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Mokaddas E, Asadzadeh M, Syed S, Albert MJ. High Prevalence of Novel Sequence Types in Streptococcus pneumoniae That Caused Invasive Diseases in Kuwait in 2018. Microorganisms 2024; 12:225. [PMID: 38276209 PMCID: PMC10819824 DOI: 10.3390/microorganisms12010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Multilocus sequence typing (MLST) is used to gain insight into the population genetics of bacteria in the form of sequence type (ST). MLST has been used to study the evolution and spread of virulent clones of Streptococcus pneumoniae in many parts of the world. Such data for S. pneumoniae are lacking for the countries of the Arabian Peninsula, including Kuwait. METHODS We determined the STs of all 31 strains of S. pneumoniae from invasive diseases received at a reference laboratory from various health centers in Kuwait during 2018 by MLST. The relationship among the isolates was determined by phylogenetic analysis. We also determined the serotypes by Quellung reaction, and antimicrobial susceptibility by Etest, against 15 antibiotics belonging to 10 classes. RESULTS There were 28 STs among the 31 isolates, of which 14 were new STs (45.2%) and 5 were rare STs (16.1%). Phylogenetic analysis revealed that 26 isolates (83.9%) were unrelated singletons, and the Kuwaiti isolates were related to those from neighboring countries whose information was gleaned from unpublished data available at the PubMLST website. Many of our isolates were resistant to penicillin, erythromycin, and azithromycin, and some were multidrug-resistant. Virulent serotype 8-ST53, and serotype 19A with new STs, were detected. CONCLUSIONS Our study detected an unusually large number of novel STs, which may indicate that Kuwait provides a milieu for the evolution of novel STs. Novel STs may arise due to recombination and can result in capsular switching. This can impact the effect of vaccination programs on the burden of invasive pneumococcal disease. This first report from the Arabian Peninsula justifies the continuous monitoring of S. pneumoniae STs for the possible evolution of new virulent clones and capsular switching.
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Affiliation(s)
| | | | | | - M. John Albert
- Department of Microbiology, College of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait; (E.M.); (M.A.); (S.S.)
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2
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Chaguza C, Yang M, Jacques LC, Bentley SD, Kadioglu A. Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms. Trends Microbiol 2022; 30:581-592. [PMID: 34949516 PMCID: PMC7613904 DOI: 10.1016/j.tim.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022]
Abstract
Streptococcus pneumoniae (the 'pneumococcus') is a significant cause of morbidity and mortality worldwide, causing life-threatening diseases such as pneumonia, bacteraemia, and meningitis, with an annual death burden of over one million. Discovered over a century ago, pneumococcal serotype 1 (S1) is a significant cause of these life-threatening diseases. Our understanding of the epidemiology and biology of pneumococcal S1 has significantly improved over the past two decades, informing the development of preventative and surveillance strategies. However, many questions remain unanswered. Here, we review the current state of knowledge of pneumococcal S1, with a special emphasis on clinical epidemiology, genomics, and disease mechanisms.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Darwin College, University of Cambridge, Silver Street, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London, UK.
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
| | - Laura C Jacques
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK.
| | - Stephen D Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK; Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, The Ronald Ross Building, West Derby St, Liverpool, UK
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3
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Chaguza C, Ebruke C, Senghore M, Lo SW, Tientcheu PE, Gladstone RA, Tonkin-Hill G, Cornick JE, Yang M, Worwui A, McGee L, Breiman RF, Klugman KP, Kadioglu A, Everett DB, Mackenzie G, Croucher NJ, Roca A, Kwambana-Adams BA, Antonio M, Bentley SD. Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci. Genome Biol Evol 2022; 14:evac052. [PMID: 35439297 PMCID: PMC9048925 DOI: 10.1093/gbe/evac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2022] [Indexed: 11/14/2022] Open
Abstract
The isolation of Streptococcus pneumoniae serotypes in systemic tissues of patients with invasive disease versus the nasopharynx of healthy individuals with asymptomatic carriage varies widely. Some serotypes are hyper-invasive, particularly serotype 1, but the underlying genetics remain poorly understood due to the rarity of carriage isolates, reducing the power of comparison with invasive isolates. Here, we use a well-controlled genome-wide association study to search for genetic variation associated with invasiveness of serotype 1 pneumococci from a serotype 1 endemic setting in Africa. We found no consensus evidence that certain genomic variation is overrepresented among isolates from patients with invasive disease than asymptomatic carriage. Overall, the genomic variation explained negligible phenotypic variability, suggesting a minimal effect on the disease status. Furthermore, changes in lineage distribution were seen with lineages replacing each other over time, highlighting the importance of continued pathogen surveillance. Our findings suggest that the hyper-invasiveness is an intrinsic property of the serotype 1 strains, not specific for a "disease-associated" subpopulation disproportionately harboring unique genomic variation.
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Affiliation(s)
- Chrispin Chaguza
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Darwin College, University of Cambridge, Silver Street, Cambridge, UK
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Chinelo Ebruke
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Madikay Senghore
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stephanie W. Lo
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peggy-Estelle Tientcheu
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Rebecca A. Gladstone
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Gerry Tonkin-Hill
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jennifer E. Cornick
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Marie Yang
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Archibald Worwui
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Lesley McGee
- Respiratory Diseases Branch, 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
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Dean B. Everett
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Grant Mackenzie
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- Murdoch Children’s Research Institute, Parkville, Melbourne, VIC, Australia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Nicholas J. Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Anna Roca
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, UK
| | - Brenda A. Kwambana-Adams
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Martin Antonio
- Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
- London School of Hygiene & Tropical Medicine, London, UK
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
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4
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Gagetti P, Lo SW, Hawkins PA, Gladstone RA, Regueira M, Faccone D, Sireva-Argentina Group, Klugman KP, Breiman RF, McGee L, Bentley SD, Corso A. Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina. Microb Genom 2021; 7. [PMID: 34586054 PMCID: PMC8715423 DOI: 10.1099/mgen.0.000636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998-1999 (pre-PCV), before the introduction of PCV13 2010-2011 (PCV7) and after the introduction of PCV13 2012-2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50 % of the isolates. Resistance to penicillin was 34.9 %, cefotaxime 10.6 %, meropenem 4.9 %, cotrimoxazole 45 %, erythromycin 21.5 %, tetracycline 15.4 % and chloramphenicol 0.4 %. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9 %) were non-susceptible to at least one antibiotic and 235(13.7 %) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococcal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0 % in pre-PCV to 3.2 % in the PCV13 period. Our analysis showed that 66.1 % (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9 % (49/413) were multidrug resistant. We found an agreement of 100 % when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4 % of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.
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Affiliation(s)
- Paula Gagetti
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Stephanie W Lo
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paulina A Hawkins
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Centers for Disease Control and Prevention, Atlanta, USA
| | - Rebecca A Gladstone
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mabel Regueira
- Bacteriology Division. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Diego Faccone
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | | | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Emory Global Health Institute, Atlanta, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Stephen D Bentley
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alejandra Corso
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
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5
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Senghore M, Tientcheu PE, Worwui AK, Jarju S, Okoi C, Suso SMS, Foster-Nyarko E, Ebruke C, Sonko M, Kourna MH, Agossou J, Tsolenyanu E, Renner LA, Ansong D, Sanneh B, Cisse CB, Boula A, Miwanda B, Lo SW, Gladstone RA, Schwartz S, Hawkins P, McGee L, Klugman KP, Breiman RF, Bentley SD, Mwenda JM, Kwambana-Adams BA, Antonio M. Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction. Microb Genom 2021; 7. [PMID: 34328412 PMCID: PMC8477402 DOI: 10.1099/mgen.0.000506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 S. pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27). The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.
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Affiliation(s)
- Madikay Senghore
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.,Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - Peggy-Estelle Tientcheu
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Archibald Kwame Worwui
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Sheikh Jarju
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Catherine Okoi
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Sambou M S Suso
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Ebenezer Foster-Nyarko
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Chinelo Ebruke
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
| | - Mohamadou Sonko
- Hopital d'Enfants Albert Royer, BP 5297, Fann, Dakar, Senegal
| | | | - Joseph Agossou
- Department of Mother and Child, Faculty of Medicine, University of Parakou, Parakou, Benin.,Borgou Regional University Teaching Hospital, Parakou, Benin
| | - Enyonam Tsolenyanu
- Laboratoire Microbiologie, Centre Hospitalier Universitaire de Tokoin Lomé, BP 57, Lomé, Togo
| | - Lorna Awo Renner
- Central Laboratory Services, Korle-Bu Teaching Hospital, P.O. Box 77, Accra, Ghana
| | - Daniel Ansong
- Komfo Anokye Teaching Hospital, P.O. Box 1934, Kumasi, Ghana
| | - Bakary Sanneh
- Edward Francis Small Teaching Hospital, Banjul, The Gambia
| | - Catherine Boni Cisse
- Laboratoire Central du CHU de Yopougon, Institut Pasteur de Cote d'Ivoire, Abidjan, Ivory Coast
| | - Angeline Boula
- Centre Mere et Enfant de la Fondation, Chantal Biya, Yaounde, Cameroon
| | - Berthe Miwanda
- Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of Congo
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Paulina Hawkins
- Centers for Disease Control and Prevention, Atlanta, GA, USA.,Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Emory Global Health Institute, Atlanta, GA, USA
| | | | - Jason M Mwenda
- World Health Organization Regional Office for Africa, BP 6, Brazzaville, Republic of Congo
| | - Brenda Anna Kwambana-Adams
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, P.O. Box 273, Banjul, The Gambia
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6
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Rodgers E, Bentley SD, Borrow R, Bratcher HB, Brisse S, Brueggemann AB, Caugant DA, Findlow J, Fox L, Glennie L, Harrison LH, Harrison OB, Heyderman RS, van Rensburg MJ, Jolley KA, Kwambana-Adams B, Ladhani S, LaForce M, Levin M, Lucidarme J, MacAlasdair N, Maclennan J, Maiden MCJ, Maynard-Smith L, Muzzi A, Oster P, Rodrigues CMC, Ronveaux O, Serino L, Smith V, van der Ende A, Vázquez J, Wang X, Yezli S, Stuart JM. The global meningitis genome partnership. J Infect 2020; 81:510-520. [PMID: 32615197 DOI: 10.1016/j.jinf.2020.06.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 10/24/2022]
Abstract
Genomic surveillance of bacterial meningitis pathogens is essential for effective disease control globally, enabling identification of emerging and expanding strains and consequent public health interventions. While there has been a rise in the use of whole genome sequencing, this has been driven predominately by a subset of countries with adequate capacity and resources. Global capacity to participate in surveillance needs to be expanded, particularly in low and middle-income countries with high disease burdens. In light of this, the WHO-led collaboration, Defeating Meningitis by 2030 Global Roadmap, has called for the establishment of a Global Meningitis Genome Partnership that links resources for: N. meningitidis (Nm), S. pneumoniae (Sp), H. influenzae (Hi) and S. agalactiae (Sa) to improve worldwide co-ordination of strain identification and tracking. Existing platforms containing relevant genomes include: PubMLST: Nm (31,622), Sp (15,132), Hi (1935), Sa (9026); The Wellcome Sanger Institute: Nm (13,711), Sp (> 24,000), Sa (6200), Hi (1738); and BMGAP: Nm (8785), Hi (2030). A steering group is being established to coordinate the initiative and encourage high-quality data curation. Next steps include: developing guidelines on open-access sharing of genomic data; defining a core set of metadata; and facilitating development of user-friendly interfaces that represent publicly available data.
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Affiliation(s)
- Elizabeth Rodgers
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK.
| | - Stephen D Bentley
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Ray Borrow
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | | | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Angela B Brueggemann
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Jamie Findlow
- Pfizer Limited, Walton Oaks, Dorking Road, Tadworth, Surrey KT20 7NS, UK
| | - LeAnne Fox
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Linda Glennie
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Robert S Heyderman
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | | | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Mucosal Pathogens Research Unit, Division of Infection & Immunity, University College London, London, UK
| | - Shamez Ladhani
- Public Health England, Immunisation and Countermeasures Division, 61 Colindale Avenue, London NW9 5EQ, UK; Paediatric Infectious Diseases Research Group (PIDRG), St. George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | | | - Jay Lucidarme
- Public Health England, Meningococcal Reference Unit, Manchester Royal Infirmary, Manchester M13 9WZ, UK
| | - Neil MacAlasdair
- Wellcome Sanger Institute, Parasites and microbes, Hinxton CB10 1SA, UK
| | - Jenny Maclennan
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | | | | | | | | | | | | | | | - Vinny Smith
- Meningitis Research Foundation, Newminster House, 27-29 Newminster House, Baldwin Street, Bristol BS1 1LT, UK
| | - Arie van der Ende
- Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam UMC and, the Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam, the Netherlands
| | | | - Xin Wang
- Meningitis and Vaccine Preventable Disease Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, United States
| | - Saber Yezli
- Ministry of Health, The Global Centre for Mass Gatherings Medicine, Riyadh, Saudi Arabia
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7
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Dunne EM, Hua Y, Salaudeen R, Hossain I, Ndiaye M, Ortika BD, Mulholland EK, Hinds J, Manna S, Mackenzie GA, Satzke C. Insights into pneumococcal pneumonia using lung aspirates and nasopharyngeal swabs collected from pneumonia patients in The Gambia. J Infect Dis 2020; 225:1447-1451. [PMID: 32319524 PMCID: PMC9016440 DOI: 10.1093/infdis/jiaa186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/21/2020] [Indexed: 11/20/2022] Open
Abstract
Background We investigated the pathogenesis of pneumococcal pneumonia using clinical specimens collected for pneumonia surveillance in The Gambia. Methods Lung aspirates and nasopharyngeal swabs from 31 patients were examined by culture, quantitative polymerase chain reaction (qPCR), whole genome sequencing, serotyping, and reverse-transcription qPCR. Results Five lung aspirates cultured pneumococci, with a matching strain identified in the nasopharynx. Three virulence genes including ply (pneumolysin) were upregulated >20-fold in the lung compared with the nasopharynx. Nasopharyngeal pneumococcal density was higher in pediatric pneumonia patients compared with controls (P < .0001). Conclusions Findings suggest that changes in pneumococcal gene expression occurring in the lung environment may be important in pathogenesis.
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Affiliation(s)
- Eileen M Dunne
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia
| | - Yinglei Hua
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Rasheed Salaudeen
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Ilias Hossain
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Malick Ndiaye
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Belinda D Ortika
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia
| | - E Kim Mulholland
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jason Hinds
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom.,BUGS Bioscience, London Bioscience Innovation Centre, London, United Kingdom
| | - Sam Manna
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Grant A Mackenzie
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.,Department of Disease Control, London School of Hygiene & Tropical Medicine, London, UK
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children's Research Institute, Parkville, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, Australia.,Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Australia
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Fitness and Productivity Increase with Ecotypic Diversity among Escherichia coli Strains That Coevolved in a Simple, Constant Environment. Appl Environ Microbiol 2020; 86:AEM.00051-20. [PMID: 32060029 PMCID: PMC7117940 DOI: 10.1128/aem.00051-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/05/2020] [Indexed: 12/11/2022] Open
Abstract
Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections. The productivity of a biological community often correlates with its diversity. In the microbial world this phenomenon can sometimes be explained by positive, density-dependent interactions such as cross-feeding and syntrophy. These metabolic interactions help account for the astonishing variety of microbial life and drive many of the biogeochemical cycles without which life as we know it could not exist. While it is difficult to recapitulate experimentally how these interactions evolved among multiple taxa, we can explore in the laboratory how they arise within one. These experiments provide insight into how different bacterial ecotypes evolve and from these, possibly new “species.” We have previously shown that in a simple, constant environment a single clone of Escherichia coli can give rise to a consortium of genetically and phenotypically differentiated strains, in effect, a set of ecotypes, that coexist by cross-feeding. We marked these different ecotypes and their shared ancestor by integrating fluorescent protein into their genomes and then used flow cytometry to show that each evolved strain is more fit than the shared ancestor, that pairs of evolved strains are fitter still, and that the entire consortium is the fittest of all. We further demonstrate that the rank order of fitness values agrees with estimates of yield, indicating that an experimentally evolved consortium more efficiently converts primary and secondary resources to offspring than its ancestor or any member acting in isolation. IMPORTANCE Polymicrobial consortia occur in both environmental and clinical settings. In many cases, diversity and productivity correlate in these consortia, especially when sustained by positive, density-dependent interactions. However, the evolutionary history of such entities is typically obscure, making it difficult to establish the relative fitness of consortium partners and to use those data to illuminate the diversity-productivity relationship. Here, we dissect an Escherichia coli consortium that evolved under continuous glucose limitation in the laboratory from a single common ancestor. We show that a partnership consisting of cross-feeding ecotypes is better able to secure primary and secondary resources and to convert those resources to offspring than the ancestral clone. Such interactions may be a prelude to a special form of syntrophy and are likely determinants of microbial community structure in nature, including those having clinical significance such as chronic infections.
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High-Risk International Clones of Carbapenem-Nonsusceptible Pseudomonas aeruginosa Endemic to Indonesian Intensive Care Units: Impact of a Multifaceted Infection Control Intervention Analyzed at the Genomic Level. mBio 2019; 10:mBio.02384-19. [PMID: 31719179 PMCID: PMC6851282 DOI: 10.1128/mbio.02384-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In low-to-middle-income countries such as Indonesia, work in intensive care units (ICUs) can be hampered by lack of resources. Conducting large epidemiological studies in such settings using genomic tools is rather challenging. Still, we were able to systematically study the transmissions of carbapenem-nonsusceptible strains of P. aeruginosa (CNPA) within and between ICUs, before and after an infection control intervention. Our data show the importance of the broad dissemination of the internationally recognized CNPA clones, the relevance of environmental reservoirs, and the mixed effects of the implemented intervention; it led to a profound change in the clonal make-up of CNPA, but it did not reduce the patients’ risk of CNPA acquisitions. Thus, CNPA epidemiology in Indonesian ICUs is part of a global expansion of multiple CNPA clones that remains difficult to control by infection prevention measures. Infection control effectiveness evaluations require detailed epidemiological and microbiological data. We analyzed the genomic profiles of carbapenem-nonsusceptible Pseudomonas aeruginosa (CNPA) strains collected from two intensive care units (ICUs) in the national referral hospital in Jakarta, Indonesia, where a multifaceted infection control intervention was applied. We used clinical data combined with whole-genome sequencing (WGS) of systematically collected CNPA to infer the transmission dynamics of CNPA strains and to characterize their resistome. We found that the number of CNPA transmissions and acquisitions by patients was highly variable over time but that, overall, the rates were not significantly reduced by the intervention. Environmental sources were involved in these transmissions and acquisitions. Four high-risk international CNPA clones (ST235, ST823, ST375, and ST446) dominated, but the distribution of these clones changed significantly after the intervention was implemented. Using resistome analysis, carbapenem resistance was explained by the presence of various carbapenemase-encoding genes (blaGES-5, blaVIM-2-8, and blaIMP-1-7-43) and by mutations within the porin OprD. Our results reveal for the first time the dynamics of P. aeruginosa antimicrobial resistance (AMR) profiles in Indonesia and additionally show the utility of WGS in combination with clinical data to evaluate the impact of an infection control intervention. (This study has been registered at www.trialregister.nl under registration no. NTR5541).
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