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

Abstract

<h3>Objectives</h3><p>Accurate identification of <em>Streptococcus</em> species is critical for clinical management and epidemiology. Misidentification of <em>Streptococcus parapneumoniae</em> as <em>Streptococcus pneumoniae</em> can hinder diagnosis and affect treatment outcomes.</p><h3>Methods</h3><p>From 385 archived <em>S. pneumoniae</em> isolates, species-specific polymerase chain reaction (PCR) was used to identify potential <em>S. parapneumoniae</em>. 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 <em>S. parapneumoniae</em>.</p><h3>Results</h3><p>Three <em>S. parapneumoniae</em> 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 <em>S. parapneumoniae</em> SP4011^T, distinct from <em>S. pneumoniae</em> (<94%). These strains possessed virulence factors similar to <em>S. pneumoniae</em>, suggesting pathogenic potential. All isolates exhibited multidrug and levofloxacin resistance, unlike local <em>S. pneumoniae</em> strains. MALDI-TOF MS identified two peaks (<em>m/z</em> 6,399 and <em>m/z</em> 6,960) unique to <em>S. parapneumoniae.</em></p><h3>Conclusions</h3><p>The multidrug resistance of <em>S. parapneumoniae</em> complicates antimicrobial resistance surveillance data and empirical treatment accuracy for <em>S. pneumoniae</em>. The identified discriminatory peaks offer promising tools for accurate species identification. The prevalence of <em>S. parapneumoniae</em> is likely underestimated; expanded surveillance is warranted to determine its true distribution and clinical significance.</p>