Whole Genome Sequencing Detects Infection Transmission in NICU

A new study has shown that whole genome sequencing (WGS) of bacterial pathogens acquired from surveillance in a neonatal intensive care unit (NICU) can reveal significant infection transmission that goes undetected by standard infection control measures. The research highlights that even in well-equipped medical facilities and in areas like the NICU where vigilant monitoring is routine, WGS provides a level of detection of transmission events that current methods cannot achieve.

Conducted by Next Gen Diagnostics (NGD, West Palm Beach, FL, USA) and researchers from Vanderbilt University Medical Center (VUMC, Nashville, TN, USA), the study analyzed 171 S. aureus samples from 132 individual patients. These samples were collected during routine surveillance in April, June, and July, and were supplemented with clinical samples. The samples were sequenced using short-read sequencing techniques and analyzed by NGD’s automated system to determine the relatedness of core genomes at the SNP level.

A stringent cutoff of 6 SNPs was used to identify potential transmission, which was then further assessed by the VUMC infection prevention team. The analysis found that 42 out of 132 patients (31.8%) with S. aureus infections were linked by transmission chains. Notably, the incidence of patients with MRSA infections connected by transmission was 46.8%, more than double the rate found in patients with MSSA infections, which stood at 21.2%. The study identified 13 distinct strains involved in these transmissions, indicating localized, undetected sources of spread rather than a ward-wide outbreak.

“We found that WGS of S. aureus isolates obtained from surveillance swabs and clinical samples revealed a significant amount of likely transmission, which provided guidance enabling our infection control team to take a series of actions with beneficial effect,” said Dr. Romney Humphries, Professor of Pathology, Microbiology and Immunology and Director of Laboratory Medicine at VUMC and senior author on the study.

“This result, along with those emerging from other medical centers, of the use of WGS to detect rather than simply verify transmission may signal a sea-change in best practice,” added Tom Talbot, Professor of Medicine and Medical Director of Infection Prevention at VUMC. “With a sufficiently low cost for sequencing and bioinformatic analysis, use of WGS to detect transmission, at least in those wards where patients are at the greatest risk, may become a more routine infection prevention practice.”

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