Pan-Indian Clinical Registry of Invasive Fungal Infections Among Patients in the Intensive Care Unit: Protocol for a Multicentric Prospective Study

BACKGROUND

Fungal infections are now a great public health threat, especially in those with underlying risk factors such as neutropenia, diabetes, high-dose steroid treatment, cancer chemotherapy, prolonged intensive care unit stay, and so on, which can lead to mycoses with higher mortality rates. The rates of these infections have been steadily increasing over the past 2 decades due to the increasing population of patients who are immunocompromised. However, the data regarding the exact burden of such infection are still not available from India. Therefore, this registry was initiated to collate systematic data on invasive fungal infections (IFIs) across the country.

OBJECTIVE

The primary aim of this study is to create a multicenter digital clinical registry and monitor trends of IFIs and emerging fungal diseases, as well as early signals of any potential fungal outbreak in any region. The registry will also capture information on the antifungal resistance patterns and the contribution of fungal infections on overall morbidity and inpatient mortality across various conditions.

METHODS

This multicenter, prospective, noninterventional observational study will be conducted by the Indian Council of Medical Research through a web-based data collection method from 8 Advanced Mycology Diagnostic and Research Centers across the country. Data on age, gender, clinical signs and symptoms, date of admission, date of discharge or death, diagnostic tests performed, identified pathogen details, antifungal susceptibility testing, outcome, and so on will be obtained from hospital records. Descriptive and multivariate statistical methods will be applied to investigate clinical manifestations, risk variables, and treatment outcomes.

RESULTS

These Advanced Mycology Diagnostic and Research Centers are expected to find the hidden cases of fungal infections in the intensive care unit setting. The study will facilitate the enhancement of the precision of fungal infection diagnosis and prompt treatment modalities in response to antifungal drug sensitivity tests. This registry will improve our understanding of IFIs, support evidence-based clinical decision-making ability, and encourage public health policies and actions.

CONCLUSIONS

Fungal diseases are a neglected public health problem. Fewer diagnostic facilities, scanty published data, and increased vulnerable patient groups make the situation worse. This is the first systematic clinical registry of IFIs in India. Data generated from this registry will increase our understanding related to the diagnosis, treatment, and prevention of fungal diseases in India by addressing pertinent gaps in mycology. This initiative will ensure a visible impact on public health in the country.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/54672.

The Development of a Clinical Registry Digital Database on Invasive Fungal Infections in India: Advancing Epidemiological Understanding and Patient Care

A well-structured digital database is essential for any national priority project as it can provide real-time data analysis and facilitate quick decision making. In recent times, particularly after the COVID-19 pandemic, invasive fungal infections (IFIs) have emerged as a significant public health challenge in India, affecting vulnerable population, including immunocompromised individuals. The lack of comprehensive and well-structured data on IFIs has hindered efforts to understand their true burden and optimize patient care. To address this critical knowledge gap, the ICMR has undertaken a Pan-India pioneer initiative to develop a network of Advanced Mycology Diagnostic research centres in different geographical zones of the country (ICMR-MycoNet). Under the aegis of this project, a clinical registry on IFIs in the ICUs is initiated. This process paper presents a detailed account of the steps involved in the establishment of a web-based data entering and monitoring platform to capture data electronically, ensuring robust and secure data collection and management. This system not only allows participating ICMR-MycoNet centres to enter patient information directly into the database using standardized Case Report Form (CRF) but also includes data validation checks to ensure the accuracy and completeness of entered data. It is complemented by a real-time, web-based, and adaptable data visualization platform. This registry aims to provide crucial epidemiological insights, promote evidence-based hospital infection control programs, and ultimately improve patient outcomes in the face of this formidable healthcare challenge.

Prevalence of antibiotic resistance in lactic acid bacteria isolated from traditional fermented Indian food products

The emergence of antimicrobial resistance (AMR) in lactic acid bacteria (LAB) raises questions on qualified presumptive safety status and poses challenge of AMR transmission in food milieu. This study focuses on isolation, identification and characterization of AMR in LAB prevalent in traditional fermented Indian food products. The analysis of 16SrRNA based phylogenetic tree showed placements of isolates among four different genera Lactobacillus, Enterococcus, Weissella and Leuconostoc. In E-strip gradient test of susceptibility to 14 different antibiotics, over 50% of isolates showed resistance to ampicillin, chloramphenicol, ciprofloxacin, erythromycin, kanamycin, linezolid, streptomycin, trimethoprim and vancomycin. A multivariate principal component analysis, an antibiogram and multiple antibiotic resistance index-values (> 0.2) indicated presence of multidrug-resistance among the isolates. This study reports prevalence of an alarmingly high rate of AMR LAB strains in traditional fermented foods and is important to regulators and public health authorities for developing strategies to control transmission in food systems.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01305-1.

Exploring Diversity and Polymer Degrading Potential of Epiphytic Bacteria Isolated from Marine Macroalgae

The macroalgae surface allows specific bacterial communities to colonize, resulting in complex biological interactions. In recent years, several researchers have studied the diversity and function of the epiphytic bacteria associated with algal host, but largely these interactions remain underexplored. In the present study we analysed the cultivable diversity and polymer degradation potential of epiphytic bacteria associated with five different marine macroalgae (Sargassum, Ulva, Padina, Dictyota and Pterocladia sp.) sampled from the central west coast of India. Out of the total 360 strains isolated, purified and preserved, about 238 strains were identified through 16S rRNA gene sequence analysis and processed for polymer (cellulose, pectin, xylan and starch) degrading activities. Phylogeny placed the strains within the classes Actinobacteria, Bacilli, Alpha-proteobacteria, and Gamma-proteobacteria and clustered them into 45 genera, wherein Vibrio, Bacillus, Pseudoalteromonas, Alteromonas, Staphylococcus and Kocuria spp. were the most abundant with 20 strains identified as potentially novel taxa within the genera Bacillus, Cellulosimicrobium, Gordonia, Marinomonas, Vibrio, Luteimonas and Pseudoalteromonas. In terms of polymer hydrolysis potential, 61.3% had xylanase activity, while 59.7%, 58.8%, and 52.2% had amylase, cellulase, and pectinase activity, respectively. Overall, 75.6% of the strains degraded more than one polysaccharide, 24% degraded all polymers, while nine strains (3.8%) degraded raw sugarcane bagasse. This study showed great potential for seaweed-associated bacteria in the bio-remediation of agro-waste based raw materials, which can be employed in the form of green technology.

Characterization and Transferability of erm and tet Antibiotic Resistance Genes in Lactobacillus spp. Isolated from Traditional Fermented Milk

Lactobacillus is a widely used bacteria and consumed through various fermented foods and beverages. Strains have been shown to carry resistance genes and mobile genetic elements with their ability to transfer the resistance to sensitive pathogenic strains. To study this, 4 cultures of Lactobacillus were isolated from traditional fermented milk. The isolates were able to grow up to 4% (w/v) NaCl concentration and 45 °C temperature, and showed > 97% 16S rRNA gene similarities with Lactobacillus fermentum. All the isolates were phenotypically screened for the presence of antibiotic resistance. Minimum inhibitory concentration (MIC) as microbiological breakpoints were observed against a varied class of antibiotics. Isolates AKO 94.6, DVM 95.7, and NIFTEM 95.8 were explicitly resistant to ampicillin, ciprofloxacin and vancomycin with MIC well beyond the maximum range of 256 µg/ml in the E-strip test. While isolate SKL1 was sensitive to ampicillin and showed MIC at 0.25 µg/ml but resistant to streptomycin and trimethoprim (MIC > 256 µg/ml). Molecular characterization showed the presence of tet(M) gene in three isolates SKL1, DVM 95.7, and NIFTEM 95.8 which was chromosomally associated resistance determinants while erm(B) resistance gene was detected in isolates DVM 95.7 and NIFTEM 95.8 only which was a plasmid associated gene and could be transferrable conjugally. Gene for Tn916 family (xis) was also observed in isolates DVM 95.7 and NIFTEM 95.8. Transferability of antibiotic resistance to pathogenic recipient strains was examined in isolates DVM 95.7 and NIFTEM 95.8 in different food matrices. The highest conjugation frequency with ~ 10^-1 was obtained in alfalfa seed sprouts. This study reports the presence of acquired gene resistance in Lactobacillus species and dissemination to susceptible strains of bacteria in different food matrices. 16S rRNA gene sequences of isolates were uploaded to the NCBI GenBank database to retrieve the accession number.

Conjugal Transfer of Antibiotic Resistances in Lactobacillus spp

Lactic acid bacteria (LAB) are a heterogeneous group of bacteria which are Gram-positive, facultative anaerobes and non-motile, non-spore forming, with varied shapes from cocci to coccobacilli and bacilli. Lactobacillus is the largest and most widely used bacterial species amongst LAB in fermented foods and beverages. The genus is a common member of human gut microbiome. Several species are known to provide benefits to the human gut via synergistic interactions with the gut microbiome and their ability to survive the gut environment. This ability to confer positive health effects provide them a status of generally recognized as safe (GRAS) microorganisms. Due to their various beneficial characteristics, other factors such as their resistance acquisition were overlooked. Overuse of antibiotics has made certain bacteria develop resistance against these drugs. Antibiotic resistance was found to be acquired mainly through conjugation which is a type of lateral gene transfer. Several in vitro methods of conjugation have been discussed previously depending on their success to transfer resistance. In this review, we have addressed methods that are employed to study the transfer of resistance genes using the conjugation phenomenon in lactobacilli.

Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius

Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8^T confirmed their separation into a novel genus with B. badius and genus Domibacillus as the closest phylogenetic relatives. The major fatty acids of the strains are iso-C_15:0 and iso-C_16:0 and MK-7 is the only quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The digital DNA-DNA hybridization (DDH) and ortho average nucleotide identity (ANI) values calculated through whole genome sequences indicated that the three strains showed low relatedness with their phylogenetic neighbours. Based on evidences from phylogenomic analyses and polyphasic taxonomic characterization we propose reclassification of the species B. thermotolerans into a novel genus named Quasibacillus thermotolerans gen. nov., comb. nov with the type strain SgZ-8^T (=CCTCC AB2012108^T=KACC 16706^T). Further our analyses also revealed that B. encimensis SGD-V-25^T is a later heterotypic synonym of Bacillus badius DSM 23^T.

Marinomonas epiphytica sp. nov., isolated from a marine intertidal macroalga

A novel Gram-stain-negative, aerobic marine bacterial strain, SAB-3T, was isolated from brown macroalgae (Dictyota sp.) growing in the Arabian sea, Goa, India. The strain grew optimally at 30 °C, with 2.0-4.0 % (w/v) NaCl and at pH 7.0 on marine agar medium. Strain SAB-3T was unable to hydrolyse aesculin and did not grow in the presence of rifamycin but showed resistance to antibiotics such as cefadroxil and co-trimoxazole. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0, and Q-8 was the major ubiquinone. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.0 mol%. 16S rRNA gene sequencing and phylogenetic analysis indicated that the strain was a member of the genus Marinomonas with Marinomonas aquiplantarum IVIA-Po-159T (97.6 % similarity), Marinomonas posidonica IVIA-Po-181T (97.5 %) and Marinomonas dokdonensis DSM 17202T (97.4 %) as the closest relatives. Whole genome relatedness determined through DNA-DNA hybridization revealed values of 40-50 % (below the 70 % threshold recommended for species delineation) with the above three species, thus confirming it as representing a distinct and novel species of the genus Marinomonas for which the name Marinomonas epiphytica sp. nov. is proposed. The type strain is SAB-3T (=JCM 31365T=KCTC 52293T=MTCC 12569T).

Quality of care in patients with diabetic kidney disease in Asia: The Joint Asia Diabetes Evaluation (JADE) Registry

AIMS

Diabetic kidney disease independently predicts cardiovascular disease and premature death. We examined the burden of chronic kidney disease (CKD, defined as an estimated GFR < 60 ml/min/1.73 m(2) ) and quality of care in a cross-sectional survey of adults (age ≥ 18 years) with Type 2 diabetes across Asia.

METHODS

The Joint Asia Diabetes Evaluation programme is a disease-management programme implemented using an electronic portal that systematically captures clinical characteristics of all patients enrolled. Between July 2007 and December 2012, data on 28 110 consecutively enrolled patients (China: 3415, Hong Kong: 15 196, India: 3714, Korea: 1651, Philippines: 3364, Vietnam: 692, Taiwan: 78) were analysed.

RESULTS

In this survey, 15.9% of patients had CKD, 25.0% had microalbuminuria and 12.5% had macroalbuminuria. Patients with CKD were less likely to achieve HbA1c < 53 mmol/mol (7.0%) (36.0% vs. 42.3%) and blood pressure < 130/80 mmHg (20.8% vs. 35.3%), and were more likely to have retinopathy (26.2% vs. 8.7%), sensory neuropathy (29.0% vs. 7.7%), cardiovascular disease (26.6% vs. 8.7%) and self-reported hypoglycaemia (18.9% vs. 8.2%). Despite high frequencies of albuminuria (74.8%) and dyslipidaemia (93.0%) among CKD patients, only 49.0% were using renin-angiotensin system inhibitors and 53.6% were on statins. On logistic regression, old age, male gender, tobacco use, long disease duration, high HbA1c , blood pressure and BMI, and low LDL cholesterol were independently associated with CKD (all P < 0.05).

CONCLUSIONS

The poor control of risk factors, suboptimal use of organ-protective drugs and high frequencies of hypoglycaemia highlight major treatment gaps in patients with diabetic kidney disease in Asia.

Pentoxifylline in perforated peritonitis: results of a randomised, placebo controlled trial

OBJECTIVES

To evaluate the role of pentoxifylline as an adjuvant to operation and routine antibiotic treatment for perforated peritonitis.

DESIGN

Randomised controlled clinical trial.

SETTINGS

University hospital, India.

SUBJECTS

36 patients with clinically diagnosed and radiologically confirmed perforated peritonitis. 22 (61%) had typhoid enteric perforations, 11 (31%) had duodenal ulcer perforations while 3 (8%) had perforated gastric ulcers.

INTERVENTION

Laparotomy with closure of perforation and lavage together with routine antibiotic treatment (ciprofloxacin and metronidazole), and random allocation to pentoxifylline 200 mg/day for 3 days in 500 ml of saline over 3-4 hours or saline alone (n = 18 in each group).

MAIN OUTCOME MEASURES

Hospital stay, APACHE II scores, and the condition of the wound during the postoperative period.

RESULTS

The baseline characteristics of the two groups were essentially similar. However, their preoperative APACHE II scores differed significantly (mean (SD) 12 (3) in the pentoxifylline group compared with 10 (2) in the saline group; p <0.01). The outcome was better in the pentoxifylline group in terms of significantly reduced hospital stay (median 8, range 6-17, compared with 11, 7-27, p=0.02) improved postoperative APACHE II scores (mean (SD) 8 (2) compared with 9 (2), p=0.02), and reduced incidence of wound infection (6/18 compared with 12/18, p=0.02).

CONCLUSION

The addition of pentoxifylline to our standard management protocol for patients with perforated peritonitis helped to improve their outcome significantly compared with a placebo-treated group.

Revisiting the stringent response, ppGpp and starvation signaling

Microbial adaptation to environmental stress plays an important role in survival. It is necessary to understand the mechanisms underlying the survival of microbes under stress, as they may eventually aid in the successful control of the growth and persistence of these organisms. During nutrient starvation, Escherichia coli elicits a stringent response to conserve energy. The hallmark of the stringent response is the accumulation of guanosine tetra- (ppGpp) and pentaphosphates (pppGpp), which probably bind RNA polymerase to regulate gene expression at certain promoters. Recently, there has been renewed interest in the stringent responses of other microbes, with a view to correlating it with sporulation, virulence and long-term persistence.

High intracellular level of guanosine tetraphosphate in Mycobacterium smegmatis changes the morphology of the bacterium

Almost one-third of the world population today harbors the tubercle bacillus asymptomatically. It is postulated that the morphology and staining pattern of the long-term persistors are different from those of actively growing culture. Interestingly, it has been found that the morphology and staining pattern of the starved in vitro population of mycobacteria is similar to the persistors obtained from the lung lesions. In order to delineate the biochemical characteristics of starved mycobacteria, Mycobacteria smegmatis was grown in 0.2% glucose as a sole carbon source along with an enriched culture in 2% glucose. Accumulation of the stringent factor guanosine tetraphosphate (ppGpp) with a concomitant change in morphology was observed for M. smegmatis under carbon-deprived conditions. In addition, M. smegmatis assumed a coccoid morphology when ppGpp was ectopically produced by overexpressing Escherichia coli relA, even in an enriched medium. The Mycobacterium tuberculosis relA and spoT homologue, when induced in M. smegmatis, also resulted in the overproduction of ppGpp with a change in the bacterium's growth characteristics.