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Microbial cellulose, especially the bacterial cellulose produced by symbiotic co-cultures of acetic acid bacteria and yeast (SCOBY) that exists in a mutualistic interaction opens plausible strategies in the field of food as well as sustainable regenerative eco-system and waste management. Cultivated on sweetened black tea, the mutually proliferating bacteria (Acetobacter xylinum, A. xylinoides, and Bacterium gluconicum) and yeast strains (Schizosaccharomyces pombe, Saccharomycodes ludwigii and Saccharomyces cerevisiae) produces a fermented liquor along with the floating bacterial cellulosic pellicle called as Kombucha. This review explores the possible applications of kombucha SCOBY to use bacterial cellulose-based engineered living materials, commercial superabsorbent spheres by various marketing ventures like food, pharmaceutics, biomedical applications for bio-sensing and bio-catalysis, crop biostimulants, biocontrol agents in the management of plant and animal illnesses, post-harvest management in crops, water purification, pollutant detection, environmental biotechnology, and production of SCOBY from alternative substrates and agrarian waste management. The plausible use of bacterial cellulose hydrogels in dryland agriculture for their exceptional water-absorbing capability, eco-friendly nature, capacity to break down naturally, and compatibility with other living organisms is also elaborated in this paper. Furthermore, diverse microbial species to enhance the variety and functional properties of SCOBY, health benefits and its influence on human welfare is vividly discussed in the paper. The very in-depth study on the uses of SCOBY also paves way for the research exploration of this under-utilized microbial boon in food and farm sector for circular based regenerative agriculture in near future.

Rapid nucleic acid assays have been approved by FDA for managing the COVID-19 pandemic, however its analytical efficiency has not been thoroughly validated. This study evaluates the detection and identification of COVID-19 virus using Abbott ID-Now to rapidly identify cases and intervention practices in comparison to nucleic acid detection. Nasopharyngeal Swabs collected from 611 participants were tested for Abbott ID-NOW and LabGun COVID-19 ExoFast RT-PCR Kit as per manufacturer’s protocol. The results from the ID NOW™ COVID-19 assay were evaluated by comparing results with the standard RT-PCR, which served as a standard reference. The infection burden of SARS-CoV-2 in the population of UAE was 11.62%. Compared to detection using real time-based platforms, the sensitivity, specificity, positive and negative predictive values of the ID-Now were 84.51%, 99.81%, 98.36% and 98.00% respectively for COVID-19. A stratified analysis was also carried out using cycle threshold (Ct) values categorizing as Ct>33 as with low viral loads while those with Ct

Increasing soil salinity depreciates the quantity of the crop produce. Looking at the tremendous potential of plant-associated microorganisms in salinity stress mitigation, it would be very useful in exploring and deciphering salt-tolerant microorganisms from halophytic plants and their utilization in cultivated plants. With this aim, in the present study, four halophytic plants were taken from Rann of Kutch, and bacterial endophytes were isolated from different plant organs. These endophytes were characterized by plant growth and health promotion features. The molecular identification was done based on 16 s rRNA sequence similarity. It was found that the endophytic bacteria isolated from 4 different halophytes found sharing phylogenetic relatedness. Four potential endophytes Alkalihalobacillus gibsonii 2H2, Achromobacter insuavis 2H18, Terribacillus halophilus 2H20, and Bacillus siamensis 4H1 were tested in tomato for salinity stress alleviation. Changes in the levels of antioxidants were analyzed. Total chlorophyll, total phenolics, malondialdehyde, and proline content indicated reduced damage in the plant system due to salinity by the application of endophytes. All the treatments exhibited low levels of electrolyte leakage. The accumulation of enzymatic reactive oxygen species scavengers was assessed from the levels of peroxidase, catalase, superoxide dismutase, phenylalanine ammonia-lyase, ascorbate peroxidase, and guiacol peroxidase. The NBT and DAB staining confirmed the findings. The reduction in the accumulation of Na+ ions in tomato leaves was visualized using Sodium Green probes under CSLM and found to be lowest in Terribacillus halophilus 2H20 and Bacillus siamensis 4H1 inoculated plants. The endophyte Terribacillus halophilus 2H20 was the most promising isolate. The colonization in tomato roots was confirmed using a cell tracker system. Results showed that the endophytes were found to have salinity stress mitigation traits. The efficiency could be further improved with the combination of other endophytes tested earlier.

Introduction: In the era of increasing antimicrobial resistance, knowing the mechanism of carbapenem resistance can aid in choosing an apt drug for treatment of patients. There are only few studies estimating the burden of carbapenem resistance and determining the mechanism of resistance among the isolates in our locale. Aim: To determine the prevalence of carbapenemase production by modified Carbapenem Inactivation Method (mCIM) among the Carbapenem Resistant Gram-Negative Bacteria (CRGNB)- Enterobacteriaceae and Pseudomonas aeruginosa isolated in our hospital. Materials and Methods: This was a prospective observational study conducted in Department of Microbiology, KMCH, Coimbatore, Tamil Nadu, India during the period of June 2021 to August 2021. A total of 165 isolates of Enterobacteriaceae family and P. aeruginosa which were resistant to one of the carbapenems (imipenem, meropenem or ertapenem) by Vitek MIC testing were included in the study. All were subjected to mCIM and EDTA-modified CIM (eCIM) test and interpreted as per the CLSI M100 S31 guidelines. Results: Among the 165 isolates, 130 (78.8%) were K. pneumoniae, 27 (16.4%) were other Enterobacteriaceae and eight (4.8%) were P. aeruginosa. Prevalence of mCIM positivity was 51.5% (85 isolates). Approximately, 98% of the mCIM positives (Carbapenemase Producing Gram-Negative Bacteria [CPGNB]) were eCIM positive indicating Metallo-Beta- Lactamase (MBL) production. Conclusion: Performing mCIM in CRGNB is important in routine practice to identify CPGNBs. Due to very high prevalence of MBL among carbapenemase producers, it is advisable to choose ceftazidime avibactam plus aztreonam as the treatment option for CPGNB in our locale.

Introduction: In the recent days, large proportion of the Intensive Care Unit (ICU) admissions ending in poor outcomes is impacted by pathological conditions like sepsis and septic shock. Hence, early diagnosis and appropriate therapy within the first hours of hospital admission plays a major role. Simple markers like C-Reactive Protein (CRP), Erythrocyte Sedimentation Rate (ESR), blood counts are still relied upon for suspected sepsis cases. Aim: To study the prevalence of sepsis and to evaluate the utility of the simple ideal markers like CRP, ESR, and blood counts for early diagnosis of sepsis in critically ill patients. Materials and Methods: This was a prospective observational study performed in the ICU of KMCH Institute of Allied Health Sciences, Coimbatore, Tamil Nadu, India, using 112 blood samples collected from patients admitted with clinical suspicion of sepsis. The samples were subjected to CRP estimation using turbidimetric immunoassay and blood culture. The data obtained were analysed using Statistical Package for the Social Sciences (SPSS) software version 21.0. The sensitivity, specificity, negative and positive predictive values were calculated. Results: Among a total of 112, the number of patients who abided the sepsis-3 definitions with positive qSOFA (quick Sepsis related Organ Failure Assessment) score was 50%. The most common comorbid condition among the sepsis patients were diabetes mellitus (39.2%). The most frequent site of infection was respiratory tract (37.5%). Majority of infections were by gram-negative organisms (82%), the commonly isolated gram negative organisms were Klebsiella pneumoniae (25.9%) and Escherichia coli (25.9%). The sensitivity of CRP was 81% and specificity was 49% while the Positive Predictive Value (PPV) and Negative Predictive Value (NPV) was 60% and 56%, respectively. The prevalence of sepsis in present study was 50%. Conclusion: The study highlights the usefulness of CRP in identifying patients with sepsis in those who present with positive qSOFA score. Also, CRP could be very useful in resource-limited places, where newer biomarkers and guidance of an intensivist or sepsis expert are not available.

Background and Objectives: Cryptococcosis is an opportunistic mycosis, caused by Cryptococcus neoformans. Cryptococcal meningitis is one of the most fatal opportunistic infections associated with human immunodeficiency virus (HIV) infection. The aim of this study was to find the prevalence of cryptococcal antigenemia in people living with HIV (PLHA) and also to find the prevalence of opportunistic infections among these patients. Materials and Methods: A total of 204 non duplicate samples were collected from people with HIV aged above 18 years. Samples with CD4 count less than 300 were included in the study. Cryptococcal antigen detection was done by CrAg Lateral flow assay. Results: None of the patients in our study were positive for cryptococcal antigen. Opportunistic infections were observed in 82 (40.2%) HIV positive patients. Candidiasis, tuberculosis and Pneumocystis jiroveci pneumonia were the most common opportunistic infections. Conclusion: This is the first study from the southern state of Kerala on the prevalence of Cryptococcal antigenemia among HIV positive individuals. The study showed that routine screening for cryptococcal antigen will not be cost effective in our population. Similar to other studies, eventhough candidiasis, tuberculosis and PCP were more commonly seen among people with CD4 count < 200 cells/mm3, there was no statistically significant association.

An enveloped double-stranded DNA monkeypox virus (MPXV) is a causative agent of the zoonotic viral disease, human monkeypox (HMPX). MPXV belongs to the genus Orthopoxviridae, a family of notorious smallpox viruses, and so it shares similar clinical pathophysiological features. The recent multicountry HMPX outbreak (May 2022 onwards) is recognized as an emerging global public health emergency by the World Health Organization, shunting its endemic status as opined over the past few decades. Re-emergence of HMPX raises concern to reassess the present clinical strategy and therapeutics as its outbreak evolves further. Keeping a check on these developments, here we provide insights into the HMPX epidemiology, pathophysiology, and clinical representation. Weighing on its early prevention, we reviewed the strategies that are being enrolled for HMPX diagnosis. In the line of expanded MPXV prevalence, we further reviewed its clinical management and the diverse employed preventive/therapeutic strategies, including vaccines (JYNNEOS, ACAM2000, VIGIV) and antiviral drugs/inhibitors (Tecovirimat, Cidofovir, Brincidofovir). Taken together, with a revised perspective of HMPX re-emergence, the present report summarizes new knowledge on its prevalence, pathology, and prevention strategies.

Background and Objectives: Resistance to methicillin in methicillin resistant strains of Staphylococcus aureus (MRSA) is due to the presence of mec-A gene ,which encodes a low affinity penicillin binding protein (PBP)-2a or PBP2. Accurate and rapid identification of MRSA in clinical specimens is essential for timely decision on effective treatment. The aim of the study was to compare three different methods for detection of MRSA namely cefoxitin disc diffusion, CHROM agar MRSA and VITEK-2 susceptibility with PCR which is the gold standard reference method and to find the antibiotic susceptibility pattern of these isolates by VITEK-2. Materials and Methods: A Total of 100 non-duplicate S. aureus isolates were collected from different clinical samples among both outpatient and inpatients. Detection of MRSA among these isolates was done by cefoxitin disc diffusion, VITEK-2, CHROM agar MRSA and PCR. Results: The sensitivity and specificity of cefoxitin disc diffusion and Vitek was found to be 97.2% and 100%, while that of CHROM agar was found to be 100% and 78.6%. The overall prevalence of MRSA in our study by PCR was 72%. Conclusion: Based on the findings in our study, isolates which show cefoxitin zone diameter < 22 mm can be reported as MRSA. However, those isolates which have a zone diameter between 22-24 mm, should ideally be confirmed by PCR.

Pathogenic potentials of the gastric pathogen, Helicobacter pylori, have been proposed, evaluated, and confirmed by many laboratories for nearly 4 decades since its serendipitous discovery in 1983 by Barry James Marshall and John Robin Warren. Helicobacter pylori is the first bacterium to be categorized as a definite carcinogen by the International Agency for Research on Cancer (IARC) of the World Health Organization (WHO). Half of the world’s population carries H. pylori, which may be responsible for severe gastric diseases like peptic ulcer and gastric cancer. These two gastric diseases take more than a million lives every year. However, the role of H. pylori as sole pathogen in gastric diseases is heavily debated and remained controversial. It is still not convincingly understood, why most (80–90%) H. pylori infected individuals remain asymptomatic, while some (10–20%) develop such severe gastric diseases. Moreover, several reports indicated that colonization of H. pylori has positive and negative associations with several other gastrointestinal (GI) and non-GI diseases. In this review, we have discussed the state of the art knowledge on “H. pylori factors” and several “other factors,” which have been claimed to have links with severe gastric and duodenal diseases. We conclude that H. pylori infection alone does not satisfy the “necessary and sufficient” condition for developing aggressive clinical outcomes. Rather, the cumulative effect of a number of factors like the virulence proteins of H. pylori, local geography and climate, genetic background and immunity of the host, gastric and intestinal microbiota, and dietary habit and history of medicine usage together determine whether the H. pylori infected person will remain asymptomatic or will develop one of the severe gastric diseases.

Background and Objectives: Hepatitis C is the most common hepatotropic viral infection that affects patients on maintenance hemodialysis. Most of the laboratories in India depend on HCV antibody detection by ELISA. PCR based studies on detection of HCV RNA among haemodialysis patients are very scanty in India. The current study was undertaken to find the prevalence of HCV among haemodialysis patients by ELISA and PCR. Materials and Methods: This prospective study was conducted from January to May 2018 in a total of 100 samples. Patients more than 18 years of age, who had undergone at least 15 sessions of dialysis were enrolled in the study. All samples were screened for HCV antibody by ELISA and HCV RNA by PCR. Data regarding age and gender of the patients, history of blood transfusion, duration of hemodialysis, total bilirubin levels were collected from medical records. Results: Among the 100 samples, only one was positive for HCV antibody by ELISA. Eight samples were positive for HCV RNA by PCR. In this study 62.5% of the HCV positives had a previous history of blood transfusion. Duration of dialysis was more among the HCV positive group but there was no statistical significance. Conclusion: This is the first study from the southern state of Kerala in India showing the prevalence of HCV among hemodialysis patients by PCR. Our study showed an overall HCV prevalence of 8% by PCR. All the PCR positive samples were negative by 3rd generation ELISA which is an alarming finding and further justifies the need for PCR for detecting HCV.

Context: Helicobacter pylori is associated with the development of a variety of gastroduodenal diseases which varies with ethnicity and the type of strains that infect the population. Aims: This study aims to evaluate the prevalence of H. pylori cagA and vacA genotypes in our region and to determine their relationship to the severity of the lesions that they cause. Settings and Design: This study was an observational cross-sectional study. Subjects and Methods: DNA was extracted from 165 gastric biopsies from patients evaluated for dyspepsia. PCR was used to detect cagA and vacA (s1, s2, m1, m2) genes of H. pylori. Statistical analysis of associations was performed between endoscopy findings and virulence genes. Statistical Analysis Used: Pearson Chi-square test and Fischer's exact test. Results: The prevalence of H. pylori infection was 37% and the dominant genotypes was vacA s1 cagA-positive strain (54.1%) in this study. The vacAs1 subtype was found in all patients with peptic ulcer disease (PUD). The entire normal study group had VacA s2 variant only. This clearly shows that vacA s1 is a significant virulence marker and patients harboring s1 strains are more prone to develop ulcers (P = 0.007). There was a significant association of cagA with s1 strain rather than s2. Variation in VacA m genotype did not seem to have any association with disease status. There was a statistically significant association between the presence of cagA gene and PUD rather than the nonulcer dyspepsia (P = 0.027). Conclusion: The predominant genotype in our population was cagA positive vacA s1, which was found to be significantly associated with patients with gastric diseases, especially PUD. VacA s1 can serve as a single best virulence marker of the disease manifestation.

Background and Objectives: Dengue and Leptospirosis were often discussed separately with rash being more common in dengue and jaundice in leptospirosis. But with increasing reports of co-infection, the situation has become worse. The main objective of this study was to look for the presence of both Dengue and Leptospira IgM antibodies in serum samples of patients, presenting with acute febrile illness. Medical records of the co-infected patients were examined to analyse the clinical features and laboratory findings. Materials and Methods: Serum samples of patients presenting with acute febrile illness were screened for the presence of Dengue IgM antibodies and Leptospira antibodies. Clinical features and laboratory parameters of patients with co-infection were compared with patients having dengue alone. Rainfall data was obtained to look for an association between rainfall and Dengue, leptospirosis and co-infected cases. Results: Co-infection was seen in 33 (3.4%) samples. There was a statistically significant association between clinical features like rashes, bleeding gums and co-infection. There was a statistically significant association between various laboratory parameters like thrombocytopenia and co-infection. There was positive correlation between rainfall and development of dengue, leptospirosis, and co-infection but it was not statistically significant. Conclusion: The overall prevalence of co-infection was 3.4%. This study re-emphasizes the fact that dengue and leptospirosis are widely prevalent in south India and clinicians should be aware that co-infection with dengue and leptospirosis is not uncommon.

Nocardia otitidiscaviarum is a rare cause of pulmonary nocardiosis. We present a case of pulmonary nocardiosis with pleural involvement in an adolescent with rheumatic heart disease and congestive cardiac failure presenting with right lower lobe consolidation and pleural effusion. Direct gram-stain of pleural fluid showed pus cells with Gram-positive filamentous branching bacilli. Empiric treatment with parenteral ceftriaxone and supportive therapy for cardiac failure was initiated. Pleural fluid culture yielded growth of N. otitidiscaviarum at 72 h. Antibiotic susceptibility testing showed resistance to cephalosporins. The patient expired due to congestive cardiac failure on the 5th day.

Introduction: Streptococcus pneumoniae (pneumococci) colonizes the nasopharynx and 94 different serotypes have been characterized on the basis of the capsular polysaccharides. Nasopharyngeal colonization is documented to be present in children more, than that seen in adults. Pneumococci cause wide range of infections with marked morbidity among children, elderly and immuno-compromised patients. The pathogenesis may be attributed to the virulence factors such as pneumolysin and autolysin. Aim: The aim of this study was to demonstrate virulence genes, pneumolysin (ply) and autolysin (lytA) in pneumococci isolated from clinical samples and nasopharyngeal carriers by Polymerase Chain Reaction (PCR). Materials and Methods: Total 15,473 clinical samples of sputum, broncho-alveolar lavage, tracheal aspirate, cerebrospinal fluid, blood, ascitic fluid, throat swab, eye discharge, ear swab and pleural fluid from infected patients, including nasopharyngeal carriers screened for pneumococci in 600 healthy school children were included in the study. Blood and CSF isolates were categorized as invasive and those isolates obtained from other clinical sites as non-invasive, respectively. Standard methods for characterisation of Streptococcus pneumoniae such as Gram stain, Optochin sensitivity, bile solubility, and inulin fermentation was done, with confirmation by automated Vitek 2. Streptococcus pneumoniae isolated from positive samples were subjected to molecular detection of virulence genes lytA and ply coding for autolysin and pneumolysin respectively. Results: In all 121 Streptococcus pneumoniae positive isolates were isolated from clinical specimens including carriers with isolation rate of 0.81%. Seventy four pneumococci isolates were randomly selected which were representative of invasive, non-invasive and carrier isolates. They were screened by PCR for lytA and ply genes using appropriate primers. All isolates tested were positive for autolysin (lytA) and 97.2% including the 15 invasive isolates were positive for pneumolysin (ply). Conclusion: This study concludes that detection of virulence genes for pneumococci in clinical samples confirms the pathophysiologic consequences of pneumococcal infections.

Occupational exposure poses a significant risk of transmission of blood-borne pathogens to healthcare workers (HCWs). Adherence to standard precautions, awareness about post exposure prophylaxis is poor in developing countries. This retrospective study analyzes the self-reported cases of occupational exposure in a tertiary care hospital. During the study period, 105 HCWs sustained occupational exposure to blood and body fluids. Majority of the victims 36 (34.2%) were interns and the clinical practice that led to the occupational exposure was withdrawal of blood (45.7%). Good infection control practices and emphasis on appropriate disposal are needed to increase the occupational safety for HCWs.

Background: Chromosome 7 aberrations in renal cell carcinoma (RCC) have been reported in papillary renal cell carcinoma (pRCC) and clear cell renal cell carcinoma (ccRCC). However, the implication of these anomalies on prognosis and survival is still unclear. RCC Chromosome 7 aberrations have commonly been detected by fluorescent in situ hybridization and chromogenic in situ hybridization but not silver in situ hybridization (SISH). Aim: The purpose was to report chromosome 7 aberrations in ccRCC and pRCC using SISH in paraffin-embedded tissues and determine the association between the anomalies with clinical and pathological features. Materials and Methods: Cases of ccRCC and pRCC from University Malaya Medical Centre (2001-2009) were analyzed. Chromosome 7 staining was performed using an automated SISH method and association tests between chromosomal anomalies, clinical features and survival were performed. Results: SISH is a feasible technique to detect chromosome 7 aberration in RCC. Chromosome 7 aberrations with nuclear grading, staging and survival yielded no significant correlation. Surprisingly, there was a significant association between gender and chromosome 7 expressions. Though grade did not reach statistical significance for survival in our RCC cases, there was a significant correlation between overall survival with race and stage. Conclusion: Chromosome 7 aberrations in ccRCC showed no prognostic significance. Nevertheless, staging and grading systems that include prognostic variables could hold better promise.

Synovium is specialized mesenchymal tissue lining the inner surface of the joint capsule and is the site for a series of pathologic processes that are characteristic, and in some cases specific, to this distinctive tissue. Hemosiderotic synovitis is a rare and inadequately defined synovial proliferative disorder, which develops with recurrent hemorrhages in the joint. The most affected joint from bleeding is the knee whatever the etiology is. Repeated hemarthrosis may produce significant structural alteration of joints leading to chronic osteoarthritis. The most common cause is hereditary clotting factor deficiency diseases like hemophilia. We report a rare case of nonhemophilic hemosiderotic synovitis of the knee joint, in which the patient lacks history of any bleeding diathesis. Its definitive diagnosis was possible only by histopathological examination. The prompt recognition of this distinct subtype of hemosiderotic synovitis and awareness of underlying causes should lead to earlier diagnosis, appropriate therapy, less joint destruction, and better outcomes.

Background and Objectives: Phenotypic methods for detection of methicillin resistant Staphylococcus aureus (MRSA) have been compared with the gold standard which, as of now, is by the detection of mecA gene and femA gene by polymerase chain reaction (PCR). Discrepancies in detection have an adverse effect on patient management, thereby highlighting the importance of accuracy in detection. Our study aims to evaluate the efficacy of cefoxitin disk diffusion test to detect MRSA and compare it with other phenotypic and molecular methods. Methodology; The study was conducted from June 2006 to December 2007 and included 610 Staphylococcus aureus (S. aureus) isolates obtained from clinical samples. All isolates were tested for MRSA using oxacillin screen agar plates with 6 µg/ml of oxacillin, cefoxitin disk diffusion using 30 µg disk and MIC of oxacillin. Selected isolates (55) were tested for presence of mecA gene and Fem A gene by PCR. Results: Out of 610 isolates, MRSA was identified in 34.09% by cefoxitin disk diffusion, 34.9% by oxacillin screen agar, 34.4% by MIC and 37.3% by oxacillin disk diffusion. When selected isolates were tested with molecular methods, the cefoxitin disk diffusion and PCR tests were comparable. Discussion: Prevalence of MRSA (34.09%) is quite high as in other studies. The oxacillin disk diffusion test which was used routinely earlier is showing low specificity (56%). Among all phenotypic methods, cefoxitin disk diffusion and PCR alone have similar sensitivity and specificity. Conclusion: Results of cefoxitin disk diffusion test are in concordance with the PCR for mecA gene. Thus, the test can be an alternative to PCR for detection of MRSA in resource constraint settings.

To date, sarcocystis has been considered an asymptomatic infection in humans. Even though cases with glomerulonephritis have been reported in animals with sarcocystis, there have been no reports of a similar occurrence in humans. We report a case of acute proliferative glomerulonephritis and leukocytoclastic vasculitis in a patient with sarcocystis infestation.

To evaluate the diagnostic efficacy of various screening tests in detecting asymptomatic bacteriuria among pregnant women. Clean catch midstream urine specimens were collected from 630 consecutive pregnant women and processed. Forty-four (7.4%) of the urine samples were culture positive, with Escherichia coli as the predominant organism isolated (57.4%). The results of the four screening tests, viz., Gram′s staining of uncentrifuged urine, pus cell count, nitrite test and leukocyte esterase (LE) test, were compared against urine culture. Gram′s stain of the uncentrifuged urine was found to be the single most useful test with a sensitivity and negative predictive value (NPV) of 85.1% and 98.8%, respectively. Pus cell count was the least sensitive. Neither the nitrite test nor the LE test alone was sensitive enough with 74.4% and 61.7%, respectively. However, when either or both tests positive were considered, it increased the sensitivity and NPV comparable with Gram′s staining results, with 82.9% and 98.8%, respectively. With the potential to be used as an office diagnostic procedure, the combined nitrite and LE dipstick test may provide an acceptable alternative.