Assistant Professor of Pediatrics/Attending Neonatologist Connecticut Children's Medical Center Hartford, Connecticut, United States
Background: Bacterial source tracking typically involves whole-genome sequencing (WGS) of cultured isolates for strain identification. We recently described a novel approach that utilizes PacBio sequencing of a ~2,500 base rRNA (StrainID) amplicon to achieve strain-level resolution of the gut microbiome in preterm infants. Objective: To determine if StrainID could be utilized as a technique to trace Klebsiella pneumoniae infections in the neonatal intensive care unit (NICU). Design/Methods: At 8-9 days of age, a set of premature twins had a deterioration in their condition. Twin B developed intestinal perforation, had a surgical drain placed, and was started on broad-spectrum antibiotics. The blood culture grew K. pneumoniae and the infant died within 48 hours due to septic shock. Twin A required increased ventilatory support and nitric oxide. The baby was started on broad-spectrum antibiotics and gradually recovered. The blood and tracheal cultures grew K. pneumoniae. Considering that the infecting organism could be from a single source, a sample of mother’s milk was cultured and grew K. pneumoniae. Around the same time, an unrelated infant in the same NICU developed conjunctivitis, and the surface culture grew K. pneumoniae. StrainID was performed on the isolates and compared to results obtained via WGS. Sequential fecal samples from twin A and the unrelated preterm infant were also analyzed by StrainID. Results: StrainID identified distinct groups of amplicon sequence variants (ASVs) comprising a unique fingerprint pattern for a given Klebsiella strain. The ASV fingerprints for the isolates recovered from the twins' blood, trachea, and mother’s milk were indistinguishable, whereas the fingerprints were different compared to the conjunctival isolate. WGS confirmed that the isolates recovered from the twins and mother’s milk were identical, and the conjunctival isolate was a different strain. StrainID further demonstrated that the fingerprint pattern of the infecting strain was present in fecal samples of twin A at the time of dissemination and persisted for 15 weeks. A different fingerprint pattern was observed in fecal samples of the unrelated infant and corresponded to the pattern observed for the conjunctival isolate.
Conclusion(s): In this case series, K. pneumoniae transmission leading to sepsis in a set of premature twins appeared to originate from the mother’s milk. We show that StrainID and ASV fingerprinting enable differentiation of closely related bacterial strains and can be used for source- and strain-tracking across complex microbiomes. Authors APM, EAJ, and MDD hold equity in Intus Biosciences.
