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Williams AN, Ma A, Croxen MA, Demczuk WHB, Martin I, Tyrrell GJ. Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993-2019. Microb Genom 2023; 9. [PMID: 38015202 DOI: 10.1099/mgen.0.001141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
In the province of Alberta, Canada, invasive disease caused by Streptococcus pneumoniae serogroup 20 (serotypes 20A/20B) has been increasing in incidence. Here, we characterize provincial invasive serogroup 20 isolates collected from 1993 to 2019 alongside invasive and non-invasive serogroup 20 isolates from the Global Pneumococcal Sequencing (GPS) Project collected from 1998 to 2015. Trends in clinical metadata and geographic location were evaluated, and serogroup 20 isolate genomes were subjected to molecular sequence typing, virulence and antimicrobial resistance factor mining, phylogenetic analysis and pangenome calculation. Two hundred and seventy-four serogroup 20 isolates from Alberta were sequenced, and analysed along with 95 GPS Project genomes. The majority of invasive Alberta serogroup 20 isolates were identified after 2007 in primarily middle-aged adults and typed predominantly as ST235, a sequence type that was rare among GPS Project isolates. Most Alberta isolates carried a full-length whaF capsular gene, suggestive of serotype 20B. All Alberta and GPS Project genomes carried molecular resistance determinants implicated in fluoroquinolone and macrolide resistance, with a few Alberta isolates exhibiting phenotypic resistance to azithromycin, clindamycin, erythromycin, tetracycline and trimethoprim-sulfamethoxazole, as well as non-susceptibility to tigecycline. All isolates carried multiple virulence factors including those involved in adherence, immune modulation and nutrient uptake, as well as exotoxins and exoenzymes. Phylogenetically, Alberta serogroup 20 isolates clustered with predominantly invasive GPS Project isolates from the USA, Israel, Brazil and Nepal. Overall, this study highlights the increasing incidence of invasive S. pneumoniae serogroup 20 disease in Alberta, Canada, and provides insights into the genetic and clinical characteristics of these isolates within a global context.
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Affiliation(s)
- Ashley N Williams
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Alberta Precision Laboratory - Public Health Laboratory, 8440 112 Street NW, Edmonton, Alberta, T6G 2B7 Canada
| | - Angela Ma
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, Ste. #1100, Salt Lake City, UT, 84112 USA
| | - Matthew A Croxen
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Alberta Precision Laboratory - Public Health Laboratory, 8440 112 Street NW, Edmonton, Alberta, T6G 2B7 Canada
- Li Ka Shing Institute of Virology, University of Alberta, 6-010 Katz Centre for Health Research, 11315 - 87 Ave NW, Edmonton, Alberta, T6G 2E1 Canada
- Women & Children's Health Research Institute (WCHRI), University of Alberta, 5-083 Edmonton Clinic Health Academy (ECHA), 11405 87 Avenue NW Edmonton, AB, T6G 1C9 Canada
| | - Walter H B Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2 Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2 Canada
| | - Gregory J Tyrrell
- Department of Laboratory Medicine and Pathology, University of Alberta, 5-411 Edmonton Clinic Health Academy, Edmonton, Alberta, T6G 1C9 Canada
- Alberta Precision Laboratory - Public Health Laboratory, 8440 112 Street NW, Edmonton, Alberta, T6G 2B7 Canada
- Li Ka Shing Institute of Virology, University of Alberta, 6-010 Katz Centre for Health Research, 11315 - 87 Ave NW, Edmonton, Alberta, T6G 2E1 Canada
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Colomba C, Garbo V, Boncori G, Albano C, Bagarello S, Condemi A, Giordano S, Canduscio LA, Gallo C, Parrinello G, Cascio A. Streptococcus mitis as a New Emerging Pathogen in Pediatric Age: Case Report and Systematic Review. Antibiotics (Basel) 2023; 12:1222. [PMID: 37508318 PMCID: PMC10376791 DOI: 10.3390/antibiotics12071222] [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: 06/28/2023] [Revised: 07/20/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Streptococcus mitis, a normal inhabitant of the oral cavity, is a member of Viridans Group Streptococci (VGS). Generally recognized as a causative agent of invasive diseases in immunocompromised patients, S. mitis is considered to have low pathogenic potential in immunocompetent individuals. We present a rare case of sinusitis complicated by meningitis and cerebral sino-venous thrombosis (CSVT) caused by S. mitis in a previously healthy 12-year-old boy with poor oral health status. With the aim of understanding the real pathogenic role of this microorganism, an extensive review of the literature about invasive diseases due to S. mitis in pediatric patients was performed. Our data define the critical role of this microorganism in invasive infections, especially in immunocompetent children and in the presence of apparently harmful conditions such as sinusitis and caries. Attention should be paid to the choice of therapy because of VGS's emerging antimicrobial resistance patterns.
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Affiliation(s)
- Claudia Colomba
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Valeria Garbo
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Giovanni Boncori
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Chiara Albano
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Sara Bagarello
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Anna Condemi
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Salvatore Giordano
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Laura A Canduscio
- Division of Pediatric Infectious Diseases, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Cristina Gallo
- Division of Radiology, "G. Di Cristina" Hospital, ARNAS Civico Di Cristina Benfratelli, 90100 Palermo, Italy
| | - Gaspare Parrinello
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
| | - Antonio Cascio
- Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, 90100 Palermo, Italy
- Infectious and Tropical Diseases Unit, AOU Policlinico "P. Giaccone", 90100 Palermo, Italy
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Nishimoto AT, Dao TH, Jia Q, Ortiz-Marquez JC, Echlin H, Vogel P, van Opijnen T, Rosch JW. Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae. Cell Rep 2022; 41:111835. [PMID: 36516783 PMCID: PMC9850807 DOI: 10.1016/j.celrep.2022.111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.
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Affiliation(s)
- Andrew T. Nishimoto
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | | | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology and Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Boston, MA 02467, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Lead contact,Correspondence:
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Moreno-Blanco A, Solano-Collado V, Ortuno-Camuñas A, Espinosa M, Ruiz-Cruz S, Bravo A. PclR is a transcriptional activator of the gene that encodes the pneumococcal collagen-like protein PclA. Sci Rep 2022; 12:11827. [PMID: 35821046 PMCID: PMC9276737 DOI: 10.1038/s41598-022-15758-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
The Gram-positive bacterium Streptococcus pneumoniae is a major human pathogen that shows high levels of genetic variability. The pneumococcal R6 genome harbours several gene clusters that are not present in all strains of the species. One of these clusters contains two divergent genes, pclA, which encodes a putative surface-exposed protein that contains large regions of collagen-like repeats, and spr1404 (here named pclR). PclA was shown to mediate pneumococcal adherence to host cells in vitro. In this work, we demonstrate that PclR (494 amino acids) is a transcriptional activator. It stimulates transcription of the pclA gene by binding to a specific DNA site upstream of the core promoter. In addition, we show that PclR has common features with the MgaSpn transcriptional regulator (493 amino acids), which is also encoded by the R6 genome. These proteins have high sequence similarity (60.3%), share the same organization of predicted functional domains, and generate multimeric complexes on linear double-stranded DNAs. However, on the PpclA promoter region, MgaSpn binds to a site different from the one recognized by PclR. Our results indicate that PclR and MgaSpn have similar DNA-binding properties but different DNA-binding specificities, pointing to a different regulatory role of both proteins.
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Affiliation(s)
- Ana Moreno-Blanco
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Virtu Solano-Collado
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain.,Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Alejandro Ortuno-Camuñas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Sofía Ruiz-Cruz
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain. .,School of Microbiology, University College Cork and APC Microbiome Ireland, Western Road, Cork, T12 YT20, Ireland.
| | - Alicia Bravo
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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5
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González-Díaz A, Berbel D, Ercibengoa M, Cercenado E, Larrosa N, Quesada MD, Casabella A, Cubero M, Marimón JM, Domínguez MÁ, Carrera-Salinas A, Càmara J, Martín-Galiano AJ, Yuste J, Martí S, Ardanuy C. Genomic features of predominant non-PCV13 serotypes responsible for adult invasive pneumococcal disease in Spain. J Antimicrob Chemother 2022; 77:2389-2398. [PMID: 35815569 DOI: 10.1093/jac/dkac199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/23/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Although pneumococcal conjugate vaccines (PCVs) effectively prevent invasive pneumococcal disease (IPD), serotype replacement has occurred. OBJECTIVES We studied the pangenome, antibiotic resistance mechanisms and presence of mobile elements in predominant non-PCV13 serotypes causing adult IPD after PCV13 vaccine introduction in Spain. METHODS We conducted a multicentre study comparing three periods in six Spanish hospitals and analysed through whole genome sequencing representative strains collected in the pre-PCV13, early-PCV13 and late-PCV13 periods. RESULTS Among 2197 cases of adult IPD identified, 110 pneumococci expressing non-PCV13 capsules were sequenced. Seven predominant serotypes accounted for 42.6% of IPD episodes in the late-PCV13 period: serotypes 8 (14.4%), 12F (7.5%), 9N (5.2%), 11A (4.1%), 22F (3.9%), 24F (3.9%) and 16F (3.6%). All predominant non-PCV13 serotypes were highly clonal, comprising one or two clonal complexes (CC). In general, CC538, CC4048, CC3016F, CC43322F and CC669N, related to predominant non-PCV13 serotypes, were antibiotic susceptible. CC15611A was associated with resistance to co-trimoxazole, penicillin and amoxicillin. CC23024F was non-susceptible to penicillin and resistant to erythromycin, clindamycin, and tetracycline. Six composite transposon structures of the Tn5252-family were found in CC23024F, CC98912F and CC3016F carrying different combinations of erm(B), tet(M), and cat. Pangenome analysis revealed differences in accessory genomes among the different CC, with most variety in CC3016F (23.9%) and more conservation in CC15611A (8.5%). CONCLUSIONS We identified highly clonal predominant serotypes responsible for IPD in adults. The detection of not only conjugative elements carrying resistance determinants but also clones previously associated with vaccine serotypes (CC15611A and CC23024F) highlights the importance of the accessory genome.
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Affiliation(s)
- Aida González-Díaz
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain.,Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Dàmaris Berbel
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain.,Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - María Ercibengoa
- Biodonostia, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group, Osakidetza Basque Health, Donostia-San Sebastian, Spain
| | - Emilia Cercenado
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain.,Clinical Microbiology and Infectious Disease Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Nieves Larrosa
- Microbiology Department, Hospital Universitari Vall d'Hebron, UAB, Barcelona, Spain.,Research Network for Infectious Diseases (CIBERINFEC), ISCIII, Madrid, Spain
| | - Mª Dolores Quesada
- Research Network for Infectious Diseases (CIBERINFEC), ISCIII, Madrid, Spain
| | - Antonio Casabella
- Microbiology Department, Clinical Laboratory North Metropolitan Area, Hospital Universitari Germans Trias i Pujol, UAB, Badalona, Spain
| | - Meritxell Cubero
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain.,Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - José María Marimón
- Biodonostia, Infectious Diseases Area, Respiratory Infection and Antimicrobial Resistance Group, Osakidetza Basque Health, Donostia-San Sebastian, Spain
| | - M Ángeles Domínguez
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain.,Research Network for Infectious Diseases (CIBERINFEC), ISCIII, Madrid, Spain.,Microbiology Department, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Anna Carrera-Salinas
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jordi Càmara
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain.,Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Antonio J Martín-Galiano
- Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - José Yuste
- Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain.,Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
| | - Sara Martí
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain.,Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain.,Department of Medicine, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari Bellvitge, IDIBELL-UB, L'Hospitalet de Llobregat, Barcelona, Spain.,Research Network for Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain.,Microbiology Department, Hospital Universitari Parc Taulí, Sabadell, Spain
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6
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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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7
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Lu G, Shan S, Zainab B, Ayaz Z, He J, Xie Z, Rashid U, Zhang D, Mehmood Abbasi A. Novel vaccine design based on genomics data analysis: A review. Scand J Immunol 2021; 93:e12986. [PMID: 33043473 DOI: 10.1111/sji.12986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/04/2020] [Accepted: 10/05/2020] [Indexed: 12/28/2022]
Abstract
Modification of pathogenic strains with the passage of time is responsible for evolution in the timeline of vaccine development for last 30 years. Recent advancements in computational vaccinology on the one hand and genome sequencing approaches on the other have generated new hopes in vaccine development. The aim of this review was to discuss the evolution of vaccines, their characteristics and limitations. In this review, we highlighted the evolution of vaccines, from first generation to the current status, pointing out how different vaccines have emerged and different approaches that are being followed up in the development of more rational vaccines against a wide range of diseases. Data were collected using Google Scholar, Web of Science, Science Direct, Web of Knowledge, Scopus and Science Hub, whereas computational tools such as NCBI, GeneMANIA and STRING were used to analyse the pathways of vaccine action. Innovative tools, such as computational tools, recombinant technologies and intra-dermal devices, are currently being investigated in order to improve the immunological response. New technologies enlightened the interactions of host proteins with pathogenic proteins for vaccine candidate development, but still there is a need of integrating transcriptomic and proteomic approaches. Although immunization with genomics data is a successful approach, its advantages must be assessed case by case and its applicability depends on the nature of the agent to be immunized, the nature of the antigen and the type of immune response required to achieve effective protection.
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Affiliation(s)
- Guangli Lu
- Institute of Business, School of Business, Henan University, Henan, China
| | - Sharui Shan
- The First Affiliated Hospital of Jinan University (Guangzhou Overseas Chinese Hospital), Guangzhou, China
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Bibi Zainab
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zainab Ayaz
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Jialiang He
- School of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Zhenxing Xie
- Basic School of Medicine, Henan University, Kaifeng, China
| | - Umer Rashid
- Department of Chemistry, COMSATS University Islamabad, Islamabad, Pakistan
| | - Dalin Zhang
- Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Arshad Mehmood Abbasi
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
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8
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Ruiz García Y, Nieto Guevara J, Izurieta P, Vojtek I, Ortega-Barría E, Guzman-Holst A. CIRCULATING CLONAL COMPLEXES AND SEQUENCE TYPES OF STREPTOCOCCUS PNEUMONIAE SEROTYPE 19A WORLDWIDE: THE IMPORTANCE OF MULTIDRUG RESISTANCE: A SYSTEMATIC LITERATURE REVIEW. Expert Rev Vaccines 2021; 20:45-57. [PMID: 33507135 DOI: 10.1080/14760584.2021.1873136] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Streptococcus pneumoniae is a major cause of morbidity and mortality, especially amongst young children and the elderly. Childhood implementation of pneumococcal conjugate vaccines (PCVs) significantly reduced the incidence of invasive pneumococcal disease (IPD), while several nonvaccine serotypes remained substantial. Although there is evidence of the impact of higher-valent PCVs on serotype 19A, 19A IPD burden and antibiotic resistance remain a major concern post-vaccination. AREAS COVERED We performed a systematic literature review to analyze the frequency and clonal distribution of serotype 19A isolates in the pre- and post-PCV era worldwide providing a scientific background on the factors that influence multidrug resistance in pneumococcal isolates. EXPERT COMMENTARY Serotype 19A IPD incidence increased in all regions following the introduction of the 7-valent PCV. The higher-valent PCVs have reduced the rates of 19A IPD isolates, but several circulating strains with diverse antibiotic resistance prevailed. Heterogeneous clonal distribution in serotype 19A was observed within countries and regions, irrespective of higher-valent PCV used. An increase of 19A isolates from pre- to post-vaccination periods were associated with frequently occurring serotype switching events and with the prevalence of multidrug resistant strains. Rational antibiotic policies must be implemented to control the emergence of resistance.Plain Language SummaryWhat is the context?Streptococcus pneumoniae is a major cause of pneumococcal diseases especially amongst young children and the elderly. Vaccination with pneumococcal conjugate vaccines has significantly reduced the incidence of invasive pneumococcal disease worldwide. However, the invasive pneumococcal disease remains an important health problem due to the increase of nonvaccine serotypes. Serotype 19A is predominant in many countries worldwide. Factors contributing to its prevalence include serotype replacement, the emergence of clones with multidrug resistance due to antibiotic overuse, and potential bacteria adaptation in response to the vaccine.What is new?We performed a systematic literature review to 1) analyze the incidence and clonal distribution of serotype 19A isolates pre- and post-vaccination worldwide, and to collect data evaluating antimicrobial resistance patterns displayed by the clones of serotype 19A. We found that 1) clonal distribution in serotype 19A was heterogeneous within countries and regions, irrespective of the vaccine used; 2) the diversity of 19A isolates increased after vaccination. It was associated with frequent serotype switching events and with the prevalence of multidrug resistant strains.What is the impact?Implementation of policies to educate on sustainable antibiotic use and infectious prevention measures may help control the emergence of antibiotic resistance. High-quality active surveillance and future molecular epidemiology studies are needed to understand rapid genetic changes.
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9
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Abstract
A description of the genetic makeup of a species based on a single genome is often insufficient because it ignores the variability in gene repertoire among multiple strains. The estimation of the pangenome of a species is a solution to this issue as it provides an overview of genes that are shared by all strains and genes that are present in only some of the genomes. These different sets of genes can then be analyzed functionally to explore correlations with unique phenotypes and adaptations. This protocol presents the usage of Roary, a Linux-native pangenome application. Roary is a straightforward software that provides 1) an overview about core and accessory genes for those interested in general trends and, also, 2) detailed information on gene presence/absence in each genome for in-depth analyses. Results are provided both in text and graphic format.
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Affiliation(s)
- Farrah Sitto
- Department of Biological Sciences, Oakland University, Rochester, MI
| | - Fabia U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester, MI
- Center for Data Science and Big Data Analytics, Oakland University, Rochester, MI
- Corresponding author: E-mail:
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10
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Nasher F, Aguilar F, Aebi S, Hermans PWM, Heller M, Hathaway LJ. Peptide Ligands of AmiA, AliA, and AliB Proteins Determine Pneumococcal Phenotype. Front Microbiol 2018; 9:3013. [PMID: 30568648 PMCID: PMC6290326 DOI: 10.3389/fmicb.2018.03013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/21/2018] [Indexed: 12/13/2022] Open
Abstract
The Ami-AliA/AliB oligopeptide permease of Streptococcus pneumoniae has been suggested to play a role in environmental sensing and colonisation of the nasopharynx by this human bacterial pathogen by binding peptides derived from bacterial neighbours of other species in the microbiota. Here, we investigated the effects of the peptide ligands of the permease’s substrate binding proteins AmiA, AliA, and AliB on pneumococcal phenotype. AmiA and AliA ligands reduced pneumococcal growth, increased biofilm production and reduced capsule size. In contrast, AliB ligand increased growth and greatly increased bacterial chain length. A decrease in transformation rate was observed in response to all three peptides. Changes in protein expression were also observed, particularly those associated with metabolism and cell wall synthesis. Understanding interspecies bacterial communication and its effect on development of colonising versus invasive phenotypes has the potential to reveal new targets to tackle and prevent pneumococcal infections.
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Affiliation(s)
- Fauzy Nasher
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Fernando Aguilar
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Suzanne Aebi
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Peter W M Hermans
- Janssen Vaccines and Prevention, Leiden, Netherlands.,Julius Center, UMC Utrecht, Utrecht, Netherlands
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Lucy J Hathaway
- Institute for Infectious Diseases, Faculty of Medicine, University of Bern, Bern, Switzerland
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11
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Hare KM, Leach AJ, Smith-Vaughan HC, Chang AB, Grimwood K. Streptococcus pneumoniae and chronic endobronchial infections in childhood. Pediatr Pulmonol 2017; 52:1532-1545. [PMID: 28922566 DOI: 10.1002/ppul.23828] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/06/2017] [Indexed: 01/03/2023]
Abstract
Streptococcus pneumoniae (pneumococcus) is the main cause of bacterial pneumonia worldwide and has been studied extensively in this context. However, its role in chronic endobronchial infections and accompanying lower airway neutrophilic infiltration has received little attention. Severe and recurrent pneumonia are risk factors for chronic suppurative lung disease (CSLD) and bronchiectasis; the latter causes considerable morbidity and, in some populations, premature death in children and adults. Protracted bacterial bronchitis (PBB) is another chronic endobronchial infection associated with substantial morbidity. In some children, PBB may progress to bronchiectasis. Although nontypeable Haemophilus influenzae is the main pathogen in PBB, CSLD and bronchiectasis, pneumococci are isolated commonly from the lower airways of children with these diagnoses. Here we review what is known currently about pneumococci in PBB, CSLD and bronchiectasis, including the importance of pneumococcal nasopharyngeal colonization and how persistence in the lower airways may contribute to the pathogenesis of these chronic pulmonary disorders. Antibiotic treatments, particularly long-term azithromycin therapy, are discussed together with antibiotic resistance and the impact of pneumococcal conjugate vaccines. Important areas requiring further investigation are identified, including immune responses associated with pneumococcal lower airway infection, alone and in combination with other respiratory pathogens, and microarray serotyping to improve detection of carriage and infection by multiple serotypes. Genome wide association studies of pneumococci from the upper and lower airways will help identify virulence and resistance determinants, including potential therapeutic targets and vaccine antigens to treat and prevent endobronchial infections. Much work is needed, but the benefits will be substantial.
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Affiliation(s)
- Kim M Hare
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Heidi C Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,Department of Respiratory Medicine, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Keith Grimwood
- School of Medicine, Griffith University, Gold Coast, Queensland, Australia.,Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia.,Gold Coast Health, Gold Coast, Queensland, Australia
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12
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Exploring the Genomic Diversity and Cariogenic Differences of Streptococcus mutans Strains Through Pan-Genome and Comparative Genome Analysis. Curr Microbiol 2017; 74:1200-1209. [PMID: 28717847 DOI: 10.1007/s00284-017-1305-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 07/11/2017] [Indexed: 10/19/2022]
Abstract
Pan-genome refers to the sum of genes that can be found in a given bacterial species, including the core-genome and the dispensable genome. In this study, the genomes from 183 Streptococcus mutans (S. mutans) isolates were analyzed from the pan-genome perspective. This analysis revealed that S. mutans has an "open" pan-genome, implying that there are plenty of new genes to be found as more genomes are sequenced. Additionally, S. mutans has a limited core-genome, which is composed of genes related to vital activities within the bacterium, such as metabolism and hereditary information storage or processing, occupying 35.6 and 26.6% of the core genes, respectively. We estimate the theoretical core-genome size to be about 1083 genes, which are fewer than other Streptococcus species. In addition, core genes suffer larger selection pressures in comparison to those that are less widely distributed. Not surprisingly, the distribution of putative virulence genes in S. mutans strains does not correlate with caries status, indicating that other factors are also responsible for cariogenesis. These results contribute to a more understanding of the evolutionary characteristics and dynamic changes within the genome components of the species. This also helps to form a new theoretical foundation for preventing dental caries. Furthermore, this study sets an example for analyzing large genomic datasets of pathogens from the pan-genome perspective.
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13
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Long Persistence of a Streptococcus pneumoniae 23F Clone in a Cystic Fibrosis Patient. mSphere 2017; 2:mSphere00201-17. [PMID: 28596991 PMCID: PMC5463027 DOI: 10.1128/msphere.00201-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023] Open
Abstract
Streptococcus pneumoniae is a common resident in the human nasopharynx. However, carriage can result in severe diseases due to a unique repertoire of pathogenicity factors that are rare in closely related commensal streptococci. We investigated a penicillin-resistant S. pneumoniae clone of serotype 23F isolated from a cystic fibrosis patient on multiple occasions over an unusually long period of over 3 years that was present without causing disease. Genome comparisons revealed an apparent nonfunctional pneumococcus-specific gene encoding a hyaluronidase, supporting the view that this enzyme adds to the virulence potential of the bacterium. The 23F clone harbored unique mosaic genes encoding penicillin resistance determinants, the product of horizontal gene transfer involving the commensal S. mitis as donor species. Sequences identical to one such mosaic gene were identified in an S. mitis strain from the same patient, suggesting that in this case S. pneumoniae played the role of donor. Streptococcus pneumoniae isolates of serotype 23F with intermediate penicillin resistance were recovered on seven occasions over a period of 37 months from a cystic fibrosis patient in Berlin. All isolates expressed the same multilocus sequence type (ST), ST10523. The genome sequences of the first and last isolates, D122 and D141, revealed the absence of two phage-related gene clusters compared to the genome of another ST10523 strain, D219, isolated earlier at a different place in Germany. Genomes of all three strains carried the same novel mosaic penicillin-binding protein (PBP) genes, pbp2x, pbp2b, and pbp1a; these genes were distinct from those of other penicillin-resistant S. pneumoniae strains except for pbp1a of a Romanian S. pneumoniae isolate. All PBPs contained mutations that have been associated with the penicillin resistance phenotype. Most interestingly, a mosaic block identical to an internal pbp2x sequence of ST10523 was present in pbp2x of Streptococcus mitis strain B93-4, which was isolated from the same patient. This suggests interspecies gene transfer from S. pneumoniae to S. mitis within the host. Nearly all genes expressing surface proteins, which represent major virulence factors of S. pneumoniae and are typical for this species, were present in the genome of ST10523. One exception was the hyaluronidase gene hlyA, which contained a 12-nucleotide deletion within the promoter region and an internal stop codon. The lack of a functional hyaluronidase might contribute to the ability to persist in the host for an unusually long period of time. IMPORTANCEStreptococcus pneumoniae is a common resident in the human nasopharynx. However, carriage can result in severe diseases due to a unique repertoire of pathogenicity factors that are rare in closely related commensal streptococci. We investigated a penicillin-resistant S. pneumoniae clone of serotype 23F isolated from a cystic fibrosis patient on multiple occasions over an unusually long period of over 3 years that was present without causing disease. Genome comparisons revealed an apparent nonfunctional pneumococcus-specific gene encoding a hyaluronidase, supporting the view that this enzyme adds to the virulence potential of the bacterium. The 23F clone harbored unique mosaic genes encoding penicillin resistance determinants, the product of horizontal gene transfer involving the commensal S. mitis as donor species. Sequences identical to one such mosaic gene were identified in an S. mitis strain from the same patient, suggesting that in this case S. pneumoniae played the role of donor.
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14
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Udaondo Z, Duque E, Ramos JL. The pangenome of the genus Clostridium. Environ Microbiol 2017; 19:2588-2603. [PMID: 28321969 DOI: 10.1111/1462-2920.13732] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 11/26/2022]
Abstract
The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.
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Affiliation(s)
- Zulema Udaondo
- Calle Energía Solar 1, Building D, Campus Palmas Altas, Abengoa Research, Biotechnology Technological Area, Sevilla, 41014, Spain.,Consejo Superior de Investigaciones Científicas, EEZ, Environmental Protection Department, C/Profesor Albareda 1, Granada, 18008, Spain
| | - Estrella Duque
- Calle Energía Solar 1, Building D, Campus Palmas Altas, Abengoa Research, Biotechnology Technological Area, Sevilla, 41014, Spain.,Consejo Superior de Investigaciones Científicas, EEZ, Environmental Protection Department, C/Profesor Albareda 1, Granada, 18008, Spain
| | - Juan-Luis Ramos
- Calle Energía Solar 1, Building D, Campus Palmas Altas, Abengoa Research, Biotechnology Technological Area, Sevilla, 41014, Spain.,Consejo Superior de Investigaciones Científicas, EEZ, Environmental Protection Department, C/Profesor Albareda 1, Granada, 18008, Spain
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15
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Comparative genomic analysis reveals genetic features related to the virulence of Bacillus cereus FORC_013. Gut Pathog 2017; 9:29. [PMID: 28515790 PMCID: PMC5433235 DOI: 10.1186/s13099-017-0175-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacillus cereus is well known as a gastrointestinal pathogen that causes food-borne illness. In the present study, we sequenced the complete genome of B. cereus FORC_013 isolated from fried eel in South Korea. To extend our understanding of the genomic characteristics of FORC_013, we conducted a comparative analysis with the published genomes of other B. cereus strains. RESULTS We fully assembled the single circular chromosome (5,418,913 bp) and one plasmid (259,749 bp); 5511 open reading frames (ORFs) and 283 ORFs were predicted for the chromosome and plasmid, respectively. Moreover, we detected that the enterotoxin (NHE, HBL, CytK) induces food-borne illness with diarrheal symptom, and that the pleiotropic regulator, along with other virulence factors, plays a role in surviving and biofilm formation. Through comparative analysis using the complete genome sequence of B. cereus FORC_013, we identified both positively selected genes related to virulence regulation and 224 strain-specific genes of FORC_013. CONCLUSIONS Through genome analysis of B. cereus FORC_013, we identified multiple virulence factors that may contribute to pathogenicity. These results will provide insight into further studies regarding B. cereus pathogenesis mechanism at the genomic level.
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16
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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17
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Robbins RJ, Krishtalka L, Wooley JC. Advances in biodiversity: metagenomics and the unveiling of biological dark matter. Stand Genomic Sci 2016; 11:69. [PMID: 27617059 PMCID: PMC5016886 DOI: 10.1186/s40793-016-0180-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 08/16/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones. RESULTS Biology, like physics, has a fundamental duality-the classical macroscale eukaryotic realm vs. the quantum microscale microbial realm-with the two realms differing profoundly, and counter-intuitively, from one another. Just as classical physics is emergent from and cannot explain the microscale realm of quantum physics, so classical biology is emergent from and cannot explain the microscale realm of prokaryotic life. Classical biology describes the familiar, macroscale realm of multi-cellular eukaryotic organisms, which constitute a highly derived and constrained evolutionary subset of the biosphere, unrepresentative of the vast, mostly unseen, microbial world of prokaryotic life that comprises at least half of the planet's biomass and most of its genetic diversity. The two realms occupy fundamentally different mega-niches: eukaryotes interact primarily mechanically with the environment, prokaryotes primarily physiologically. Further, many foundational tenets of classical biology simply do not apply to prokaryotic biology. CONCLUSIONS Classical genetics one held that genes, arranged on chromosomes like beads on a string, were the fundamental units of mutation, recombination, and heredity. Then, molecular analysis showed that there were no fundamental units, no beads, no string. Similarly, classical biology asserts that individual organisms and species are fundamental units of ecology, evolution, and biodiversity, composing an evolutionary history of objectively real, lineage-defined groups in a single-rooted tree of life. Now, metagenomic tools are forcing a recognition that there are no completely objective individuals, no unique lineages, and no one true tree. The newly revealed biosphere of microbial dark matter cannot be understood merely by extending the concepts and methods of eukaryotic macrobiology. The unveiling of biological dark matter is allowing us to see, for the first time, the diversity of the entire biosphere and, to paraphrase Darwin, is providing a new view of life. Advancing and understanding that view will require major revisions to some of the most fundamental concepts and theories in biology.
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Affiliation(s)
- Robert J. Robbins
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045 USA
- University of California, San Diego, USA
| | - Leonard Krishtalka
- Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045 USA
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18
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Donati C, Zolfo M, Albanese D, Tin Truong D, Asnicar F, Iebba V, Cavalieri D, Jousson O, De Filippo C, Huttenhower C, Segata N. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing. Nat Microbiol 2016; 1:16070. [PMID: 27572971 DOI: 10.1038/nmicrobiol.2016.70] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 04/19/2016] [Indexed: 12/18/2022]
Abstract
Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes. We applied these tools to 520 oral metagenomes from the Human Microbiome Project, finding evidence of site tropism and temporal intra-subject strain retention. Although the opportunistic pathogen Neisseria meningitidis is enriched for colonization in the throat, N. flavescens and N. subflava populate the tongue dorsum, and N. sicca, N. mucosa and N. elongata the gingival plaque. The buccal mucosa appeared as an intermediate ecological niche between the plaque and the tongue. The resulting approaches to metagenomic strain profiling are generalizable and can be extended to other organisms and microbiomes across environments.
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Affiliation(s)
- Claudio Donati
- Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele All'adige, Italy
| | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Davide Albanese
- Computational Biology Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010 San Michele All'adige, Italy
| | - Duy Tin Truong
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Francesco Asnicar
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Valerio Iebba
- Department of Public Health and Infectious Diseases, Institute Pasteur Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy.,Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Firenze, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Carlotta De Filippo
- Institute of Biometeorology, National Research Council (IBIMET-CNR), Via Caproni 8, 50145 Firenze, Italy
| | - Curtis Huttenhower
- Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
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19
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Provorov NA, Tikhonovich IA, Vorobyov NI. Symbiogenesis as a model for reconstructing the early stages of genome evolution. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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20
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The evolution and epidemiology of Listeria monocytogenes in Europe and the United States. INFECTION GENETICS AND EVOLUTION 2015; 35:172-83. [DOI: 10.1016/j.meegid.2015.08.008] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 11/20/2022]
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21
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Abnave P, Mottola G, Gimenez G, Boucherit N, Trouplin V, Torre C, Conti F, Ben Amara A, Lepolard C, Djian B, Hamaoui D, Mettouchi A, Kumar A, Pagnotta S, Bonatti S, Lepidi H, Salvetti A, Abi-Rached L, Lemichez E, Mege JL, Ghigo E. Screening in planarians identifies MORN2 as a key component in LC3-associated phagocytosis and resistance to bacterial infection. Cell Host Microbe 2015; 16:338-50. [PMID: 25211076 DOI: 10.1016/j.chom.2014.08.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 06/13/2014] [Accepted: 07/10/2014] [Indexed: 01/21/2023]
Abstract
Dugesia japonica planarian flatworms are naturally exposed to various microbes but typically survive this challenge. We show that planarians eliminate bacteria pathogenic to Homo sapiens, Caenorhabditis elegans, and/or Drosophila melanogaster and thus represent a model to identify innate resistance mechanisms. Whole-transcriptome analysis coupled with RNAi screening of worms infected with Staphylococcus aureus or Legionella pneumophila identified 18 resistance genes with nine human orthologs, of which we examined the function of MORN2. Human MORN2 facilitates phagocytosis-mediated restriction of Mycobacterium tuberculosis, L. pneumophila, and S. aureus in macrophages. MORN2 promotes the recruitment of LC3, an autophagy protein also involved in phagocytosis, to M. tuberculosis-containing phagosomes and subsequent maturation to degradative phagolysosomes. MORN2-driven trafficking of M. tuberculosis to single-membrane, LC3-positive compartments requires autophagy-related proteins Atg5 and Beclin-1, but not Ulk-1 and Atg13, highlighting the importance of MORN2 in LC3-associated phagocytosis. These findings underscore the value of studying planarian defenses to identify immune factors.
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Affiliation(s)
- Prasad Abnave
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France; INSERM, U1065, C3M, Université de Nice Sophia-Antipolis, Equipe labellisée ligue contre le cancer, 06204 Nice Cedex 3, France
| | - Giovanna Mottola
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France; Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II," Via S. Pansini 5, 80131 Naples, Italy
| | - Gregory Gimenez
- Otago Genomics & Bioinformatics Facility, Department of Biochemistry, University of Otago, PO Box 56, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Nicolas Boucherit
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Virginie Trouplin
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Cedric Torre
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Filippo Conti
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France; INSERM, U1065, C3M, Université de Nice Sophia-Antipolis, Equipe labellisée ligue contre le cancer, 06204 Nice Cedex 3, France
| | - Amira Ben Amara
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Catherine Lepolard
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Benjamin Djian
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Daniel Hamaoui
- INSERM, U1065, C3M, Université de Nice Sophia-Antipolis, Equipe labellisée ligue contre le cancer, 06204 Nice Cedex 3, France
| | - Amel Mettouchi
- INSERM, U1065, C3M, Université de Nice Sophia-Antipolis, Equipe labellisée ligue contre le cancer, 06204 Nice Cedex 3, France
| | - Atul Kumar
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France; INSERM, U1065, C3M, Université de Nice Sophia-Antipolis, Equipe labellisée ligue contre le cancer, 06204 Nice Cedex 3, France
| | - Sophie Pagnotta
- Centre Commun de Microscopie Appliquée (CCMA) Université de Nice Sophia Antipolis, Faculté des Sciences, Parc Valrose, 06108 Nice Cedex 2, France
| | - Stefano Bonatti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II," Via S. Pansini 5, 80131 Naples, Italy
| | - Hubert Lepidi
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, Unity of Experimental Biology and Genetics, University of Pisa, Via Volta 4, 56126 Pisa, Italy
| | - Laurent Abi-Rached
- Centre National de la Recherche Scientifique, Laboratoire d'Analyse, Topologie, Probabilités - Unité Mixte de Recherche 7353, Equipe ATIP, Aix-Marseille Université, 13331 Marseille, France
| | - Emmanuel Lemichez
- INSERM, U1065, C3M, Université de Nice Sophia-Antipolis, Equipe labellisée ligue contre le cancer, 06204 Nice Cedex 3, France
| | - Jean-Louis Mege
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
| | - Eric Ghigo
- CNRS UMR 7278, IRD198, INSERM U1095, Aix-Marseille Université, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France.
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22
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Teixeira AS, Monteiro PT, Carriço JA, Ramirez M, Francisco AP. Not seeing the forest for the trees: size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis. PLoS One 2015; 10:e0119315. [PMID: 25799056 PMCID: PMC4370493 DOI: 10.1371/journal.pone.0119315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 12/18/2014] [Indexed: 11/23/2022] Open
Abstract
Trees, including minimum spanning trees (MSTs), are commonly used in phylogenetic studies. But, for the research community, it may be unclear that the presented tree is just a hypothesis, chosen from among many possible alternatives. In this scenario, it is important to quantify our confidence in both the trees and the branches/edges included in such trees. In this paper, we address this problem for MSTs by introducing a new edge betweenness metric for undirected and weighted graphs. This spanning edge betweenness metric is defined as the fraction of equivalent MSTs where a given edge is present. The metric provides a per edge statistic that is similar to that of the bootstrap approach frequently used in phylogenetics to support the grouping of taxa. We provide methods for the exact computation of this metric based on the well known Kirchhoff’s matrix tree theorem. Moreover, we implement and make available a module for the PHYLOViZ software and evaluate the proposed metric concerning both effectiveness and computational performance. Analysis of trees generated using multilocus sequence typing data (MLST) and the goeBURST algorithm revealed that the space of possible MSTs in real data sets is extremely large. Selection of the edge to be represented using bootstrap could lead to unreliable results since alternative edges are present in the same fraction of equivalent MSTs. The choice of the MST to be presented, results from criteria implemented in the algorithm that must be based in biologically plausible models.
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Affiliation(s)
- Andreia Sofia Teixeira
- INESC-ID Lisboa, Lisbon, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Pedro T. Monteiro
- INESC-ID Lisboa, Lisbon, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - João A Carriço
- INESC-ID Lisboa, Lisbon, Portugal
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Mário Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandre P. Francisco
- INESC-ID Lisboa, Lisbon, Portugal
- Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- * E-mail:
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23
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Abstract
Kingella kingae is a common etiology of pediatric bacteremia and the leading agent of osteomyelitis and septic arthritis in children aged 6 to 36 months. This Gram-negative bacterium is carried asymptomatically in the oropharynx and disseminates by close interpersonal contact. The colonized epithelium is the source of bloodstream invasion and dissemination to distant sites, and certain clones show significant association with bacteremia, osteoarthritis, or endocarditis. Kingella kingae produces an RTX (repeat-in-toxin) toxin with broad-spectrum cytotoxicity that probably facilitates mucosal colonization and persistence of the organism in the bloodstream and deep body tissues. With the exception of patients with endocardial involvement, children with K. kingae diseases often show only mild symptoms and signs, necessitating clinical acumen. The isolation of K. kingae on routine solid media is suboptimal, and detection of the bacterium is significantly improved by inoculating exudates into blood culture bottles and the use of PCR-based assays. The organism is generally susceptible to antibiotics that are administered to young patients with joint and bone infections. β-Lactamase production is clonal, and the local prevalence of β-lactamase-producing strains is variable. If adequately and promptly treated, invasive K. kingae infections with no endocardial involvement usually run a benign clinical course.
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Affiliation(s)
- Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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24
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Andam CP, Hanage WP. Mechanisms of genome evolution of Streptococcus. INFECTION GENETICS AND EVOLUTION 2014; 33:334-42. [PMID: 25461843 DOI: 10.1016/j.meegid.2014.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 11/05/2014] [Accepted: 11/07/2014] [Indexed: 10/24/2022]
Abstract
The genus Streptococcus contains 104 recognized species, many of which are associated with human or animal hosts. A globally prevalent human pathogen in this group is Streptococcus pneumoniae (the pneumococcus). While being a common resident of the upper respiratory tract, it is also a major cause of otitis media, pneumonia, bacteremia and meningitis, accounting for a high burden of morbidity and mortality worldwide. Recent findings demonstrate the importance of recombination and selection in driving the population dynamics and evolution of different pneumococcal lineages, allowing them to successfully evade the impacts of selective pressures such as vaccination and antibiotic treatment. We highlight the ability of pneumococci to respond to these pressures through processes including serotype replacement, capsular switching and horizontal gene transfer (HGT) of antibiotic resistance genes. The challenge in controlling this pathogen also lies in the exceptional genetic and phenotypic variation among different pneumococcal lineages, particularly in terms of their pathogenicity and resistance to current therapeutic strategies. The widespread use of pneumococcal conjugate vaccines, which target only a small subset of the more than 90 pneumococcal serotypes, provides us with a unique opportunity to elucidate how the processes of selection and recombination interact to generate a remarkable level of plasticity and heterogeneity in the pneumococcal genome. These processes also play an important role in the emergence and spread of multi-resistant strains, which continues to pose a challenge in disease control and/or eradication. The application of population of genomic approaches at different spatial and temporal scales will help improve strategies to control this global pathogen, and potentially other pathogenic streptococci.
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Affiliation(s)
- Cheryl P Andam
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - William P Hanage
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.
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25
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Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure. Proc Natl Acad Sci U S A 2014; 111:5439-44. [PMID: 24706866 DOI: 10.1073/pnas.1403353111] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen.
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26
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Dorella FA, Gala-Garcia A, Pinto AC, Sarrouh B, Antunes CA, Ribeiro D, Aburjaile FF, Fiaux KK, Guimarães LC, Seyffert N, El-Aouar RA, Silva R, Hassan SS, Castro TLP, Marques WS, Ramos R, Carneiro A, de Sá P, Miyoshi A, Azevedo V, Silva A. Progression of 'OMICS' methodologies for understanding the pathogenicity of Corynebacterium pseudotuberculosis: the Brazilian experience. Comput Struct Biotechnol J 2013; 6:e201303013. [PMID: 24688721 PMCID: PMC3962224 DOI: 10.5936/csbj.201303013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/06/2013] [Accepted: 09/08/2013] [Indexed: 11/22/2022] Open
Abstract
Since the first successful attempt at sequencing the Corynebacterium pseudotuberculosis genome, large amounts of genomic, transcriptomic and proteomic data have been generated. C. pseudotuberculosis is an interesting bacterium due to its great zoonotic potential and because it causes considerable economic losses worldwide. Furthermore, different strains of C. pseudotuberculosis are capable of causing various diseases in different hosts. Currently, we seek information about the phylogenetic relationships between different strains of C. pseudotuberculosis isolates from different hosts across the world and to employ these data to develop tools to diagnose and eradicate the diseases these strains cause. In this review, we present the latest findings on C. pseudotuberculosis that have been obtained with the most advanced techniques for sequencing and genomic organization. We also discuss the development of in silico tools for processing these data to prompt a better understanding of this pathogen.
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Affiliation(s)
- Fernanda A Dorella
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Alfonso Gala-Garcia
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Anne C Pinto
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Boutros Sarrouh
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Camila A Antunes
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Dayana Ribeiro
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Flavia F Aburjaile
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Karina K Fiaux
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Luis C Guimarães
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Núbia Seyffert
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Rachid A El-Aouar
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Renata Silva
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Syed S Hassan
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Thiago L P Castro
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Wanderson S Marques
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Rommel Ramos
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Adriana Carneiro
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Pablo de Sá
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
| | - Anderson Miyoshi
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Artur Silva
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém-PA, Brazil
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27
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Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, van Hylckama Vlieg JET, Siezen RJ. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One 2013; 8:e68731. [PMID: 23894338 PMCID: PMC3716772 DOI: 10.1371/journal.pone.0068731] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 05/31/2013] [Indexed: 12/11/2022] Open
Abstract
Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link the distribution pattern of a specific phenotype to the presence/absence of specific sets of genes.
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28
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Song L, Wang W, Conrads G, Rheinberg A, Sztajer H, Reck M, Wagner-Döbler I, Zeng AP. Genetic variability of mutans streptococci revealed by wide whole-genome sequencing. BMC Genomics 2013; 14:430. [PMID: 23805886 PMCID: PMC3751929 DOI: 10.1186/1471-2164-14-430] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Accepted: 06/12/2013] [Indexed: 01/09/2023] Open
Abstract
Background Mutans streptococci are a group of bacteria significantly contributing to tooth decay. Their genetic variability is however still not well understood. Results Genomes of 6 clinical S. mutans isolates of different origins, one isolate of S. sobrinus (DSM 20742) and one isolate of S. ratti (DSM 20564) were sequenced and comparatively analyzed. Genome alignment revealed a mosaic-like structure of genome arrangement. Genes related to pathogenicity are found to have high variations among the strains, whereas genes for oxidative stress resistance are well conserved, indicating the importance of this trait in the dental biofilm community. Analysis of genome-scale metabolic networks revealed significant differences in 42 pathways. A striking dissimilarity is the unique presence of two lactate oxidases in S. sobrinus DSM 20742, probably indicating an unusual capability of this strain in producing H2O2 and expanding its ecological niche. In addition, lactate oxidases may form with other enzymes a novel energetic pathway in S. sobrinus DSM 20742 that can remedy its deficiency in citrate utilization pathway. Using 67 S. mutans genomes currently available including the strains sequenced in this study, we estimates the theoretical core genome size of S. mutans, and performed modeling of S. mutans pan-genome by applying different fitting models. An “open” pan-genome was inferred. Conclusions The comparative genome analyses revealed diversities in the mutans streptococci group, especially with respect to the virulence related genes and metabolic pathways. The results are helpful for better understanding the evolution and adaptive mechanisms of these oral pathogen microorganisms and for combating them.
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Affiliation(s)
- Lifu Song
- Institute of Bioprocess and Biosystems, Technical University Hamburg Harburg, Hamburg Harburg, Germany
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29
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Cornejo OE, Lefébure T, Pavinski Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol 2013; 30:881-93. [PMID: 23228887 PMCID: PMC3603310 DOI: 10.1093/molbev/mss278] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Streptococcus mutans is widely recognized as one of the key etiological agents of human dental caries. Despite its role in this important disease, our present knowledge of gene content variability across the species and its relationship to adaptation is minimal. Estimates of its demographic history are not available. In this study, we generated genome sequences of 57 S. mutans isolates, as well as representative strains of the most closely related species to S. mutans (S. ratti, S. macaccae, and S. criceti), to identify the overall structure and potential adaptive features of the dispensable and core components of the genome. We also performed population genetic analyses on the core genome of the species aimed at understanding the demographic history, and impact of selection shaping its genetic variation. The maximum gene content divergence among strains was approximately 23%, with the majority of strains diverging by 5-15%. The core genome consisted of 1,490 genes and the pan-genome approximately 3,296. Maximum likelihood analysis of the synonymous site frequency spectrum (SFS) suggested that the S. mutans population started expanding exponentially approximately 10,000 years ago (95% confidence interval [CI]: 3,268-14,344 years ago), coincidental with the onset of human agriculture. Analysis of the replacement SFS indicated that a majority of these substitutions are under strong negative selection, and the remainder evolved neutrally. A set of 14 genes was identified as being under positive selection, most of which were involved in either sugar metabolism or acid tolerance. Analysis of the core genome suggested that among 73 genes present in all isolates of S. mutans but absent in other species of the mutans taxonomic group, the majority can be associated with metabolic processes that could have contributed to the successful adaptation of S. mutans to its new niche, the human mouth, and with the dietary changes that accompanied the origin of agriculture.
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Affiliation(s)
- Omar E. Cornejo
- Department of Genetics, School of Medicine, Stanford University
| | - Tristan Lefébure
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Paulina D. Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Ping Lang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Vincent P. Richards
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Kirsten Eilertson
- Department of Biological Statistics and Computational Biology, Cornell University
| | - Thuy Do
- Department of Microbiology, King’s College London Dental Institute and NIHR Biomedical Research Centre at Guy's and St. Thomas’s NHS Foundation Trust, Guy’s Hospital, London, United Kingdom
| | - David Beighton
- Department of Microbiology, King’s College London Dental Institute and NIHR Biomedical Research Centre at Guy's and St. Thomas’s NHS Foundation Trust, Guy’s Hospital, London, United Kingdom
| | - Lin Zeng
- Department of Oral Biology, University of Florida
| | | | | | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University
| | | | - Michael J. Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
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30
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Donati C, Rappuoli R. Reverse vaccinology in the 21st century: improvements over the original design. Ann N Y Acad Sci 2013; 1285:115-32. [PMID: 23527566 DOI: 10.1111/nyas.12046] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Reverse vaccinology (RV), the first application of genomic technologies in vaccine research, represented a major revolution in the process of discovering novel vaccines. By determining their entire antigenic repertoire, researchers could identify protective targets and design efficacious vaccines for pathogens where conventional approaches had failed. Bexsero, the first vaccine developed using RV, has recently received positive opinion from the European Medicines Agency. The use of RV initiated a cascade of changes that affected the entire vaccine development process, shifting the focus from the identification of a list of vaccine candidates to the definition of a set of high throughput screens to reduce the need for costly and labor intensive tests in animal models. It is now clear that a deep understanding of the epidemiology of vaccine candidates, and their regulation and role in host-pathogen interactions, must become an integral component of the screening workflow. Far from being outdated by technological advancements, RV still represents a paradigm of how high-throughput technologies and scientific insight can be integrated into biotechnology research.
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31
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Shak JR, Vidal JE, Klugman KP. Influence of bacterial interactions on pneumococcal colonization of the nasopharynx. Trends Microbiol 2012; 21:129-35. [PMID: 23273566 DOI: 10.1016/j.tim.2012.11.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 11/13/2012] [Accepted: 11/19/2012] [Indexed: 12/11/2022]
Abstract
Streptococcus pneumoniae (the pneumococcus) is a common commensal inhabitant of the nasopharynx and a frequent etiologic agent in serious diseases such as pneumonia, otitis media, bacteremia, and meningitis. Multiple pneumococcal strains can colonize the nasopharynx, which is also home to many other bacterial species. Intraspecies and interspecies interactions influence pneumococcal carriage in important ways. Co-colonization by two or more pneumococcal strains has implications for vaccine serotype replacement, carriage detection, and pneumonia diagnostics. Interactions between the pneumococcus and other bacterial species alter carriage prevalence, modulate virulence, and affect biofilm formation. By examining these interactions, this review highlights how the bacterial ecosystem of the nasopharynx changes the nature and course of pneumococcal carriage.
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Affiliation(s)
- Joshua R Shak
- Molecules to Mankind Program and Graduate Program in Population Biology, Ecology, and Evolution, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
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32
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Tibayrenc M, Ayala FJ. Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. Proc Natl Acad Sci U S A 2012; 109:E3305-13. [PMID: 22949662 PMCID: PMC3511763 DOI: 10.1073/pnas.1212452109] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. The two main manifestations of clonal evolution are strong linkage disequilibrium (LD) and widespread genetic clustering ("near-clading"). We hypothesize that this pattern is not mainly due to natural selection, but originates chiefly from in-built genetic properties of pathogens, which could be ancestral and could function as alternative allelic systems to recombination genes ("clonality/sexuality machinery") to escape recombinational load. The clonal framework of species of pathogens should be ascertained before any analysis of biomedical phenotypes (phylogenetic character mapping). In our opinion, this model provides a conceptual framework for the population genetics of any micropathogen.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, Institut de Rercherche pour le Développement 224, Centre National de la Recherche Scientifique 5290, Universités Montpellier 1 and 2, 34394 Montpellier Cedex 5, France; and
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697
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33
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Selection of resistance at lethal and non-lethal antibiotic concentrations. Curr Opin Microbiol 2012; 15:555-60. [DOI: 10.1016/j.mib.2012.07.005] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 11/23/2022]
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Abstract
The comparative genomics of prokaryotes has shown the presence of conserved regions containing highly similar genes (the 'core genome') and other regions that vary in gene content (the 'flexible' regions). A significant part of the latter is involved in surface structures that are phage recognition targets. Another sizeable part provides for differences in niche exploitation. Metagenomic data indicates that natural populations of prokaryotes are composed of assemblages of clonal lineages or "meta-clones" that share a core of genes but contain a high diversity by varying the flexible component. This meta-clonal diversity is maintained by a collection of phages that equalize the populations by preventing any individual clonal lineage from hoarding common resources. Thus, this polyclonal assemblage and the phages preying upon them constitute natural selection units.
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Affiliation(s)
- Francisco Rodriguez-Valera
- Departmento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain
| | - David W Ussery
- Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby, Denmark
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Amit U, Porat N, Basmaci R, Bidet P, Bonacorsi S, Dagan R, Yagupsky P. Genotyping of Invasive Kingella kingae Isolates Reveals Predominant Clones and Association With Specific Clinical Syndromes. Clin Infect Dis 2012; 55:1074-9. [DOI: 10.1093/cid/cis622] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Yalcin B, Adams DJ, Flint J, Keane TM. Next-generation sequencing of experimental mouse strains. Mamm Genome 2012; 23:490-8. [PMID: 22772437 PMCID: PMC3463794 DOI: 10.1007/s00335-012-9402-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 05/24/2012] [Indexed: 12/24/2022]
Abstract
Since the turn of the century the complete genome sequence of just one mouse strain, C57BL/6J, has been available. Knowing the sequence of this strain has enabled large-scale forward genetic screens to be performed, the creation of an almost complete set of embryonic stem (ES) cell lines with targeted alleles for protein-coding genes, and the generation of a rich catalog of mouse genomic variation. However, many experiments that use other common laboratory mouse strains have been hindered by a lack of whole-genome sequence data for these strains. The last 5 years has witnessed a revolution in DNA sequencing technologies. Recently, these technologies have been used to expand the repertoire of fully sequenced mouse genomes. In this article we review the main findings of these studies and discuss how the sequence of mouse genomes is helping pave the way from sequence to phenotype. Finally, we discuss the prospects for using de novo assembly techniques to obtain high-quality assembled genome sequences of these laboratory mouse strains, and what advances in sequencing technologies may be required to achieve this goal.
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Affiliation(s)
- Binnaz Yalcin
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
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Olsen RJ, Long SW, Musser JM. Bacterial genomics in infectious disease and the clinical pathology laboratory. Arch Pathol Lab Med 2012; 136:1414-22. [PMID: 22439809 DOI: 10.5858/arpa.2012-0025-ra] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Throughout history, technologic advancements have fueled the engine of innovation, which, in turn, has driven discovery. Accordingly, recent advancements in DNA sequencing technology are revolutionizing bacterial genomics. OBJECTIVE To review important developments from the literature. The current state of bacterial genomics, with an emphasis on human pathogens and the clinical pathology laboratory, will be discussed. DATA SOURCES A comprehensive review was performed of the relevant literature indexed in PubMed (National Library of Medicine) and referenced medical texts. CONCLUSIONS Many important discoveries bearing on infectious disease research and pathology laboratory practice have been achieved through whole-genome sequencing strategies. Bacterial genomics has improved our understanding of molecular pathogenesis, host-pathogen interactions, and antibiotic-resistance mechanisms. Bacterial genomics has also facilitated the study of population structures, epidemics and outbreaks, and newly identified pathogens. Many opportunities now exist for clinical pathologists to contribute to bacterial genomics, including in the design of new diagnostic tests, therapeutic agents, and vaccines.
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Affiliation(s)
- Randall J Olsen
- Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX 77030, USA.
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