Test Developed for Healthcare-Acquired Infections Validated

Healthcare-acquired infections (HAIs) kill tens of thousands of people each year and add significantly to healthcare costs. Multidrug resistant and epidemic strains are a large proportion of HAI agents, and multidrug resistant strains of Klebsiella pneumoniae, a leading HAI agent, have become an urgent public health crisis.

In the healthcare environment, patient colonization of K. pneumoniae precedes infection, and transmission via colonization leads to outbreaks. Periodic patient screening for K. pneumoniae colonization has the potential to curb the number of HAIs, which affect hundreds of thousands of patients annually and add nearly USD10 billion in associated healthcare costs.


Scientists at the Translational Genomics Research Institute (Flagstaff, AZ, USA) and their colleagues acquired isolates for target identification and assay validation, and DNA extracted from clinical specimens were acquired through collaborations with a large hospital reference laboratory. This laboratory receives specimens from ten system-wide medical centers in Arizona, and from a high volume private reference laboratory that receives specimens from regional inpatient, long-term care, and outpatient facilities.

Isolates were identified using the VITEK 2 system (bioMérieux, Marcy-l'Étoile, France). Clinical specimen types included various respiratory specimens, nasal, ear, and throat swabs, sputa, tracheal aspirates, and bronchial alveolar lavages, urine, and wound swabs or tissue. Unlike traditional assays that require growing a live culture in a laboratory setting, which adds days to the testing process and layers on cost, the new method called KlebSeq employs a technique called amplicon sequencing that identifies the presence of Klebsiella and stratifies its characteristics, such as strain type and whether it may be antibiotic resistant.

KlebSeq can be used for routine screening and surveillance, enabling healthcare staff to make more informed patient decisions, and curb outbreak situations by rapidly identifying transmissions prior to patients showing signs of infection. Classifying the type of infection in each patient would help enable an institution to decide when and which intervention procedures to enact. The study results suggest that KlebSeq would be especially helpful for high-risk patients, such as those in intensive-care units, centers specializing in bone marrow transplantation or chronically immunosuppressed patients, long-term care facilities, and travelers returning from endemic regions. The results also suggest that KlebSeq could be easily modified to detect other healthcare-acquired infectious agents, and identify those with antimicrobial resistance.

Paul Keim, PhD, Director of TGen North and senior author of the study said, “The sensitivity of KlebSeq is superior to culture-based methods. KlebSeq is an important step toward a comprehensive, yet accessible, tool for all pathogen identification and characterization.” The study was published on August 10, 2016, in the Journal of Clinical Microbiology.

Related Links:
Translational Genomics Research Institute
bioMérieux