1887
Surveillance Open Access
Like 0

Abstract

Background

Modern laboratory methods such as next generation sequencing and MALDI-TOF allow identification of novel bacterial species. This can affect surveillance of infections and antimicrobial resistance. From 2017, increasing numbers of medical microbiology laboratories in Switzerland differentiated from complex using updated MALDI-TOF databases, whereas many laboratories still report them as or complex.

Aim

Our study explored whether separate reporting of and the complex affected the ANRESIS surveillance database.

Methods

We analysed antibiotic susceptibility rates and specimen types of and non-- complex isolates reported by Swiss medical laboratories to the ANRESIS database (Swiss Centre for Antibiotic Resistance) from January 2017 to June 2022.

Results

Analysis of Swiss antimicrobial resistance data revealed increased susceptibility rates of compared with species of the complex other than in all six antibiotic classes tested. This can lead to underestimated resistance rates of complex in laboratories that do not specifically identify . Furthermore, strains were significantly more often reported from blood and primarily sterile specimens than isolates of the complex other than indicating increased invasiveness of .

Conclusion

Our data suggest that refined differentiation of the complex can improve our understanding of its taxonomy, susceptibility, epidemiology and clinical significance, thus providing more precise information to clinicians and epidemiologists.

Loading

Article metrics loading...

/content/10.2807/1560-7917.ES.2022.27.45.2200104
2022-11-10
2022-12-10
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2022.27.45.2200104
Loading
Loading full text...

Full text loading...

/deliver/fulltext/eurosurveillance/27/45/eurosurv-27-45-2.html?itemId=/content/10.2807/1560-7917.ES.2022.27.45.2200104&mimeType=html&fmt=ahah

References

  1. Munson E, Carroll KC. An update on the novel genera and species and revised taxonomic status of bacterial organisms described in 2016 and 2017. J Clin Microbiol. 2019;57(2):e01181-18.  https://doi.org/10.1128/JCM.01181-18  PMID: 30257907 
  2. Munson E, Carroll KC. Summary of novel bacterial isolates derived from human clinical specimens and nomenclature revisions published in 2018 and 2019. J Clin Microbiol. 2021;59(2):e01309-20.  https://doi.org/10.1128/JCM.01309-20  PMID: 32967902 
  3. Torres-Sangiao E, Leal Rodriguez C, García-Riestra C. Application and perspectives of MALDI-TOF mass spectrometry in clinical microbiology laboratories. Microorganisms. 2021;9(7):1539.  https://doi.org/10.3390/microorganisms9071539  PMID: 34361974 
  4. Giraud-Gatineau A, Texier G, Fournier PE, Raoult D, Chaudet H. Using MALDI-TOF spectra in epidemiological surveillance for the detection of bacterial subgroups with a possible epidemic potential. BMC Infect Dis. 2021;21(1):1109.  https://doi.org/10.1186/s12879-021-06803-3  PMID: 34711189 
  5. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci USA. 2015;112(27):E3574-81.  https://doi.org/10.1073/pnas.1501049112  PMID: 26100894 
  6. Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol. 2020;18(6):344-59.  https://doi.org/10.1038/s41579-019-0315-1  PMID: 32055025 
  7. Long SW, Linson SE, Ojeda Saavedra M, Cantu C, Davis JJ, Brettin T, et al. Whole-genome sequencing of a human clinical isolate of the novel species Klebsiella quasivariicola sp. nov. Genome Announc. 2017;5(42):e01057-17.  https://doi.org/10.1128/genomeA.01057-17  PMID: 29051239 
  8. Potter RF, Lainhart W, Twentyman J, Wallace MA, Wang B, Burnham CA, et al. Population structure, antibiotic resistance, and uropathogenicity of Klebsiella variicola. MBio. 2018;9(6):e02481-18.  https://doi.org/10.1128/mBio.02481-18  PMID: 30563902 
  9. Rodríguez-Medina N, Barrios-Camacho H, Duran-Bedolla J, Garza-Ramos U. Klebsiella variicola: an emerging pathogen in humans. Emerg Microbes Infect. 2019;8(1):973-88.  https://doi.org/10.1080/22221751.2019.1634981  PMID: 31259664 
  10. Andrade BGN, de Veiga Ramos N, Marin MF, Fonseca EL, Vicente AC. The genome of a clinical Klebsiella variicola strain reveals virulence-associated traits and a pl9-like plasmid. FEMS Microbiol Lett. 2014;360(1):13-6.  https://doi.org/10.1111/1574-6968.12583  PMID: 25135672 
  11. Maatallah M, Vading M, Kabir MH, Bakhrouf A, Kalin M, Nauclér P, et al. Klebsiella variicola is a frequent cause of bloodstream infection in the Stockholm area, and associated with higher mortality compared to K. pneumoniae. PLoS One. 2014;9(11):e113539.  https://doi.org/10.1371/journal.pone.0113539  PMID: 25426853 
  12. Barrios-Camacho H, Aguilar-Vera A, Beltran-Rojel M, Aguilar-Vera E, Duran-Bedolla J, Rodriguez-Medina N, et al. Molecular epidemiology of Klebsiella variicola obtained from different sources. Sci Rep. 2019;9(1):10610.  https://doi.org/10.1038/s41598-019-46998-9  PMID: 31337792 
  13. World Health Organisation (WHO). Antimicrobial resistance. Geneva: WHO; 2021. Available from: https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance
  14. Barnsteiner S, Baty F, Albrich WC, Babouee Flury B, Gasser M, Plüss-Suard C, et al. Antimicrobial resistance and antibiotic consumption in intensive care units, Switzerland, 2009 to 2018. Euro Surveill. 2021;26(46):2001537.  https://doi.org/10.2807/1560-7917.ES.2021.26.46.2001537  PMID: 34794535 
  15. European Committee on Antimicrobial Susceptibility Testing (EUCAST). New definitions of S, I and R from 2019. Växjö: EUCAST. [Accessed: 7 Jul 2022]; Available from: https://www.eucast.org/newsiandr
  16. R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2021. Available from: https://www.R-project.org
  17. Cuénod A, Wüthrich D, Seth-Smith HMB, Ott C, Gehringer C, Foucault F, et al. Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study. Genome Med. 2021;13(1):150.  https://doi.org/10.1186/s13073-021-00960-5  PMID: 34517886 
  18. Yang J, Long H, Hu Y, Feng Y, McNally A, Zong Z. Klebsiella oxytoca complex: update on taxonomy, antimicrobial resistance, and virulence. Clin Microbiol Rev. 2022;35(1):e0000621.  https://doi.org/10.1128/CMR.00006-21  PMID: 34851134 
  19. World Health Organization Regional Office for Europe (WHO/Europe)/European Centre for Disease Prevention and Control. Antimicrobial resistance surveillance in Europe 2022 – 2020 data. 2022, Copenhagen: WHO/Europe; 2022. Available from: https://www.ecdc.europa.eu/en/publications-data/antimicrobial-resistance-surveillance-europe-2022-2020-data
  20. Liao H, Friman VP, Geisen S, Zhao Q, Cui P, Lu X, et al. Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting. Sci Total Environ. 2019;660:841-50.  https://doi.org/10.1016/j.scitotenv.2018.12.353  PMID: 30743970 
  21. Broaders E, Gahan CG, Marchesi JR. Mobile genetic elements of the human gastrointestinal tract: potential for spread of antibiotic resistance genes. Gut Microbes. 2013;4(4):271-80.  https://doi.org/10.4161/gmic.24627  PMID: 23651955 
  22. Murray CJL, Ikuta KS, Sharara F, Swetschinski L, Robles Aguilar G, Gray A, et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 2022;399(10325):629-55.  https://doi.org/10.1016/S0140-6736(21)02724-0  PMID: 35065702 
  23. Kim JI, Maguire F, Tsang KK, Gouliouris T, Peacock SJ, McAllister TA, et al. Machine learning for antimicrobial resistance prediction: current practice, limitations, and clinical perspective. Clin Microbiol Rev. 2022;e0017921.  PMID: 35612324 
  24. Nathwani D, Varghese D, Stephens J, Ansari W, Martin S, Charbonneau C. Value of hospital antimicrobial stewardship programs [ASPs]: a systematic review. Antimicrob Resist Infect Control. 2019;8(1):35.  https://doi.org/10.1186/s13756-019-0471-0  PMID: 30805182 
  25. Rodrigues C, Passet V, Rakotondrasoa A, Brisse S. Identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola and related phylogroups by MALDI-TOF mass spectrometry. Front Microbiol. 2018;9:3000.  https://doi.org/10.3389/fmicb.2018.03000  PMID: 30581423 
/content/10.2807/1560-7917.ES.2022.27.45.2200104
Loading

Data & Media loading...

Supplementary data

Submit comment
Close
Comment moderation successfully completed
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