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Bhatia M, Shamanna V, Nagaraj G, Gupta P, Omar BJ, Diksha, Rohilla R, Ravikumar KL. Assessment of in vitro colistin susceptibility of carbapenem-resistant clinical Gram-negative bacterial isolates using four commercially available systems & Whole-genome sequencing: A diagnostic accuracy study. Diagn Microbiol Infect Dis 2024; 108:116155. [PMID: 38219381 DOI: 10.1016/j.diagmicrobio.2023.116155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024]
Abstract
AIM To analyze the diagnostic utility of commercially available platforms and Whole-genome sequencing (WGS) for accurate determination of colistin susceptibility test results. MATERIAL & METHODS An exploratory diagnostic accuracy study was conducted in which sixty carbapenem-resistant Gram-negative bacteria were subjected to identification and AST using MALDI-TOF MS & MicroScan walkaway 96 Plus. Additional AST was performed using the BD Phoenix system and Mikrolatest colistin kit. The test isolates were subjected to Vitek-2 and WGS at CRL, Bengaluru. RESULTS There was no statistically significant agreement between the colistin susceptibility results obtained by WGS, with those of commercial phenotypic platforms. The MicroScan 96 Plus had the highest sensitivity (31 %) & NPV (77 %), and the BD Phoenix system had the highest specificity (97 %) and PPV (50 %), respectively, for determining colistin resistance. CONCLUSION The utility of WGS as a tool in AMR surveillance and validation of phenotypic AST methods should be explored further.
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Affiliation(s)
- Mohit Bhatia
- Department of Microbiology, Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi, 110029, India.
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India; Department of Biotechnology, NMAM Institute of Technology, Nitte, Udupi, Karnataka 574110, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences Deoghar, Jharkhand 814152, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Diksha
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Ranjana Rohilla
- Department of Microbiology, Sri Guru Ram Rai Institute of Medical & Health Science, Dehradun, Uttarakhand 248001, India
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
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Shincy MR, Vandana G, Akhila MM, Shilpa R, Ravikumar KL. Validation and comprehensive analysis of Streptococcus pneumoniae IgG WHO enzyme-linked immunosorbent assay in an Indian reference laboratory. Bioanalysis 2024; 16:191-201. [PMID: 38315628 DOI: 10.4155/bio-2023-0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Monitoring serotype-specific IgG levels against pneumococci is crucial for assessing immunity, vaccine efficacy, and evaluating vaccination programs. The WHO ELISA for pneumococci is a standardized assay ensuring consistency in testing and comparability of results across laboratories. It involves a rigorous testing process to confirm accurate, precise and reliable detection of antibodies. We validated the protocol 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 excellent performance. Our findings imply that the method employed is appropriate for evaluating 13 valent pneumococcal conjugate vaccine which is introduced in the national immunization program by comparing pre-and post-vaccination IgG response.
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Affiliation(s)
- Mettingal Ramakrishnan Shincy
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
- Department of Biotechnology and Genetics, School of Sciences, JAIN (Deemed-to-be University), Bangalore, India
| | - Govindan Vandana
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | | | - Ravindran Shilpa
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
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Bhatia M, Shamanna V, Nagaraj G, Sravani D, Gupta P, Omar BJ, Singh A, Rani D, Ravikumar KL. An insight into whole genome sequencing data of methicillin-resistant Staphylococcus aureus circulating in a teaching hospital in North India. Indian J Med Microbiol 2023; 44:100365. [PMID: 37356847 DOI: 10.1016/j.ijmmb.2023.100365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/31/2023] [Accepted: 03/14/2023] [Indexed: 06/27/2023]
Abstract
PURPOSE To provide an insight into the Whole-genome sequencing (WGS) data of MRSA strains circulating in a teaching hospital in north India. METHODS An exploratory study was conducted in which fifty non-repetitive MRSA isolates obtained from pus samples of inpatients from July 2018 to February 2019 were subjected to preliminary identification (ID) and antibiotic susceptibility testing (AST) at our centre. These isolates were later sent to Central Research Laboratory, India for further testing using the VITEK-2 compact system followed by WGS. Only eighteen isolates were eventually considered for final analysis and the rest (n = 32) were excluded due to various technical reasons. RESULTS The WGS confirmed MRSA isolates predominantly belonged to CC22 (56.25%) and CC30 (31.25%). The CC22 MRSA strains carried SCCmec types IVa (77.8%) & IVc (22.2%) and belonged to spa types t005 (44.4%), t4584 (22.2%), t11808 (11.1%), t1328 (11.1%) and t309 (11.1%), respectively. The MRSA isolates of CC30 carried SCCmec types IVa (60%), IVg (20%) & V (20%) and belonged to spa types t021 (80%) & t2575 (20%), respectively. One MRSA isolate carried a novel SCCmec type V. The luk-PV and tsst-1 genes were present in 93.75% and 33.33% of MRSA isolates, respectively. The concordance between the phenotypic and genotypic AST results was 100% for Beta-lactams, Fluoroquinolones, Tetracyclines & Lipoglycopeptides, respectively. CONCLUSIONS Through this study, we intend to embark upon a relatively newer avenue of clinical-genomic surveillance of nosocomial bacterial isolates like MRSA, which would help us improve the existing infection control and antibiotic stewardship practices in our hospital.
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Affiliation(s)
- Mohit Bhatia
- Department of Microbiology, Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi 110029, India.
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| | - Dharmavaram Sravani
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences Deoghar, Jharkhand 814142, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Arpana Singh
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Diksha Rani
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
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Govindan V, Ganaie FA, Ramakrishnan SM, Ravindran S, Mavuppadi AM, Ravikumar KL. Estimation of baseline IgG antibody levels to 23 pneumococcal vaccine-type capsular polysaccharides in healthy vaccine naïve Indian adults. Vaccine 2023:S0264-410X(23)00497-8. [PMID: 37173269 DOI: 10.1016/j.vaccine.2023.04.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Since immunological responses to pneumococcal vaccines are assessed by a fold-increase in antibody levels relative to pre-immunization levels, it is therefore critical to determine baseline antibody levels to establish putative threshold as a measure of normal response. Herein, for the first time, we measured baseline IgG antibody levels in 108 healthy unvaccinated Indian adults using WHO-recommended ELISA. Median baseline IgG concentration ranged between 0.54 µg/mL to 12.35 µg/mL. Highest levels of baseline capsule polysaccharide (cPS)-specific IgG were found against types 14, 19A, and 33F. Whereas, lowest baseline IgG levels were observed against types 3, 4, and 5. Overall, ∼79 % of study population had median baseline IgG levels ≥1.3 µg/mL against 74 % of cPS's. Substantial baseline antibody levels in unvaccinated adults were observed. The study would be critical in bridging gaps in baseline immunogenicity data and may offer a valuable foundation for evaluating immune response of Indian adults to pneumococcal vaccination.
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Affiliation(s)
- Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Feroze A Ganaie
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care, University of Alabama at Birmingham, AL, USA
| | - Shincy M Ramakrishnan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Shilpa Ravindran
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Akhila M Mavuppadi
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India.
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Lo SW, Mellor K, Cohen R, Alonso AR, Belman S, Kumar N, Hawkins PA, Gladstone RA, von Gottberg A, Veeraraghavan B, Ravikumar KL, Kandasamy R, Pollard SAJ, Saha SK, Bigogo G, Antonio M, Kwambana-Adams B, Mirza S, Shakoor S, Nisar I, Cornick JE, Lehmann D, Ford RL, Sigauque B, Turner P, Moïsi J, Obaro SK, Dagan R, Diawara I, Skoczyńska A, Wang H, Carter PE, Klugman KP, Rodgers G, Breiman RF, McGee L, Bentley SD, Almagro CM, Varon E, Corso A, Davydov A, Maguire A, Kiran A, Moiane B, Beall B, Zhao C, Aanensen D, Everett D, Faccone D, Foster-Nyarko E, Bojang E, Egorova E, Voropaeva E, Sampane-Donkor E, Sadowy E, Nagaraj G, Mucavele H, Belabbès H, Elmdaghri N, Verani J, Keenan J, Lees J, N Nair Thulasee Bhai J, Ndlangisa K, Zerouali K, Bentley L, Titov L, De Gouveia L, Alaerts M, Ip M, de Cunto Brandileone MC, Hasanuzzaman M, Paragi M, Nurse-Lucas M, du Plessis M, Ali M, Croucher N, Wolter N, Givon-Lavi N, Porat N, Köseoglu Eser Ö, Ho PL, Eberechi Akpaka P, Gagetti P, Tientcheu PE, Law P, Benisty R, Mostowy R, Malaker R, Grassi Almeida SC, Doiphode S, Madhi S, Devi Sekaran S, Clarke S, Srifuengfung S, Nzenze S, Kastrin T, Ochoa T, Hryniewicz W, Urban Y. Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study. Lancet Microbe 2022; 3:e735-e743. [PMID: 35985351 PMCID: PMC9519462 DOI: 10.1016/s2666-5247(22)00158-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context. METHODS Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018. To provide a global context, we included an additional collection of 24F isolates in the Global Pneumococcal Sequencing (GPS) project database for analysis. A Global Pneumococcal Sequence Cluster (GPSC) and a clonal complex (CC) were assigned to each genome. Phylogenetic, evolutionary, and spatiotemporal analysis were conducted using the same 24F collection and supplemented with a global collection of genomes belonging to the lineage of interest from the GPS project database (n=25 590). FINDINGS Serotype 24F was identified in numerous countries mainly due to the clonal spread of three lineages: GPSC10 (CC230), GPSC16 (CC156), and GPSC206 (CC7701). GPSC10 was the only multidrug-resistant lineage. GPSC10 drove the increase in 24F in France and had high invasive disease potential. The international dataset of GPSC10 (n=888) revealed that this lineage expressed 16 other serotypes, with only six included in 13-valent PCV (PCV13). All serotype 24F isolates were clustered in a single clade within the GPSC10 phylogeny and long-range transmissions were detected from Europe to other continents. Spatiotemporal analysis showed GPSC10-24F took 3-5 years to spread across France and a rapid change of serotype composition from PCV13 serotype 19A to 24F during the introduction of PCV13 was observed in neighbouring country Spain. INTERPRETATION Our work reveals that GPSC10 alone is a challenge for serotype-based vaccine strategy. More systematic investigation to identify lineages like GPSC10 will better inform and improve next-generation preventive strategies against pneumococcal diseases. FUNDING Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control and Prevention.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK,Correspondence to: Dr Stephanie W Lo, Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kate Mellor
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Robert Cohen
- ACTIV, Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés, France,GPIP, Groupe de Pathologie Infectieuse Pédiatrique, Paris, France,AFPA, Association Française de Pédiatrie Ambulatoire, Saint-Germain-en-Laye, France,Université Paris Est, IMRB-GRC GEMINI, Créteil, France,Clinical Research Center, Centre Hospitalier Intercommunal de Créteil, Créteil, France,Unité Court Séjour, Petits nourrissons, Service de Néonatalogie, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Alba Redin Alonso
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Sophie Belman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Narender Kumar
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Rebecca A Gladstone
- Department of Biostatistics, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK,School of Women and Children's Health, University of New South Wales, Sydney, NSW, Australia,Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Sir Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Churchill Hospital, Oxford, UK,NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Brenda Kwambana-Adams
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Shaper Mirza
- Microbiology and Immunology Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Jennifer E Cornick
- Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Deborah Lehmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Rebecca L Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Stephen K Obaro
- Division of Pediatric Infectious Disease, University of Nebraska Medical Center Omaha, Omaha, NE, USA,International Foundation against Infectious Diseases in Nigeria, Abuja, Nigeria
| | - Ron Dagan
- Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Idrissa Diawara
- Department of Microbiology, Faculty of Medicine and Pharmacy of Casablanca, Hassan II University of Casablanca, Casablanca, Morocco,National Reference Laboratory, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Anna Skoczyńska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Hui Wang
- Peking University People ‘s Hospital, Beijing, China
| | - Philip E Carter
- Institute of Environmental Science and Research Limited, Kenepuru Science Centre, Porirua, New Zealand
| | - Keith P Klugman
- Rollins School Public Health, Emory University, Atlanta, GA, USA
| | - Gail Rodgers
- Pneumonia Program, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Robert F Breiman
- Rollins School Public Health, Emory University, Atlanta, GA, USA,Emory Global Health Institute, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Carmen Muñoz Almagro
- Department of RDI Microbiology, Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain,Spanish Network of Epidemiology and Public Health, CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Emmanuelle Varon
- National Reference Center for Pneumococci, Centre Hospitalier Intercommunal de Créteil, Créteil, France
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Bhatia M, Shamanna V, Nagaraj G, Sravani D, Gupta P, Omar BJ, Chakraborty D, Ravikumar KL. Molecular characterisation of carbapenem-resistant Klebsiella pneumoniae clinical isolates: preliminary experience from a tertiary care teaching hospital in the Himalayas. Trans R Soc Trop Med Hyg 2022; 116:655-662. [PMID: 35029688 PMCID: PMC9259183 DOI: 10.1093/trstmh/trab189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/13/2021] [Accepted: 12/21/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND There is a lack of whole-genome sequencing (WGS) data on multidrug-resistant (MDR) bacteria from the Uttarakhand region of India. The aim of this study was to generate WGS data of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates recovered from patients in Uttarakhand's tertiary care centre. METHODS A cross-sectional study included 29 MDR K. pneumoniae test isolates obtained from various clinical samples submitted to the bacteriology laboratory for culture and sensitivity testing from July 2018 to August 2019. After preliminary identification and antibiotic susceptibility testing, these isolates were subjected to WGS. RESULTS A total of 27 of 29 isolates were CRKP. ST14 was the most common sequence type (n=8 [29.6%]). Carbapenem resistance was mainly encoded by OXA-48-like genes (21/27 [77.8%]). All isolates had a varied arsenal of resistance genes to different antibiotic classes. KL2 (9/27 [33.3%]) and KL51 (8/27 [29.6%]) were dominant K loci types. O1 and O2 together accounted for 88.9% (n=27) of CRKP isolates. Genes encoding yersiniabactin (ybt) and aerobactin (iuc) were identified in 88.9% (24/27) and 29.6% (8/27) of isolates. The predominant plasmid replicons present were ColKP3 (55.5%), IncFII(K) (51.8%) and IncFIB(pQil) (44.4%). CONCLUSIONS This study emphasises the need for continued genomic surveillance of MDR bacteria that could be instrumental in developing treatment guidelines based on integrating phenotypic and molecular methods.
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Affiliation(s)
- Mohit Bhatia
- Corresponding author: Tel: +918750549280; E-mail: ;
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
| | - Dharmavaram Sravani
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India 249203
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India 249203
| | - Deepika Chakraborty
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India 249203
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
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Argimón S, David S, Underwood A, Abrudan M, Wheeler NE, Kekre M, Abudahab K, Yeats CA, Goater R, Taylor B, Harste H, Muddyman D, Feil EJ, Brisse S, Holt K, Donado-Godoy P, Ravikumar KL, Okeke IN, Carlos C, Aanensen DM. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch. Clin Infect Dis 2021; 73:S325-S335. [PMID: 34850838 PMCID: PMC8634497 DOI: 10.1093/cid/ciab784] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. METHODS We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR. RESULTS Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse. CONCLUSIONS Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
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Affiliation(s)
- Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicole E Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Corin A Yeats
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Richard Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ben Taylor
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Harry Harste
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Dawn Muddyman
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathryn Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pilar Donado-Godoy
- Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars), CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitatá–Mosquera, Cundinamarca, Colombia
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Celia Carlos
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
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Aanensen DM, Carlos CC, Donado-Godoy P, Okeke IN, Ravikumar KL. Implementing Whole-Genome Sequencing for Ongoing Surveillance of Antimicrobial Resistance: Exemplifying Insights Into Klebsiella pneumoniae. Clin Infect Dis 2021; 73:S255-S257. [PMID: 34850830 PMCID: PMC8634455 DOI: 10.1093/cid/ciab795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In this Supplement, we detail outputs of the National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance project, covering practical implementation of whole-genome sequencing across our consortium, which consists of laboratories in Colombia, India, Nigeria, and the Philippines.
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Affiliation(s)
- David M Aanensen
- Centre
for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Celia C Carlos
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Pilar Donado-Godoy
- Colombian Integrated Program for Antimicrobial Resistance Surveillance–Coipars, CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, Tibaitatá–Mosquera, Cundinamarca, Colombia
| | - Iruka N Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
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Nagaraj G, Shamanna V, Govindan V, Rose S, Sravani D, Akshata KP, Shincy MR, Venkatesha VT, Abrudan M, Argimón S, Kekre M, Underwood A, Aanensen DM, Ravikumar KL. High-Resolution Genomic Profiling of Carbapenem-Resistant Klebsiella pneumoniae Isolates: A Multicentric Retrospective Indian Study. Clin Infect Dis 2021; 73:S300-S307. [PMID: 34850832 PMCID: PMC8634558 DOI: 10.1093/cid/ciab767] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India because of its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India. MATERIALS AND METHODS We characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013-2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, multilocus sequence type, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism phylogeny were inferred from their whole genome sequences. RESULTS Phylogenetic analysis of the 325 Klebsiella isolates that passed quality control revealed 3 groups: K. pneumoniae sensu stricto (n = 307), K. quasipneumoniae (n = 17), and K. variicola (n = 1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates, respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%) and Col group (35.0%). CONCLUSION Our study documents for the first time the genetic diversity of K and O antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these transmissible lineages.
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Affiliation(s)
- Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Steffimole Rose
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - D Sravani
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - K P Akshata
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - M R Shincy
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - V T Venkatesha
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Genome Campus, Hinxton, UK
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
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Harste HJ, Kiff G, Okeke IN, Adebiyi AO, Ravikumar KL, Nagaraj G, Ajiboye JJ, Osma Castro ECD, Herrera E, Aanensen DM. Good Financial Grant Practice: A Tool for Developing and Demonstrating Institutional Financial and Grant Management Capacity in Global Health. Clin Infect Dis 2021; 73:S275-S282. [PMID: 34850833 PMCID: PMC8634540 DOI: 10.1093/cid/ciab768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The administration and governance of grant funding across global health organizations presents enormous challenges. Meeting these challenges is crucial to ensuring that funds are used in the most effective way to improve health outcomes, in line with the United Nations' Sustainable Development Goal 3, "Ensure healthy lives and promote well-being for all at all ages." The Good Financial Grant Practice (GFGP) Standard (ARS 1651) is the world's first and, currently, only international standard for the financial governance and management of grant funding. Through consensus building and global harmonization between both low- and middle-income and high-income country players, the GFGP Standard has achieved a leveling impact: GFGP applies equally to, and can be implemented by, all types of organization, regardless of location, size, or whether they predominantly give or receive funding. GFGP can be used as a tool for addressing some of the challenges of the current funding model. Here, we describe our experiences and lessons learned from implementing GFGP across 4 diverse research institutions in India, Nigeria, Colombia, and the Philippines as part of our National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance.
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Affiliation(s)
- Harry J Harste
- Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom; Wellcome Genome Campus, Hinxton, United Kingdom
| | - Genevieve Kiff
- Oxford University Clinical Research Unit, Hanoi, Vietnam; African Academy of Sciences, Nairobi, Kenya
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College Research and Innovation Management, College of Medicine, University of Ibadan, Nigeria
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Jolaade J Ajiboye
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Erik C D Osma Castro
- AGROSAVIA (Corporación Colombiana de Investigación Agropecuaria), Bogotá, Colombia
| | - Elmer Herrera
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute of Tropical Medicine, Manila, Philippines
| | - David M Aanensen
- Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom; Wellcome Genome Campus, Hinxton, United Kingdom
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Nagaraj G, Govindan V, Ganaie F, Venkatesha VT, Hawkins PA, Gladstone RA, McGee L, Breiman RF, Bentley SD, Klugman KP, Lo SW, Ravikumar KL. Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach. Microb Genom 2021; 7. [PMID: 34494953 PMCID: PMC8715438 DOI: 10.1099/mgen.0.000645] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Globally, India has a high burden of pneumococcal disease, and pneumococcal conjugate vaccine (PCV) has been rolled out in different phases across the country since May 2017 in the national infant immunization programme (NIP). To provide a baseline for assessing the impact of the vaccine on circulating pneumococci in India, genetic characterization of pneumococcal isolates detected prior to introduction of PCV would be helpful. Here we present a population genomic study of 480 Streptococcus pneumoniae isolates collected across India and from all age groups before vaccine introduction (2009–2017), including 294 isolates from pneumococcal disease and 186 collected through nasopharyngeal surveys. Population genetic structure, serotype and antimicrobial susceptibility profile were characterized and predicted from whole-genome sequencing data. Our findings revealed high levels of genetic diversity represented by 110 Global Pneumococcal Sequence Clusters (GPSCs) and 54 serotypes. Serotype 19F and GPSC1 (CC320) was the most common serotype and pneumococcal lineage, respectively. Coverage of PCV13 (Pfizer) and 10-valent Pneumosil (Serum Institute of India) serotypes in age groups of ≤2 and 3–5 years were 63–75 % and 60–69 %, respectively. Coverage of PPV23 (Merck) serotypes in age groups of ≥50 years was 62 % (98/158). Among the top five lineages causing disease, GPSC10 (CC230), which ranked second, is the only lineage that expressed both PCV13 (serotypes 3, 6A, 14, 19A and 19F) and non-PCV13 (7B, 13, 10A, 11A, 13, 15B/C, 22F, 24F) serotypes. It exhibited multidrug resistance and was the largest contributor (17 %, 18/103) of NVTs in the disease-causing population. Overall, 42 % (202/480) of isolates were penicillin-resistant (minimum inhibitory concentration ≥0.12 µg ml−1) and 45 % (217/480) were multidrug-resistant. Nine GPSCs (GPSC1, 6, 9, 10, 13, 16, 43, 91, 376) were penicillin-resistant and among them six were multidrug-resistant. Pneumococci expressing PCV13 serotypes had a higher prevalence of antibiotic resistance. Sequencing of pneumococcal genomes has significantly improved our understanding of the biology of these bacteria. This study, describing the pneumococcal disease and carriage epidemiology pre-PCV introduction, demonstrates that 60–75 % of pneumococcal serotypes in children ≤5 years are covered by PCV13 and Pneumosil. Vaccination against pneumococci is very likely to reduce antibiotic resistance. A multidrug-resistant pneumococcal lineage, GPSC10 (CC230), is a high-risk clone that could mediate serotype replacement.
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Affiliation(s)
- Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Feroze Ganaie
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - V T Venkatesha
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bangalore, India
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12
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Lo SW, Gladstone RA, van Tonder AJ, Du Plessis M, Cornick JE, Hawkins PA, Madhi SA, Nzenze SA, Kandasamy R, Ravikumar KL, Elmdaghri N, Kwambana-Adams B, Almeida SCG, Skoczynska A, Egorova E, Titov L, Saha SK, Paragi M, Everett DB, Antonio M, Klugman KP, Li Y, Metcalf BJ, Beall B, McGee L, Breiman RF, Bentley SD, von Gottberg A. A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa. J Antimicrob Chemother 2021; 75:512-520. [PMID: 31789384 PMCID: PMC7021099 DOI: 10.1093/jac/dkz477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions. METHODS We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth-death model. RESULTS We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth-death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage. CONCLUSIONS The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Andries J van Tonder
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mignon Du Plessis
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jennifer E Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,Institute of Infection & Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan A Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - K L Ravikumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Centre, Bangalore, India
| | - Naima Elmdaghri
- Department of Microbiology, Faculty of Medicine and Pharmacy, B.P. 9154, Hassan II University of Casablanca, Casablanca, Morocco.,Bacteriology-Virology and Hospital Hygiene Laboratory, University Hospital Centre Ibn Rochd, Casablanca, Morocco
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.,WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Samanta Cristine Grassi Almeida
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil
| | - Anna Skoczynska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Ekaterina Egorova
- Laboratory of Clinical Microbiology and Biotechnology, Moscow Research Institute for Epidemiology and Microbiology, Moscow, Russian Federation
| | - Leonid Titov
- Laboratory of Clinical and Experimental Microbiology, The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Samir K Saha
- Department of Microbiology, Dhaka Shishu (Children's) Hospital, Child Health Research Foundation, Dhaka, Bangladesh
| | - Metka Paragi
- Department for Public Health Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Dean B Everett
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,University of Edinburgh, The Queens Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Keith P Klugman
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Yuan Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Emory Global Health Institute, Emory University, Atlanta, GA 30322, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anne von Gottberg
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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Arya BK, Bhattacharya SD, Harigovind G, Das RS, Khan T, Ganaie F, Niyogi SK, Ravikumar KL, Manoharan A, Bhattacharyya S, Panda S, Mandal S, Acharya B. Streptococcus pneumoniae Acquisition and Carriage in Vaccine Naïve Indian Children with HIV and their Parents: A Longitudinal Household Study. Indian J Pediatr 2019; 86:1002-1010. [PMID: 31222554 DOI: 10.1007/s12098-019-02995-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/22/2019] [Indexed: 02/01/2023]
Abstract
OBJECTIVES To investigate the difference in pneumococcal carriage, acquisition, antibiotic resistance profiles and serotype distribution, in human immunodeficiency virus (HIV) affected and unaffected families. METHODS A prospective cohort study was conducted in children with and without HIV in West Bengal from March 2012 through August 2014, prior to 13-valent pneumococcal conjugate vaccine (PCV-13) immunization. One thousand four hundred forty one nasopharyngeal swabs were collected and cultured at five-time points from children and their parents for pneumococcal culture, and serotyping by Quellung method. RESULTS One hundred twenty five HIV infected children and their parents, and 47 HIV uninfected children and their parents participated. Two hundred forty pneumococcal isolates were found. In children under 6 y, the point prevalence of colonization was 31% in children living with HIV (CLH) and 32% in HIV uninfected children (HUC), p = 0.6. The most common vaccine type (VT) serotypes were 6A, 6B and 19A. All isolates from parents and 71% from children in the HIV uninfected cohort were PCV-13 representative, compared to 33% of isolates from CLH and their parents. Acquisition rate in children was 1.77 times that of parents (OR = 1.77, 95%CI: 1.18-2.65). The HIV status of child or parent did not affect acquisition. Isolates from CLH were more frequently resistant to multiple antibiotics (p = 0.02). CONCLUSIONS While the rate of pneumococcal carriage and acquisition did not differ between CLH and HUC, HIV affected families had exposure to a wider range of serotypes including non-vaccine type serotypes and antibiotic resistant serotypes, than HIV unaffected families.
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Affiliation(s)
- Bikas K Arya
- School of Medical Science & Technology, Indian Institute of Technology-Kharagpur, IIT Kharagpur Campus, Kharagpur, West Bengal, 721302, India
| | - Sangeeta Das Bhattacharya
- School of Medical Science & Technology, Indian Institute of Technology-Kharagpur, IIT Kharagpur Campus, Kharagpur, West Bengal, 721302, India.
| | - Gautam Harigovind
- School of Medical Science & Technology, Indian Institute of Technology-Kharagpur, IIT Kharagpur Campus, Kharagpur, West Bengal, 721302, India
| | - Ranjan S Das
- School of Medical Science & Technology, Indian Institute of Technology-Kharagpur, IIT Kharagpur Campus, Kharagpur, West Bengal, 721302, India
| | - Tila Khan
- School of Medical Science & Technology, Indian Institute of Technology-Kharagpur, IIT Kharagpur Campus, Kharagpur, West Bengal, 721302, India
| | - Feroze Ganaie
- Department of Microbiology, Kempegowda Institute of Medical Sciences, KR Road, VV Puram, Bengaluru, Karnataka, India
| | - Swapan K Niyogi
- National Institute of Cholera and Enteric Diseases (NICED)/Indian Council of Medical Research (ICMR), P- C.I.T. Scheme XM, Beleghata, 33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata, West Bengal, India
| | - K L Ravikumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences, KR Road, VV Puram, Bengaluru, Karnataka, India
| | - Anand Manoharan
- Medicine Unit I & ID, Christian Medical College & Hospital, Vellore, Ida Scudder Road, Vellore, Tamil Nadu, India.,CHILDS Trust Medical Research Foundation, Chennai, India
| | - Subhasish Bhattacharyya
- Department of Pediatrics, Midnapore Medical College and Hospital, Vidyasagar Road, Paschim Medinipur, Medinipur, West Bengal, India.,Department of Pediatrics College of Medicine and Sagore Dutta Hospital, Kamarhati, Kolkata, India
| | - Samiran Panda
- National Institute of Cholera and Enteric Diseases (NICED)/Indian Council of Medical Research (ICMR), P- C.I.T. Scheme XM, Beleghata, 33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata, West Bengal, India.,National AIDS Research Institute Pune (NARI/ICMR), Plot No 73, G-block, M I D C, Bhosari, Pune, Maharashtra, India
| | - Sutapa Mandal
- National Institute of Cholera and Enteric Diseases (NICED)/Indian Council of Medical Research (ICMR), P- C.I.T. Scheme XM, Beleghata, 33, CIT Rd, Subhas Sarobar Park, Phool Bagan, Beleghata, Kolkata, West Bengal, India
| | - Banuja Acharya
- School of Medical Science & Technology, Indian Institute of Technology-Kharagpur, IIT Kharagpur Campus, Kharagpur, West Bengal, 721302, India
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14
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Nagaraj G, Ganaie F, Govindan V, Ravikumar KL. Development of PCRSeqTyping-a novel molecular assay for typing of Streptococcus pneumoniae. Pneumonia (Nathan) 2017; 9:8. [PMID: 28702310 PMCID: PMC5471960 DOI: 10.1186/s41479-017-0032-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 05/01/2017] [Indexed: 11/25/2022] Open
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.
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Affiliation(s)
- Geetha Nagaraj
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
| | - Feroze Ganaie
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
| | - Vandana Govindan
- Central Research Laboratory, KIMS Hospital and Research Centre, KR Road, VV Purum, Bangalore, Karnataka 560 004 India
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Giridhara Upadhyaya PM, Umapathy BL, Ravikumar KL. Comparative study for the presence of enterococcal virulence factors gelatinase, hemolysin and biofilm among clinical and commensal isolates of enterococcus faecalis. J Lab Physicians 2011; 2:100-4. [PMID: 21346906 PMCID: PMC3040082 DOI: 10.4103/0974-2727.72159] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Biofilm production, gelatinase and hemolysin are the potential virulence factors of Enterococci. Gelatinase and hemolysin producing strains of Enterococcus Faecalis have been shown to cause severe infections in animal models. Biofilm production has been shown to enhance the persistence of E. faecalis in urinary bladder and other medical indwelling devices infections. Aims: To compare the presence of gelatinase, hemolysin and biofilm formation among clinical and commensal isolates and to study the co-relation between virulence factors with respect to different clinical specimens. Settings and Design: During the study period of 2 years from July 2004 to July 2006, 200 clinical isolates from nosocomial infections and 100 commensal isolates of E. faecalis were taken for the study. Materials and Methods: The clinical and commensal isolates were tested for the presence of gelatinase, hemolysin and biofilm and compared. The presence of these virulence factors among different clinical isolates was also studied. Statistical Analysis: Chi-square and likelihood ratio analysis were carried out using SSPS version 5.1 software. Results: The clinical isolates produced 39, 16.5 and 32.5% of gelatinase, hemolysin and biofilm, respectively, as compared to 31, 19 and 16% produced by the commensal isolates, respectively. Endotracheal tube infection, urinary tract infection, umbilical catheter tip infected isolates produced 60.8, 86.6 and 100% biofilm, respectively. Conclusion: Significant difference in the production of biofilm (P<0.001) was noted between clinical and commensal isolates. Organism isolated from medically indwelling devices produced high amount of biofilm, confirming its role in colonization and causing nosocomial infections.
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Affiliation(s)
- P M Giridhara Upadhyaya
- Department of Microbiology, Kempegowda Institute of Medical Sciences, Bangalore, Karnataka, India
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Abstract
Brucellosis is a zoonotic infection transmitted from animals to humans by the ingestion of infected food products, direct contact with an infected animal or inhalation of aerosols. The last method is remarkably efficient given the relatively low concentration of organisms (10 - 100 bacteria) needed to establish infection in humans, and has brought renewed attention to this old disease. Brucella is a facultative intracellular pathogen that has the ability to survive and multiply in the phagocytes and cause abortion in cattle and undulant fever in humans. Brucella spp particularly B. melitensis, B. abortus, and B. suis represent a significant public health concern. At present, B. melitensis is the principle cause of human brucellosis in India. Molecular studies have demonstrated the phylogenetic affiliation of Brucella to Agrobacterium, Ochrobactrum, and Rhizobium. Human brucellosis still presents scientists and clinicians with several challenges, with regard to the understanding of its pathogenic mechanism, severity, progression, and development of improved treatment regimens. Molecular studies have now highlighted the pathogenesis of Brucella, for the development of newer diagnostic tools that will be useful in developing countries where brucellosis is a common, but often a neglected disease. This review compiles all these issues in general and the pathogenicity and newer diagnostic tools in particular.
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Affiliation(s)
- Supriya Christopher
- Department of Microbiology, Kempegowda Institute of Medical Sciences, BSK II Stage, Bangalore, India
| | - B L Umapathy
- Department of Microbiology, Kempegowda Institute of Medical Sciences, BSK II Stage, Bangalore, India
| | - K L Ravikumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences, BSK II Stage, Bangalore, India
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Giridhara Upadhyaya PM, Ravikumar KL, Umapathy BL. Review of virulence factors of enterococcus: an emerging nosocomial pathogen. Indian J Med Microbiol 2009; 27:301-5. [PMID: 19736397 DOI: 10.4103/0255-0857.55437] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Enterococcus, considered a normal commensal of intestinal tract, is fast emerging as a pathogen causing serious and life threatening hospital borne infections. This is attributed to acquisition of multi drug resistance and virulence factors of the organisms. The sequencing of Enterococcus faecalis has given a lot of insight into its genetic makeup. The E. faecalis strain V583, which has been sequenced, contains a total of 3182 open reading frames (ORFs) with 1760 of these showing similarity to known proteins and 221 of unknown functions. Strikingly unique to this genome is the fact that over 25% of the genome is made up of mobile and exogenously acquired DNA which includes a number of conjugative and composite transposons, a pathogenicity island, integrated plasmid genes and phage regions, and a high number of insertion sequence (IS) elements. This review addresses the genomic arrangement and the study of virulence factors that have occurred since the sequencing of the genome.
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Affiliation(s)
- P M Giridhara Upadhyaya
- Department of Microbiology, Kempe Gowda Institute of Medical Sciences, BSK II Stage, Bangalore-560 070, India.
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