Population structure and drug resistance patterns of emerging non-PCV-13 Streptococcus pneumoniae serotypes 22F, 15A, and 8 isolated from adults in Ontario, Canada

Infection, Genetics and Evolution

Volumn 42, Issue , 2016, Pages 1-8

  Duvvuri, Venkata R ^a   Deng, Xianding ^a,b   Teatero, Sarah ^a   Memari, Nader ^a   Athey, Taryn ^a   Fittipaldi, Nahuel ^a,b   Gubbay, Jonathan B ^a,b,c,d  

^a PUBLIC HEALTH ONTARIO   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

^d MOUNT SINAI HOSPITAL   (Canada)

Author keywords

Antimicrobial resistance; Invasive pneumococcal disease; Non PCV 13 serotypes; Streptococcus pneumoniae; Whole genome sequencing

Indexed keywords

AZITHROMYCIN; CEPHALOSPORIN DERIVATIVE; CLINDAMYCIN; ERYTHROMYCIN; PENICILLIN DERIVATIVE; PNEUMOCOCCUS VACCINE; QUINOLONE DERIVATIVE; TETRACYCLINE; 13-VALENT PNEUMOCOCCAL VACCINE; ANTIINFECTIVE AGENT; MACROLIDE;

ADULT; AGED; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; GENE SEQUENCE; GENETIC VARIABILITY; GENOME ANALYSIS; GENOMICS; HUMAN; MICROBIAL POPULATION DYNAMICS; MULTIDRUG RESISTANCE; NONHUMAN; PHENOTYPE; POPULATION STRUCTURE; PRIORITY JOURNAL; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS PNEUMONIAE SEROTYPE 15A; STREPTOCOCCUS PNEUMONIAE SEROTYPE 22F; STREPTOCOCCUS PNEUMONIAE SEROTYPE 8; CLASSIFICATION; DRUG EFFECTS; GENETIC RECOMBINATION; GENETICS; IMMUNOLOGY; ISOLATION AND PURIFICATION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MOLECULAR EVOLUTION; ONTARIO; PHYLOGENY; PNEUMOCOCCAL INFECTIONS; PREVALENCE; SEROTYPE; SEROTYPING;

ADULT; ANTI-BACTERIAL AGENTS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; EVOLUTION, MOLECULAR; GENOME, BACTERIAL; HUMANS; MACROLIDES; MICROBIAL SENSITIVITY TESTS; ONTARIO; PHYLOGENY; PNEUMOCOCCAL INFECTIONS; PNEUMOCOCCAL VACCINES; PREVALENCE; RECOMBINATION, GENETIC; SEROGROUP; SEROTYPING; STREPTOCOCCUS PNEUMONIAE;

EID: 84964413694     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2016.04.007     Document Type: Article

References (47)

1. Alikhan N.F., Petty N.K., Ben Zakour N.L., Beatson S.A. BLAST ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011, 12:402.
2. Andam C.P., Hanage W.P. Mechanisms of genome evolution of Streptococcus. Infect. Genet. Evol. 2015, 33:334-342.
3. Ardanuy C., de la Campa A.G., García E., Fenoll A., Calatayud L., Cercenado E., Pérez-Trallero E., Bouza E., Liñares J. Spread of Streptococcus pneumoniae serotype 8-ST63 multidrug-resistant recombinant clone, Spain. Emerg. Infect. Dis. 2014, 20:1848-1856.
4. Austrian R. The quellung reaction, a neglected microbiologic technique. Mt Sinai J. Med. 1976, 43:699-709.
5. Brueggemann A.B., Pai R., Crook D.W., Beall B. Vaccine escape recombinants emerge after pneumococcal vaccination in the United States. PLoS Pathog. 2007, 3:e168.
6. Caierão J., Hawkins P., Sant'anna F.H., da Cunha G.R., d'Azevedo P.A., McGee L., Dias C. Serotypes and genotypes of invasive Streptococcus pneumoniae before and after PCV10 implementation in Southern Brazil. PLoS One 2014, 9.
7. Calix J.J., Porambo R.J., Brady A.M., Larson T.R., Yother J., Abeygunwardana C., Nahm M.H. Biochemical, genetic, and serological characterization of two capsule subtypes among Streptococcus pneumoniae serotype 20 strains: discovery of a new pneumococcal serotype. J. Biol. Chem. 2012, 287:27885-27894.
8. Chang Q., Stevenson A.E., Croucher N.J., Lee G.M., Pelton S.I., Lipsitch M., Finkelstein J.A., Hanage W.P. Stability of the pneumococcal population structure in Massachusetts as PCV-13 was introduced. BMC Infect. Dis. 2015, 15:68.
9. Clinical and Laboratory Standards Institute Performance Standards for Antimicrobial Susceptibility Testing: twenty-Fifth Informational Supplement M100-S25 2015, CLSI, Wayne, PA, USA.
10. Croucher N.J., Finkelstein J.A., Pelton S.I., Mitchell P.K., Lee G.M., Parkhill J., Bentley S.D., Hanage W.P., Lipsitch M. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat. Genet. 2013, 45:656-663.
11. Croucher N.J., Harris S.R., Fraser C., Quail M.A., Burton J., van der Linden M., McGee L., von Gottberg A., Song J.H., Ko K.S., Pichon B., Baker S., Parry C.M., Lambertsen L.M., Shahinas D., Pillai D.R., Mitchell T.J., Dougan G., Tomasz A., Klugman K.P., Parkhill J., Hanage W.P., Bentley S.D. Rapid pneumococcal evolution in response to clinicalinterventions. Science 2011, 331:430-434.
12. Daly M.M., Doktor S., Flamm R., Shortridge D. Characterization and prevalence of MefA, MefE, and the associated msr(D) gene in Streptococcus pneumoniae clinical isolates. J. Clin. Microbiol. 2004, 42:3570-3574.
13. Darling A.E., Mau B., Perna N.T. Progressive mauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010, 5.
14. Del Grosso M., Iannelli F., Messina C., Santagati M., Petrosillo N., Stefani S., Pozzi G., Pantosti A. Macrolide efflux genes mef(A) and mef(E) are carried by different genetic elements in Streptococcus pneumoniae. J. Clin. Microbiol. 2002, 40:774-778.
15. Del Grosso M., Camilli R., Iannelli F., Pozzi G., Pantosti A. The mef(E)-carrying genetic element (mega) of Streptococcus pneumoniae: insertion sites and association with other genetic elements. Antimicrob. Agents Chemother. 2006, 50:3361-3366.
16. Demczuk W.H., Martin I., Griffith A., Lefebvre B., McGeer A., Lovgren M., Tyrrell G.J., Desai S., Sherrard L., Adam H., Gilmour M., Zhanel G.G., Toronto Bacterial Diseases Network., Canadian Public Health Laboratory Network Serotype distribution of invasive Streptococcus pneumoniae in Canada after the introduction of the 13-valent pneumococcal conjugate vaccine, 2010-2012. Can. J. Microbiol. 2013, 59:778-788.
17. Deng X., Arya G., Memari N., Mackenzie R., MacMullin G., Low D.E., Pillai D.R., Gubbay J.B. Genetic analysis of invasive pneumococcal isolates from children in Ontario, Canada, 2007-2012. Pediatr. Infect. Dis. J. 2015, 34:594-598.
18. Desai S., McGeer A., Quach-Thanh, Elliott D. An advisory committee statement (ACS) National Advisory Committee on Immunization (NACI) update on the use of conjugate pneumococcal vaccines in childhood. Can. Commun. Dis. Rep. 2010, 36(ACS 12):1-21.
19. Fenoll A., Granizo J.J., Aguilar L., Giménez M.J., Aragoneses-Fenoll L., Hanquet G., Casal J., Tarragó D. Temporal trends of invasive Streptococcus pneumoniae serotypes and antimicrobial resistance patterns in Spain from 1979 to 2007. J. Clin. Microbiol. 2009, 47:1012-1020.
20. Geno K.A., Gilbert G.L., Song J.Y., Skovsted I.C., Klugman K.P., Jones C., Konradsen H.B., Nahm M.H. Pneumococcal capsules and their types: past, present, and future. Clin. Microbiol. Rev. 2015, 28:871-899.
21. Golden A.R., Adam H.J., Gilmour M.W., Baxter M.R., Martin I., Nichol K.A., Demczuk W.H., Hoban D.J., Zhanel G.G. Assessment of multidrug resistance, clonality and virulence in non-PCV-13 Streptococcus pneumoniae serotypes in Canada, 2011-13. J. Antimicrob. Chemother. 2015, 70:1960-1964.
22. Golden A.R., Rosenthal M., Fultz B., Nichol K.A., Adam H.J., Gilmour M.W., Baxter M.R., Hoban D.J., Karlowsky J.A., Zhanel G.G. Characterization of MDR and XDR Streptococcus pneumoniae in Canada, 2007-13. J. Antimicrob. Chemother. 2015, 70:2199-2202.
23. Huang S.S., Hinrichsen V.L., Stevenson A.E., Rifas-Shiman S.L., Kleinman K., Pelton S.I., Lipsitch M., Hanage W.P., Lee G.M., Finkelstein J.A. Continued impact of pneumococcal conjugate vaccine on carriage in young children. Pediatrics 2009, 124:e1-11.
24. Inouye M., Conway T.C., Zobel J., Holt K.E. Short read sequence typing (SRST): multi-locus sequence types from short reads. BMC Genomics 2012, 13:338.
25. Jefferies J.M., Johnston C.H., Kirkham L.A., Cowan G.J., Ross K.S., Smith A., Clarke S.C., Brueggemann A.B., George R.C., Pichon B., Pluschke G., Pfluger V., Mitchell T.J. Presence of nonhemolytic pneumolysin in serotypes of Streptococcus pneumoniae associated with disease outbreaks. J. Infect. Dis. 2007, 196:936-944.
26. Leclercq R., Courvalin P. Bacterial resistance to macrolide, lincosamide, and streptogramin antibiotics by target modification. Antimicrob. Agents Chemother. 1991, 35:1267-1272.
27. Lim G.H., Wormsbecker A.E., McGeer A., Pillai D.R., Gubbay J.B., Rudnick W., Low D.E., Green K., Crowcroft N.S., Deeks S.L. Have changing pneumococcal vaccination programmes impacted disease in Ontario?. Vaccine 2013, 31:2680-2685.
28. Lynch J.P., Zhanel G.G. Streptococcus pneumoniae: epidemiology, risk factors, and strategies for prevention. Semin. Respir. Crit. Care Med. 2009, 30:189-209.
29. Marttinen P., Baldwin A., Hanage W.P., Dowson C., Mahenthiralingam E., Corander J. Bayesian modeling of recombination events in bacterial populations. BMC Bioinf. 2008, 9:421.
30. Nusbaum C., Ohsumi T.K., Gomez J., Aquadro J., Victor T.C., Warren R.M., Hung D.T., Birren B.W., Lander E.S., Jaffe D.B. Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing. Nat. Methods 2009, 6:67-69.
31. O'Brien K.L., Wolfson L.J., Watt J.P., Henkle E., Deloria-Knoll M., McCall N., Lee E., Mulholland K., Levine O.S., Cherian T. Hib and Pneumococcal Global Burden of Disease Study team. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet 2009, 374:893-902.
32. Ontario Ministry of Health and Long-Term Care Memo re: SynflorixTM vaccine to replace Prevnar® vaccine for the immunization of infants and children up to 24 months of age. October 2009, 6:2009.
33. Pichon B., Ladhani S.N., Slack M.P., Segonds-Pichon A., Andrews N.J., Waight P.A., Miller E., George R. Changes in molecular epidemiology of Streptococcus pneumoniae causing meningitis following introduction of pneumococcal conjugate vaccination in England and Wales. J. Clin. Microbiol. 2013, 51:820-827.
34. Pilishvili T., Lexau C., Farley M.M., Hadler J., Harrison L.H., Bennett N.M., Reingold A., Thomas A., Schaffner W., Craig A.S., Smith P.J., Beall B.W., Whitney C.G., Moore M.R., Active Bacterial Core Surveillance/Emerging Infections Program Network Sustained reductions in invasive pneumococcal disease in the era of conjugate vaccine. J. Infect. Dis. 2010, 201:32-41.
35. Public Health Agency of Canada National Surveillance of Invasive Streptococcus pneumoniae and Streptococcus pyogenes in Canada. Annual Summary 2012 2012, (ISSN: 2292-2709). http://publications.gc.ca/collections/collection_2014/aspc-phac/HP57-2-2012-eng.pdf (accessed 23 June 2015).
36. Public Health Agency of Canada National Surveillance of Invasive Streptococcal Disease in Canada. Annual Summary 2013 2013, (ISBN: 2368-9854). http://www.healthycanadians.gc.ca/publications/drugs-products-medicaments-produits/2013-streptococcus/alt/surveillance-streptococca-eng.pdf (Accessed on 17 July 2015).
37. Rosen J.B., Thomas A.R., Lexau C.A., Reingold A., Hadler J.L., Harrison L.H., Bennett N.M., Schaffner W., Farley M.M., Beall B.W., Moore M.R., CDC Emerging Infections Program Network Geographic variation in invasive pneumococcal disease following pneumococcal conjugate vaccine introduction in the United States. Clin. Infect. Dis. 2011, 53:137-143.
38. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014, 30:2068-2069.
39. Sleeman K.L., Griffiths D., Shackley F., Diggle L., Gupta S., Maiden M.C., Moxon E.R., Crook D.W., Peto T.E. Capsular serotype-specific attack rates and duration of carriage of Streptococcus pneumoniae in a population of children. J. Infect. Dis. 2006, 194:682-688.
40. Statistics Canada (Accessed on 14-Dec-2015). http://www12.statcan.gc.ca/census-recensement/index-eng.cfm.
41. Sutcliffe J., Tait-Kamradt A., Wondrack L. Streptococcus pneumoniae and streptococcus pyogenes resistant to macrolides but sensitive to clindamycin: a common resistance pattern mediated by an efflux system. Antimicrob. Agents Chemother. 1996, 40:1817-1824.
42. Tritt A., Eisen J.A., Facciotti M.T., Darling A.E. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 2012, 7.
43. Tyrrell G.J., Lovgren M., Chui N., Minion J., Garg S., Kellner J.D., Marrie T.J. Serotypes and antimicrobial susceptibilities of invasive Streptococcus pneumoniae pre- and post-seven valent pneumococcal conjugate vaccine introduction in Alberta, Canada, 2000-2006. Vaccine 2009, 27:3553-3560.
44. van Hoek A.H., Mevius D., Guerra B., Mullany P., Roberts A.P., Aarts H.J. Acquired antibiotic resistance genes: an overview. Front. Microbiol. 2011, 2:203.
45. Weinberger D.M., Malley R., Lipsitch M. Serotype replacement in disease after pneumococcal vaccination. Lancet 2011, 378:1962-1973.
46. Zerbino D.R., Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008, 18:821-829.
47. Zhao Y., Wu J., Yang J., Sun S., Xiao J., Yu J. PGAP: pan-genomes analysispipeline. Bioinformatics 2012, 28:416-418.