SARS-CoV-2 specific antibody prevalence in health care personnel in a tertiary care teaching hospital treating COVID-19 patients

Background: Serosurvey is a salient method for estimating infection rates and monitoring the progression of a pandemic. This study was done to determine the extent of seroprevalence of SARS-COV-2 antibodies among health care personnel of a tertiary care hospital.Methods: Serum samples of 532 participants working in a teaching hospital which provides tertiary care services to the poor were tested for SARS-CoV-2-IgG antibodies. A questionnaire was used to collect demographic details and hygiene practices.Results: 160 (30%) out of the 532 participants had IgG levels above the positive cut off value. The seroprevalence was higher in the nurses when compared to other class of staff working in the hospital.Conclusions: The present study shows that the overall seroprevalence of SARS-CoV-2 in healthcare workers of a tertiary hospital in Bengaluru is high. This indicates that there is a need for the health care workers to take better precautions while treating COVID patients and emphasis should be given in training them to adhere to more stringent hygienic practices

Global diversity and antimicrobial resistance of typhoid fever pathogens : insights from a meta-analysis of 13,000 Salmonella Typhi genomes

DATA AVAILABILITY : All data analysed during this study are publicly accessible. Raw Illumina sequence reads have been submitted to the European Nucleotide Archive (ENA), and individual sequence accession numbers are listed in Supplementary file 2. The full set of n=13,000 genome assemblies generated for this study are available for download from FigShare: https://doi.org/10.26180/21431883. All assemblies of suitable quality (n=12,849) are included as public data in the online platform Pathogenwatch (https://pathogen.watch). The data are organised into collections, which each comprise a neighbour-joining phylogeny annotated with metadata, genotype, AMR determinants, and a linked map. Each contributing study has its own collection, browsable at https://pathogen.watch/collections/all?organismId= 90370. In addition, we have provided three large collections, each representing roughly a third of the total dataset presented in this study: Typhi 4.3.1.1 (https://pathogen.watch/collection/ 2b7mp173dd57-clade-4311), Typhi lineage 4 (excluding 4.3.1.1) (https://pathogen.watch/collection/ wgn6bp1c8bh6-clade-4-excluding-4311), and Typhi lineages 0-3 (https://pathogen.watch/collection/ 9o4bpn0418n3-clades-0-1-2-and-3). In addition, users can browse the full set of Typhi genomes in Pathogenwatch and select subsets of interest (e.g. by country, genotype, and/or resistance) to generate a collection including neighbour-joining tree for interactive exploration.SUPPLEMENTARY FILES : Available at https://elifesciences.org/articles/85867/figures#content. SUPPLEMENTARY FILE 1. Details of local ethical approvals provided for studies that were unpublished at the time of contributing data to this consortium project. Most data are now published, and the citations for the original studies are provided here. National surveillance programs in Chile (Maes et al., 2022), Colombia (Guevara et al., 2021), France, New Zealand, and Nigeria (Ikhimiukor et al., 2022b) were exempt from local ethical approvals as these countries allow sharing of non-identifiable pathogen sequence data for surveillance purposes. The US CDC Internal Review Board confirmed their approval was not required for use in this project (#NCEZID-ARLT- 10/ 20/21-fa687). SUPPLEMENTARY FILE 2. Line list of 13,000 genomes included in the study. SUPPLEMENTARY FILE 3. Source information recorded for genomes included in the study. ^Indicates cases included in the definition of ‘assumed acute illness’. SUPPLEMENTARY FILE 4. Summary of genomes by country. SUPPLEMENTARY FILE 5. Genotype frequencies per region (N, %, 95% confidence interval; annual and aggregated, 2010–2020). SUPPLEMENTARY FILE 6. Genotype frequencies per country (N, %, 95% confidence interval; annual and aggregated, 2010–2020). SUPPLEMENTARY FILE 7. Antimicrobial resistance (AMR) frequencies per region (N, %, 95% confidence interval; aggregated 2010–2020). SUPPLEMENTARY FILE 8. Antimicrobial resistance (AMR) frequencies per country (N, %, 95% confidence interval; annual and aggregated, 2010–2020). SUPPLEMENTARY FILE 9. Laboratory code master list. Three letter laboratory codes assigned by the consortium.BACKGROUND : The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS : This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS : Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS : The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.Fellowships from the European Union (funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council.https://elifesciences.org/am2024Medical MicrobiologySDG-03:Good heatlh and well-bein

Development of PCRSeqTyping—a novel molecular assay for typing of Streptococcus pneumoniae

Abstract Background Precise serotyping of pneumococci is essential for vaccine development, to better understand the pathogenicity and trends of drug resistance. Currently used conventional and molecular methods of serotyping are expensive and time-consuming, with limited coverage of serotypes. An accurate and rapid serotyping method with complete coverage of serotypes is an urgent necessity. This study describes the development and application of a novel technology that addresses this need. Methods Polymerase chain reaction (PCR) was performed, targeting 1061 bp cpsB region, and the amplicon was subjected to sequencing. The sequence data was analyzed using the National Centre for Biotechnology Information database. For homologous strains, a second round of PCR, sequencing, and data analysis was performed targeting 10 group-specific genes located in the capsular polysaccharide region. Ninety-one pneumococcal reference strains were analyzed with PCRSeqTyping and compared with Quellung reaction using Pneumotest Kit (SSI, Denmark). Results A 100% correlation of PCRSeqTyping results was observed with Pneumotest results. Fifty-nine reference strains were uniquely identified in the first step of PCRSeqTyping. The remaining 32 homologous strains out of 91 were also uniquely identified in the second step. Conclusion This study describes a PCRSeqTyping assay that is accurate and rapid, with high reproducibility. This assay is amenable for clinical testing and does not require culturing of the samples. It is a significant improvement over other methods because it covers all pneumococcal serotypes, and it has the potential for use in diagnostic laboratories and surveillance studies

A comparative clinical study of efficacy of microimmuno assay with WIDAL-test in enteric fever in children

The diagnosis of typhoid fever in young children is also a dilemma because of its manifestations and typical presentation may not be seen in all cases. Antibodies to Salmonella typhi antigen are developed in the human body, which can be detected as a diagnostic test for the enteric fever. Objective: This study was undertaken to compare the efficacy of WIDAL-test with micro-immunoassay (dot enzyme immunosorbent assay). Method: 40 cases of clinically suspected enteric fever cases were included in this study. Result: In the present study, nearly 92% were positive for micro immunoassay (dot-enzyme immunosorbent assay) by Enterocheck-WB kit, 80% were positive for WIDAL and only 15% were culture positive. Immunoassay positive, but WIDAL negative cases were 20%, whereas WIDAL positive and immunoassay negative cases were only 7.5%. The positive predictivity of micro-immunoassay in diagnosing enteric fever is better than WIDAL both in 1st and 2nd week of illness. Micro-immunoassay done in the study was rapid in diagnosing the case. Conclusion: It is concluded from the present study that the micro-immunoassay (Enterocheck-WB) is better than WIDAL-test in the diagnosis of enteric fever in children

Validation and comprehensive analysis ofStreptococcus pneumoniae IgG WHOenzyme linked immunosorbent assay in anIndian reference laboratory: supplementary data

Monitoring serotype-specific IgG levels against pneumococci is crucial for assessing immunity, vaccineefficacy, and evaluating vaccination programs. The WHO ELISA for pneumococci is a standardized assayensuring consistency in testing and comparability of results across laboratories. It involves a rigoroustesting process to confirm accurate, precise, and reliable detection of antibodies. We validated theprotocol for 13 pneumococcal serotypes by assessing its specificity, reproducibility (coefficient of variation≤15%), repeatability (coefficient of variation ≤20%) , accuracy, lower limit of quantification, stability,and robustness. We found these parameters were within acceptable ranges and showed excellentperformance. Our findings imply that the method employed is appropriate for evaluating 13 valentpneumococcal conjugate vaccine which is introduced in the national immunization program by comparingpre-and post-vaccination IgG response.</p

Circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, India

We report the persistent circulation of third-generation cephalosporin resistant Salmonella Typhi in Mumbai, linked to the acquisition and maintenance of a previously characterized IncX3 plasmid carrying the ESBL gene blaSHV-12 and the fluoroquinolone resistance gene qnrB7 in the genetic context of a triple mutant also associated with fluoroquinolone resistance

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

BACKGROUND: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal sentinel surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (&gt;1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS: The consortiums aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. FUNDING: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Unions Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210])

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

Peer reviewed: TrueFunder: Canadian Institutes of Health Research; FundRef: http://dx.doi.org/10.13039/501100000024Funder: National Institute for Health Research; FundRef: http://dx.doi.org/10.13039/501100000272Funder: Institut Pasteur and Santé Publique FranceFunder: Bill and Melinda Gates Foundation; FundRef: http://dx.doi.org/10.13039/100000865Funder: Indian Council of Medical Research; FundRef: http://dx.doi.org/10.13039/501100001411Funder: World Health Organization and Gavi, the Vaccine AllianceFunder: Department for Health and Social Care, the Department for International Development/Global Challenges Research Fund, the UK Medical Research Council, and the Wellcome TrustFunder: Wellcome; FundRef: http://dx.doi.org/10.13039/100010269BACKGROUND: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. FUNDING: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210])