Tina Damodar

Chikungunya virus (CHIKV) is an emerging cause of acute encephalitis syndrome (AES) in India, with limited data on its role in childhood AES in southern India. We systematically evaluated children with AES in southern India during a non‐epidemic period for CHIKV. Serum and cerebrospinal fluid (CSF) samples were tested for CHIKV using IgM ELISA and real‐time reverse transcriptase PCR. Amplicon sequencing was performed on PCR‐positive samples. Clinical and laboratory features were compared between children with and without CSF CHIKV positivity (PCR/IgM antibodies). Of 376 children with AES, 20 (5.3%) had positive CHIKV tests. Co‐infections were common, particularly with scrub typhus. Children presented with diverse symptoms affecting various organ systems. Neurological manifestations included meningism, seizures, cerebellar signs, behavioral abnormalities, cranial nerve involvement, involuntary movements, and hemiparesis/hemiplegia. Children with CSF CHIKV positivity showed more focal neurological deficits and transaminitis, and less musculoskeletal symptoms. Sequencing confirmation of CHIKV was made in all patients with positive CHIKV PCR, revealing a close relationship with 2016 Kenyan and Indian strains, albeit in a different clade within the East/Central/South African genotype. Along with important mutations known to impact CHIKV infectivity, four novel amino acid substitutions were detected in envelope protein coding regions. Our findings underscore the importance of routine and comprehensive CHIKV testing for children with AES, irrespective of season/outbreak. The high rate of co‐infections warrants further research. Continued genomic surveillance is essential to monitor emerging mutations with epidemic potential, increased severity and the risk of neurological disease.

COVID‐19 severely impacts children in India, with many developing severe pneumonia or multisystem inflammatory syndrome (MIS‐C). Concurrently, non‐COVID‐19 respiratory viruses causing community‐acquired pneumonia (CAP) have resurged. These conditions present similarly, challenging accurate diagnosis. This study aims to compare inflammatory markers and clinical parameters in children with severe COVID‐19 pneumonia, non‐COVID‐19 CAP, and COVID‐associated MIS‐C. We assessed 12 mediators in serum from 14 children with severe COVID‐19 pneumonia, 16 with severe non‐COVID‐19 CAP, and 9 with MIS‐C. Clinical characteristics and routine laboratory findings at admission were recorded. Children with MIS‐C had significantly higher levels of IL‐1RA, IL‐8, and TNF compared with those with severe COVID‐19 pneumonia; and higher levels of CCL2, HGF, M‐CSF, and IL‐8 compared with severe non‐COVID‐19 CAP. GROα levels tended to be higher in severe COVID‐19 pneumonia. Clinical presentations were similar, but MIS‐C patients had distinct laboratory findings, including lower platelet counts and albumin levels, and higher creatinine and liver enzyme levels. MIS‐C exhibited a unique inflammatory profile. IL‐8 emerged as a potential biomarker for MIS‐C, while increased GROα levels in severe COVID‐19 pneumonia merit further exploration. Combining inflammatory markers with routine laboratory parameters may improve the diagnosis and differentiation of these conditions, enhancing patient management.

Acute encephalitis syndrome (AES) in children poses a significant public health challenge in India. This study aims to explore the utility of host inflammatory mediators and neurofilament (NfL) levels in distinguishing etiologies, assessing disease severity, and predicting outcomes in AES. We assessed 12 mediators in serum (n = 58) and 11 in cerebrospinal fluid (CSF) (n = 42) from 62 children with AES due to scrub typhus, viral etiologies, and COVID‐associated multisystem inflammatory syndrome (MIS‐C) in Southern India. Additionally, NfL levels in serum (n = 20) and CSF (n = 18) were examined. Clinical data, including Glasgow coma scale (GCS) and Liverpool outcome scores, were recorded. Examining serum and CSF markers in the three AES etiology groups revealed notable distinctions, with scrub typhus differing significantly from viral and MIS‐C causes. Viral causes had elevated serum CCL11 and CCL2 compared with scrub typhus, while MIS‐C cases showed higher HGF levels than scrub typhus. However, CSF analysis showed a distinct pattern with the scrub typhus group exhibiting elevated levels of IL‐1RA, IL‐1β, and TNF compared with MIS‐C, and lower CCL2 levels compared with the viral group. Modeling the characteristic features, we identified that age ≥3 years with serum CCL11 < 180 pg/mL effectively distinguished scrub typhus from other AES causes. Elevated serum CCL11, HGF, and IL‐6:IL‐10 ratio were associated with poor outcomes (p = 0.038, 0.005, 0.02). Positive CSF and serum NfL correlation, and negative GCS and serum NfL correlation were observed. Median NfL levels were higher in children with abnormal admission GCS and poor outcomes. Measuring immune mediators and brain injury markers in AES provides valuable diagnostic insights, with the potential to facilitate rapid diagnosis and prognosis. The correlation between CSF and serum NfL, along with distinctive serum cytokine profiles across various etiologies, indicates the adequacy of blood samples alone for assessment and monitoring. The association of elevated levels of CCL11, HGF, and an increased IL‐6:IL‐10 ratio with adverse outcomes suggests promising avenues for therapeutic exploration, warranting further investigation.

Background: Africa has one of the highest incidences of gonorrhoea, but not much information is available on the relatedness with strains from other geographical locations. Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major public health threat, with the bacteria gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing is an efficient way of predicting AMR determinants and their spread in the human population. Previous studies on Kenyan gonococcal samples have focused on plasmid-mediated drug resistance and fluoroquinolone resistance using Illumina sequencing. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. However, long-reads are error-prone. The increasing accuracy ofbase-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer in remote areas is leading to the adoption of the MinION sequencer (ONT), for routine microbial genome sequencing. Methods: To investigate whether MinION-only sequencing is sufficient for diagnosis, genome sequencing and downstream analysis like inferring phylogenetic relationships and detection of AMR in resource-limited settings, we sequenced the genomes of fourteen clinical isolates suspected to be N. gonorrhoeae from Nairobi, Kenya. The isolates were tested using standard bacteriological methods for identification, interpreted using analytical profile index and antibiotic susceptibility tests had indicated ciprofloxacin and gentamycin resistance. Using whole-genome sequencing, the isolates were confirmed to be cases of N. gonorrhoeae (n=12), Additionally, we identified reads from N. meningitidis (n=2) and both of N. gonorrhoeae and Moraxella osloensis (n=3) in the sample (co-infections) respectively, which have been implicated in sexually transmitted infections in the recent years. The near-complete N. gonorrhoeae genomes (n=10) were analysed further for mutations/factors causing AMR using an in-house database of mutations curated from the literature. We attempted to understand the basis of drug resistance using homology modelling of AMR proteins, using known structures from other bacteria. Results: We observe that Ciprofloxacin resistance is associated with multiple mutations in both gyrA and parC . We identified mutations conferring tetracycline ( rpsJ ) and Sulfonamide ( folA ) resistance in all the isolates and plasmids encoding beta-lactamase and tet (M) were identified in almost all of the strains. Phylogenetic analysis clustered the nine isolates into clades containing previously sequenced genomes from Kenya and countries across the world. Conclusion: Here, we demonstrate the utility of mobile DNA sequencing technology supplemented with reference-based assembly in sequence typing and elucidating the basis of AMR. Bioinformatics profiling to predict AMR can be used along with routine AMR susceptibility tests in clinics. The workflow followed in the study, including AMR mutation dataset creation and the genome identification, assembly and analysis, can be used for the genome assembly and analysis of any clinical isolate. Further studies are required to determine the utility of real-time sequencing in the outbreak investigations, diagnosis and management of infections, especially in resource-limited settings. Data availability: The raw reads generated for this study have been deposited in BioProject Accession: PRJNA660404 ( https://www.ncbi.nlm.nih.gov ). The biosample details are available under the ids SAMN15960547, SAMN15960548, SAMN15960549, SAMN15960550, SAMN15960551, SAMN15960552, SAMN15960553, SAMN15960554, SAMN15960555. The genomes and annotation files are available under the bioproject.

An earlier version of this manuscript was removed owing to inclusion of confidential information relating to an individual

Early ante-mortem laboratory confirmation of human rabies is essential to aid patient management and institute public health measures. Few studies have highlighted the diagnostic value of antibody detection in CSF/serum in rabies, and its utility is usually undermined owing to the late seroconversion and short survival in infected patients. This study was undertaken to examine the ante-mortem diagnostic utility and prognostic value of antibody detection by rapid fluorescent focus inhibition test (RFFIT) in cerebrospinal fluid (CSF)/serum samples received from clinically suspected human rabies cases from January 2015 to December 2017. Samples collected ante-mortem and post-mortem from 130 and 6 patients with clinically suspected rabies respectively, were received in the laboratory during the study period. Ante-mortem laboratory confirmation was achieved in 55/130 (42.3%) cases. Real time PCR for detection of viral nucleic acid performed on saliva, nuchal skin, brain tissue and CSF samples could confirm the diagnosis in 15 (27.2%) of the 55 laboratory confirmed cases. Ante-mortem diagnosis could be achieved by RFFIT (in CSF and/or serum) in 45 (34.6%) of the 130 clinically suspected cases, accounting for 81.8% of the total 55 laboratory confirmed cases. The sensitivity of CSF RFFIT increased with the day of sample collection (post-onset of symptoms) and was found to be 100% after 12 days of illness. Patients who had received prior vaccination had an increased probability of a positive RFFIT and negative PCR result. Patients who were positive by RFFIT alone at initial diagnosis had longer survival (albeit with neurological sequelae) than patients who were positive by PCR alone or both RFFIT and PCR. Detection of antibodies in the CSF/serum is a valuable ante-mortem diagnostic tool in human rabies, especially in patients who survive beyond a week. It was also found to have a limited role as a prognostic marker to predict outcomes in patients. Ante-mortem diagnosis of human rabies is essential for patient management and public health measures. The detection of virus specific antibodies in the CSF/serum of patients with suspected rabies is thought to have a limited diagnostic role owing to late seroconversion and short survival in rabies. We examined the diagnostic and prognostic utility of antibody detection by rapid fluorescent focus inhibition test (RFFIT) in CSF/serum samples received from clinically suspected human rabies cases (2015–2017). RFFIT (in CSF and/or serum) could confirm ante-mortem diagnosis in 45 (34.6%) of the 130 clinically suspected cases, accounting for 81.8% of the total 55 laboratory confirmed cases. The sensitivity of CSF RFFIT increased with the day of sample collection (post-onset of symptoms) and was found to be 100% after 12 days of illness. Patients who had received prior vaccination had an increased likelihood of a positive RFFIT and negative PCR result. Patients who were positive by RFFIT alone at initial diagnosis had longer duration of survival, although with poor functional outcomes. Antibody detection by RFFIT in CSF/serum was found to have a diagnostic utility especially in patients who survived beyond a week and a limited prognostic role in human rabies.

Rabies, a zoonotic viral encephalitis, continues to be a serious public health problem in India and several other countries in Asia and Africa. Survival is rarely reported in rabies, which is considered to be almost universally fatal. We report the clinical and radiological findings of eight patients with laboratory-confirmed rabies who survived the illness. With the exception of one patient who recovered with mild sequelae, all survivors had poor functional outcomes. The reported survival from rabies in recent years may reflect an increased awareness of the disease and greater access to better critical care facilities in rabies-endemic countries. Nonetheless, there is an urgent need to focus on preventive strategies to reduce the burden of this dreadful disease in rabies-endemic countries.

Neurol India is an peer-reviewed biomedical periodical of Neurological Society of India.