Evaluation of an 'all-in-one' seven-day whole-genome sequencing solution in the investigation of a Staphylococcus aureus outbreak in a neonatal intensive care unit

C Rouard; N Bourgeois-Nicolaos; L Rahajamanana; O Romain; L Pouga; V Derouin; D De Luca; F Doucet-Populaire

doi:10.1016/j.jhin.2019.01.029

Evaluation of an 'all-in-one' seven-day whole-genome sequencing solution in the investigation of a Staphylococcus aureus outbreak in a neonatal intensive care unit

J Hosp Infect. 2019 Jul;102(3):297-303. doi: 10.1016/j.jhin.2019.01.029. Epub 2019 Feb 14.

Authors

C Rouard¹, N Bourgeois-Nicolaos², L Rahajamanana³, O Romain⁴, L Pouga³, V Derouin³, D De Luca⁵, F Doucet-Populaire⁶

Affiliations

¹ AP-HP, Hôpitaux Universitaires Paris Sud, Hôpital Antoine Béclère, Service de Bactériologie-Hygiène, Clamart, France; EA4043, Bactéries pathogènes et santé, Faculté de Pharmacie, Université Paris Sud, Chatenay-Malabry, France.
² AP-HP, Hôpitaux Universitaires Paris Sud, Hôpital Antoine Béclère, Service de Bactériologie-Hygiène, Clamart, France; EA4043, Bactéries pathogènes et santé, Faculté de Pharmacie, Université Paris Sud, Chatenay-Malabry, France; Institute of Integrative Biology of the Cell, CNRS, CEA, Université Paris Sud, Paris Saclay University, Gif sur Yvette, France.
³ AP-HP, Hôpitaux Universitaires Paris Sud, Hôpital Antoine Béclère, Service de Bactériologie-Hygiène, Clamart, France.
⁴ AP-HP, Hôpitaux Universitaires Paris Sud, Hôpital Antoine Béclère, Division of Paediatrics and Neonatal Intensive Care, Clamart, France.
⁵ AP-HP, Hôpitaux Universitaires Paris Sud, Hôpital Antoine Béclère, Division of Paediatrics and Neonatal Intensive Care, Clamart, France; INSERM-U999 LabEx - LERMIT, Clamart, France.
⁶ AP-HP, Hôpitaux Universitaires Paris Sud, Hôpital Antoine Béclère, Service de Bactériologie-Hygiène, Clamart, France; EA4043, Bactéries pathogènes et santé, Faculté de Pharmacie, Université Paris Sud, Chatenay-Malabry, France; Institute of Integrative Biology of the Cell, CNRS, CEA, Université Paris Sud, Paris Saclay University, Gif sur Yvette, France. Electronic address: florence.doucet-populaire@aphp.fr.

PMID: 30771369
DOI: 10.1016/j.jhin.2019.01.029

Abstract

Background: Meticillin-susceptible and -resistant Staphylococcus aureus (MSSA and MRSA) are responsible for outbreaks in intensive care units. MSSA infections have the same morbidity and mortality rate as MRSA infections but are studied less often. Whole-genome sequencing (WGS) is used increasingly for outbreak monitoring, but still requires specific installation and trained personnel to obtain and analyse the data.

Aim: To evaluate the workflow and benefits of EpiSeq solution (bioMérieux, Marcy l'Etoile, France) in exploring the increased incidence of S. aureus bloodstream infections in a neonatal intensive care unit (NICU).

Methods: Four S. aureus bacteraemia isolates and 27 colonization isolates obtained between January and July 2016 were submitted to the 'all in one solution' EpiSeq [WGS, quality data assessment, multi-locus sequence typing (MLST), spa typing, virulome and resistome characterization, and phylogenetic tree construction]. More in-depth analyses were performed (whole-genome MLST and whole-genome single nucleotide polymorphism (wgSNP)] with BioNumerics software (Applied Maths, Sint-Martens-Latem, Belgium).

Findings: Nine different sequence types and 13 different spa types were found among the 31 isolates studied. Among those isolates, 11 (seven patients) were ST146 spa type t002, five (four patients) were ST30 and four (four patients) were ST398. The 11 ST146 isolates had a maximum of seven pairwise SNP differences.

Conclusion: Use of EpiSeq solution allowed fast demonstration of the polyclonal profile of the MSSA population in neonates, and enabled the suspicion of a global outbreak to be ruled out. However, wgSNP analysis showed the transmission and persistence of one sequence type for over six months in the NICU, and enabled the infection control team to adapt its response.

Keywords: Neonatal intensive care unit; Outbreak; Sepsis; Staphylococcus aureus; Whole-genome sequencing; bioMérieux EpiSeq.

MeSH terms

Bacteremia / epidemiology
Bacteremia / microbiology
Cross Infection / epidemiology
Cross Infection / microbiology
Disease Outbreaks*
Disease Transmission, Infectious
France / epidemiology
Genetic Variation
Genotype
Humans
Incidence
Infant
Intensive Care Units, Neonatal
Molecular Epidemiology
Molecular Typing*
Staphylococcal Infections / epidemiology*
Staphylococcal Infections / microbiology
Staphylococcus aureus / classification*
Staphylococcus aureus / genetics
Staphylococcus aureus / isolation & purification*
Whole Genome Sequencing*