Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein

The SARS-CoV-2 omicron variants keep accumulating a large number of mutations in the spike (S) protein, which contributes to greater transmissibility and a rapid rise to dominance within populations. The identification of mutations and their affinity to the cellular angiotensin-converting enzyme-2 (ACE-2) receptor and immune evasion in the Delhi NCR region was under-acknowledged. The study identifies some mutations (Y505 reversion, G339H, and R346T/N) in genomes from Delhi, India, and their probable implications for altering the immune response and binding affinity for ACE-2. The spike mutations have influenced the neutralizing activity of antibodies against the omicron variant, which shows partial immune escape. However, researchers are currently exploring various mitigation strategies to tackle the potential decline in efficacy or effectiveness against existing and future variants of SARS-CoV-2. These strategies include modifying vaccines to target specific variants, such as the omicron variant, developing multivalent vaccine formulations, and exploring alternative delivery methods. To address this, it is also necessary to understand the impact of these mutations from a different perspective, especially in terms of alterations in antigenic determinants. In this study, we have done whole genome sequencing (WGS) of SARS-CoV-2 in COVID-19 samples from Delhi, NCR, and analyzed the spike's mutation with an emphasis on antigenic alterations. The impact of mutation in terms of epitope formation, loss/gain of efficiency, and interaction of epitopes with antibodies has been studied. Some of the mutations or variant genomes seem to be the progenitors of the upcoming variants in India. Our analyses suggested that weakening interactions with antibodies may lead to immune resistance in the circulating genomes.

Liquid Biopsies: Emerging role and clinical applications in solid tumours

Late detection and lack of precision diagnostics are the major challenges in cancer prevention and management. Biomarker discovery in specific cancers, especially at the pre-invasive stage, is vital for early diagnosis, positive treatment response, and good disease prognosis. Traditional diagnostic measures require invasive procedures such as tissue excision using a needle, an endoscope, and/or surgical resection which can be unsafe, expensive, and painful. Additionally, the presence of comorbid conditions in individuals might render them ineligible for undertaking a tissue biopsy, and in some cases, it is difficult to access tumours depending on the site of occurrence. In this context, liquid biopsies are being explored for their clinical significance in solid malignancies management. These non-invasive or minimally invasive methods are being developed primarily for identification of biomarkers for early diagnosis and targeted therapeutics. In this review, we have summarised the use and importance of liquid biopsy as significant tool in diagnosis, prognosis prediction, and therapeutic development. We have also discussed the challenges that are encountered and future perspective.

Insights from establishing a high throughput viral diagnostic laboratory for SARS-CoV-2 RT-PCR testing facility: challenges and experiences

Background: The World Health Organization declared the coronavirus disease 2019 (COVID-19) a global pandemic on 11 March 2020. Identifying the infected people and isolating them was the only measure that was available to control the viral spread, as there were no standardized treatment interventions available. Various public health measures, including vaccination, have been implemented to control the spread of the virus worldwide. India, being a densely populated country, required laboratories in different zones of the country with the capacity to test a large number of samples and report test results at the earliest. The Indian Council of Medical Research (ICMR) took the lead role in developing policies, generating advisories, formulating guidelines, and establishing and approving testing centers for COVID-19 testing. With advisories of ICMR, the National Institute of Cancer Prevention and Research (NICPR) established a high-throughput viral diagnostic laboratory (HTVDL) for RT-PCR-based diagnosis of SARS-CoV-2 in April 2020. HTVDL was established during the first lockdown to serve the nation in developing and adopting rapid testing procedures and to expand the testing capacity using "Real-Time PCR." The HTVDL provided its testing support to the national capital territory of Delhi and western Uttar Pradesh, with a testing capacity of 6000 tests per day. The experience of establishing a high-throughput laboratory with all standard operating procedures against varied challenges in a developing country such as India is explained in the current manuscript which will be useful globally to enhance the knowledge on establishing an HTVDL in pandemic or non-pandemic times.

Genomic analysis of Fosfomycin resistance in multi-drug resistant uropathogens and comparison of in-vitro susceptibility methods uropathogens

BACKGROUND AND OBJECTIVES

Urinary tract infection is one of the most common bacterial infections causing high morbidity and mortality. The alarming rise of multidrug-resistant uropathogens worldwide forced the clinician to rethink the old drugs like Fosfomycin for its therapeutic management. Our objective was to compare agar dilution, disc diffusion and E-test method for antimicrobial susceptibility testing of Fosfomycin against different drug-resistant uropathogens.

MATERIALS AND METHODS

Consecutive 181 uropathogens were tested for Fosfomycin susceptibility using agar dilution, disc diffusion and E-test. Results were interpreted using Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. Whole genome sequencing analysis was done on the 4 XDR/PDR Fosfomycin resistant Klebsiella pneumoniae isolates.

RESULTS

Escherichia coli was found as the most common (62.4%) uropathogen followed by Klebsiella pneumoniae (21%). Considering agar dilution as the gold standard, 6.1% of isolates were resistant to Fosfomycin. Following CLSI breakpoints, the susceptibility of Escherichia coli, Klebsiella pneumoniae, other Enterobacterales and Pseudomonas aeruginosa were 92.9%, 92.1%, 100%, 100%; whereas using EUCAST breakpoints the susceptibility rates were 85.7%, 86.9%, 92.9%, and 100%, respectively. The essential agreement, categorical agreement, major error, and very major error for E-test/disc diffusion for all the organisms were 91.2%/Not Applicable, 95%/93.9%, 1.8%/4.7%, 9.1%/9.1%, respectively. Whole-genome sequencing showed mutation UhpT gene as well as the presence of plasmid-mediated fosA5 or fosA6 genes conferring Fosfomycin resistance.

CONCLUSION

This result supports very low resistance of Enterobacterales against Fosfomycin; hence should be considered a valuable option to treat multidrug-resistant uropathogens. Disc diffusion was observed to be a convenient method for Fosfomycin susceptibility testing compared to agar dilution.

Analysis of colistin resistance in carbapenem-resistant Enterobacterales and XDR Klebsiella pneumoniae

Introduction:

Increasing occurrence of infections caused by multidrug-resistant Gram-negative bacteria resulted in colistin being the last agent for treatment. Apart from plasmid-mediated mcr genes, mutations involving several genes like mgrB, phoP/phoQ, pmrA, pmrB, pmrC, and crrABC genes, are leading causes of colistin resistance. Four colistin susceptibility testing methods were compared against broth microdilution (BMD) and determined the presence of the mcr1-5 gene.

Methodology:

A total of 100 carbapenem-resistant Enterobacterales isolates were tested for colistin susceptibility by commercial broth microdilution (cBMD), E-test, VITEK-2, and rapid polymyxin NP assay (RPNP) and compared with BMD. The presence of the mcr1-5 gene was determined by modified RPNP and PCR. Two non-mcr colistin-resistant XDR isolates were subjected to whole-genome sequencing using Illumina MiSeq sequencing platform.

Results:

Among 100 carbapenem-resistant Enterobacterales isolates, 15% were resistant to colistin. Essential agreement, categorical agreement, major error, and very major error for cBMD/E-test/VITEK-2/RPNP were 96%/73%/82%/NA; 99%/86%/88%/91%, 1.2%/9.4%/11.8%/8.2% and 0%/40%/13.3%/13.3%, respectively. Only one Klebsiella pneumoniae isolate harbored the mcr-1 gene, observed by both methods. Whole-genome sequencing of two non-mcr XDR Klebsiella pneumoniae showed multiple mutations in 10 genes responsible for lipopolysaccharide biosynthesis.

Conclusions:

The performance of cBMD was excellent, whereas the E-test was unacceptable. VITEK-2 and RPNP performed better but remained unreliable due to high error rates. Multiple mutations in the target proteins involving lipopolysaccharide formation, modification, and regulation were seen, resulting in colistin resistance.

Infective Endocarditis Caused by C. sordellii: The First Case Report from India

Clostridium sordellii is a gram-positive anaerobic bacteria most commonly isolated from skin and soft tissue infection, penetrating injurious and intravenous drug abusers. The exotoxins produced by the bacteria are associated with toxic shock syndrome. We report here a first case of infective endocarditis due to C. sordellii from a female patient with ventricular septal defect from India.

Clostridioides difficile from intracardiac vegetation

Extracolonic manifestations by Clostridioides difficile are uncommon. Here, we report a case of monomicrobial C. difficile intracardiac vegetation in a 11-year-old girl with a predisposed heart disease who responded well to the treatment. C. difficile has been isolated from a variety of specimens outside the intestinal tract and is not always associated with gastrointestinal symptoms.

SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients: a retrospective observational study

BACKGROUND

despite being in the 5th month of pandemic, knowledge with respect to viral dynamics, infectivity and RT-PCR positivity continues to evolve.

AIM

to analyse the SARS CoV-2 nucleic acid RT-PCR profiles in COVID-19 patients.

DESIGN

it was a retrospective, observational study conducted at COVID facilities under AIIMS, New Delhi.

METHODS

patients admitted with laboratory confirmed COVID-19 were eligible for enrolment. Patients with incomplete details, or only single PCR tests were excluded. Data regarding demographic details, comorbidities, treatment received and results of SARS-CoV-2 RT-PCR performed on nasopharyngeal and oropharyngeal swabs, collected at different time points, was retrieved from the hospital records.

RESULTS

a total of 298 patients were included, majority were males (75·8%) with mean age of 39·07 years (0·6-88 years). The mean duration from symptom onset to first positive RT-PCR was 4·7 days (SD 3·67), while that of symptom onset to last positive test was 17·83 days (SD 6·22). Proportions of positive RT-PCR tests were 100%, 49%, 24%, 8·7% and 20·6% in the 1st, 2nd, 3rd, 4th and >4 weeks of illness. A total of 12 symptomatic patients had prolonged positive test results even after 3 weeks of symptom onset. Age > = 60 years was associated with prolonged RT-PCR positivity (statistically significant).

CONCLUSION

this study showed that the average period of PCR positivity is more than 2 weeks in COVID-19 patients; elderly patients have prolonged duration of RT-PCR positivity and requires further follow up.

Pleural effusion due to Chryseobacterium indologenes: Case report and review of literature

Chryseobacterium indologenes is found ubiquitously in the environment; it rarely causes human disease. Hence, we report a case of C. indologenes-associated pleural effusion in a patient with aortic dissection. Postoperatively, the patient developed massive right-sided pleural effusion with underlying consolidated lung. Culture of the pleural fluid yielded pure growth of C. indologenes which was susceptible to cotrimoxazole, minocycline, and tigecycline. Therapy was modified; tigecycline and cotrimoxazole were started following which the patient showed improvement, and subsequent cultures of the pleural fluid were sterile. This report promotes awareness of this organism as an emerging pathogen in lung infections and emphasizes the importance of targeted therapy.

Comparative analysis of syndromic case management and polymerase chain reaction based diagnostic assays for treatment of Neisseria gonorrhoeae, Chlamydia trachomatis and genital mycoplasmas in patients of genitourinary discharge

To respond to the situation of high prevalence and need for effective treatment for sexually transmitted infections (STIs) in low-resource settings, syndromic diagnostic approach was recommended by the World Health Organization and was adopted by National AIDS Control Organization at the primary health centre level. A retrospective study was undertaken in symptomatic patients attending an STI clinic to validate the syndromic approach for genitourinary discharge syndrome. For aetiological diagnosis, culture and/or polymerase chain reaction was used. An infective aetiology could be established in only 20% (106 of 530) patients. The present data call for an early appraisal and review of the diagnostic policy by national authorities on syndromic case management.

Decreasing trend of seroprevalence of leptospirosis at All India Institute of Medical Sciences New Delhi: 2014-2018

Background

Leptospirosis is an important emerging public health problem in India. There is limited information regarding the seroprevalence of leptospirosis in population from northern states of India. This study reports result of a 4-year-retrospective sero-epidemiological survey of leptospirosis conducted in a teaching tertiary care hospital in New Delhi, India. The aim of our study was to explore seroprevalence and clinical pattern of disease occurrence in suspected cases of leptospirosis and to search for any co-existing infections in northern areas such as New Delhi, India.

Methods

The patients with clinically suspected leptospirosis who attended outpatient or admitted to the Departments of Medicine, Gastroenterology, Pediatrics and Neurology, etc. of our hospital were retrospectively analyzed. The qualitative determination of anti-leptospira-specific immunoglobulin (IgM) antibodies was carried out using commercially available enzyme-linked immunosorbent assay (ELISA) kit (Panbio Diagnostics, Brisbane, Australia).

Results

Of these 1545 patients, 6.47% (100/1545) were seropositive for anti-leptospira-specific immunoglobulin (IgM) antibodies. Using modified Faine's criteria, a diagnosis of presumptive and possible leptospirosis was made in 79/100 (79%) and 21/100 (21%) patients. Significant declining trend of seroprevalence rate of leptospirosis from 26.90% in 2000-2010 and 20% in 2011-2014 to 6.47% in 2014-2018 (P value <0.05) in our referral tertiary care center. Seventeen patients showed co-infection with other common pathogen prevailing locally.

Conclusion

There is a need to increase awareness among public and clinicians, however, more region/province-wise studies on seroprevalence of leptospirosis are required to improve our understanding of the actual burden.

A case of sterile pyuria caused by Chlamydia trachomatis and Mycoplasma hominis: A diagnostic challenge

Sterile pyuria is a highly prevalent condition with a wide aetiological spectrum, which often challenges the diagnostician. We describe the case of a middle-aged female admitted to the medical Intensive Care Unit for acute gastroenteritis, whose urinalysis revealed persistent sterile pyuria. Polymerase chain reaction assay in urine was positive for Chlamydia trachomatis and Mycoplasma hominis. She responded to antimicrobial therapy. We hereby reflect on the approach to a case of sterile pyuria and review the available literature on this entity.

Analysis of laboratory testing results for Chlamydia trachomatis infection in an STI clinic in India: Need for extragenital screening

BACKGROUND

Extragenital sites are believed to serve as hidden reservoirs for ongoing transmission of infection. In addition, treatment for rectal Chlamydia infection is different from that of genital Chlamydia infection. Many cases may be missed if only genital testing is performed.

METHODS

Between September 2015 and August 2016, all male and female attendees at an STI clinic of a tertiary care hospital with genital and or extragenital discharge were screened for CT infection. Samples included endocervical swabs in women, urethral swabs and urine samples in men. Rectal and pharyngeal samples were collected wherever indicated.

RESULTS

Of total of 439 samples collected from 417 patients (245 women and 172 men), samples from women had a high positivity rate than men. (13.6% and 11%). High rates of rectal CT was detected nearly 30.43%. All rectal positive cases except one had no concomitant genital infection.

CONCLUSIONS

Prevalence of extragenital Chlamydia is increasing in men as well as women. What needs to be stressed on is the sexual behaviour of an individual and not the sexual identity. Further studies are needed to help formulate guidelines and recommendations for extragenital screening in a population.

Mental incapacity in hospitalised patients undergoing percutaneous endoscopic gastrostomy insertion

BACKGROUND & AIMS

Decisions to insert percutaneous endoscopic gastrostomy (PEG) tubes may be difficult because patients have serious underlying disease, and the procedure has associated risks. Patients may also lack mental capacity to consent to PEG insertion. This study aimed to prospectively determine the prevalence of mental incapacity in hospitalised patients undergoing PEG insertion.

METHODS

Mental capacity was assessed using the MacArthur Competence Assessment Tool for Treatment (MacCAT-T) in 72 consecutive inpatients referred for PEG insertion. Cognitive function was measured using the Mini-Mental State Examination (MMSE). Sixty eight inpatients and 69 outpatients having diagnostic upper gastrointestinal (UGI) endoscopy were similarly studied.

RESULTS

Thirty nine of the PEG patients had suffered stroke, and none had a primary diagnosis of dementia. Seventy four % (53/72) of inpatients referred for PEG, 22% (15/68) of inpatients having UGI endoscopy, and 3% (2/69) of outpatients having UGI endoscopy, lacked mental capacity, p < 0.001. MMSE scores were normal in just 18% of inpatients having PEG, in 72% of inpatients having UGI endoscopy, and in 91% of outpatients having UGI endoscopy, p < 0.001.

CONCLUSION

Amongst inpatients undergoing PEG insertion there is a high prevalence (three-quarters patients) of mental incapacity to consent to this important intervention. Decisions have to be made on behalf of most inpatients referred for PEG insertion.

Diversity of Veillonella spp. from sound and carious sites in children

Detailed data on the distribution of Veillonella in caries-free and caries-active subjects are scarce. We hypothesized that the diversity of the genus would be lower in caries lesions than in plaque from caries-free individuals. The proportions of Veillonella were not significantly different in the two groups. All isolates (n = 1308) were genotyped by REP-PCR, and different genotypes (n = 170) were identified by 16S rRNA, dnaK, and rpoB sequencing. V. parvula, V. dispar, and V. atypica were in both groups, V. denticariosi only in caries lesions, and V. rogosae only from the caries-free individuals (p < 0.009). Lesions were more likely to harbor a single predominant species (p = 0.0018). The mean number of genotypes in the lesions was less than in the fissure (p < 0.001) or buccal (p = 0.011) sites. The Veillonella from caries-free sites were more diverse than those from caries lesions, and may be related to the acidic environment of caries lesions.

Microbiological assessment of occlusal brown-spot lesions in primary molars

Conventional cultural methods were used to compare the plaque flora and the level of infection of the dentine underlying 51 occlusal brown-spot lesions and 21 sound occlusal sites on the primary dentition. Freshly extracted primary molar teeth were used, and occlusal brown-spot lesions and sound occlusal sites were identified using laser fluorescence (LF) and clinical visual methods. A standardized plaque sample was taken from each site, and an LF score was recorded for one discrete site per tooth. The teeth were carefully opened at each predetermined site to determine the clinical status of the underlying dentine, and samples were collected using a sterile bur. The microbiota of the plaque and dentine samples were enumerated and identified. The mean LF scores for the sound sites and brown-spot lesions were 1.2 and 30.5 (p < 0.001), and all the sound sites exhibited hard sound dentine, but 6 out of 51 brown spots exhibited softened dentine. Overall there was no significant (p > 0.1) difference between the level of infection of the dentine of the sound and brown-spot sites, although some sites in the brown-spot lesions yielded high numbers of bacteria. However, the numbers of bacteria as log10(CFU per sample + 1) +/- SE recovered from the plaque above the brown-spot lesions were significantly greater than above the sound sites, i.e. 2.89 +/- 0.24 and 0.89 +/- 0.33, respectively. These data indicate that brown-spot lesions may be more plaque retentive than sound sites and that they are either arrested or arresting lesions, which may require preventive intervention.

Hepatic involvement with typhoid fever: a report of nine patients

Salmonella typhi has been reported to cause hepatic involvement. We studied nine patients with positive blood cultures in order to identify characteristic features of typhoid hepatitis which may help in early diagnosis. Patients who had an illness resembling enteric fever but negative cultures for Salmonella typhi were excluded. No specific clinical features were found consistently and liver function tests were widely variable. Other biochemical abnormalities occurred due to vomiting and renal involvement. Liver biopsy showed focal hepatocellular necrosis and non specific inflammation. Although most responded to conventional antibiotics, it was generally a delayed response. It is recommended that patients with fever greater than 38.5 degrees C and liver abnormalities should undergo blood, urine, stool and/or bone marrow cultures. Liver biopsy may help to differentiate typhoid hepatitis from acute viral hepatitis.