Introduction Nontyphoidal Salmonella encompasses over 2500 serotypes of S. enterica subsp. enterica capable of causing asymptomatic infection, self-limited gastroenteritis, or invasive disease. Neonates are at high risk for invasive disease given the immaturity of their gastrointestinal tract and cell-mediated immunity. They also excrete bacteria longer after infection than older individuals. In nurseries, outbreaks may last months to years. Serotyping is essential for tracking outbreaks and can predict both severity of illness and source of infection. While traditional serotyping uses DNA fingerprinting, Salmonella surveillance is moving towards whole genome sequencing (WGS) for more precise characterization of isolates. Laptop-compatible sequencing technology and open-source bioinformatics make WGS accessible to clinical investigators at the site of outbreak. Here we present cases of an unusual serotype, Salmonella ser. Agbeni, affecting 5 infants in the neonatal intensive care unit (NICU), along with the first WGS data for this serotype. Cases Four infants evaluated for bradycardia episodes were found to be bacteremic with Salmonella ser. Agbeni in a span of 36 hours (Fig. 1A). All were extremely or very low birth weight (ELBW, VLBW) and premature at delivery (25w0d to 30w1d). Only one developed bloody stool early in illness. All improved clinically with negative blood cultures within 24 hours of IV antibiotic initiation, continued for 14 days. Contact precautions were enforced until 3 days after the end of therapy per Illinois Department of Public Health recommendations. A fifth infant developed Salmonella sepsis 10 days after contact precautions had been lifted on affected infants, all four of whom were still inpatient (Fig. 1B-C). This infant was VLBW, premature (32w4d), and improved within 24 hours of IV antibiotic therapy. All infants demonstrated Salmonella stool shedding up to 28 days after completing antibiotic therapy. Only two stool samples (negative for Salmonella) could be obtained from parents. One untested parent owned 3 bearded dragons. WGS We sequenced genomic DNA from Salmonella ser. Agbeni from the fifth infant’s blood culture using a Nanopore MinION. Reads were assembled using Canu v1.8 to a 4.56 Mb chromosome (33.7x coverage) consistent in length with Salmonella enterica (Fig. 2). Annotation with Prokka 1.13.3 included genes known to promote Salmonella pathogenicity, including invasion of intestinal epithelium (invG), IL-8-mediated inflammation (sipA), and a Type III secretion system (spiA). We performed all sequencing and bioinformatics at the outbreak site. Conclusion Salmonella ser. Agbeni caused invasive disease that rapidly resolved with IV antibiotics in 5 of 5 ELBW and VLBW premature infants. Stool cultures confirmed shedding up to a month after treatment, explaining the recurrence after discontinuing contact precautions. Bearded dragons may have been the source, considering previous reports of Agbeni in pet reptiles. WGS will provide the basis for evaluating this hypothesis and analyzing the relatedness of future outbreaks.

Timing and distribution of clinical cases

Timing and distribution of clinical cases

Close modal

A) Clinical timelines for first 4 Salmonella ser. Agbeni sepsis cases. B) Clinical timeline for fifth Agbeni sepsis case. C) Distribution of Agbeni sepsis cases in the neonatal intensive care unit.

Salmonella ser. Agbeni whole genome sequencing

Salmonella ser. Agbeni whole genome sequencing

Close modal

Map of isolate chromosome, annotated with genes implicated in pathogenicity. Blue, coding regions on forward strand; green, coding regions on reverse strand; purple, higher G:C content; gold, lower G:C content.