Comparison of integron mediated antimicrobial resistance in clinical isolates of Escherichia coli from urinary and bacteremic sources.

BACKGROUND: Antimicrobial resistance (AMR) is a global threat driven mainly by horizontal gene transfer (HGT) mechanisms through mobile genetic elements (MGEs) including integrons. The variable region (VR) of an integron can acquire or excise gene cassettes (GCs) that confer resistance to antibiotics based on the selection pressure. Escherichia coli plays a significant role in the genetic transfer of resistance determinants to other Gram-negative bacteria. Current study is aimed to detect and compare integron-mediated resistance in clinical isolates of E. coli. Unique isolates of E. coli from urine or blood cultures were studied for their antimicrobial resistance patterns and integrons were detected using polymerase chain reaction assays followed by Sanger sequencing of GCs. RESULTS: During the study period, a total of 470 E. coli isolates were obtained, 361 (76.8%) from urinary and 109 (23.1%) from bacteremic sources. Class 1 integrons were detected in 66 (18.2%) and 26 (23.8%) isolates respectively. Urinary isolates of E. coli harbouring Class 1 integrons demonstrated significantly higher rates of resistance (p < 0.05) for most antibiotics (12/16, 75%) compared to integron negative isolates. Although not statistically significant, similar differences were observed in bacteremic isolates. Among the urinary isolates, 27 (40.9%) had a VR, in which the most common GC array detected was DfrA17-AadA5 (n = 14), followed by DfrA5 (n = 4) and DfrA12 (n = 3). Among bacteremic isolates, only 4 (15.3%) had a VR, all of which were carrying DfrA17. The detected GC array correlated with the respective isolates' phenotypic resistance patterns. CONCLUSION: We found a strong correlation between integron positivity and trimethoprim resistance among E. coli from urinary sources. Although higher rates of resistance were observed in bacteremic isolates, they mostly carried empty integrons.

Optimization of an allelic discrimination real-time RT-PCR assay for detection of H275Y oseltamivir resistance gene mutation among influenza A(H1N1)pdm09 patients from 2020 to 2022.

Influenza virus is known to cause mild to severe respiratory infections and is also prone to genetic mutations. Of all the mutations, neuraminidase (NA) gene mutations are a matter of concern, as most approved antivirals target this protein. During the 2020 influenza season, an emergence of mutation in the NA gene, affecting the binding of the World Health Organization (WHO)-recommended probes to the specific site of the NA gene, was reported by our group. As a result of this mutation, the WHO-recommended allelic discrimination real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was unable to detect wild-type (H275) or mutant oseltamivir-resistant (Y275) strains of influenza A(H1N1)pmd09 viruses. In the current study, the WHO-recommended probes were redesigned according to the mutation in the probe binding site. Fifty undetermined samples (2020-2021) from the previous study were retested with the newly designed probes and found to be positive for H275 and/or Y275. The results obtained were similar to the Sanger sequencing results from the previous study, suggesting that the redesigned probes were efficient in discriminating between wild-type and mutant-type viruses. Furthermore, 133 samples from 2022, making a total of 183 samples (2020-2022), were tested using improved allelic discrimination real-time RT-PCR, and the overall prevalence rate of oseltamivir resistance in 2020-2022 was found to be 0.54%.

Disposable electrochemical biosensors for the detection of bacteria in the light of antimicrobial resistance.

Persistent and inappropriate use of antibiotics is causing rife antimicrobial resistance (AMR) worldwide. Common bacterial infections are thus becoming increasingly difficult to treat without the use of last resort antibiotics. This has necessitated a situation where it is imperative to confirm the infection to be bacterial, before treating it with antimicrobial speculatively. Conventional methods of bacteria detection are either culture based which take anywhere between 24 and 96 hor require sophisticated molecular analysis equipment with libraries and trained operators. These are difficult propositions for resource limited community healthcare setups of developing or less developed countries. Customized, inexpensive, point-of-care (PoC) biosensors are thus being researched and developed for rapid detection of bacterial pathogens. The development and optimization of disposable sensor substrates is the first and crucial step in development of such PoC systems. The substrates should facilitate easy charge transfer, a high surface to volume ratio, be tailorable by the various bio-conjugation chemistries, preserve the integrity of the biorecognition element, yet be inexpensive. Such sensor substrates thus need to be thoroughly investigated. Further, if such systems were made disposable, they would attain immunity to biofouling. This article discusses a few potential disposable electrochemical sensor substrates deployed for detection of bacteria for environmental and healthcare applications. The technologies have significant potential in helping reduce bacterial infections and checking AMR. This could help save lives of people succumbing to bacterial infections, as well as improve the overall quality of lives of people in low- and middle-income countries.

Detection of H275Y oseltamivir resistance gene mutation among Influenza A(H1N1)pdm09 patients by allelic discrimination real-time RT-PCR.

Influenza viruses can mutate genetically and cause a range of respiratory ailments. The H275Y mutation in the neuraminidase (NA) gene reduces the effectiveness of oseltamivir, a widely used drug for the treatment of Influenza A and B virus infection. The World Health Organization (WHO) recommends single-nucleotide polymorphism assays to detect this mutation. The present study aims to estimate the prevalence of H275Y mutation conferring oseltamivir resistance in Influenza A(H1N1)pdm09 virus among hospitalized patients from June 2014 to December 2021. Following the WHO protocol, allelic discrimination real-time RT-PCR was performed for 752 samples. Out of the 752 samples, 1 tested positive for Y275 gene mutation by allelic discrimination real-time RT-PCR. In samples of years 2020 and 2021, neither the H275 nor Y275 genotype was detected. Sequencing of the NA gene of all negative samples showed a mismatch between the NA sequence and the probes used in the allelic discrimination assay. Also, Y275 mutation was detected in only 1 sample from 2020. The prevalence of oseltamivir resistance was estimated as 0.27% among the Influenza A(H1N1)pdm09 patients during 2014-2021. The study highlights that the WHO-recommended probes for detecting H275Y mutation may not be useful to detect 2020 and 2021 circulating strains of Influenza A(H1N1)pdm09, emphasizing the need for continuous monitoring of mutations in the influenza virus.

Preventing Risks of Infections and Medication Errors in IV therapy (PRIME): a patient safety initiative.

BACKGROUND: Two major avoidable reasons for adverse events in hospital are medication errors and intravenous therapy-induced infections or complications. Training for clinical staff and compliance to patient safety principles could address these. METHODS: Joint Commission International (JCI) consultants created a standardised, 6-month training programme for clinical staff in hospitals. Twenty-one tertiary care hospitals from across south-east Asia took part. JCI trained the clinical consultants, who trained hospital safety champions, who trained nursing staff. Compliance and knowledge were assessed, and monthly audits were conducted. RESULTS: There was an overall increase of 29% in compliance with parameters around medication preparation and vascular access device management. CONCLUSION: The programme improved safe practice around preparing medications management and managing vascular access devices. The approach could be employed as a continuous quality improvement initiative for the prevention of medication errors and infusion-associated complications.

Burkholderia pseudomallei in Environment of Adolescent Siblings with Melioidosis, Kerala, India, 2019.

In 2019, Burkholderia pseudomallei was isolated from the backyard of 2 siblings with melioidosis in Kerala, India. This finding highlights the value of healthcare providers being aware of risk for melioidosis in febrile patients, of residents taking precautions when outside, and of increasing environmental surveillance for B. pseudomallei in this region.

Genotyping of Burkholderia pseudomallei Isolated From Patients in South-Western Coastal Region of India.

Burkholderia pseudomallei is the causative agent of melioidosis. Various tools have been used to determine the genetic diversity in B. pseudomallei isolates. In this study, Random Amplified Polymorphic DNA (RAPD)-PCR and flagellin gene (fliC) based PCR-Restriction Fragment Length Polymorphism (RFLP) were used to genotype Indian clinical B. pseudomallei isolates. A total of 89 clinical isolates could be grouped in 6 groups (A through F) by RAPD-PCR analysis. Some of the isolates in various groups had identical banding pattern suggesting them to be epidemiologically related. The RAPD groups also correlated with MLST sequence types suggesting the utility of this easy to do typing method. The PCR- RFLP analysis suggested Type III to be the predominant type which is different from other RFLP types reported from Southeast Asia. In conclusion, the results of this study show that RAPD-PCR, a simple genotyping method, may be used for analyzing the B. pseudomallei isolates and also establish epidemiological relevant relatedness among them. The results of fliC PCR-RFLP further suggest the Indian isolates are different from other Southeast Asian isolates.

Evaluation of clinical, diagnostic features and therapeutic outcome of neurobrucellosis: a case series and review of literature.

AIM: In this study, we aimed to discuss the clinical features, laboratory findings, treatment and outcome of seven cases of neurobrucellosis from a tertiary care center and review the available global literature. MATERIALS AND METHODS: The diagnosis of neurobrucellosis was established using the following criteria in our setting: (1) signs and symptoms of neurological infection with examination of cerebrospinal fluid (CSF) revealing signs of meningitis, (2) isolation of Brucella spp. from blood and/or CSF and/or antibody titer ≥1:160 in serum using standard agglutination test (SAT) and/or the presence of anti-Brucella antibodies in CSF and/or detection of Brucella spp.-specific DNA from CSF using PCR. A literature search was performed to review previous cases of neurobrucellosis published worldwide during the last 30 years. RESULTS: The proportion of neurobrucellosis was 2.8% in our setting. Fever with headache and altered sensorium were the major presenting complaints. Brucella melitensis was isolated from blood culture in 6 patients. From the literature search, a total of 221 cases of neurobrucellosis were reviewed and analyzed. Meningitis (32.6%), loss of hearing (25.8%) and encephalitis (14.9%) were the most common clinical features. Involvement of cranial nerves, polyradiculopathy and paraplegia were the major complications found in patients with neurobrucellosis. CONCLUSIONS: Neurobrucellosis should always be considered in the differential diagnosis of befitting neurological, rheumatological, and neuropsychiatric presentations in endemic regions for brucellosis. To prevent morbidity and mortality associated with neurobrucellosis, a multimodal diagnostic approach is essential for early and accurate diagnosis and effective treatment.

Vitamin D in Prevention and Treatment of COVID-19: Current Perspective and Future Prospects.

Vitamin D deficiency (VDD) partly explains geographical differences in COVID-19 susceptibility, severity, and mortality. VDD among African-Americans, diabetics, hypertensive, and aged populations possibly explain the higher death rate, aggravated by cocooning. Vitamin D is pleiotropic, mediating bone metabolism, calcium homeostasis, and immune functions, whereas VDD is associated with inflammatory reactions and immune dysfunction, predisposing individuals to severe infections. Vitamin D modulates innate and adaptive immunity via the expression of genes that code antimicrobial peptides (AMPs). And the expression of cluster of differentiation (CD)14, the co-receptor for epidermal toll-like receptor (TLR)4. AMPs stimulate TLR2 in macrophages, increasing the conversion of vitamin D into its active form by cytochrome P450 27B1. Antiviral properties of vitamin D-induced AMPs can shift the polarization of the adaptive immune response from helper T cells (Th)1 to the more regulatory Th2 responses that suppress immune over-reactivity by preventing cytokine storm, which is already demonstrated during the Spanish flu episode. Vitamin D induces antiviral effects by both direct and indirect mechanisms via AMPs, immunomodulation, the interplay between major cellular and viral elements, induction of autophagy and apoptosis, variation of genetic and epigenetic factors. The crosstalk between vitamin D and intracellular signaling pathways may operate as a primary regulatory action on viral gene transcription. VDD may increase the likelihood of infection with enveloped viruses, including retrovirus, hepatitis, and dengue. Global data correlates severe VDD with COVID-19 associated coagulopathy, disrupted immune response and mortality, reduced platelet count, and prolonged prothrombin time, suggesting benefits from supplementation.Key teaching pointsVitamin D induces antiviral effects by direct and indirect mechanisms via AMPs, immunomodulation, induction of autophagy, etc.Epidemiology of VDD partly explains geographical differences in COVID-19 susceptibility, severity, and mortality.Global data correlates severe VDD with COVID-19 associated coagulopathy, disrupted immune response and mortality, reduced platelet count, and prolonged prothrombin time, together suggesting benefits from supplementation.Many clinical trials are underway globally to delineate the role of vitamin D in both prevention and treatment of COVID-19.

Structure, staffing, and factors affecting infection control nurses: Hospital based exploratory survey- A study protocol.

AIM: The overall aim of the study is to develop a module for the structure, staffing, job responsibilities, training and workflow for the hospital Infection Control Department. DESIGN: An exploratory research design in two phases. Phase 1: Hospital based exploratory survey design. Phase 2: Delphi technique with Focus Group Discussion. METHOD: Data will be collected through interviewing Infection Control Nurses (ICNs) or infection control in-charge using Infection Prevention and Control Assessment Framework (IPCAF) released by World Health Organization (WHO) in the first phase and Delphi technique in the second phase to determine the problems and solutions for the concerns pertaining to the ICNs. The study is funded by Indian Council of Medical Research from 15 October 2019 for 3 years duration. DISCUSSION: Healthcare Associated Infection (HAI) affects the care quality of millions of people around the globe. Many researchers have explored the evidence for causes and measures to contain infection. However, there are hardly few researches from the perspective to structure, staffing pattern and factors affecting ICNs. As staffing is considered as a vital component in infection prevention, there is a necessity for optimization to reduce the global burden related to HAI. IMPACT: This protocol on Structure, staffing, and factors affecting ICN will provide insight into developing strategy, policy or educational module for the ICNs across the country. TRIAL REGISTRATION: The trial is registered with Central Trial Registry of India (CTRI) with reference ID: CTRI/2020/07/026286.

Interplay between Hepatitis E Virus and Host Cell Pattern Recognition Receptors.

Hepatitis E virus (HEV) usually causes self-limiting acute hepatitis, but the disease can become chronic in immunocompromised individuals. HEV infection in pregnant women is reported to cause up to 30% mortality, especially in the third trimester. Additionally, extrahepatic manifestations like neuronal and renal diseases and pancreatitis are also reported during the course of HEV infection. The mechanism of HEV pathogenesis remains poorly understood. Innate immunity is the first line of defense triggered within minutes to hours after the first pathogenic insult. Growing evidence based on reverse genetics systems, in vitro cell culture models, and representative studies in animal models including non-human primates, has implicated the role of the host's innate immune response during HEV infection. HEV persists in presence of interferons (IFNs) plausibly by evading cellular antiviral defense. This review summarizes our current understanding of recognizing HEV-associated molecular patterns by host cell Pattern Recognition Receptors (PRRs) in eliciting innate immune response during HEV infection as well as mechanisms of virus-mediated immune evasion.

Melioidosis: A Neglected Cause of Community-Acquired Pneumonia.

Melioidosis, caused by the facultative intracellular gram-negative pathogen Burkholderia pseudomallei, is an emerging cause of community-acquired pneumonia across the tropics. The majority of patients present with pneumonia with or without sepsis, but localized and asymptomatic infection is also well recognized. Recent modeling and epidemiological studies have demonstrated the widespread presence of B. pseudomallei in otherwise unrecognized regions with a predicted mortality of 90,000 deaths worldwide. Innovative environmental studies are also uncovering how hydrodynamic, pedology, fauna, and weather events influence geographic distribution and incidence of melioidosis cases. Of concern is the changes associated with global warming, which will be conducive to B. pseudomallei in combination with the global diabetes pandemic. In fact, over 80% of patient developing melioidosis have underlying comorbidities. For this great mimicker, culture remains the mainstay of diagnosis and despite availability of other assays, challenges still remain in reducing time to diagnosis and avoiding misdiagnosis. With institution of timely antimicrobials such as ceftazidime and supportive intensive care, overall mortality can be reduced to 10%, although this can still be as high as 50% in poorly resourced areas. Promise is on the horizon with the first human vaccine trials being planned for 2021. Meanwhile new multiomics techniques are giving us a better understanding of the role of virulence and host-pathogen interactions on patient outcomes.

Community-acquired bacterial pneumonia in adults: An update.

Community-acquired pneumonia (CAP) is the prominent cause of mortality and morbidity with important clinical impact across the globe. India accounts for 23 per cent of global pneumonia burden with case fatality rates between 14 and 30 per cent, and Streptococcus pneumoniae is considered a major bacterial aetiology. Emerging pathogens like Burkholderia pseudomallei is increasingly recognized as an important cause of CAP in Southeast Asian countries. Initial management in the primary care depends on clinical assessment while the hospitalized patients require combinations of clinical scores, chest radiography and various microbiological and biomarker assays. This comprehensive diagnostic approach together with additional sampling and molecular tests in selected high-risk patients should be practiced. Inappropriate therapy in CAP in hospitalized patients lengthens hospital stay and increases cost and mortality. In addition, emergence of multidrug-resistant organisms poses tough challenges in deciding empirical as well as definitive therapy. Developing local evidence on the cause and management should be a priority to improve health outcomes in CAP.

The global impact and cost-effectiveness of a melioidosis vaccine.

BACKGROUND: Every year, 90,000 people may die from melioidosis. Vaccine candidates have not proceeded past animal studies, partly due to uncertainty around the potential market size. This study aims to estimate the potential impact, cost-effectiveness and market size for melioidosis vaccines. METHODS: Age-structured decision tree models with country-specific inputs were used to estimate net costs and health benefits of vaccination, with health measured in quality-adjusted life years (QALYs). Four target groups of people living in endemic regions were considered: (i) people aged over 45 years with chronic renal disease, (ii) people aged over 45 years with diabetes, (iii) people aged over 45 years with diabetes and/or chronic renal disease, (iv) everyone aged over 45 years. Melioidosis risk was estimated using Bayesian evidence synthesis of 12 observational studies. In the base case, vaccines were assumed to have 80% efficacy, to have 5-year mean protective duration and to cost USD10.20-338.20 per vaccine. RESULTS: Vaccination could be cost-effective (with incremental cost-effectiveness ratio below GDP per capita) in 61/83 countries/territories with local melioidosis transmission. In these 61 countries/territories, vaccination could avert 68,000 lost QALYs, 8300 cases and 4400 deaths per vaccinated age cohort, at an incremental cost of USD59.6 million. Strategy (ii) was optimal in most regions. The vaccine market may be worth USD268 million per year at its threshold cost-effective price in each country/territory. CONCLUSIONS: There is a viable melioidosis vaccine market, with cost-effective vaccine strategies in most countries/territories with local transmission.

Invasive nontyphoidal Salmonella disease in southern India: a 5-year experience from a tertiary care hospital

Background/aim: The current study was carried out to describe the clinical presentation, antimicrobial susceptibility pattern, and outcome of invasive nontyphoidal Salmonella disease (iNTS) in a tertiary care center. Materials and methods: A 5-year hospital-based retrospective study was carried out on blood culture-confirmed cases of iNTS. Medical records of patients were reviewed to obtain information on demography, clinical manifestations, comorbidities, complications, immune status, treatment, and clinical outcome. Results: A total of 40 blood culture-confirmed cases of iNTS were diagnosed during the study period. Among these 40 isolates, 9 (22.5%) were identified as Salmonella Typhimurium. Fever (67.5%) with gastrointestinal disturbance (40%) was the most common clinical presentation. The majority of the patients were immunosuppressed (75%). All isolates were susceptible to all the antimicrobials tested. Ceftriaxone (92.5%) was the most common antimicrobial used in our setting. A total of 15% patients died during the hospital stay. Conclusion: We conclude that iNTS disease is a severe infection prevailing in India with a high mortality rate. Anemia and diabetes were the two most common comorbidities. Though all NTS organisms isolated were sensitive to all the antimicrobials tested, we suggest that continued surveillance is necessary to monitor the presence of multidrug-resistant strains.

Improved detection of Burkholderia pseudomallei from non-blood clinical specimens using enrichment culture and PCR: narrowing diagnostic gap in resource-constrained settings.

OBJECTIVES: To evaluate the diagnostic utility of enrichment culture and PCR for improved case detection rates of non-bacteraemic form of melioidosis in limited resource settings. METHODS: Clinical specimens (n = 525) obtained from patients presenting at a tertiary care hospital of South India with clinical symptoms suggestive of community-acquired pneumonia, lower respiratory tract infections, superficial or internal abscesses, chronic skin ulcers and bone or joint infections were tested for the presence of Burkholderia pseudomallei using conventional culture (CC), enrichment culture (EC) and PCR. Sensitivity, specificity, positive and negative predictive values of CC and PCR were initially deduced using EC as the gold standard method. Further, diagnostic accuracies of all the three methods were analysed using Bayesian latent class modelling (BLCM). RESULTS: Detection rates of B. pseudomallei using CC, EC and PCR were 3.8%, 5.3% and 6%, respectively. Diagnostic sensitivities and specificities of CC and PCR were 71.4, 98.4% and 100 and 99.4%, respectively in comparison with EC as the gold standard test. With Bayesian latent class modelling, EC and PCR demonstrated sensitivities of 98.7 and 99.3%, respectively, while CC showed a sensitivity of 70.3% for detection of B. pseudomallei. An increase of 1.6% (95% CI: 1.08-4.32%) in the case detection rate of melioidosis was observed in the study population when EC and/or PCR were used in adjunct to the conventional culture technique. CONCLUSIONS: Our study findings underscore the diagnostic superiority of enrichment culture and/or PCR over conventional microbiological culture for improved case detection of melioidosis from non-blood clinical specimens.

Melioidosis diagnostic workshop, 2013.

Melioidosis is a severe disease that can be difficult to diagnose because of its diverse clinical manifestations and a lack of adequate diagnostic capabilities for suspected cases. There is broad interest in improving detection and diagnosis of this disease not only in melioidosis-endemic regions but also outside these regions because melioidosis may be underreported and poses a potential bioterrorism challenge for public health authorities. Therefore, a workshop of academic, government, and private sector personnel from around the world was convened to discuss the current state of melioidosis diagnostics, diagnostic needs, and future directions.

Optimization and validation of indirect ELISA using truncated TssB protein for the serodiagnosis of glanders amongst equines.

OBJECTIVE: To express truncated TssB protein of Burkholderia mallei and to evaluate its diagnostic efficacy for serological detection of glanders among equines. MATERIALS AND METHODS: In an attempt to develop recombinant protein based enzyme-linked immunosorbent assay (ELISA), N-terminal 200 amino acid sequences of B. mallei TssB protein-a type 6 secretory effector protein--were expressed in prokaryotic expression system. Diagnostic potential of recombinant TssB protein was evaluated in indirect ELISA using a panel of glanders positive (n = 49), negative (n = 30), and field serum samples (n = 1811). Cross-reactivity of the assay was assessed with equine disease control serum and human melioidosis positive serum. RESULTS: In comparison to CFT, diagnostic sensitivity and specificity of ELISA were 99.7% and 100%, respectively. CONCLUSIONS: The indirect ELISA method using the truncated TssB offered safer and more rapid and efficient means of serodiagnosis of glanders in equines. These data highlight the use of TssB as potential diagnostic antigen for serological diagnosis of glanders.

Recent cluster of neonatal enteroviral myocarditis cases in the United Kingdom of Great Britain and Northern Ireland - current scenario and counteracting prospects.

Objectives: Neonatal myocarditis is a rare but life-threatening complication of enterovirus infection that presents like bacterial sepsis. Outbreak: A sudden upsurge in cases of neonatal enteroviral myocarditis, reported from South West England and South Wales between June 2022 and April 2023 has alerted health agencies to bring in counteracting measures. Impact: In view of this outbreak situation, the World Health Organisation advisory has urged clinicians seeing neonates and infants with shock may consider myocarditis as a differential diagnosis and test for enteroviruses.

The hidden burden of melioidosis in Nepal: a paradigm for the urgent need to implement a simple laboratory algorithm to detect Burkholderia pseudomallei in low-resource endemic areas.

Melioidosis, an emerging infectious disease caused by the Gram-negative bacillus Burkholderia pseudomallei, is massively underdiagnosed in many low- and middle-income countries. The disease is clinically extremely variable, has a high case fatality rate, and is assumed to be highly endemic in South Asian countries, including Nepal. The reasons for underdiagnosis include the lack of awareness among clinicians and laboratory staff and limited microbiological capacities. Because costly laboratory equipment and consumables are likely to remain a significant challenge in many melioidosis-endemic countries in the near future, it will be necessary to make optimum use of available tools and promote their stringent implementation. Therefore, we suggest that health facilities in resource-poor countries, such as Nepal, introduce a simple and low-cost diagnostic laboratory algorithm for the identification of B. pseudomallei cultures. This screening algorithm should be applied specifically to samples from patients with fever of unknown origin and risk factors for melioidosis, such as diabetes. In addition, there could also be a role of low-cost, novel, promising serological point-of-care tests, which are currently under research and development.