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Management and investigation of a Serratia marcescens outbreak in a neonatal unit in Switzerland – the role of hand hygiene and whole genome sequencing

  • Walter Zingg1Email author,
  • Isabelle Soulake1,
  • Damien Baud2,
  • Benedikt Huttner1, 3,
  • Riccardo Pfister4,
  • Gesuele Renzi5,
  • Didier Pittet1,
  • Jacques Schrenzel2, 5 and
  • Patrice Francois2, 5
Antimicrobial Resistance & Infection Control20176:125

https://doi.org/10.1186/s13756-017-0285-x

Received: 28 June 2017

Accepted: 28 November 2017

Published: 11 December 2017

The Correction to this article has been published in Antimicrobial Resistance & Infection Control 2018 7:6

Abstract

Background

Many outbreaks due to Serratia marcescens among neonates have been described in the literature but little is known about the role of whole genome sequencing in outbreak analysis and management.

Methods

Between February and March 2013, 2 neonates and 2 infants previously hospitalised in the neonatal unit of a tertiary care centre in Switzerland, were found to be colonised with S. marcescens. An investigation was launched with extensive environmental sampling and neonatal screening in four consecutive point prevalence surveys between April and May 2013. All identified isolates were first investigated by fingerprinting and later by whole genome sequencing. Audits of best practices were performed and a hand hygiene promotion programme was implemented.

Results

Twenty neonates were colonised with S. marcescens. No invasive infection due to S. marcescens occurred. All 231 environmental samples were negative. Hand hygiene compliance improved from 51% in April 2013 to 79% in May 2013 and remained high thereafter. No S. marcescens was identified in point prevalence surveys in June and October 2013. All strains were identical in the fingerprinting analysis and closely related according to whole genome sequencing.

Conclusions

Improving best practices and particularly hand hygiene proved effective in terminating the outbreak. Whole genome sequencing is a helpful tool for genotyping because it allows both sufficient discrimination of strains and comparison to other outbreaks through the use of an emerging international database.

Keywords

NeonatesNeonatal intensive care unit Serratia Marcescens OutbreakHand hygieneIsolationInfection controlWhole genome sequencingCross-transmissionHealthcare-associated infection

Background

Serratia marcescens has long been recognized as an important pathogen in neonatal intensive care units (NICUs). It is the third most common pathogen identified in published NICU outbreaks [1], and it has been found to account for 15% of all culture-positive nosocomial infections in this setting [2]. The large number of outbreak reports underestimates the true occurrence of S. marcescens in neonatology units and NICUs. According to the results of the mandatory surveillance of healthcare-associated infections (HAIs) in very low birth weight infants in Germany from 2006 to 2011, at least one to two Serratia outbreaks per year are expected for Germany alone [3].

S. marcescens causes a wide range of clinical manifestations in neonates, from asymptomatic colonization to infections such as urinary tract infections, pneumonia, sepsis or meningitis [4, 5]. Risk factors for Serratia spp. acquisition by neonates are related to immaturity, prolonged hospital stay, antibiotic use, and mechanical ventilation [4, 6].

The objective of this outbreak report was to summarize the investigation and successful management of a S. marcescens outbreak in neonates and to investigate the contribution of using whole genome sequencing. This report follows the ORION (Outbreak Reports and Intervention Studies Of Nosocomial infection) statement [7].

Methods

Setting

The University of Geneva Hospitals (HUG), are a 1′800-bed primary and tertiary care center with about 47,000 admissions accounting for 660,000 patient-days per year. At the time of the outbreak it offered 17 places in the NICU, and 12 places in the geographically separate pediatric intensive care unit (PICU), where neonates are cared for when mechanical ventilation is needed. Neonates who are clinically stable but need prolonged stay for non-medical reasons are transferred to the unit for child development (UCD).

Outbreak

The outbreak started in February 2013 and ended in June 2013 (Fig. 1). Between February and March 2013, two neonates in the NICU and 2 infants in the UCD were found with S. marcescens (2 vascular catheters, 2 eye swabs, and 1 urine sample). Given the organizational ties and the patient flow between NICU, PICU, and UCD, an investigation was launched by a first point prevalence survey in the three units (Fig. 2) on 23 April 2013. Eight out of 41 screened children were identified as cases in this survey, one in the PICU, 3 in the UCD and 4 in the NICU. All new cases were neonates with a present or past history of stay in the NICU. Based on these findings, we focused further activity on the NICU with extensive environmental sampling and neonatal screening during 4 consecutive prevalence surveys.
Fig. 1

Epidemic curve – Serratia marcescens outbreak at the University of Geneva Hospitals, 2013

Fig. 2

Cases – Serratia marcescens outbreak at the University of Geneva Hospitals, 2013

Outbreak management

Audits of best practices in the use of surface disinfectants, ointments and cosmetic products were performed, as well as weekly direct hand hygiene observations (439 opportunities in total). An intensive hand hygiene promotion programme was offered to the staff working in the NICU: daily presence in the NICU, education and training, and weekly hand hygiene audits with individual feedback.

Microbiological investigation/genotyping

In 2013, the genomes of the S. marcescens isolates obtained in the prevalence surveys were tested by a commercial fingerprinting assay (DiversiLab®, Biomerieux, France). In 2016, the genomes S. marcescens isolates were fully sequenced using an Illumina HiSeq 2500 sequencer as previously described [8].

Results

A total of 232 neonatal screenings (117 stool samples, 115 nasal swabs) [9] were performed. In addition to the 4 index cases and the 8 cases identified in the first prevalence survey, an additional three, four and one cases were identified in the second, third and fourth prevalence surveys in April and May, respectively (Fig. 2). The proportions of positive rectal and nasal swabs were 11.1% (13/117) and 6.1% (7/115), respectively. Five infants had a positive result for both rectal and nasal swabs. All cases were preterm-, and seven were very-low-birth weight infants. No new S. marcescens cases were identified until October 2016, including two further prevalence surveys, which were performed in June and October. There was no invasive infection due to S. marcescens, neither during the outbreak nor until end of December 2013. A total of 231 environmental samplings were performed (Table 1). All tested products, materials and surfaces were negative for S. marcescens. Hand hygiene compliance improved from 51% in April 2013 to 79% in May 2013 following the promotion programme. Compliance remained above 65% in the following months (Fig. 1).
Table 1

Products, materials and surfaces tested for microbiological growth – Serratia marcescens outbreak at the University of Geneva Hospitals, 2013

Products, materials and surfaces

N (%)

Hand and skin disinfectants

66 (28.6)

Hypochlorite solution 225 ppm to disinfect pacifiers and nipple shields

25 (10.8)

Ointments and body lotions

25 (10.8)

Computer keyboards

20 (8.7)

Medicated and non-medicated soaps

20 (8.7)

Bowls for body care

17 (7.4)

Water from incubators

11 (4.8)

Tap water

10 (4.3)

Tubs

9 (3.9)

Sinks

9 (3.9)

Water from CPAPa tubes

6 (2.6)

Other materials or surfaces

13 (5.6)

Total

231 (100)

There was no growth for S. marcescens on any of the tested products, materials or surfaces

aCPAP continuous positive airway pressure

Fingerprinting of 24 isolates from 16 neonates showed identical strains (Fig. 3). Whole genome sequencing was carried out on the set of 24 S. marcescens strains (Sm01-Sm24) belonging to the outbreak. The sequencing on an Illumina HiSeq produced on average a total of 13 million 150 bp reads per sample, exhibiting very high theoretical coverage values (between 300 and 900 fold). Assembly was achieved using SPAdes 3.9.0 software, after read quality trimming and filtering was applied to the raw reads. The assembly produced very similar results for each strain from the outbreak, resulting in an average genome size of 5′080’124 bp with a standard deviation of 1097 bp. This shows extreme similarity between the strains of the outbreak. Moreover, pairwise comparisons using MUMmer software were performed between each couple of strains and showed similarity above 99.999% [10]. Figure 4 shows an unrooted tree displaying all the isolates from the outbreak (Sm01-24), and one representative strain isolated in Germany during a SM outbreak in 2016 (SMB2099) [11].
Fig. 3

Fingerprinting of S. marcescens strains using the DiversiLab® kit – Serratia marcescens outbreak at the University of Geneva Hospitals, 2013

Fig. 4

Whole genome SNP based phylogenetic analysis of Serratia marcescens strains – Serratia marcescens outbreak at the University of Geneva Hospitals, 2013

Discussion

This report suggests that focusing on and improving hand hygiene is effective in terminating a S. marcescens outbreak among neonates. Whole genome sequencing is a useful tool for outbreak investigation because it is more discriminative than standard fingerprinting tests and allows benchmarking with other outbreaks thanks to a growing gene bank.

The source of S. marcescens outbreaks in NICUs is rarely identified. A review summarizing 48 NICU outbreaks reported an identified source in only 40% (19/48), the most frequent being a colonized or infected index patient (8/48), followed by equipment for patient care (6/48), an (unspecified) environment (4/48), and food (1/48) [12]. Colonized or infected patients are thought to represent the most important reservoir of S. marcescens outbreaks in NICUs [4, 13]. In the currently described situation, the investigation revealed two additional NICU cases prior to the outbreak. A mother of one of them hadan amnion infection syndrome due to S. marcescens three months before the start of the outbreak, and thus, may have been the most likely source [12]. In the literature, healthcare workers were never identified as a source, but few studies investigated this specifically [14]. Like in our study, extensive environmental screening rarely yielded positive results in the reported outbreaks, suggesting that environmental contamination may play a limited role.

The clinical implication of colonization with S. marcescens in neonates and its implication in outbreaks is not always clear. A number of studies reported that S. marcescens is rather commonly isolated in stool of preterm neonates within the first weeks of life [6, 15, 16]. However, the pathogen was not isolated consistently in preterm neonates either [17], and S. marcescens has not been isolated in healthy term babies [18]. Thus, while the finding of S. marcescens in neonatal stool can be considered a regular event in NICUs, the pathogen per se is not part of the normal early gut flora of healthy newborns in the community. Once the intestines of a neonate are colonized with S. marcescens from the (pathologic) outside, they can become the “source” of an outbreak. This makes control of Serratia outbreaks very difficult, and underlines the importance of hands in the transmission of the pathogen and the possible successful management of an outbreak.

Already in 1981, contaminated hand-washing brushes were reported to be implicated in a S. marcescens outbreak, indirectly pointing to the pivotal role of hand hygiene in the spread of the pathogen [19]. Contaminated soaps were identified in another report [20]. Interventions to control outbreaks included always both hand hygiene and environmental control [9, 2128]. Given that all environmental samples were negative in our outbreak investigation and work had been done in the past to dedicate equipment, drugs, ointments and other cosmetic products to individual neonates (avoiding multivials) [29], our intervention focused on hand hygiene improvement. This was all the more justified because a decrease of hand hygiene compliance had been identified as part of the investigation; hand hygiene compliance was 72% in the year before the outbreak.

Whole genome sequencing technology emerged as a powerful tool to identify clonality among outbreak isolates. The genome of a S. marcescens strain that sparked an outbreak among infants in Germany was reported very recently [11, 12]. Comparison with our index case revealed a moderate difference around 200 SNPs. Other isolates identified from our institution and not related to the outbreak were sequenced and the number of SNPs was higher than 100′000 (data not shown).

There are limitations in our outbreak investigation. First, environmental sampling was large but we did not consistently use neutralizing agents for testing the different cosmetic products, resulting in potential underreporting. However, cosmetic products were strictly confined to the neonates and no multivials were in use. A positive finding of a product with a case would not have been prove of the product being the source. Second, we did not produce formal records from the audits other than hand hygiene.

Conclusions

Improving best practice and particularly hand hygiene are effective in terminating the outbreak. This highlights the role of hand hygiene in the cause but also in the successful management of S. marcescens outbreaks in neonates. Whole genome sequencing is a helpful tool for genotyping because it allows both sufficient discrimination of strains within the outbreak and comparison to other outbreaks through an emerging international database.

Notes

Abbreviations

HAI: 

Healthcare-associated infection

HUG: 

University of Geneva hospitals

NICU: 

Neonatal intensive care unit

ORION: 

Outbreak reports and intervention studies of nosocomial infection

PICU: 

Pediatric intensive care unit

SNP: 

Single nucleotide polymorphism

UCD: 

Unit for child development

Declarations

Acknowledgments

We would like to thank Delphine Scalia-Perreard, Claude Ginet, and Sylvie Touveneau for the outbreak investigation.

Funding

No external funding.

Availability of data and materials

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

Authors’ contributions

BH, IS, and WZ organised and performed the investigation and management of the outbreak. DB, GR and PF performed the microbiological investigation and whole genome sequencing. WZ, DB, and PF did the data analysis. WZ wrote the first draft of the manuscript. WZ, IS, DB, BH, RP, GR, DP, JS, and PF reviewed and contributed to subsequent drafts. All authors approved the final version for publication.

Ethics approval and consent to participate

Not applicable (outbreak report; no interventions humans).

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

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Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
Infection Control Program and WHO Collaborating Center for Patient Safety, |University of Geneva Hospitals, Geneva, Switzerland
(2)
Genomic Research Laboratory, Division of Infectious Diseases, University of Geneva Hospitals, Geneva, Switzerland
(3)
Division of Infectious Diseases, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
(4)
Neonatal Intensive Care Unit, Department of Paediatrics, University of Geneva Hospitals, Geneva, Switzerland
(5)
Bacteriology Laboratory, Department of Genetics and Laboratory Medicine, University of Geneva Hospitals, Geneva, Switzerland

References

  1. Gastmeier P, Loui A, Stamm-Balderjahn S, Hansen S, Zuschneid I, Sohr D, Behnke M, Obladen M, Vonberg RP, Ruden H. Outbreaks in neonatal intensive care units - they are not like others. Am J Infect Control. 2007;35(3):172–6.View ArticlePubMedGoogle Scholar
  2. Raymond J, Aujard Y. Nosocomial infections in pediatric patients: a European, multicenter prospective study. European study group. Infect Control Hosp Epidemiol. 2000;21(4):260–3.View ArticlePubMedGoogle Scholar
  3. Schwab F, Geffers C, Piening B, Haller S, Eckmanns T, Gastmeier P. How many outbreaks of nosocomial infections occur in German neonatal intensive care units annually? Infection. 2014;42(1):73–8.View ArticlePubMedGoogle Scholar
  4. Voelz A, Muller A, Gillen J, Le C, Dresbach T, Engelhart S, Exner M, Bates CJ, Simon A. Outbreaks of Serratia Marcescens in neonatal and pediatric intensive care units: clinical aspects, risk factors and management. Int J Hyg Environ Health. 2010;213(2):79–87.View ArticlePubMedGoogle Scholar
  5. David MD, Weller TM, Lambert P, Fraise AP. An outbreak of Serratia Marcescens on the neonatal unit: a tale of two clones. J Hosp Infect. 2006;63(1):27–33.View ArticlePubMedGoogle Scholar
  6. Moles L, Gomez M, Heilig H, Bustos G, Fuentes S, de Vos W, Fernandez L, Rodriguez JM, Jimenez E. Bacterial diversity in meconium of preterm neonates and evolution of their fecal microbiota during the first month of life. PLoS One. 2013;8(6):e66986.View ArticlePubMedPubMed CentralGoogle Scholar
  7. Stone SP, Cooper BS, Kibbler CC, Cookson BD, Roberts JA, Medley GF, Duckworth G, Lai R, Ebrahim S, Brown EM, et al. The ORION statement: guidelines for transparent reporting of outbreak reports and intervention studies of nosocomial infection. Lancet Infect Dis. 2007;7(4):282–8.View ArticlePubMedGoogle Scholar
  8. Von Dach E, Diene SM, Fankhauser C, Schrenzel J, Harbarth S, Francois P. Comparative genomics of community-associated Methicillin-resistant Staphylococcus Aureus shows the emergence of clone ST8-USA300 in Geneva, Switzerland. J Infect Dis. 2016;213(9):1370–9.View ArticlePubMedGoogle Scholar
  9. Steppberger K, Walter S, Claros MC, Spencker FB, Kiess W, Rodloff AC, Vogtmann C. Nosocomial neonatal outbreak of Serratia Marcescens--analysis of pathogens by pulsed field gel electrophoresis and polymerase chain reaction. Infection. 2002;30(5):277–81.View ArticlePubMedGoogle Scholar
  10. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12.View ArticlePubMedPubMed CentralGoogle Scholar
  11. Serratia marcescens SMB2099 complete genome; GenBank: HG738868.1. https://www.ncbi.nlm.nih.gov/nuccore/HG738868.1. Accessed 1 Dec 2017.
  12. Gastmeier P. Serratia Marcescens: an outbreak experience. Front Microbiol. 2014;5:81.View ArticlePubMedPubMed CentralGoogle Scholar
  13. Duggan TG, Leng RA, Hancock BM, Cursons RT. Serratia Marcescens in a newborn unit--microbiological features. Pathology. 1984;16(2):189–91.View ArticlePubMedGoogle Scholar
  14. Assadian O, Berger A, Aspock C, Mustafa S, Kohlhauser C, Hirschl AM. Nosocomial outbreak of Serratia Marcescens in a neonatal intensive care unit. Infect Control Hosp Epidemiol. 2002;23(8):457–61.View ArticlePubMedGoogle Scholar
  15. Moles L, Gomez M, Jimenez E, Fernandez L, Bustos G, Chaves F, Canton R, Rodriguez JM, Del Campo R. Preterm infant gut colonization in the neonatal ICU and complete restoration 2 years later. Clin Microbiol Infect. 2015;21(10):e931–10. 936View ArticleGoogle Scholar
  16. Drell T, Lutsar I, Stsepetova J, Parm U, Metsvaht T, Ilmoja ML, Simm J, Sepp E. The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing. Gut Microbes. 2014;5(3):304–12.View ArticlePubMedPubMed CentralGoogle Scholar
  17. Aujoulat F, Roudiere L, Picaud JC, Jacquot A, Filleron A, Neveu D, Baum TP, Marchandin H, Jumas-Bilak E. Temporal dynamics of the very premature infant gut dominant microbiota. BMC Microbiol. 2014;14:325.View ArticlePubMedPubMed CentralGoogle Scholar
  18. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5(7):e177.View ArticlePubMedPubMed CentralGoogle Scholar
  19. Anagnostakis D, Fitsialos J, Koutsia C, Messaritakis J, Matsaniotis N. A nursery outbreak of Serratia Marcescens infection. Evidence of a single source of contamination. Am J Dis Child. 1981;135(5):413–4.View ArticlePubMedGoogle Scholar
  20. Archibald LK, Corl A, Shah B, Schulte M, Arduino MJ, Aguero S, Fisher DJ, Stechenberg BW, Banerjee SN, Jarvis WR. Serratia Marcescens outbreak associated with extrinsic contamination of 1% chlorxylenol soap. Infect Control Hosp Epidemiol. 1997;18(10):704–9.View ArticlePubMedGoogle Scholar
  21. Al Jarousha AM, El Qouqa IA, El Jadba AH, Al Afifi AS. An outbreak of Serratia Marcescens septicaemia in neonatal intensive care unit in Gaza City Palestine. J Hosp Infect. 2008;70(2):119–26.View ArticlePubMedGoogle Scholar
  22. Bates CJ, Pearse R. Use of hydrogen peroxide vapour for environmental control during a Serratia outbreak in a neonatal intensive care unit. J Hosp Infect. 2005;61(4):364–6.View ArticlePubMedGoogle Scholar
  23. Braver DJ, Hauser GJ, Berns L, Siegman-Igra Y, Muhlbauer B. Control of a Serratia Marcescens outbreak in a maternity hospital. J Hosp Infect. 1987;10(2):129–37.View ArticlePubMedGoogle Scholar
  24. Buffet-Bataillon S, Rabier V, Betremieux P, Beuchee A, Bauer M, Pladys P, Le Gall E, Cormier M, Jolivet-Gougeon A. Outbreak of Serratia Marcescens in a neonatal intensive care unit: contaminated unmedicated liquid soap and risk factors. J Hosp Infect. 2009;72(1):17–22.View ArticlePubMedGoogle Scholar
  25. Casolari C, Pecorari M, Fabio G, Cattani S, Venturelli C, Piccinini L, Tamassia MG, Gennari W, Sabbatini AM, Leporati G, et al. A simultaneous outbreak of Serratia Marcescens and Klebsiella Pneumoniae in a neonatal intensive care unit. J Hosp Infect. 2005;61(4):312–20.View ArticlePubMedGoogle Scholar
  26. Gillespie EE, Bradford J, Brett J, Kotsanas D. Serratia Marcescens bacteremia - an indicator for outbreak management and heightened surveillance. J Perinat Med. 2007;35(3):227–31.View ArticlePubMedGoogle Scholar
  27. Jang TN, Fung CP, Yang TL, Shen SH, Huang CS, Lee SH. Use of pulsed-field gel electrophoresis to investigate an outbreak of Serratia Marcescens infection in a neonatal intensive care unit. J Hosp Infect. 2001;48(1):13–9.View ArticlePubMedGoogle Scholar
  28. Sarvikivi E, Lyytikainen O, Salmenlinna S, Vuopio-Varkila J, Luukkainen P, Tarkka E, Saxen H. Clustering of Serratia Marcescens infections in a neonatal intensive care unit. Infect Control Hosp Epidemiol. 2004;25(9):723–9.View ArticlePubMedGoogle Scholar
  29. Pessoa-Silva CL, Hugonnet S, Pfister R, Touveneau S, Dharan S, Posfay-Barbe K, Pittet D. Reduction of health care associated infection risk in neonates by successful hand hygiene promotion. Pediatrics. 2007;120(2):e382–90.View ArticlePubMedGoogle Scholar

Copyright

© The Author(s). 2017

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