Backhaus E, Berg S, Andersson R, Ockborn G, Malmström P, Dahl M, et al. Epidemiology of invasive pneumococcal infections: manifestations, incidence and case fatality rate correlated to age, gender and risk factors. BMC Infect Dis. 2016;16:367.
Google Scholar
Bogaert D, de Groot R, Hermans P. Streptococcus pneumoniae colonisation: the key to pneumococcal disease. Lancet Infect Dis. 2004;4:144–54.
Google Scholar
Wahl B, O’Brien KL, Greenbaum A, Majumder A, Liu L, Chu Y, et al. Burden of Streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: global, regional, and national estimates for 2000-15. Lancet Glob Health. 2018;6:e744–57.
Google Scholar
McAllister DA, Liu L, Shi T, Chu Y, Reed C, Burrows J, et al. Global, regional, and national estimates of pneumonia morbidity and mortality in children younger than 5 years between 2000 and 2015: a systematic analysis. Lancet Glob Health. 2019;7:e47–57.
Google Scholar
Abdullahi O, Karani A, Tigoi CC, Mugo D, Kungu S, Wanjiru E, et al. The prevalence and risk factors for pneumococcal colonization of the nasopharynx among children in Kilifi District, Kenya. PloS ONE. 2012;7:e30787.
Google Scholar
Kelly MS, Surette MG, Smieja M, Rossi L, Luinstra K, Steenhoff AP, et al. Pneumococcal colonization and the nasopharyngeal microbiota of children in Botswana. Pediatr Infect Dis J. 2018;37:1176–83.
Google Scholar
Huang SS, Hinrichsen VL, Stevenson AE, Rifas-Shiman SL, Kleinman K, Pelton SI, et al. Continued impact of pneumococcal conjugate vaccine on carriage in young children. Pediatrics 2009;124:e1–e11.
Google Scholar
van Hoek AJ, Sheppard CL, Andrews NJ, Waight PA, Slack MP, Harrison TG, et al. Pneumococcal carriage in children and adults two years after introduction of the thirteen valent pneumococcal conjugate vaccine in England. Vaccine.2014;32:4349–55.
Google Scholar
Almeida ST, Nunes S, Paulo ACS, Valadares I, Martins S, Breia F, et al. Low prevalence of pneumococcal carriage and high serotype and genotype diversity among adults over 60 years of age living in Portugal. PloS ONE 2014;9:e90974.
Google Scholar
Kaplan SL, Mason EO, Wald ER, Schutze GE, Bradley JS, Tan TQ, et al. Decrease of invasive pneumococcal infections in children among 8 children’s hospitals in the United States after the introduction of the 7-valent pneumococcal conjugate vaccine. Pediatrics.2004;113:443–9.
Google Scholar
Hammitt LL, Etyang AO, Morpeth SC, Ojal J, Mutuku A, Mturi N, et al. Effect of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya: a longitudinal surveillance study. Lancet.2019;393:2146–54.
Google Scholar
Cutts F, Zaman S, Enwere GY, Jaffar S, Levine O, Okoko J, et al. Efficacy of nine-valent pneumococcal conjugate vaccine against pneumonia and invasive pneumococcal disease in The Gambia: randomised, double-blind, placebo-controlled trial. Lancet.2005;365:1139–46.
Google Scholar
Congdon M, Hong H, Young RR, Cunningham CK, Enane LA, Arscott-Mills T, et al. Effect of Haemophilus influenzae type b and 13-valent pneumococcal conjugate vaccines on childhood pneumonia hospitalizations and deaths in Botswana. Clin Infect Dis. 2020; e-pub ahead of print 8 July 2020; https://doi.org/10.1093/cid/ciaa919.
Eskola J, Kilpi T, Palmu A, Jokinen J, Eerola M, Haapakoski J, et al. Efficacy of a pneumococcal conjugate vaccine against acute otitis media. N. Engl J Med. 2001;344:403–9.
Google Scholar
Pelton SI, Huot H, Finkelstein JA, Bishop CJ, Hsu KK, Kellenberg J, et al. Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine. Pediatr Infect Dis J. 2007;26:468–72.
Google Scholar
Pichichero ME, Casey JR. Emergence of a multiresistant serotype 19A pneumococcal strain not included in the 7-valent conjugate vaccine as an otopathogen in children. JAMA.2007;298:1772–8.
Google Scholar
Neves FP, Cardoso NT, Snyder RE, Marlow MA, Cardoso CA, Teixeira LM, et al. Pneumococcal carriage among children after four years of routine 10-valent pneumococcal conjugate vaccine use in Brazil: the emergence of multidrug resistant serotype 6C. Vaccine.2017;35:2794–800.
Google Scholar
Bradshaw JL, McDaniel LS. Selective pressure: rise of the nonencapsulated pneumococcus. PLoS Pathog. 2019;15:e1007911.
Google Scholar
Ladhani SN, Collins S, Djennad A, Sheppard CL, Borrow R, Fry NK, et al. Rapid increase in non-vaccine serotypes causing invasive pneumococcal disease in England and Wales, 2000–17: a prospective national observational cohort study. Lancet Infect Dis. 2018;18:441–51.
Google Scholar
Ouldali N, Levy C, Varon E, Bonacorsi S, Béchet S, Cohen R, et al. Incidence of paediatric pneumococcal meningitis and emergence of new serotypes: a time-series analysis of a 16-year French national survey. Lancet Infect Dis. 2018;18:983–91.
Google Scholar
Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI, et al. Host-bacterial coevolution and the search for new drug targets. Curr Opin Chem Biol. 2008;12:109–14.
Google Scholar
de Steenhuijsen Piters WA, Binkowska J, Bogaert D. Early life microbiota and respiratory tract infections. Cell Host Microbe. 2020;28:223–32.
Google Scholar
Bogaert D, van Belkum A, Sluijter M, Luijendijk A, de Groot R, Rümke H, et al. Colonisation by Streptococcus pneumoniae and Staphylococcus aureus in healthy children. Lancet.2004;363:1871–2.
Google Scholar
Pettigrew MM, Gent JF, Revai K, Patel JA, Chonmaitree T. Microbial interactions during upper respiratory tract infections. Emerg Infect Dis. 2008;14:1584.
Google Scholar
Shiri T, Nunes MC, Adrian PV, Van Niekerk N, Klugman KP, Madhi SA. Interrelationship of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus colonization within and between pneumococcal-vaccine naïve mother–child dyads. BMC Infect Dis. 2013;13:483.
Google Scholar
Jacoby P, Watson K, Bowman J, Taylor A, Riley TV, Smith DW, et al. Modelling the co-occurrence of Streptococcus pneumoniae with other bacterial and viral pathogens in the upper respiratory tract. Vaccine.2007;25:2458–64.
Google Scholar
Nzenze S, Shiri T, Nunes M, Klugman K, Kahn K, Twine R, et al. Temporal association of infant immunisation with pneumococcal conjugate vaccine on the ecology of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus nasopharyngeal colonisation in a rural South African community. Vaccine.2014;32:5520–30.
Google Scholar
Faden H, Stanievich J, Brodsky L, Bernstein J, Ogra PL. Changes in nasopharyngeal flora during otitis media of childhood. Pediatr Infect Dis J. 1990;9:623–6.
Google Scholar
Shekhar S, Khan R, Schenck K, Petersen FC. Intranasal Immunization with the commensal Streptococcus mitis confers protective immunity against pneumococcal lung infection. Appl Environ Microbiol. 2019;85:e02235–18.
Google Scholar
Cangemi de Gutierrez R, Santos V, Nader-Macias ME. Protective effect of intranasally inoculated Lactobacillus fermentum against Streptococcus pneumoniae challenge on the mouse respiratory tract. FEMS Immunol Med Microbiol. 2001;31:187–95.
Google Scholar
Wong SS, Quan Toh Z, Dunne EM, Mulholland EK, Tang ML, Robins-Browne RM, et al. Inhibition of Streptococcus pneumoniae adherence to human epithelial cells in vitro by the probiotic Lactobacillus rhamnosus GG. BMC Res Notes. 2013;6:135.
Google Scholar
Laufer AS, Metlay JP, Gent JF, Fennie KP, Kong Y, Pettigrew MM. Microbial communities of the upper respiratory tract and otitis media in children. mBio.2011;2:e00245–10.
Google Scholar
Bomar L, Brugger SD, Yost BH, Davies SS, Lemon KP. Corynebacterium accolens releases antipneumococcal free fatty acids from human nostril and skin surface triacylglycerols. mBio.2016;7:e01725–15.
Google Scholar
Cope EK, Goldstein-Daruech N, Kofonow JM, Christensen L, McDermott B, Monroy F, et al. Regulation of virulence gene expression resulting from Streptococcus pneumoniae and nontypeable Haemophilus influenzae interactions in chronic disease. PloS ONE. 2011;6:e28523.
Google Scholar
Lysenko ES, Ratner AJ, Nelson AL, Weiser JN. The role of innate immune responses in the outcome of interspecies competition for colonization of mucosal surfaces. PloS Pathog. 2005;1:e1.
Google Scholar
Weimer KE, Juneau RA, Murrah KA, Pang B, Armbruster CE, Richardson SH, et al. Divergent mechanisms for passive pneumococcal resistance to β-lactam antibiotics in the presence of Haemophilus influenzae. J Infect Dis. 2011;203:549–55.
Google Scholar
Tikhomirova A, Kidd SP. Haemophilus influenzae and Streptococcus pneumoniae: living together in a biofilm. Pathog Dis. 2013;69:114–26.
Google Scholar
Brugger SD, Eslami SM, Pettigrew MM, Escapa IF, Henke MT, Kong Y, et al. Dolosigranulum pigrum cooperation and competition in human nasal microbiota. mSphere. 2020;5.
Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host Microbe. 2015;17:704–15.
Google Scholar
Mika M, Mack I, Korten I, Qi W, Aebi S, Frey U, et al. Dynamics of the nasal microbiota in infancy: a prospective cohort study. J Allergy Clin Immunol. 2015;135:905–12.
Google Scholar
Biesbroek G, Tsivtsivadze E, Sanders EA, Montijn R, Veenhoven RH, Keijser BJ, et al. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am J Respir Crit Care Med. 2014;190:1283–92.
Google Scholar
Bosch AA, Levin E, van Houten MA, Hasrat R, Kalkman G, Biesbroek G, et al. Development of upper respiratory tract microbiota in infancy is affected by mode of delivery. EBioMedicine.2016;9:336–45.
Google Scholar
Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA. 2010;107:11971–5.
Google Scholar
Biesbroek G, Bosch AA, Wang X, Keijser BJ, Veenhoven RH, Sanders EA, et al. The impact of breastfeeding on nasopharyngeal microbial communities in infants. Am J Respir Crit Care Med. 2014;190:298–308.
Google Scholar
Bogaert D, Keijser B, Huse S, Rossen J, Veenhoven R, Van Gils E, et al. Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PloS ONE. 2011;6:e17035.
Google Scholar
Bruce N, Perez-Padilla R, Albalak R. Indoor air pollution in developing countries: a major environmental and public health challenge. Bull World Health Organ. 2000;78:1078–92.
Google Scholar
Pelissari DM, Diaz-Quijano FA. Household crowding as a potential mediator of socioeconomic determinants of tuberculosis incidence in Brazil. PloS ONE. 2017;12:e0176116.
Google Scholar
Mannucci PM, Franchini M. Health effects of ambient air pollution in developing countries. Int J Environ Res Public Health. 2017;14:1048.
Google Scholar
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature.2012;486:222–7.
Google Scholar
Ferretti P, Pasolli E, Tett A, Asnicar F, Gorfer V, Fedi S, et al. Mother-to-infant microbial transmission from different body sites shapes the developing infant gut microbiome. Cell Host Microbe. 2018;24:133–45.
Google Scholar
Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SS, McCulle SL, et al. Vaginal microbiome of reproductive-age women. Proc Natl Acad Sci USA. 2011;108:4680–7.
Google Scholar
Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, et al. Multivariable association discovery in population-scale meta-omics studies. bioRxiv. 2021. https://doi.org/10.1101/2021.01.20.427420.
Hojsak I, Snovak N, Abdović S, Szajewska H, Mišak Z, Kolaček S. Lactobacillus GG in the prevention of gastrointestinal and respiratory tract infections in children who attend day care centers: a randomized, double-blind, placebo-controlled trial. Clin Nutr. 2010;29:312–6.
Google Scholar
Gluck U, Gebbers JO. Ingested probiotics reduce nasal colonization with pathogenic bacteria (Staphylococcus aureus, Streptococcus pneumoniae, and beta-hemolytic streptococci). Am J Clin Nutr. 2003;77:517–20.
Google Scholar
Feleszko W, Jaworska J, Rha RD, Steinhausen S, Avagyan A, Jaudszus A, et al. Probiotic-induced suppression of allergic sensitization and airway inflammation is associated with an increase of T regulatory-dependent mechanisms in a murine model of asthma. Clin Exp Allergy. 2007;37:498–505.
Google Scholar
Nhan T-X, Parienti J-J, Badiou G, Leclercq R, Cattoir V. Microbiological investigation and clinical significance of Corynebacterium spp. in respiratory specimens. Diagn Microbiol Infect Dis. 2012;74:236–41.
Google Scholar
Díez-Aguilar M, Ruiz-Garbajosa P, Fernández-Olmos A, Guisado P, Del Campo R, Quereda C, et al. Non-diphtheriae Corynebacterium species: an emerging respiratory pathogen. Eur J Clin Microbiol Infect Dis. 2013;32:769–72.
Google Scholar
Teutsch B, Berger A, Marosevic D, Schönberger K, Lâm T-T, Hubert K, et al. Corynebacterium species nasopharyngeal carriage in asymptomatic individuals aged ≥ 65 years in Germany. Infection.2017;45:607–11.
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinforma. 2009;10:421.
Google Scholar
Turner P, Turner C, Green N, Ashton L, Lwe E, Jankhot A, et al. Serum antibody responses to pneumococcal colonization in the first 2 years of life: results from an SE Asian longitudinal cohort study. Clin Microbiol Infect. 2013;19:e551–8.
Google Scholar
Numminen E, Chewapreecha C, Turner C, Goldblatt D, Nosten F, Bentley SD, et al. Climate induces seasonality in pneumococcal transmission. Sci Rep. 2015;5:11344.
Google Scholar
Kelly MS, Smieja M, Luinstra K, Wirth KE, Goldfarb DM, Steenhoff AP, et al. Association of respiratory viruses with outcomes of severe childhood pneumonia in Botswana. PloS ONE. 2015;10:e0126593.
Google Scholar
le Roux DM, Myer L, Nicol MP, Zar HJ. Incidence and severity of childhood pneumonia in the first year of life in a South African birth cohort: the Drakenstein Child Health Study. Lancet Glob Health. 2015;3:e95–103.
Google Scholar
von Mollendorf C, von Gottberg A, Tempia S, Meiring S, de Gouveia L, Quan V, et al. Increased risk and mortality of invasive pneumococcal disease in HIV-exposed-uninfected infants <1 year of age in South Africa, 2009-2013. Clin Infect Dis. 2015;60:1346–56.
Google Scholar
Farley JJ, King JC Jr., Nair P, Hines SE, Tressler RL, Vink PE. Invasive pneumococcal disease among infected and uninfected children of mothers with human immunodeficiency virus infection. J Pediatr. 1994;124:853–8.
Google Scholar
Kinabo GD, van der Ven A, Msuya LJ, Shayo AM, Schimana W, Ndaro A, et al. Dynamics of nasopharyngeal bacterial colonisation in HIV-exposed young infants in Tanzania. Trop Med Int Health. 2013;18:286–95.
Google Scholar
Koliou MG, Andreou K, Lamnisos D, Lavranos G, Iakovides P, Economou C, et al. Risk factors for carriage of Streptococcus pneumoniae in children. BMC Pediatr. 2018;18:1–8.
Google Scholar
List of prokaryotic names with standing in nomenclature. Available at: http://www.bacterio.net/corynebacterium.html. Accessed 4 February 2021.
Efstratiou A, George R. Microbiology and epidemiology of diphtheria. Rev Med Microbiol. 1996;7:31–42.
Google Scholar
Spach DH, Opp DR, Gabre-Kidan T. Bacteremia due to Corynebacterium jeikeium in a patient with AIDS. Rev Infect Dis. 1991;13:342–3.
Google Scholar
Wang C, Mattson D, Wald A. Corynebacterium jeikeium bacteremia in bone marrow transplant patients with Hickman catheters. Bone Marrow Transplant. 2001;27:445.
Google Scholar
Morris A, Guild I. Endocarditis due to Corynebacterium pseudodiphtheriticum: five case reports, review, and antibiotic susceptibilities of nine strains. Rev Infect Dis. 1991;13:887–92.
Google Scholar
Bookani KR, Marcus R, Cheikh E, Parish M, Salahuddin U. Corynebacterium jeikeium endocarditis: a case report and comprehensive review of an underestimated infection. IDCases.2018;11:26–30.
Google Scholar
Renom F, Gomila M, Garau M, Gallegos M, Guerrero D, Lalucat J, et al. Respiratory infection by Corynebacterium striatum: epidemiological and clinical determinants. N. Microbes N. Infect. 2014;2:106–14.
Google Scholar
Bittar F, Cassagne C, Bosdure E, Stremler N, Dubus J-C, Sarles J, et al. Outbreak of Corynebacterium pseudodiphtheriticum infection in cystic fibrosis patients, France. Emerg Inf Dis. 2010;16:1231.
Google Scholar
Stubbendieck RM, May DS, Chevrette MG, Temkin MI, Wendt-Pienkowski E, Cagnazzo J, et al. Competition among nasal bacteria suggests a role for siderophore-mediated interactions in shaping the human nasal microbiota. Appl Environ Microbiol. 2019;85:e02406–18.
Google Scholar
Kiryukhina N, Melnikov V, Suvorov A, Morozova YA, Ilyin V. Use of Corynebacterium pseudodiphtheriticum for elimination of Staphylococcus aureus from the nasal cavity in volunteers exposed to abnormal microclimate and altered gaseous environment. Probiotics Antimicrob Proteins. 2013;5:233–8.
Google Scholar
Lappan R, Peacock CS. Corynebacterium and Dolosigranulum: future probiotic candidates for upper respiratory tract infections. Microbiol Aust. 2019;40:172–7.
Neal EFG, Nguyen C, Ratu FT, Matanitobua S, Dunne EM, Reyburn R, et al. A comparison of pneumococcal nasopharyngeal carriage in very young Fijian infants born by vaginal or cesarean delivery. JAMA Netw Open. 2019;2:e1913650.
Google Scholar
UN Interagency Group for Child Mortality Estimation. Levels & trends in child mortality, report 2020. Available at: https://childmortality.org/wp-content/uploads/2020/09/UNICEF-2020-Child-Mortality-Report.pdf. Accessed 3 Nov 2020.
United Nations Children’s Fund, World Health Organization. Botswana: WHO and UNICEF estimates of immunization coverage, 2019 revision. Available at: https://www.who.int/immunization/monitoring_surveillance/data/bwa.pdf. Accessed 18 Jan 2021.
Statistics Botswana. 2011 Population and Housing Census Analytical Report. Available at: http://www.cso.gov.bw/images/analytical_report.pdf. Accessed 24 July 2016.
Joint United Nations Programme on HIV/AIDS. UNAIDS estimates 2019: Botswana. Available at: http://www.unaids.org/en/regionscountries/countries/botswana. Accessed 3 Feb 2021.
McAvin JC, Reilly PA, Roudabush RM, Barnes WJ, Salmen A, Jackson GW, et al. Sensitive and specific method for rapid identification of Streptococcus pneumoniae using real-time fluorescence PCR. J Clin Microbiol. 2001;39:3446–51.
Google Scholar
Gueye SB, Diop-Ndiaye H, Diallo MM, Ly O, Sow-Ndoye A, Diagne-Gueye ND, et al. Performance of Roche CAP/CTM HIV-1 qualitative test version 2.0 using dried blood spots for early infant diagnosis. J Virol Methods. 2016;229:12–15.
Google Scholar
Gilbert JA, Meyer F, Antonopoulos D, Balaji P, Brown CT, Brown CT, et al. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Stand Genom Sci. 2010;3:243–8.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics.2014;30:2114–20.
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581.
Google Scholar
Escapa IF, Huang Y, Chen T, Lin M, Kokaras A, Dewhirst FE, et al. Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets. Microbiome.2020;8:1–16.
Google Scholar
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome.2018;6:226.
Google Scholar
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS ONE. 2013;8:e61217.
Google Scholar
Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package. Community Ecol Package. 2007;10:719.
Anderson MJ. A new method for non‐parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.
Biesbroek G, Wang X, Keijser BJ, Eijkemans RM, Trzcinski K, Rots NY, et al. Seven-valent pneumococcal conjugate vaccine and nasopharyngeal microbiota in healthy children. Emerg Infect Dis. 2014;20:201–10.
Google Scholar
Bender JM, Li F, Martelly S, Byrt E, Rouzier V, Leo M, et al. Maternal HIV infection influences the microbiome of HIV-uninfected infants. Sci Transl Med. 2016;8:349ra100.
Google Scholar
Rosas-Salazar C, Shilts MH, Tovchigrechko A, Schobel S, Chappell JD, Larkin EK, et al. Differences in the nasopharyngeal microbiome during acute respiratory tract infection with human rhinovirus and respiratory syncytial virus in infancy. J Infect Dis. 2016;214:1924–8.
Google Scholar
Therneau T. A package for survival analysis in R. R package version 3.2.11, https://CRAN.R-project.org/package=survival.
Source: Ecology - nature.com