Identifying Invasive Pneumococci in Pediatric Infections Utilizing Whole Genome Sequencing
This method represents a significant advancement in case management for this population. In our latest From Pathogen to Infectious Disease Diagnosis Podcast, Jose Alexander, MD, ABMM, ABAIM, FCCM, CIC, ASCP, BCMAS, provides insights on its capabilities and how it can potentially aid clinicians in reducing antimicrobial resistance.
Streptococcus pneumoniae (pneumococcus) is a major cause of infections, including pneumonia, sepsis, and meningitis, which can severely impact young children. According to the World Health Organization, pneumococcal pneumonia caused 1,189,937 deaths and 197.05 million incidents in 2016, globally. In looking at the mortality, nearly a third—341,029 of these deaths—occurred in children under 5 years of age.¹
Identifying this bacterium in children can be especially challenging. “Microbiological identification is challenging, since collecting respiratory samples in children is more problematic compared to adults,” Rueda et al. write. “Some microbiological tests have low sensitivities in children. Previous research has shown different etiologic attributions depending on the anatomical origin of collected specimens (induced sputum, nasopharyngeal or oropharyngeal aspirate or swab, blood, and/or urine) and the diagnostic tests employed (PCR, acute or convalescent serology, cultures, direct or indirect immunofluorescence).”2
Jose Alexander, MD, ABMM, ABAIM, FCCM, CIC, ASCP, BCMAS, medical director of the microbiology laboratory at AdventHealth in Orlando, FL, points out that there is even a greater burden in low- and middle-income countries as they have limited access to screening.
“Low-income countries have no access to specialized microbiology laboratories. Isolation, identification, and even basic imaging or testing can be really challenging,” Alexander said.
Having experience both as a practicing physician and now as a laboratorian, Alexander is able to utilize his clinical and diagnostic expertise in patient care. He recently authored an article, Genotyping Invasive Pneumococci: A Game-Changer in Pediatric Infection Management, which he posted on LinkedIn.
In his piece, he notes that vaccines have led to a sharp decline in invasive pneumococcal disease (IPD). Still, he explains, IPD evolves—especially as unvaccinated serotypes quickly fill the void. While newer vaccines are being developed to address these emerging serotypes, the importance of robust testing cannot be overlooked.
He sees WGS as a game-changer because it provides a complete genetic blueprint of the bacterium, helping to identify antimicrobial resistance.
Alexander emphasizes that this level of specificity can provide real-time, more precise information, leading to better patient outcomes. “We don’t want the patient to get these reports 2 or 3 months later,” Alexander said. “We want to be able to provide this result while the patient is still in the hospital.”
Alexander asked clinicians at his institution what it would mean if they could receive WGS results while the patient was still hospitalized. His clinical team responded that they could, “use this information to adjust, improve, escalate, or optimize treatment.”
