Multimodal analysis of the COVID-19-associated mucormycosis outbreak in Delhi, India indicates the convergence of clinical and environmental risk factors.

BACKGROUND: The aetiology of the major outbreak of COVID-19-associated mucormycosis (CAM) in India in spring 2021 remains incompletely understood. Herein, we provide a multifaceted and multi-institutional analysis of clinical, pathogen-related, environmental and healthcare-related factors during CAM outbreak in the metropolitan New Delhi area. METHODS: We reviewed medical records of all patients diagnosed with biopsy-proven CAM (n = 50) at 7 hospitals in the New Delhi, and NCR area in April-June 2021. Two multivariate logistic regression models were used to compare clinical characteristics of CAM cases with COVID-19-hospitalised contemporary patients as controls (n = 69). Additionally, meteorological parameters and mould spore concentrations in outdoor air were analysed. Selected hospital fomites were cultured. Mucorales isolates from CAM patients were analysed by ITS sequencing and whole-genome sequencing (WGS). RESULTS: Independent risk factors for CAM identified by multivariate analysis were previously or newly diagnosed diabetes mellitus, active cancer and severe COVID-19 infection. Supplemental oxygen, remdesivir therapy and ICU admission for COVID-19 were associated with reduced CAM risk. The CAM incidence peak was preceded by an uptick in environmental spore concentrations in the preceding 3-4 weeks that correlated with increasing temperature, high evaporation and decreasing relative humidity. Rhizopus was the most common genus isolated, but we also identified two cases of the uncommon Mucorales, Lichtheimia ornata. WGS found no clonal population of patient isolates. No Mucorales were cultured from hospital fomites. CONCLUSIONS: An intersection of host and environmental factors contributed to the emergence of CAM. Surrogates of access to advanced COVID-19 treatment were associated with lower CAM risk.

India-discovered levonadifloxacin & alalevonadifloxacin: A review on susceptibility testing methods, CLSI quality control and breakpoints along with a brief account of their emerging therapeutic profile as a novel standard-of-care.

BACKGROUND: Levonadifloxacin (intravenous) and alalevonadifloxacin (oral prodrug) are novel antibiotics based on benzoquinolizine subclass of fluoroquinolone, licensed for clinical use in India in 2019. The active moiety, levonadifloxacin, is a broad-spectrum antibiotic with a high potency against methicillin-resistant Staphylococcus. aureus, multi-drug resistant pneumococci and anaerobes. OBJECTIVE: This review, for the first time, critically analyses the antimicrobial susceptibility testing methods, Clinical Laboratory & Standards Institute (CLSI)-quality control of susceptibility testing and breakpoints of levonadifloxacin. Further, the genesis, discovery and developmental aspects as well as therapeutic profile of levonadifloxacin and alalevonadifloxacin are briefly described. CONTENTS: In order to aid the scientific and clinician communities with a single comprehensive overview on all the key aspects of levonadifloxacin and alalevonadifloxacin, the present article covers the reference MIC and disk diffusion methods for levonadifloxacin susceptibility testing that were approved by CLSI and the reference ranges for quality control strains published in the CLSI M100 document. The breakpoints of levonadifloxacin were derived in concordance to US FDA, European Committee on Antibiotic Susceptibility Testing (EUCAST) and CLSI approaches. Further, the article provides a brief account of challenges encountered during the discovery stages of levonadifloxacin and alalevonadifloxacin, activity spectrum and safety benefits accruing from structural novelty-linked mechanism of action. Further, the review also covers in vitro and in vivo activities, registrational clinical studies and patient-friendly features of levonadifloxacin/alalevonadifloxacin. Cumulatively, levonadifloxacin has a potential to offer a long awaited new standard-of-care treatment for the resistant Gram-positive bacterial infections.

In vitro activity of a novel antibacterial agent, levonadifloxacin, against clinical isolates collected in a prospective, multicentre surveillance study in India during 2016-18.

BACKGROUND: Levonadifloxacin is a novel antibiotic belonging to the benzoquinolizine subclass of fluoroquinolones with potent activity against MRSA and quinolone-resistant Staphylococcus aureus. IV levonadifloxacin and its oral prodrug alalevonadifloxacin have recently been approved in India for the treatment of acute bacterial skin and skin structure infections (ABSSSIs) including diabetic foot infections. OBJECTIVES: To investigate the in vitro activity of levonadifloxacin against contemporary clinical isolates collected from multiple tertiary care hospitals across India in the Antimicrobial Susceptibility Profiling of Indian Resistotypes (ASPIRE) surveillance study. METHODS: A total of 1376 clinical isolates, consisting of staphylococci (n = 677), streptococci (n = 178), Enterobacterales (n = 320), Pseudomonas aeruginosa (n = 140) and Acinetobacter baumannii (n = 61), collected (2016-18) from 16 tertiary hospitals located across 12 states in India, were included in the study. The MICs of levonadifloxacin and comparator antibiotics were determined using the reference agar dilution method and broth microdilution method. RESULTS: Levonadifloxacin exhibited potent activity against MSSA (MIC50/90: 0.5/1 mg/L), MRSA (MIC50/90: 0.5/1 mg/L) and levofloxacin-resistant S. aureus (MIC50/90: 1/1 mg/L) isolates. Similarly, potent activity of levonadifloxacin was also observed against CoNS including MDR isolates (MIC50/90: 1/2 mg/L). Against Streptococcus pneumoniae, levonadifloxacin (MIC50/90: 0.5/0.5 mg/L) showed superior activity compared with levofloxacin (MIC50/90: 1/2 mg/L). Among levofloxacin-susceptible Enterobacterales, 80.6% of isolates were inhibited at ≤2 mg/L levonadifloxacin. CONCLUSIONS: Levonadifloxacin displayed potent activity against contemporary MRSA and fluoroquinolone-resistant staphylococcal isolates, thus offering a valuable IV as well as an oral therapeutic option for the treatment of ABSSSIs. Furthermore, levonadifloxacin exhibited a broad-spectrum activity profile as evident from its activity against streptococci and levofloxacin-susceptible Gram-negative isolates.

Effect of carbapenem resistance on outcomes of bloodstream infection caused by Enterobacteriaceae in low-income and middle-income countries (PANORAMA): a multinational prospective cohort study.

BACKGROUND: Low-income and middle-income countries (LMICs) are under-represented in reports on the burden of antimicrobial resistance. We aimed to quantify the clinical effect of carbapenem resistance on mortality and length of hospital stay among inpatients in LMICs with a bloodstream infection due to Enterobacteriaceae. METHODS: The PANORAMA study was a multinational prospective cohort study at tertiary hospitals in Bangladesh, Colombia, Egypt, Ghana, India, Lebanon, Nepal, Nigeria, Pakistan, and Vietnam, recruiting consecutively diagnosed patients with carbapenem-susceptible Enterobacteriaceae (CSE) and carbapenem-resistant Entero-bacteriaceae (CRE) bloodstream infections. We excluded patients who had previously been enrolled in the study and those not treated with curative intent at the time of bloodstream infection onset. There were no age restrictions. Central laboratories in India and the UK did confirmatory testing and molecular characterisation, including strain typing. We applied proportional subdistribution hazard models with inverse probability weighting to estimate the effect of carbapenem resistance on probability of discharge alive and in-hospital death, and multistate modelling for excess length of stay in hospital. All patients were included in the analysis. FINDINGS: Between Aug 1, 2014, and June 30, 2015, we recruited 297 patients from 16 sites in ten countries: 174 with CSE bloodstream infection and 123 with CRE bloodstream infection. Median age was 46 years (IQR 15-61). Crude mortality was 20% (35 of 174 patients) for patients with CSE bloodstream infection and 35% (43 of 123 patients) for patients with CRE bloodstream infection. Carbapenem resistance was associated with an increased length of hospital stay (3·7 days, 95% CI 0·3-6·9), increased probability of in-hospital mortality (adjusted subdistribution hazard ratio 1·75, 95% CI 1·04-2·94), and decreased probability of discharge alive (0·61, 0·45-0·83). Multilocus sequence typing showed various clades, with marginal overlap between strains in the CRE and CSE clades. INTERPRETATION: Carbapenem resistance is associated with increased length of hospital stay and mortality in patients with bloodstream infections in LMICs. These data will inform global estimates of the burden of antimicrobial resistance and reinforce the need for better strategies to prevent, diagnose, and treat CRE infections in LMICs. FUNDING: bioMérieux.

Direct testing by VITEK® 2: A dependable method to reduce turnaround time in Gram-negative bloodstream infections.

CONTEXT: Bloodstream infections pose a major health-care burden worldwide. Routine microbiological methods are time-consuming, thereby delaying appropriate treatment. AIMS: The aim of this study is to evaluate the method of direct testing of identification (ID) and antimicrobial susceptibility testing (AST) of positive blood culture bottles by VITEK®2. SETTINGS AND DESIGN: This was a prospective study at a tertiary level hospital. SUBJECTS AND METHODS: One hundred positive BACTEC blood culture bottles with monomicrobial Gram-negative organisms on microscopy were tested in parallel by direct ID/AST as well as conventional method. Results obtained by two methods were compared in terms of ID/AST and turnaround time (TAT). RESULTS: Of the 100 isolates tested, only one was misidentified by the direct method and there was no unidentified isolate. The AST results demonstrated 99.74% categorical and 99.65% essential agreement. Of 1144 organism-antibiotic combinations, there were 0.44% major error, no very major error, or minor error observed. CONCLUSIONS: While conventional method is the gold standard, the direct ID/AST methods have demonstrated that it can be successfully utilized to decrease TAT to the final results by 18-24 h, without sacrificing test accuracy. This technique will help to tailor antimicrobial therapy, thereby reducing patient morbidity, mortality, and antibiotic resistance, as well.

First neonatal case of fungaemia due to Pseudozyma aphidis and a global literature review.

The Ustilaginomycetous basidiomycete yeast, Pseudozyma aphidis has recently been implicated in potentially fatal disorders ranging from subcutaneous mycoses to disseminated infections. Till date a solitary case of P. aphidis fungaemia in a paediatric patient has been reported. We present a case of fungaemia due to P. aphidis in a rhesus factor-isoimmunised, low-birth-weight neonate. The isolate was identified by sequencing the D1/D2 domain of the LSU region. Antifungal susceptibility of the isolate revealed susceptibility to amphotericin B, voriconazole, itraconazole, isavuconazole and posaconazole. It had high minimum inhibitory concentrations of fluconazole and was resistant to flucytosine and echinocandins. Consequently, the patient was successfully treated with intravenous amphotericin B. Although the source of infection could not be traced, as the neonate developed fungaemia on the first day of life, it could possibly be from the maternal urogenital tract or intrahospital transmission. A review of previously published cases revealed that risk factors for invasive Pseudozyma spp. infections were similar to those previously reported for non-albicans Candida spp. Pseudozyma species are underreported due to the difficulty of identifying this rare yeast pathogen by commercial identification systems. Considering that Pseudozyma spp. cause invasive fungal infections globally and are resistant to flucytosine, fluconazole and echinocandins, this pathogen assumes a greater clinical significance.

Clinically lesser known entity in India: A Report of two cases of Melioidosis.

Melioidosis is endemic in the South Asian regions, like Thailand, Singapore Malaysia and Australia. The disease is more pronounced in the southern part of the country. It is caused by Burkholderia pseudomallei which causes systemic involvement, morbidity and mortality associated with the disease is high. Due to highly varied clinical presentation, and low general awareness this infection is largely underdiagnosed and under reported in our country. Most laboratories in the country still rely on conventional culturing methods with their low sensitivity, adding to the under reporting. To enhance physician awareness we describe here two cases who presented to our institute after months of misdiagnosis.

Gas chromatographic-mass spectrometric analysis of chemical volatiles in buffalo (Bubalus bubalis) urine.

Isolation of active fraction and characterization of chemosignals from urine have been attempted in several mammalian species in the recent years. The objective of this study was to identify the urinary volatiles across various reproductive stages of buffalo cow, namely, estrus, diestrus, and pregnancy, and in bull, by chemical extraction followed by gas chromatography-linked mass spectrometry (GC-MS). Urine samples were collected from six buffalo cows at two different phases of estrous cycle, namely, estrus and diestrus. Besides, urinary samples were collected from five pregnant buffalo cows (60-75 days after artificial insemination (AI)) and six adult bulls. Thin-layer chromatography was performed as a preliminary test for qualitative comparison of different compounds extracted by organic solvents. Identification of the urinary compounds was carried out in a gas chromatograph (Perkin Elmer, Autosystem XL) linked to a mass spectrometer (Turbomass). The results of GC-MS analysis indicated the presence of 21 compounds with varying molecular weights and retention time, which were further categorized as diestrus-specific, pregnancy-specific, and bull-specific urinary compounds. No compound, however, could be identified as estrus-specific. We concluded that qualitative differences do exist in estrus, diestrus, and pregnant buffalo cow urine and in bull urine, as evidenced by GC-MS.

Melioidosis: a case report.

Burkhloderia pseudomallei has recently gained importance as an emerging pathogen in India. It causes various clinical manifestations like pneumoniae, septicaemia, arthritis, abscess etc. Cases have been reported from Southeast Asia mainly Thailand, Malaysia, Vietnam, etc. In India, few cases have been reported mainly from the southern part of the country. Patient was a 65-year-old male and presented with fever 1 month back, cough and breathlessness for same period, swelling on both ankles from 7 days. B. pseudomallei was isolated from endotracheal secretions, blood cultures, leg wound. He was successfully treated with Imipenem and Doxycycline and put on maintenance therapy now, and is currently doing well.

Study of a novel method to assist in early reporting of sepsis from the microbiology laboratory.

INTRODUCTION: Microbiology laboratories must provide accurate blood culture reports with rapid turnaround time (TAT) to effectively manage patients with sepsis. In this study three methods are compared for reporting blood culture results: a manual method that included use of a serum separator tube (SST), the conventional manual, and an automated method for identification and susceptibility (ID/AST). METHODOLOGY: Broth from positive blood culture bottles was added to an SST and then centrifuged. The pellet obtained was used to directly inoculate biochemical tests for identification and agar plates for AST on the first day of positivity. Biochemicals and AST plates were read the next day and final results reported on the second day at 24 hours. For conventional disk diffusion testing, the newly positive blood culture broth was also inoculated on solid media on the first day and incubated overnight. The next day AST by was performed as well as biochemical tests from pure colonies. These colonies were also used to inoculate panels for ID/AST using the automated MicroScan 40SI System. These results were recorded on the third day and results reported at 48 hours. RESULTS: The study included 851 samples Out of 106 (12.4%) positive blood cultures, 102 were included in the study; Comparison of the 3 methods showed good correlation. Identification was correctly reported in 95 (93.1%) isolates. The overall AST error rate was 3.8%. CONCLUSIONS: The use of SST and direct from pellet inoculation reduced TAT for identification and AST results between 18 and 24 hours.

Antimicrobial consumption and impact of "Reserve antibiotic indent form" in an intensive care unit.

OBJECTIVE: To study the antimicrobial (AM) consumption, record the AM sensitivity pattern, and evaluate impact of "Reserve AM indent form" in the intensive care unit (ICU). MATERIALS AND METHODS: The study was carried out in medical ICU over 4 months period at a tertiary care hospital. AM consumption was determined by defined daily dose (DDD) per 100 bed days for each month for consecutive 4 months. The average total AM consumption was calculated. The laboratory samples were processed, and the sensitivity pattern was determined. Some of the newer AM were categorised as "Reserve" and an indent form was made mandatory to be filled up prior to prescription. RESULTS: The total AM consumption was 232 per 100 bed days. The commonly used AM were penicillin with ß-lactamase inhibitor (21%) followed by antifungal drugs (13.4%), cephalosporins and macrolides (11.7%) each. The most common organism isolated was Acinetobacter (26.1%) followed by Candida (23.8%) and Pseudomonas (21.4%). The average occupancy index was 0.53, and the average duration of ICU stay was 6 days. The consumption of carbapenems (new AM) and antifungals decreased from 18.8/100 to 10.6/100 and 56.1/100 to 22.1/100 bed days, respectively, after the introduction of indent form. CONCLUSION: The "Reserve AM indent form" was helpful in reducing the AM consumption during the study period. The AM indent form can be used as an important tool to combat irrational use, AM resistance and can be implemented in AM stewardship programmes.

A study of phage based diagnostic technique for tuberculosis.

BACKGROUND: Tuberculosis (TB) is a leading infectious disease in India. Diagnosis of TB has always been a problem due to slow rate of growth of Mycobacterium tuberculosis. In this study we have compared the conventional tools for diagnosis of TB with the new Fast Plaque TB TM MATERIAL AND METHODS: Two hundred and twelve clinically suspected cases of TB were enrolled for the study. Three consecutive early morning sputum samples were collected from each patient. Sputum smears were examined after staining with ZN stain and the sputum samples were later subjected to culture and phage assay. RESULTS: It was seen from the study that out of the total 212 cases, 106 were phage positive and 106 were phage negative. Sensitivity of the phage test with respect to AFB smear is 94.34% and specificity of the phage test is 93.88%. A total of 120 specimens grew on LJ media, of which 112 were Mycobacterium tuberculosis, 2 were Mycobacterium Kansasii, 4 were Mycobacterium avium complex and 2 grew Mycobacteriumfortuitum group. Out of these 120 specimens which grew on LJ, 104 were also positive for phage assay. All the 8 Non-Tubercular Mycobacteria were negative by the Fast Plaque Assay. Out of the 92 which were negative on LJ, 2 were positive by phage assay. Sensitivity and specificity of phage assay with respect to growth on LJ was 92.86% and 97.83% respectively. CONCLUSION: The study showed that phage assay is a rapid, reliable and cost effective method in diagnosing pulmonary tuberculosis from clinical samples.