Surface Microbes in the Neonatal Intensive Care Unit: Changes with Routine Cleaning and over Time

Abstract

Premature infants in neonatal intensive care units (NICUs) are highly susceptible to infection due to the immaturity of their immune systems, and nosocomial infections are a significant risk factor for death and poor neurodevelopmental outcome in this population. To investigate the impact of cleaning within a NICU, a high-throughput short-amplicon-sequencing approach was used to profile bacterial and fungal surface communities before and after cleaning. Intensive cleaning of surfaces in contact with neonates decreased the total bacterial load and the percentage of Streptococcus species with similar trends for total fungal load and Staphylococcus species; this may have clinical relevance since staphylococci and streptococci are the most common causes of nosocomial NICU infections. Surfaces generally had low levels of other taxa containing species that commonly cause nosocomial infections (e.g., Enterobacteriaceae) that were not significantly altered with cleaning. Several opportunistic yeasts were detected in the NICU environment, demonstrating that these NICU surfaces represent a potential vector for spreading fungal pathogens. These results underline the importance of routine cleaning as a means of managing the microbial ecosystem of NICUs and of future opportunities to minimize exposures of vulnerable neonates to potential pathogens and to use amplicon-sequencing tools for microbial surveillance and hygienic testing in hospital environments. P remature infants in neonatal intensive care units (NICUs) are highly vulnerable to infections due to the immaturity of virtually every aspect of their innate and adaptive immune systems. The importance of hospital surfaces and the cleaning of these surfaces in interrupting outbreaks of specific organisms in NICUs (1, 2) and in eliminating reservoirs of potential pathogens (3-5) has been emphasized. However, most studies to date have relied on culture-based techniques, which can give incomplete and biased assessments of mixed microbial communities (6).The increasing ease and decreasing costs of high-throughput short-amplicon-sequencing technologies are propelling efforts to describe the microbial communities of surfaces on a massive scale (7). By parallel sequencing of short amplicons, typically 16S rRNA genes in bacteria and internal transcribed spacer (ITS) domains in fungi (8), it is possible to comprehensively profile the microbial composition of diverse environments. Microbial communities in intensive care units (ICUs) (9), hospitals (10), public restrooms (11), wineries (12), and office spaces (13) have been explored using high-throughput amplicon sequencing, advancing our knowledge of microbial trafficking and colonization in these systems. A recent report on bacterial communities on the surfaces in two NICUs demonstrated significant diversity and supported the hypothesis that colonies of pathogens on NICU surfaces may increase the risk of infection for premature infants (14).Stringent cleaning protocols for the surfaces in NICUs have been in place for many years, ...

Potential NICU Environmental Influences on the Neonate's Microbiome

“…Four studies examined several aspects of the NICU environment in an effort to better understand how they might impact the infant microbiome. 16,29,30,34 Specific measures utilized within these studies included sampling before and after cleaning with antibacterial wipes, 16 cold versus warm spot sampling in incubators, 34 predominant NICU organisms living within specific nurseries regardless of routine cleaning and hand washing, 29 and lack of hand washing and routine cleaning before and after implementing standard precautions. 30 Microbiome samples of environmental surfaces revealed complex and diverse environments and included species associated with nosocomial infections common in the neonatal population.…”

“…Every NICU has its own genera of microbes which can include commensal and pathogenic organisms. 16,17 With the NICU genera as the context for microbiome development, the infant’s ongoing interaction with multiple healthcare providers and caregiving processes have the potential to impact microbial colonization. A recent study showed that the risk of acquiring nasal colonization with coagulase-negative Staphylococcus (CoNS) for all neonates admitted in a NICU was 55.9%.…”

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City

“…Studies of the built environment have sought to understand how building architecture and engineering, in conjunction with human behavior, may influence the microbes that we encounter during our time spent indoors (which represents 87% of our time on average [8]). Such studies have aimed at capturing the microbial communities associated with both air and surfaces in homes (9, 10), hospitals (11, 12), classrooms (13), offices (14, 15), and restrooms (16), as well as community assemblages within plumbing systems (17–19) and an expanding set of other indoor microhabitats.…”

Pilot study of sources and concentrations of size-resolved airborne particles in a neonatal intensive care unit

“…The importance of surfaces and their cleaning for controlling outbreaks of specific organisms and eradicating sources of potential pathogens in NICUs has been highlighted in a few prior studies [9][10][11]. Other NICU environmental parameters previously studied in relation to prevention of nosocomial infections have included noise, illumination, medical equipment hygiene, microbes on surfaces, overcrowding, and the importance of inhibiting free mixing across rooms [11][12][13][14][15][16].…”