Microfluidic PCR platform promises early detection of neonatal sepsis

A digital microfluidic (DMF) device can reduce time to detect bacteria by as much as 9 hours, speeding up the diagnosis of neonatal sepsis, as shown in a study presented at IDWeek 2022 in Washington, DC, US.

Combining blood culture and polymerase chain reaction (PCR)-based pathogen identification, the device features a custom-built blood culture bottle incubator. This incubator is linked to a disposable cartridge that performs sample preparation and PCR.

According to Dr Vamsee Pamula, the presenting author of the study and the president and founder of Baebies, Inc, the DMF device takes advantage of PCR sensitivity to determine growth rather than fluorescence in blood culture bottles. As a result, the time to pathogen identification is brought down from 12 hours to 3 hours.

“Early administration of antibiotics significantly reduces risk of infant mortality and morbidity, and, therefore, speeding up culture-to-identification is highly desirable,” Pamula added.

To test the device, Pamula and colleagues inoculated standard blood culture bottles with Klebsiella pneumoniae then incubated them in either the DMF device or a traditional blood culture device (BD BACTEC 9050). They drew samples from the DMF bottle at 3, 4, and 5 hours and loaded in the cartridge for automated sample processing and PCR.

Time-to-positivity was determined using cycle threshold and compared with the traditional method, which used fluorescence from the blood culture bottle followed by PCR on a separate device.

With the DMF device, bacterial presence could be detected as early as 3 hours after inoculation with five replicates of K. pneumoniae samples. In comparison, detection took more than 12 hours with the traditional method (10.5-hour culture and 2-hour PCR identification). [IDWeek 2022, abstract 885]

“We observed Ct values of 34, 31, and 28 at 3, 4, and 5 hours post inoculation, [respectively]. Error bars denote reproducibility over all 5 replicates at each time point,” Pamula said.

Moreover, he noted that the DMF and the traditional blood culture device had similar growth curves for all five common pathogens that cause neonatal sepsis (K. pneumoniae, Escherichia coli, Staphylococcus aureus, Streptococcus agalactiae, Staphylococcus epidermidis). 

“To our knowledge, this is the first demonstration of using an integrated microfluidic PCR platform to speed up culture and identification,” according to Pamula.

Sepsis is one of the leading causes of mortality and morbidity in neonates, and antibiotics may be life-saving for the few infants who are truly infected. [Front Pediatr 2018;6:285]

Pamula believes that by accelerating culture-to-identification, their device will help prevent the administration of empirical antibiotic therapy in infants with clinical suspicion of sepsis but negative blood culture. This should avert the adverse outcomes associated with prolonged antibiotic exposure, including disruption of the developing microbiome and increased carriage of antibiotic resistance genes.