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Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates

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Abstract

Streptococcus pneumoniae can cause several diseases including otitis media, sinusitis, pneumonia, sepsis and meningitis. The introduction of pneumococcal vaccines has changed the molecular epidemiological and antibiotic resistance profiles of related diseases. Analysis of molecular patterns and genome sequences of clinical strains may facilitate the identification of novel drug resistance mechanism. Three multidrug resistance 19A isolates were verified, serotyped and the complete genomes were sequenced combining the Pacific Biosciences and the Illumina Miseq platform. Genomic annotation revealed that similar central networks were found in the clinical isolates, and Mauve alignments indicated high similarity between different strains. The pan-genome analysis showed the shared and unique cluster in the strains. Mobile elements were predicted in the isolates including prophages and CRISPER systems, which may participate in the virulence and antibiotic resistance of the strains. The presence of 31 virulence factor genes was predicted from other pathogens for PRSP 19339 and 19343, while 30 for PRSP 19087. Meanwhile, 33 genes antibiotic resistance genes were predicted including antibiotic resistance genes, antibiotic-target genes and antibiotic biosynthesis genes. Further analysis of the antibiotic resistance genes revealed new mutations in the isolates. By comparative genomic analysis, we contributed to the understanding of resistance mechanism of the clinical isolates with other serotype strains, which could facilitate the concrete drug resistance mechanism study.

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References

  1. Weiser JN, Ferreira DM, Paton JC (2018) Streptococcus pneumoniae: transmission, colonization and invasion. Nat Rev Microbiol 16:355–367

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Chen YY, Hsieh YC, Gong YN, Liao WC, Li SW, Chang IY, Lin TL, Huang CT, Chiu CH, Wu TL et al (2020) Genomic Insight into the Spread of Meropenem-Resistant Streptococcus pneumoniae Spain(23F)-ST81. Taiwan Emerg Infect Dis 26:711–720

    Article  PubMed  Google Scholar 

  3. Leonard A, Gierok P, Methling K, Gomez-Mejia A, Hammerschmidt S, Lalk M (2018) Metabolic inventory of Streptococcus pneumoniae growing in a chemical defined environment. Int J Med Microbiol 308:705–712

    Article  CAS  PubMed  Google Scholar 

  4. Acebo P, Martin-Galiano AJ, Navarro S, Zaballos A, Amblar M (2012) Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae. RNA 18:530–546

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Geno KA, Gilbert GL, Song JY, Skovsted IC, Klugman KP, Jones C, Konradsen HB, Nahm MH (2015) Pneumococcal capsules and their types: past, present, and future. Clin Microbiol Rev 28:871–899

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Mehr S, Wood N (2012) Streptococcus pneumoniae–a review of carriage, infection, serotype replacement and vaccination. Paediatr Respir Rev 13:258–264

    Article  PubMed  Google Scholar 

  7. Perez-Maya AA, Hinojosa-Robles RM, Barcenas-Walls JR, Vignau-Cantu A, Barrera-Saldana HA, Ortiz-Lopez R (2016) Complete Genome Sequence of Streptococcus pneumoniae Serotype 19A, a Blood Clinical Isolate from Northeast Mexico. Genome Announc 4.

  8. Agudelo CI, DeAntonio R, Castaneda E (2018) Streptococcus pneumoniae serotype 19A in Latin America and the Caribbean 2010–2015: a systematic review and a time series analysis. Vaccine 36:4861–4874

    Article  PubMed  Google Scholar 

  9. Isturiz R, Sings HL, Hilton B, Arguedas A, Reinert RR, Jodar L (2017) Streptococcus pneumoniae serotype 19A: worldwide epidemiology. Expert Rev Vaccines 16:1007–1027

    Article  CAS  PubMed  Google Scholar 

  10. Kim L, McGee L, Tomczyk S, Beall B (2016) Biological and Epidemiological Features of Antibiotic-Resistant Streptococcus pneumoniae in Pre- and Post-Conjugate Vaccine Eras: a United States Perspective. Clin Microbiol Rev 29:525–552

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Guitor AK, Wright GD (2018) Antimicrobial resistance and respiratory infections. Chest 154:1202–1212

    Article  PubMed  Google Scholar 

  12. Macheboeuf P, Di Guilmi AM, Job V, Vernet T, Dideberg O, Dessen A (2005) Active site restructuring regulates ligand recognition in class A penicillin-binding proteins. Proc Natl Acad Sci U S A 102:577–582

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Diawara I, Nayme K, Katfy K, Barguigua A, Kettani-Halabi M, Belabbes H, Timinouni M, Zerouali K, Elmdaghri N (2018) Analysis of amino acid motif of penicillin-binding proteins 1a, 2b, and 2x in invasive Streptococcus pneumoniae nonsusceptible to penicillin isolated from pediatric patients in Casablanca. Morocco BMC Res Notes 11:632

    Article  PubMed  Google Scholar 

  14. Hakenbeck R, Grebe T, Dorothea ZaÈhner, Stock JB (1999) b-Lactam resistance in Streptococcus pneumoniae penicillin-binding proteins and non-penicillin-binding proteins. Mol Microbiol 33:673–678

    Article  CAS  PubMed  Google Scholar 

  15. Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK (2019) High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res 47:e103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Clinical and Laboratory Standards Institute, (CLSI) (2020) Performance standards for antimicrobial susceptibility testing. CLSI

  17. European committee on antimicrobial susceptibility testing (EUCAST) (2021) Clinical breakpoints - breakpoints and guidance.

  18. Pai R, Gertz RE, Beall B (2006) Sequential multiplex PCR approach for determining capsular serotypes of Streptococcus pneumoniae isolates. J Clin Microbiol 44:124–131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lindgreen S (2012) AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res Notes 5:337

    Article  PubMed  PubMed Central  Google Scholar 

  20. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18

    Article  PubMed  PubMed Central  Google Scholar 

  21. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Coil D, Jospin G, Darling AE (2015) A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics (Oxford, England) 31:587–589

    CAS  Google Scholar 

  23. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK et al (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963

    Article  PubMed  PubMed Central  Google Scholar 

  25. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41:D226-232

    Article  CAS  PubMed  Google Scholar 

  29. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P (2007) CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8:209

    Article  PubMed  PubMed Central  Google Scholar 

  30. Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS (2016) PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 44:W16-21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Langille MG, Brinkman FS (2009) IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics (Oxford, England) 25:664–665

    CAS  Google Scholar 

  32. Chen L, Xiong Z, Sun L, Yang J, Jin Q (2012) VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 40:D641-645

    Article  CAS  PubMed  Google Scholar 

  33. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L et al (2013) The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348–3357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Blake JD, Cohen FE (2001) Pairwise sequence alignment below the twilight zone. J Mol Biol 307:721–735

    Article  CAS  PubMed  Google Scholar 

  35. Conesa A, Götz S (2008) Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant genom 2008:619832

    Google Scholar 

  36. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182-185

    Article  PubMed  PubMed Central  Google Scholar 

  37. Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M et al (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 42:D231-239

    Article  CAS  PubMed  Google Scholar 

  38. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics (Oxford, England) 21:537–539

    CAS  Google Scholar 

  39. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M (2020) List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70:5607–5612

    Article  PubMed  PubMed Central  Google Scholar 

  40. Kosowska K, Jacobs MR, Bajaksouzian S, Koeth L, Appelbaum PC (2004) Alterations of penicillin-binding proteins 1A, 2X, and 2B in Streptococcus pneumoniae isolates for which amoxicillin MICs are higher than penicillin MICs. Antimicrob Agents Chemother 48:4020–4022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Diawara I, Barguigua A, Katfy K, Nayme K, Belabbes H, Timinouni M, Zerouali K, Elmdaghri N (2017) Molecular characterization of penicillin non-susceptible Streptococcus pneumoniae isolated before and after pneumococcal conjugate vaccine implementation in Casablanca. Morocco Ann Clin Microbiol Antimicrob 16:23

    Article  PubMed  Google Scholar 

  42. Ma M, Yuan M, Li M, Li X, Huang H, Wang H, Li J, Du T, Huang R (2021) Serotype distribution and characteristics of the minimum inhibitory concentrations of Streptococcus pneumoniae isolated from pediatric patients in Kunming, China. Curr Microbiol 78:954–960

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Chen K, Zhang X, Shan W, Zhao G, Zhang T (2018) Serotype distribution of Streptococcus pneumoniae and potential impact of pneumococcal conjugate vaccines in China: a systematic review and meta-analysis. Hum Vaccin Immunother 14:1453–1463

    Article  PubMed  PubMed Central  Google Scholar 

  44. Hoskins J, Alborn WE Jr, Arnold J, Blaszczak LC, Burgett S, DeHoff BS, Estrem ST, Fritz L, Fu DJ, Fuller W et al (2001) Genome of the bacterium Streptococcus pneumoniae strain R6. J Bacteriol 183:5709–5717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631–637

    Article  CAS  PubMed  Google Scholar 

  46. Rezaei Javan R, Ramos-Sevillano E, Akter A, Brown J, Brueggemann AB (2019) Prophages and satellite prophages are widespread in Streptococcus and may play a role in pneumococcal pathogenesis. Nat Commun 10:4852

    Article  PubMed  PubMed Central  Google Scholar 

  47. Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ et al (2001) Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293:498–506

    Article  CAS  PubMed  Google Scholar 

  48. Hakenbeck R, Brückner R, Denapaite D, Maurer P (2012) Molecular mechanisms of beta-lactam resistance in Streptococcus pneumoniae. Future Microbiol 7:395–410

    Article  CAS  PubMed  Google Scholar 

  49. Tait-Kamradt AG, Cronan M, Dougherty TJ (2009) Comparative genome analysis of high-level penicillin resistance in Streptococcus pneumoniae. Microb Drug Resist 15:69–75

    Article  CAS  PubMed  Google Scholar 

  50. Schroeder MR, Stephens DS (2016) Macrolide resistance in Streptococcus pneumoniae. Front Cell Infect Microbiol 6:98

    Article  PubMed  PubMed Central  Google Scholar 

  51. Beheshti M, Jabalameli F, Feizabadi MM, Hahsemi FB, Beigverdi R, Emaneini M (2020) Molecular characterization, antibiotic resistance pattern and capsular types of invasive Streptococcus pneumoniae isolated from clinical samples in Tehran. Iran BMC Microbiol 20:167

    Article  CAS  PubMed  Google Scholar 

  52. Cornick JE, Harris SR, Parry CM, Moore MJ, Jassi C, Kamng’ona A, Kulohoma B, Heyderman RS, Bentley SD, Everett DB (2014) Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi. J Antimicrob Chemother 69:368–374

    Article  CAS  PubMed  Google Scholar 

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Funding

This work was supported by grants from the Scientific and Technological Projects of Henan Province (202102310395), the National Natural Science Foundation of China (31900116) and the Medical Science and Technology Projects of Henan Province (LHGJ20190955).

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Authors and Affiliations

  1. Henan Neurodevelopment Engineering Research Center for Children, Henan Key Laboratory of Children’s Genetics and Metabolic Diseases, Children’s Hospital Affiliated To Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China

    Lifeng Li, Wancun Zhang & Zhidan Yu

  2. Departments of Neonatology, Children’s Hospital Affiliated To Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China

    Lifeng Li, Mingchao Li, Zengyuan Yu, Ping Cheng & Huiqing Sun

  3. Zhengzhou Key Laboratory of Children’s Infection and Immunity, Department of Laboratory Medicine, Children’s Hospital Affiliated To Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China

    Juanjuan Zhou, Kaijie Gao, Junwen Yang & Junmei Yang

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  1. Lifeng Li
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Contributions

LL: Conceptualization, Methodology, Writing-original draft, Funding acquisition. JZ: Investigation, Resources. ML: Methodology, Formal analysis. ZY: Resources, Data curation. KG: Investigation, Resources. JY: Investigation, Resources. PC: Methodology, Formal analysis. JY: Resources, Supervision. WZ: Supervision, Writing—review & editing; ZY: Supervision, Conceptualization; HS: Supervision, Writing—review & editing. All the authors have revised the manuscript critically and approved the submission.

Corresponding authors

Correspondence to Junmei Yang, Wancun Zhang, Zhidan Yu or Huiqing Sun.

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The authors declare no conflict of interests.

Ethical approval

The study was approved by the Ethics Committee of Henan Children’s Hospital (approval number: 2021-K-079). Because the samples were collected in the formal clinical diagnosis and treatment with informed consent, the reuse of the stored strains isolated from the samples does not need further consent to be signed according to the Ethics Committee of Henan Children’s Hospital.

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Li, L., Zhou, J., Li, M. et al. Comparative Genomic Analysis of Streptococcus pneumoniae Strains: Penicillin Non-susceptible Multi-drug-Resistant Serotype 19A Isolates. Curr Microbiol 79, 49 (2022). https://doi.org/10.1007/s00284-021-02715-2

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