1887

Abstract

() was long known as an easy-to-treat bacterium, but increasing resistance against beta-lactams and other critically important antibiotics is now a growing concern. We describe here the whole-genome sequencing (WGS) analysis of three non-typeable isolates received in 2018–2019 by the Belgian National Reference Centre (NRC) for , as they presented an unusual multi-resistant profile.

All three isolates were sequenced by WGS and mapped to the reference isolate Rd KW20. Shorten uptake signal sequences (USSs) known to be associated with homologous recombination were sought in and genes, and inner partial sequences were compared against the nucleotide database to look for similarity with other species. Their antimicrobial resistance (AMR) genotype was studied. Core-genome multilocus sequence typing (MLST) was performed on the NTHi database pubMLST to place our isolates in the actual worldwide epidemiology.

The isolates also harboured interspecies recombination patterns in the region involved in cell wall synthesis. The three isolates were multidrug resistant and two of them were also resistant to amoxicillin–clavulanic acid and showed a reduced susceptibility to meropenem. All three isolates belonged to the MLST clonal complex (CC) 422, and WGS revealed that the three were very similar. They harboured mobile genetic elements (carrying , and genes associated with resistance), mutations in and linked to fluoroquinolone resistance as well as remodelling events in that might be related to lower carbapenem susceptibility.

The evolution towards antimicrobial multiresistance (AMR) is a complex and poorly understood phenomenon, although probably linked to a large degree to the presence of USSs and exchange within the family . To better understand the respective roles of clonal expansion, horizontal gene transfers, spontaneous mutations and interspecies genetic rearrangements in shaping AMR, both analysis of communities over time within individuals and worldwide monitoring of non-typeable causing infections should be conducted.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/acmi/10.1099/acmi.0.000649.v3
2024-02-12
2024-02-26
Loading full text...

Full text loading...

/deliver/fulltext/acmi/6/2/acmi000649.v3.html?itemId=/content/journal/acmi/10.1099/acmi.0.000649.v3&mimeType=html&fmt=ahah

References

  1. Heinz E. The return of Pfeiffer’s bacillus: rising incidence of ampicillin resistance in Haemophilus influenzae. Microb Genom 2018; 4:e000214 [View Article] [PubMed]
    [Google Scholar]
  2. Deghmane A-E, Hong E, Chehboub S, Terrade A, Falguières M et al. High diversity of invasive Haemophilus influenzae isolates in France and the emergence of resistance to third generation cephalosporins by alteration of ftsI gene. J Infect 2019; 79:7–14 [View Article] [PubMed]
    [Google Scholar]
  3. Hegstad K, Mylvaganam H, Janice J, Josefsen E, Sivertsen A et al. Role of horizontal gene transfer in the development of multidrug resistance in Haemophilus influenzae. mSphere 2020; 5:e00969-19 [View Article] [PubMed]
    [Google Scholar]
  4. Witherden EA, Bajanca-Lavado MP, Tristram SG, Nunes A. Role of inter-species recombination of the ftsI gene in the dissemination of altered penicillin-binding-protein-3-mediated resistance in Haemophilus influenzae and Haemophilus haemolyticus. J Antimicrob Chemother 2014; 69:1501–1509 [View Article] [PubMed]
    [Google Scholar]
  5. Whittaker R, Economopoulou A, Dias JG, Bancroft E, Ramliden M et al. Epidemiology of invasive Haemophilus influenzae disease, Europe, 2007-2014. Emerg Infect Dis 2017; 23:396–404 [View Article] [PubMed]
    [Google Scholar]
  6. Ubukata K, Shibasaki Y, Yamamoto K, Chiba N, Hasegawa K et al. Association of amino acid substitutions in penicillin-binding protein 3 with beta-lactam resistance in beta-lactamase-negative ampicillin-resistant Haemophilus influenzae. Antimicrob Agents Chemother 2001; 45:1693–1699 [View Article] [PubMed]
    [Google Scholar]
  7. Takahata S, Ida T, Senju N, Sanbongi Y, Miyata A et al. Horizontal gene transfer of ftsI, encoding penicillin-binding protein 3, in Haemophilus influenzae. Antimicrob Agents Chemother 2007; 51:1589–1595 [View Article] [PubMed]
    [Google Scholar]
  8. Ma C, Redfield RJ. Point mutations in a peptidoglycan biosynthesis gene cause competence induction in Haemophilus influenzae. J Bacteriol 2000; 182:3323–3330 [View Article] [PubMed]
    [Google Scholar]
  9. Skaare D, Anthonisen IL, Caugant DA, Jenkins A, Steinbakk M et al. Multilocus sequence typing and ftsI sequencing: a powerful tool for surveillance of penicillin-binding protein 3-mediated beta-lactam resistance in nontypeable Haemophilus influenzae. BMC Microbiol 2014; 14:131 [View Article] [PubMed]
    [Google Scholar]
  10. Redfield RJ, Findlay WA, Bossé J, Kroll JS, Cameron ADS et al. Evolution of competence and DNA uptake specificity in the Pasteurellaceae. BMC Evol Biol 2006; 6:82 [View Article] [PubMed]
    [Google Scholar]
  11. Søndergaard A, Witherden EA, Nørskov-Lauritsen N, Tristram SG. Interspecies transfer of the penicillin-binding protein 3-encoding gene ftsI between Haemophilus influenzae and Haemophilus haemolyticus can confer reduced susceptibility to β-lactam antimicrobial agents. Antimicrob Agents Chemother 2015; 59:4339–4342 [View Article] [PubMed]
    [Google Scholar]
  12. Tanaka E, Wajima T, Nakaminami H, Noguchi N. Whole-genome sequence of Haemophilus influenzae ST422 outbreak clone strain 2018-Y40 with low quinolone susceptibility isolated from a paediatric patient. J Glob Antimicrob Resist 2020; 22:759–761 [View Article] [PubMed]
    [Google Scholar]
  13. Lâm T-T, Nürnberg S, Claus H, Vogel U. Molecular epidemiology of imipenem resistance in invasive Haemophilus influenzae infections in Germany in 2016. J Antimicrob Chemother 2020; 75:2076–2086 [View Article] [PubMed]
    [Google Scholar]
  14. Wang H-J, Wang C-Q, Hua C-Z, Yu H, Zhang T et al. Antibiotic resistance profiles of Haemophilus influenzae isolates from children in 2016: a multicenter study in China. Can J Infect Dis Med Microbiol 2019; 2019:6456321 [View Article] [PubMed]
    [Google Scholar]
  15. Cherkaoui A, Diene SM, Renzoni A, Emonet S, Renzi G et al. Imipenem heteroresistance in nontypeable Haemophilus influenzae is linked to a combination of altered PBP3, slow drug influx and direct efflux regulation. Clin Microbiol Infect 2017; 23:118 [View Article] [PubMed]
    [Google Scholar]
  16. Cherkaoui A, Diene SM, Fischer A, Leo S, François P et al. Transcriptional modulation of penicillin-binding protein 1b, outer membrane protein P2 and efflux pump (AcrAB-TolC) during heat stress is correlated to enhanced bactericidal action of imipenem on non-typeable Haemophilus influenzae. Front Microbiol 2017; 8:2676 [View Article] [PubMed]
    [Google Scholar]
  17. The European Committee on antimicrobial susceptibility testing Breakpoint tables for interpretation of Mics and zone diameters; 2018 http://www.eucast.org
  18. Sottnek FO, Albritton WL. Haemophilus influenzae biotype VIII. J Clin Microbiol 1984; 20:815–816 [View Article] [PubMed]
    [Google Scholar]
  19. Falla TJ, Crook DW, Brophy LN, Maskell D, Kroll JS et al. PCR for capsular typing of Haemophilus influenzae. J Clin Microbiol 1994; 32:2382–2386 [View Article] [PubMed]
    [Google Scholar]
  20. Coughlan H, Reddington K, Tuite N, Boo TW, Cormican M et al. Comparative genome analysis identifies novel nucleic acid diagnostic targets for use in the specific detection of Haemophilus influenzae. Diagn Microbiol Infect Dis 2015; 83:112–116 [View Article] [PubMed]
    [Google Scholar]
  21. Muyldermans A, Crombé F, Bosmans P, Cools F, Piérard D et al. Serratia marcescens outbreak in a neonatal intensive care unit and the potential of whole-genome sequencing. J Hosp Infect 2021; 111:148–154 [View Article] [PubMed]
    [Google Scholar]
  22. Vanstokstraeten R, Crombé F, Piérard D, Castillo Moral A, Wybo I et al. Molecular characterization of extraintestinal and diarrheagenic Escherichia coli blood isolates. Virulence 2022; 13:2032–2041 [View Article] [PubMed]
    [Google Scholar]
  23. Argudín MA, Deplano A, Nonhoff C, Yin N, Michel C et al. Epidemiology of the Staphylococcus aureus CA-MRSA USA300 in Belgium. Eur J Clin Microbiol Infect Dis 2021; 40:2335–2347 [View Article] [PubMed]
    [Google Scholar]
  24. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  25. Johansson MHK, Bortolaia V, Tansirichaiya S, Aarestrup FM, Roberts AP et al. Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. J Antimicrob Chemother 2021; 76:101–109 [View Article] [PubMed]
    [Google Scholar]
  26. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124 [View Article] [PubMed]
    [Google Scholar]
  27. Osaki Y, Sanbongi Y, Ishikawa M, Kataoka H, Suzuki T et al. Genetic approach to study the relationship between penicillin-binding protein 3 mutations and Haemophilus influenzae beta-lactam resistance by using site-directed mutagenesis and gene recombinants. Antimicrob Agents Chemother 2005; 49:2834–2839 [View Article] [PubMed]
    [Google Scholar]
  28. Hoshino T, Takeuchi N, Ohkusu M, Hachisu Y, Hirose S et al. Identification of Haemophilus influenzae serotype e strains missing the fucK gene in clinical isolates from Japan. J Med Microbiol 2019; 68:1534–1539 [View Article] [PubMed]
    [Google Scholar]
  29. Mora M, Mell JC, Ehrlich GD, Ehrlich RL, Redfield RJ. Genome-wide analysis of DNA uptake across the outer membrane of naturally competent Haemophilus influenzae. iScience 2021; 24:102007 [View Article] [PubMed]
    [Google Scholar]
  30. National Library of Medicine Basic Local Alignment Search Tool, Nucleotide BLAST. n.d https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_SPEC=GeoBlast&PAGE_TYPE=BlastSearch
  31. Tanaka E, Wajima T, Hirai Y, Nakaminami H, Noguchi N. Dissemination of quinolone low-susceptible Haemophilus influenzae ST422 in Tokyo, Japan. J Infect Chemother 2021; 27:962–966 [View Article] [PubMed]
    [Google Scholar]
  32. Georgiou M, Muñoz R, Román F, Cantón R, Gómez-Lus R et al. Ciprofloxacin-resistant Haemophilus influenzae strains possess mutations in analogous positions of GyrA and ParC. Antimicrob Agents Chemother 1996; 40:1741–1744 [View Article] [PubMed]
    [Google Scholar]
  33. Watts SC, Judd LM, Carzino R, Ranganathan S, Holt KE. Genomic diversity and antimicrobial resistance of Haemophilus colonizing the airways of young children with cystic fibrosis. mSystems 2021e0017821 [View Article] [PubMed]
    [Google Scholar]
  34. Power PM, Bentley SD, Parkhill J, Moxon ER, Hood DW. Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants. BMC Microbiol 2012; 12:273 [View Article] [PubMed]
    [Google Scholar]
  35. Giufrè M, Daprai L, Cardines R, Bernaschi P, Ravà L et al. Carriage of Haemophilus influenzae in the oropharynx of young children and molecular epidemiology of the isolates after fifteen years of H. influenzae type b vaccination in Italy. Vaccine 2015; 33:6227–6234 [View Article] [PubMed]
    [Google Scholar]
  36. Mizoguchi A, Hitomi S. Cefotaxime-non-susceptibility of Haemophilus influenzae induced by additional amino acid substitutions of G555E and Y557H in altered penicillin-binding protein 3. J Infect Chemother Off J Jpn Soc Chemother 2019; 25:509–513 [View Article] [PubMed]
    [Google Scholar]
  37. Francis F, Ramirez-Arcos S, Salimnia H, Victor C, Dillon JR. Organization and transcription of the division cell wall (dcw) cluster in Neisseria gonorrhoeae. Gene 2000; 251:141–151 [View Article] [PubMed]
    [Google Scholar]
  38. Tanaka E, Wajima T, Uchiya K-I, Nakaminami H. Quinolone resistance is transferred horizontally via uptake signal sequence recognition in Haemophilus influenzae. Antimicrob Agents Chemother 2022; 66:e01967-21 [View Article] [PubMed]
    [Google Scholar]
  39. Bakkali M, Chen T-Y, Lee HC, Redfield RJ. Evolutionary stability of DNA uptake signal sequences in the Pasteurellaceae. Proc Natl Acad Sci U S A 2004; 101:4513–4518 [View Article] [PubMed]
    [Google Scholar]
  40. Regelink AG, Dahan D, Möller LV, Coulton JW, Eijk P et al. Variation in the composition and pore function of major outer membrane pore protein P2 of Haemophilus influenzae from cystic fibrosis patients. Antimicrob Agents Chemother 1999; 43:226–232 [View Article] [PubMed]
    [Google Scholar]
  41. Das S, Rosas LE, Jurcisek JA, Novotny LA, Green KB et al. Improving patient care via development of a protein-based diagnostic test for microbe-specific detection of chronic rhinosinusitis. Laryngoscope 2014; 124:608–615 [View Article] [PubMed]
    [Google Scholar]
  42. Hiltke TJ, Schiffmacher AT, Dagonese AJ, Sethi S, Murphy TF. Horizontal transfer of the gene encoding outer membrane protein P2 of nontypeable Haemophilus influenzae, in a patient with chronic obstructive pulmonary disease. J Infect Dis 2003; 188:114–117 [View Article] [PubMed]
    [Google Scholar]
  43. Honda H, Sato T, Shinagawa M, Fukushima Y, Nakajima C et al. In Vitro derivation of fluoroquinolone-resistant mutants from multiple lineages of Haemophilus influenzae and identification of mutations associated with fluoroquinolone resistance. Antimicrob Agents Chemother 2020; 64:e01500-19 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/acmi/10.1099/acmi.0.000649.v3
Loading
/content/journal/acmi/10.1099/acmi.0.000649.v3
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error