Hostname: page-component-586b7cd67f-dsjbd Total loading time: 0 Render date: 2024-11-25T01:45:00.273Z Has data issue: false hasContentIssue false
  • English
  • Français

Evolution of the environmental microbiota of a new neonatal intensive care unit (NICU) and implications for infection prevention and control

Published online by Cambridge University Press:  28 August 2020

Philip Zachariah Open the ORCID record for Philip Zachariah [Opens in a new window] ,
Felix D. Rozenberg ,
Stephania Stump ,
Dagmara I. Moscoso ,
Ganga Krishnamurthy ,
Lisa Saiman ,
Anne-Catrin Uhlemann  and
Daniel E. Freedberg Open the ORCID record for Daniel E. Freedberg [Opens in a new window]
Philip Zachariah*
Affiliation:
Department of Pediatrics, Columbia University Irving Medical Center, New York, New York Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, New York, New York
Felix D. Rozenberg
Affiliation:
Microbiome & Pathogen Genomics Core, Department of Medicine, Columbia University Irving Medical Center, New York, New York
Stephania Stump
Affiliation:
Microbiome & Pathogen Genomics Core, Department of Medicine, Columbia University Irving Medical Center, New York, New York
Dagmara I. Moscoso
Affiliation:
Department of Medicine, Columbia University Irving Medical Center, New York, New York
Ganga Krishnamurthy
Affiliation:
Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
Lisa Saiman
Affiliation:
Department of Pediatrics, Columbia University Irving Medical Center, New York, New York Department of Infection Prevention and Control, NewYork-Presbyterian Hospital, New York, New York
Anne-Catrin Uhlemann
Affiliation:
Microbiome & Pathogen Genomics Core, Department of Medicine, Columbia University Irving Medical Center, New York, New York Department of Medicine, Columbia University Irving Medical Center, New York, New York
Daniel E. Freedberg
Affiliation:
Department of Medicine, Columbia University Irving Medical Center, New York, New York
*
Author for correspondence: Philip Zachariah, E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Objective:

To describe changes in the environmental microbiota of a new neonatal intensive care unit (NICU) and potential implications for infection prevention and control (IPC) efforts.

Design:

Prospective observational study.

Setting:

A newly constructed level IV neonatal cardiac intensive care unit (NCICU) before and after patient introduction and the original NICU prior to patient transfer.

Methods:

Environmental samples were obtained from the original NICU prior to patient transfer to a new NCICU. Serial sampling of patient rooms and provider areas of the new NICU was conducted immediately prior to patient introduction and over an 11-month study period. Microbiota at each sampling point were characterized using Illumina sequencing of the V3/V4 region of the 16S rRNA gene. Microbiota characteristics (α and β diversity and differential abundance) were compared based on time, location, and clinical factors (room-level antibiotic use and patient turnover).

Results:

An immediate increase in the environmental differential abundance of gut anaerobes were seen after patient introduction. There was an increase in the relative abundance of Staphylococcus spp, Klebsiella spp, Pseudomonas spp, and Streptococcus spp over time. The new NCICU consistently showed more diverse microbiota and remained distinct from the original NICU. The microbiota of the provider areas of the NCICU eventually formed a cluster separate from the patient rooms. Patient turnover increased room-level microbiota diversity.

Conclusion:

Microbiota characteristics of the new NICU were distinct from the original ICU despite housing similar patients. Patient and provider areas developed distinct microbiota profiles. Non–culture-based methods may be a useful adjunct to current IPC practice.

Type
Original Article
Information
Infection Control & Hospital Epidemiology , Volume 42 , Issue 2 , February 2021 , pp. 156 - 161
Check for updates
Copyright
© 2020 by The Society for Healthcare Epidemiology of America. All rights reserved.

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Brooks, B, Olm, MR, Firek, BA, et al. The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms. Microbiome 2018;6:112.CrossRefGoogle ScholarPubMed
Brooks, B, Olm, MR, Firek, BA, et al. Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. Nat Commun 2017;8:1814.CrossRefGoogle ScholarPubMed
Hourigan, SK, Subramanian, P, Hasan, NA, et al. Comparison of infant gut and skin microbiota, resistome and virulome between neonatal intensive care unit (NICU) environments. Front Microbiol 2018;9:1361.CrossRefGoogle ScholarPubMed
Hartz, LE, Bradshaw, W, Brandon, DH. Potential NICU environmental influences on the neonate’s microbiome: a systematic review. Adv Neonatal Care 2015;15:324–335.CrossRefGoogle ScholarPubMed
Patel, AL, Mutlu, EA, Sun, Y, et al. Longitudinal survey of microbiota in hospitalized preterm very-low-birth-weight infants. J Pediatr Gastroenterol Nutr 2016;62:292–303.CrossRefGoogle ScholarPubMed
ElRakaiby, MT, Gamal-Eldin, S, Amin, MA, Aziz, RK. Hospital microbiome variations as analyzed by high-throughput sequencing. OMICS 2019;23:426–438.CrossRefGoogle ScholarPubMed
Christoff, AP, Sereia, AF, Hernandes, C, de Oliveira, LF. Uncovering the hidden microbiota in hospital and built environments: new approaches and solutions. Exp Biol Med (Maywood) 2019;244:534–542.CrossRefGoogle ScholarPubMed
Lax, S, Sangwan, N, Smith, D, et al. Bacterial colonization and succession in a newly opened hospital. Sci Transl Med 2017;9.Google Scholar
Klindworth, A, Pruesse, E, Schweer, T, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 2013;41:e1.CrossRefGoogle ScholarPubMed
Weber, N, Liou, D, Dommer, J, et al. Nephele: a cloud platform for simplified, standardized and reproducible microbiome data analysis. Bioinformatics 2018;34:1411–1413.CrossRefGoogle ScholarPubMed
Ani, OE, Ekandem, GJ, Singh, SP. Specific landmarks on radiographs as diagnostic tools in determining hip diseases in the Cross River State of Nigeria. Australas Radiol 1987;31:208–211.CrossRefGoogle ScholarPubMed
DeSantis, TZ, Hugenholtz, P, Larsen, N, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006;72:5069–5072.CrossRefGoogle ScholarPubMed
Love, MI, Huber, W, Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014;15:550.CrossRefGoogle ScholarPubMed
Gritz, EC, Bhandari, V. The human neonatal gut microbiome: a brief review. Front Pediatr 2015;3:17.Google ScholarPubMed
Oberauner, L, Zachow, C, Lackner, S, Hogenauer, C, Smolle, KH, Berg, G. The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing. Sci Rep 2013;3:1413.CrossRefGoogle ScholarPubMed
Vickery, K, Deva, A, Jacombs, A, Allan, J, Valente, P, Gosbell, IB. Presence of biofilm containing viable multiresistant organisms despite terminal cleaning on clinical surfaces in an intensive care unit. J Hosp Infect 2012;80:52–55.CrossRefGoogle Scholar
Poza, M, Gayoso, C, Gomez, MJ, et al. Exploring bacterial diversity in hospital environments by GS-FLX titanium pyrosequencing. PLoS One 2012;7:e44105.Google ScholarPubMed
Zou, ZH, Liu, D, Li, HD, et al. Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units. Ann Clin Microbiol Antimicrob 2018;17:9.CrossRefGoogle ScholarPubMed