Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

AJ van Tonder, 2016, Putatively novel serotypes and the potential for reduced vaccine effectiveness: capsular locus diversity revealed among 5405 pneumococcal genomes, Microb Genomics, 2, 000090, 10.1099/mgen.0.000090

AB Brueggemann, 2003, Clonal relationships between invasive and carriage Streptococcus pneumoniae and serotype- and clone-specific differences in invasive disease potential, J Infect Dis, 187, 1424, 10.1086/374624

P Martens, 2004, Serotype-specific mortality from invasive Streptococcus pneumoniaedisease revisited, BMC Infect Dis. BioMed Central, 4, 21, 10.1186/1471-2334-4-21

MG Täuber, 1991, Differences of pathophysiology in experimental meningitis caused by three strains of Streptococcus pneumoniae, J Infect Dis, 163, 806, 10.1093/infdis/163.4.806

DE Briles, 1992, Strong association between capsular type and virulence for mice among human isolates of Streptococcus pneumoniae, Infect Immun. American Society for Microbiology (ASM), 60, 111, 10.1128/IAI.60.1.111-116.1992

MR Moore, 2015, Effect of use of 13-valent pneumococcal conjugate vaccine in children on invasive pneumococcal disease in children and adults in the USA: analysis of multisite, population-based surveillance, Lancet Infect Dis, 15, 301, 10.1016/S1473-3099(14)71081-3

R Dagan, 2013, Comparative Immunogenicity and Efficacy of 13-Valent and 7-Valent Pneumococcal Conjugate Vaccines in Reducing Nasopharyngeal Colonization: A Randomized Double-Blind Trial, Clin Infect Dis, 57, 952, 10.1093/cid/cit428

NJ Andrews, 2014, Serotype-specific effectiveness and correlates of protection for the 13-valent pneumococcal conjugate vaccine: a postlicensure indirect cohort study, Lancet Infect Dis, 14, 839, 10.1016/S1473-3099(14)70822-9

SL Kaplan, 2013, Early Trends for Invasive Pneumococcal Infections in Children After the Introduction of the 13-valent Pneumococcal Conjugate Vaccine, Pediatr Infect Dis J, 32, 203, 10.1097/INF.0b013e318275614b

NJ Andrews, 2014, Serotype—specifi c eff ectiveness and correlates of protection for the 13—valent pneumococcal conjugate vaccine: a postlicensure indirect cohort study, Serotype—specifi c eff ectiveness and correlates of protection for the 13—valent pneumococcal conjugate vaccine: a postlicensure indirect cohort study

C Donati, 2010, Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species, Genome Biol, 11, R107, 10.1186/gb-2010-11-10-r107

NJ Croucher, 2013, Population genomics of post-vaccine changes in pneumococcal epidemiology, Nat Genet, 45, 656, 10.1038/ng.2625

L Cheng, 2013, Hierarchical and spatially explicit clustering of DNA sequences with BAPS software, Mol Biol Evol, 30, 1224, 10.1093/molbev/mst028

TJ Coffey, 1998, Recombinational exchanges at the capsular polysaccharide biosynthetic locus lead to frequent serotype changes among natural isolates of Streptococcus pneumoniae, Mol Microbiol, 27, 73, 10.1046/j.1365-2958.1998.00658.x

BG Spratt, 2004, Displaying the relatedness among isolates of bacterial species—the eBURST approach, FEMS Microbiol Lett, 241, 129, 10.1016/j.femsle.2004.11.015

JF Mosser, 2014, Nasopharyngeal carriage and transmission of <italic>Streptococcus pneumoniae</italic> in American Indian households after a decade of pneumococcal conjugate vaccine use, PLoS One. Public Library of Science, 9, e79578, 10.1371/journal.pone.0079578

SC Clarke, 2004, Serotypes and sequence types of pneumococci causing invasive disease in Scotland prior to the introduction of pneumococcal conjugate polysaccharide vaccines, J Clin Microbiol. American Society for Microbiology, 42, 4449, 10.1128/JCM.42.10.4449-4452.2004

NJ Croucher, 2013, Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection, PLoS Genet, 9, e1003868, 10.1371/journal.pgen.1003868

S Imai, 2009, High prevalence of multidrug-resistant Pneumococcal molecular epidemiology network clones among Streptococcus pneumoniae isolates from adult patients with community-acquired pneumonia in Japan, Clin Microbiol Infect, 15, 1039, 10.1111/j.1469-0691.2009.02935.x

KM Mothibeli, 2010, An unusual pneumococcal sequence type is the predominant cause of serotype 3 invasive disease in South Africa, J Clin Microbiol. American Society for Microbiology, 48, 184, 10.1128/JCM.01011-09

NJ Croucher, 2013, Population genomics of post-vaccine changes in pneumococcal epidemiology, Nat Genet. Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved, 45, 656

R Lapidot, 2017, Impact of PCV13 on Serotype 3 Invasive Pneumococcal Disease and Nasopharyngeal Colonization in Massachusetts’ children, San Diego, California: IDWeek

P Mitchell, 2017, Population genomics of pneumococcal carriage in Massachusetts children following PCV-13 introduction, bioRxiv. Cold Spring Harbor Laboratory

EH Choi, 2016, Capsular Polysaccharide (CPS) Release by Serotype 3 Pneumococcal Strains Reduces the Protective Effect of Anti-Type 3 CPS Antibodies, Clin Vaccine Immunol. American Society for Microbiology, 23, 162, 10.1128/CVI.00591-15

Y Li, 2013, Surface charge of <italic>Streptococcus pneumoniae</italic> predicts serotype distribution, Infect Immun. American Society for Microbiology (ASM), 81, 4519, 10.1128/IAI.00724-13

WB WOOD, 1949, The inhibition of surface phagocytosis by the capsular slime layer of pneumococcus type III, J Exp Med, 90, 85, 10.1084/jem.90.1.85

T Azarian, 2016, Pneumococcal protein antigen serology varies with age and may predict antigenic profile of colonizing isolates, J Infect Dis

P Mitchell, 2017, Population genomics of pneumococcal carriage in Massachusetts children following PCV-13 introduction, bioRxiv

T Azarian, 2018, The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome, PLOS Pathog. Public Library of Science, 14, e1006966, 10.1371/journal.ppat.1006966

Minka T. Estimating a Dirichlet distribution. Technical report, MIT; 2000.

DR Zerbino, 2008, Velvet: algorithms for de novo short read assembly using de Bruijn graphs, Genome Res, 18, 821, 10.1101/gr.074492.107

A Bankevich, 2012, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J Comput Biol, 19, 455, 10.1089/cmb.2012.0021

T Seemann, 2014, Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068, 10.1093/bioinformatics/btu153

AJ Page, 2015, Roary: Rapid large-scale prokaryote pan genome analysis, Bioinformatics, 31

H Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352

NJ Croucher, 2012, A high-resolution view of genome-wide pneumococcal transformation, PLoS Pathog, 8, e1002745, 10.1371/journal.ppat.1002745

NJ Croucher, 2014, Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins, Nucleic Acids Res

M Krzywinski, 2009, Circos: an information aesthetic for comparative genomics, Genome Res. Cold Spring Harbor Lab, 19, 1639

A Stamatakis, 2005, RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, 21, 456, 10.1093/bioinformatics/bti191

R Camilli, 2011, Complete genome sequence of a serotype 11A, ST62 Streptococcus pneumoniae invasive isolate, BMC Microbiol. BioMed Central, 11, 25, 10.1186/1471-2180-11-25

MD Hall, 2016, The effects of sampling strategy on the quality of reconstruction of viral population dynamics using Bayesian skyline family coalescent methods: A simulation study, Virus Evol, 2

S Duchêne, 2015, The performance of the date-randomization test in phylogenetic analyses of time-structured virus data, Mol Biol Evol. Oxford University Press, 32, 1895, 10.1093/molbev/msv056

C Ramsden, 2008, High rates of molecular evolution in hantaviruses, Mol Biol Evol. Oxford University Press, 25, 1488, 10.1093/molbev/msn093

AJ Drummond, 2012, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol Biol Evol, 1

R Bouckaert, 2014, BEAST 2: a software platform for Bayesian evolutionary analysis, PLoS Comput Biol, 10, e1003537, 10.1371/journal.pcbi.1003537

TG Vaughan, 2014, Efficient Bayesian inference under the structured coalescent, Bioinformatics

AG McArthur, 2013, The comprehensive antibiotic resistance database, Antimicrob Agents Chemother. Am Soc Microbiol, 57, 3348, 10.1128/AAC.00419-13

SK Gupta, 2014, ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes, Antimicrob Agents Chemother. Am Soc Microbiol, 58, 212, 10.1128/AAC.01310-13

Y Li, 2016, Penicillin-Binding Protein Transpeptidase Signatures for Tracking and Predicting β-Lactam Resistance Levels in Streptococcus pneumoniae, MBio. American Society for Microbiology, 7, e00756

EH Choi, 2016, Capsular Polysaccharide (CPS) Release by Serotype 3 Pneumococcal Strains Reduces the Protective Effect of Anti-Type 3 CPS Antibodies, Clin Vaccine Immunol. American Society for Microbiology (ASM), 23, 162, 10.1128/CVI.00591-15

CC Daniels, 2013, Modified opsonization, phagocytosis, and killing assays to measure potentially protective antibodies against pneumococcal surface protein A, Clin Vaccine Immunol, 20, 1549, 10.1128/CVI.00371-13

F Zhang, 2013, Multiple antigen-presenting system (MAPS) to induce comprehensive B- and T-cell immunity, Proc Natl Acad Sci U S A. National Academy of Sciences, 110, 13564, 10.1073/pnas.1307228110

NJ Croucher, 2011, Rapid pneumococcal evolution in response to clinical interventions, Science, 331, 430, 10.1126/science.1198545

P Romero, 2009, Comparative genomic analysis of ten Streptococcus pneumoniae temperate bacteriophages, J Bacteriol, 191, 4854, 10.1128/JB.01272-08

ST Chancey, 2015, Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae, Front Microbiol. Frontiers Media SA, 6, 26

A Chastanet, 2001, Regulation of Streptococcus pneumoniae clp genes and their role in competence development and stress survival, Journal of Bacteriology. American Society for Microbiology, 7295, 10.1128/JB.183.24.7295-7307.2001

C Donati, 2010, Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species, Genome Biol, 11, R107, 10.1186/gb-2010-11-10-r107

SK Hollingshead, 2000, Diversity of PspA: Mosaic Genes and Evidence for Past Recombination in Streptococcus pneumoniae, Infect Immun, 68, 5889, 10.1128/IAI.68.10.5889-5900.2000

F Iannelli, 2002, Allelic variation in the highly polymorphic locus pspC of Streptococcus pneumoniae, Gene, 284, 63, 10.1016/S0378-1119(01)00896-4

BJ Metcalf, 2016, Using whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States, Clin Microbiol Infect, 22, 1002.e1, 10.1016/j.cmi.2016.08.001

LB Rice, 2007, Characterization of Tn5386, a Tn916-related mobile element, Plasmid, 58, 61, 10.1016/j.plasmid.2007.01.002

R Isozumi, 2008, Molecular characteristics of serotype 3 Streptococcus pneumoniae isolates among community-acquired pneumonia patients in Japan, J Infect Chemother, 14, 258, 10.1007/s10156-008-0600-9

G Gherardi, 2007, Antibiotic-resistant invasive pneumococcal clones in Italy, J Clin Microbiol. American Society for Microbiology, 45, 306, 10.1128/JCM.01229-06

WP Hanage, 2010, Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete, Epidemics, 2, 80, 10.1016/j.epidem.2010.03.005

DM Weinberger, 2011, Serotype replacement in disease after pneumococcal vaccination, Lancet, 378, 1962, 10.1016/S0140-6736(10)62225-8

S Lehtinen, 2017, Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage, Proc Natl Acad Sci. National Academy of Sciences, 114, 1075, 10.1073/pnas.1617849114

A-C Uhlemann, 2014, Molecular tracing of the emergence, diversification, and transmission of <italic>S</italic>. <italic>aureus</italic> sequence type 8 in a New York community, Proc Natl Acad Sci

L a. Hicks, 2011, Outpatient Antibiotic Prescribing and Nonsusceptible Streptococcus pneumoniae in the United States, 1996–2003, Clin Infect Dis, 53, 631, 10.1093/cid/cir443

HK DeBardeleben, 2014, Tolerance of a phage element by Streptococcus pneumoniae leads to a fitness defect during colonization, J Bacteriol. American Society for Microbiology (ASM), 196, 2670

L-M Bobay, 2013, The Adaptation of Temperate Bacteriophages to Their Host Genomes, Mol Biol Evol. Oxford University Press, 30, 737, 10.1093/molbev/mss279

R Wilson, 2017, Naturally Acquired Human Immunity to Pneumococcus Is Dependent on Antibody to Protein Antigens, PLOS Pathog. Saunders, 13, e1006137, 10.1371/journal.ppat.1006137

P Turner, 2013, Serum antibody responses to pneumococcal colonization in the first 2 years of life: results from an SE Asian longitudinal cohort study, Clin Microbiol Infect, 19, E551, 10.1111/1469-0691.12286

B Ren, 2003, Both family 1 and family 2 PspA proteins can inhibit complement deposition and confer virulence to a capsular serotype 3 strain of Streptococcus pneumoniae, Infect Immun. American Society for Microbiology, 71, 75, 10.1128/IAI.71.1.75-85.2003

B Ren, 2003, Both family 1 and family 2 PspA proteins can inhibit complement deposition and confer virulence to a capsular serotype 3 strain of Streptococcus pneumoniae, Infect Immun. American Society for Microbiology, 71, 75, 10.1128/IAI.71.1.75-85.2003

M Georgieva, 2018, Antigenic Variation in Streptococcus pneumoniae PspC Promotes Immune Escape in the Presence of Variant-Specific Immunity, MBio. Am Soc Microbiol, 9, e00264

L McGee, 2001, Nomenclature of Major Antimicrobial-Resistant Clones of Streptococcus pneumoniae Defined by the Pneumococcal Molecular Epidemiology Network, J Clin Microbiol, 39, 2565, 10.1128/JCM.39.7.2565-2571.2001

R Mostowy, 2014, Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution, PLoS Genet. Public Library of Science, 10, e1004300, 10.1371/journal.pgen.1004300

Y-C Hsieh, 2006, Serotype competence and penicillin resistance in Streptococcus pneumoniae, Emerg Infect Dis, 12, 1709, 10.3201/eid1211.060414

FM Hui, 1995, Competence for genetic transformation in Streptococcus pneumoniae: organization of a regulatory locus with homology to two lactococcin A secretion genes, Gene, 153, 25, 10.1016/0378-1119(94)00841-F

MF Polz, 2013, Horizontal gene transfer and the evolution of bacterial and archaeal population structure, Trends Genet, 29, 170, 10.1016/j.tig.2012.12.006

GG Perron, 2011, Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations, Proc Biol Sci, 1477

WP Hanage, 2009, Hyper-recombination, diversity, and antibiotic resistance in pneumococcus, Science, 324, 1454, 10.1126/science.1171908

J Corander, 2017, Frequency-dependent selection in vaccine-associated pneumococcal population dynamics, Nat Ecol Evol. Nature Publishing Group, 1, 1950, 10.1038/s41559-017-0337-x

S Cobey, 2012, Niche and Neutral Effects of Acquired Immunity Permit Coexistence of Pneumococcal Serotypes, Science (80-), 335, 1376, 10.1126/science.1215947

ER Watkins, 2015, Vaccination Drives Changes in Metabolic and Virulence Profiles of Streptococcus pneumoniae, PLoS Pathog. Public Library of Science, 11, e1005034, 10.1371/journal.ppat.1005034

MR Moore, 2015, Effect of use of 13-valent pneumococcal conjugate vaccine in children on invasive pneumococcal disease in children and adults in the USA: analysis of multisite, population-based surveillance, Lancet Infect Dis. Elsevier, 15, 301, 10.1016/S1473-3099(14)71081-3