to neurological impairment/death. In cases of unexplained BM/E, the metagenomic NGS (mNGS) offers an advantage over conventional methods, especially when a rare pathogen is implicated or the patient is on antibiotics. This study aims to evaluate and compare the diagnostic efficacy of mNGS for the diagnosis of BM/E using cerebrospinal fluid (CSF) specimens versus a composite reference standard (CRS). The electronic databases (Embase, PubMed, and Web of Science) were searched up to 15 June 2021. Studies such as cohort, case-control, prospective, or retrospective studies that assessed the diagnostic efficacy of mNGS in suspected bacterial meningitis/encephalitis cases were included. Ten studies met the inclusion criteria, including three retrospective and seven prospective studies. The sensitivity of mNGS for diagnosis of BM/E from CSF samples ranged from 33 (95% CI: 13-62) to 98% (95% CI: 76-99). The specificity of mNGS ranged from 67 (95% CI: 55-78) to 98% (95% CI: 95-99). The estimated AUC (area under curve) by hierarchical summary receiver operating characteristic (HSROC) of the studies being analyzed was 0.912. The meta-regression analysis demonstrated that the different types of studies (single-center vs. multi-center) had an effect on the specificity of mNGS for BM/E compared with CRS (90% vs. 96%, meta-regression P < 0.05). The current analysis revealed moderate diagnostic accuracy of mNGS. This approach can be helpful, especially in cases of undiagnosed BM/E by identification of organism and subsequently accelerating the patient management.