Potential application of MALDI-TOF MS to identify Streptococcus parapneumoniae, an emerging pathogen previously misidentified as Streptococcus pneumoniae

Abstract

Objectives

Accurate identification of Streptococcus species is critical for clinical management and epidemiology. Misidentification of Streptococcus parapneumoniae as Streptococcus pneumoniae can hinder diagnosis and affect treatment outcomes.

Methods

From 385 archived S. pneumoniae isolates, species-specific polymerase chain reaction (PCR) was used to identify potential S. parapneumoniae. Confirmatory species determination, virulence, and antimicrobial resistance profile analyses were performed through whole-genome sequencing (WGS), phylogenomic, and comparative genomic analyses. Matrix-associated laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral analysis aimed to identify biomarkers for S. parapneumoniae.

Results

Three S. parapneumoniae strains, representing a novel species first identified in Japan in 2024, were isolated from patients with respiratory infections in Hong Kong. WGS showed >99% average nucleotide identity (ANI) with S. parapneumoniae SP4011^T, distinct from S. pneumoniae (<94%). These strains possessed virulence factors similar to S. pneumoniae, suggesting pathogenic potential. All isolates exhibited multidrug and levofloxacin resistance, unlike local S. pneumoniae strains. MALDI-TOF MS identified two peaks (m/z 6,399 and m/z 6,960) unique to S. parapneumoniae.

Conclusions

The multidrug resistance of S. parapneumoniae complicates antimicrobial resistance surveillance data and empirical treatment accuracy for S. pneumoniae. The identified discriminatory peaks offer promising tools for accurate species identification. The prevalence of S. parapneumoniae is likely underestimated; expanded surveillance is warranted to determine its true distribution and clinical significance.