MOLECULAR DIAGNOSTICS


effective vaccination strategies. With the ability to perform serotype-level analysis, researchers can beter evaluate and refine vaccine coverage and effectiveness, as well as detect non-vaccine-type replacement and emerging resistant clones at an early stage. Evolving serotype and strain


The Instituto Adolfo Lutz in São Paulo, Brazil, a national reference laboratory for bacterial meningitis and invasive pneumococcal disease, has integrated IR spectral analysis for fast and effective routine pneumococcal surveillance in Brazil.


quickly discriminate at strain level, FTIR spectroscopy and dedicated classifiers can be vital components in surveillance. As dominant serotypes vary over time and previously rare serotypes can emerge and increase, the development of the classifier began with a prevalence survey of S. pneumoniae serotypes in Brazil from 2022 to 2024. The survey revealed the 12 most prevalent serotypes which together accounted for more than 71.4% of invasive isolates. These serotypes were then confirmed using either WGS or the Quellung reaction before being incorporated into the classifier. The S. pneumoniae classifier was


trained to achieve optimal performance using a sample preparation technique which has been optimised by the Instituto Adolfo Lutz according to its needs. A sample set of invasive S. pneumoniae isolates was analysed using FTIR spectroscopy, generating 1,110 spectra and achieving complete accuracy across the 12 serotypes. Subsequent linear discriminant analysis of the spectra yielded clear separation between serotypes, indicating that the newly developed S. pneumoniae classifier has strong discriminatory power at the serotype level. Following development of the classifier,


the laboratory performed comprehensive validation using a set of 265 isolates. The set comprised both trained serotypes (included in the classifier) and non-trained serotypes (excluded from the classifier). Validation demonstrated overall concordance of 99.6% with only one discordant result, emphasising the high performance of the classifier. Using validation results, the reference


laboratory conducted a reliability ranking to measure the extent to which unknown isolates fit into the classifier model. Serotypes with a score above 80


show high reliability and can be used with confidence, while those above 60 display moderate reliability and require a confirmatory test. The majority of results atained a score of at least 80, supporting the implementation of the S. pneumoniae classifier into routine use in a public health seting. The Instituto Adolfo Lutz’s successful


development of a 12-serotype classifier reflecting the most prevalent pneumococcal serotypes in Brazil demonstrates the suitability of IR-based classifiers for routine surveillance workflows, particularly as validation findings indicate that FTIR spectroscopy generates robust and highly reliable results. These developments raise important questions about how best to deploy an expanded toolkit of microbiological techniques, spanning classical serology, genomics, and IR-based phenotyping, to support rapid outbreak response and long-term vaccine strategy.


Moving towards integrated surveillance Integrating rapid phenotyping methods, such as FTIR spectroscopy, into national and global networks could support faster and more comprehensive bacterial surveillance. IR-based strain-level typing complements species-level MALDI-TOF MS and molecular methods, such as PCR and WGS, to create a tiered, multi-layer approach which can accelerate outbreak detection, track infection transmission and monitor serotype shifts post- vaccination. Low-cost and easy to deploy, phenotypic platforms are especially well suited to bacterial surveillance in resource-limited reference laboratory setings. Improved bacterial surveillance in


turn facilitates the development of more 40 WWW.PATHOLOGYINPRACTICE.COM August 2026


landscapes, such as those associated with pneumococcal disease, are an ongoing public health threat and demand flexible, fast and scalable laboratory tools that can keep pace with the latest developments. The use of IR-based strain-typing, as evidenced by the Brazilian S. pneumoniae classifier, can help bridge the gap between traditional microbiology and genomic sequencing and could play a crucial role in combating invasive infectious diseases like pneumococcal disease.


References 1 Vaccine Knowledge. Pneumococcal disease.


(Oxford Vaccine Group, 2025) htps:// vaccineknowledge.ox.ac.uk/pneumococcal- disease


2 Ghaffar F, Friedland IR, McCracken GH Jr. Dynamics of nasopharyngeal colonization by Streptococcus pneumoniae. Pediatr Infect Dis J. 1999;18(7):638-646. doi:10.1097/00006454-199907000-00016


3 Pachito DV, Longato M, Cordeiro G, Almeida PHRF, Ferreira RM, Burian APN. Hospitalization due to pneumococcal disease in the Unified Health System in Brazil: A retrospective analysis of administrative data. Braz J Infect Dis. 2025;29(1):104482. doi:10.1016/j.bjid.2024.104482


4 Kfouri RA, Brandileone MC, Sáfadi MAP, et al. Chronic medical conditions associated with invasive pneumococcal diseases in inpatients in teaching hospitals in São Paulo city: Estimating antimicrobial susceptibility and serotype-coverage of pneumococcal vaccines. Braz J Infect Dis. 2023;27(2):102746. doi:10.1016/j. bjid.2023.102746


About Dr Carolyn Moonen Carolyn GJ Moonen PhD, is Scientific Product Specialist IR Biotyper at Bruker Daltonics, based in Amsterdam, the Netherlands, covering Europe, the Middle East and Africa. She obtained her PhD in immunology and microbiology from the University of Amsterdam and completed a postdoctoral fellowship in Otawa, Canada, before joining Bruker in 2020.


About Dr Markus Meyer Markus Meyer PhD, is Head of the Business Unit Hygiene/Epidemiology at Bruker Microbiology and Infection Diagnostics (BMID) in Bremen, Germany. He has been with Bruker Daltonics since 2010 as a Product Manager for various life science mass spectrometry instruments before joining the BMID team as Global Product Manager for consumables in 2018.


PPi


By Gsbhalla - Own work, CC BY-SA 4.0


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