Acta Paediatrica · 2018 · 23 citations · 15 references
MedicineInfectious DiseasesMicrobiologyMedical MicrobiologyMolecular EpidemiologyOutbreak InvestigationBacterial InfectionsHealthcare-associated Outbreak InvestigationInfection SurveillanceNeonatal InfectionsNeonatal Infectious DiseasesPathogen DetectionIntensive Care Unit OutbreaksIsolationMolecular Outbreak InvestigationNeonatal Infection EpidemiologyNeonatal Infectious Disease EpidemiologyNeonatal Intensive Care Unit AdmissionPathogen Genome SequencingRoutine Screening
AIM: Klebsiella spp. have been stated to be the most frequent cause of neonatal intensive care unit (NICU) outbreaks. We report an outbreak of Klebsiella oxytoca in a NICU at a tertiary care hospital in Norway between April 2016 and April 2017. This study describes the outbreak, infection control measures undertaken and the molecular methods developed. METHODS: The outbreak prompted detailed epidemiological and microbial investigations, where whole-genome sequencing (WGS) was particularly useful for both genotyping and development of two new K. oxytoca-specific real-time PCR assays. Routine screening of patients, as well as sampling from numerous environmental sites, was performed during the outbreak. A bundle of infection control measures was instigated to control the outbreak, among them strict cohort isolation. RESULTS: Five neonates had symptomatic infection, and 17 were found to be asymptomatically colonised. Infections varied in severity from conjunctivitis to a fatal case of pneumonia. A source of the outbreak could not be determined. CONCLUSION: This report describes K. oxytoca as a significant pathogen in a NICU outbreak setting and highlights the importance of developing appropriate microbiological screening methods and implementing strict infection control measures to control the outbreak in a setting where the source could not be identified.
15
Prokka: rapid prokaryotic genome annotation
Torsten Seemann · Bioinformatics · 2014 · 19.6K citations
Roary: rapid large-scale prokaryote pan genome analysis
Andrew J. Page, Carla Cummins, Martin Hunt et al. · Bioinformatics · 2015 · 5.9K citations · Full text