Dataset Information

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.

SUBMITTER: Bokulich NA

PROVIDER: S-EPMC3719657 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature

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Surface microbes in the neonatal intensive care unit: changes with routine cleaning and over time.

Bokulich Nicholas A NA Mills David A DA Underwood Mark A MA

Journal of clinical microbiology 20130605 8

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 ...[more]

PMID: 23740726

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Project description:BACKGROUND: The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonates via conventional broad-spectrum antibiotic treatment. We hypothesize the built environment (BE), specifically room surfaces frequently touched by humans, is a predominant source of colonizing microbes in the gut of premature VLBW infants. Here, we present the first matched fecal-BE time series analysis of two preterm VLBW neonates housed in a neonatal intensive care unit (NICU) over the first month of life. RESULTS: Fresh fecal samples were collected every 3 days and metagenomes sequenced on an Illumina HiSeq2000 device. For each fecal sample, approximately 33 swabs were collected from each NICU room from 6 specified areas: sink, feeding and intubation tubing, hands of healthcare providers and parents, general surfaces, and nurse station electronics (keyboard, mouse, and cell phone). Swabs were processed using a recently developed 'expectation maximization iterative reconstruction of genes from the environment' (EMIRGE) amplicon pipeline in which full-length 16S rRNA amplicons were sheared and sequenced using an Illumina platform, and short reads reassembled into full-length genes. Over 24,000 full-length 16S rRNA sequences were produced, generating an average of approximately 12,000 operational taxonomic units (OTUs) (clustered at 97% nucleotide identity) per room-infant pair. Dominant gut taxa, including Staphylococcus epidermidis, Klebsiella pneumoniae, Bacteroides fragilis, and Escherichia coli, were widely distributed throughout the room environment with many gut colonizers detected in more than half of samples. Reconstructed genomes from infant gut colonizers revealed a suite of genes that confer resistance to antibiotics (for example, tetracycline, fluoroquinolone, and aminoglycoside) and sterilizing agents, which likely offer a competitive advantage in the NICU environment. CONCLUSIONS: We have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. The approach enabled identification of discrete ICU reservoirs of microbes that also colonized the infant gut and provided evidence for the presence of certain organisms in the room prior to their detection in the gut.

Project description:BackgroundEarly reports suggest the number of cardiac intensive care unit (CICU) patients with primary noncardiac diagnoses is rising in the United States, but no national data currently exist. We examined changes in primary noncardiac diagnoses among elderly patients admitted to a CICU during the past decade.Methods and resultsUsing 2003 to 2013 Medicare data, we grouped elderly patients admitted to CICUs into 2 categories based on principal diagnosis at discharge: (1) primary noncardiac diagnoses and (2) primary cardiac diagnoses. We examined changes in patient demographics, comorbidities, procedure use, and risk-adjusted in-hospital mortality. Among 3.4 million admissions with a CICU stay, primary noncardiac diagnoses rose in prevalence from 38.0% to 51.7% between 2003 and 2013. The fastest rising primary noncardiac diagnoses were infectious diseases (7.8%-15.1%) and respiratory diseases (6.0%-7.6%; P<0.001 for both), whereas the fastest declining primary cardiac diagnosis was coronary artery disease (32.3%-19.0%; P<0.001). Simultaneously, the prevalence of both cardiovascular and noncardiovascular comorbidities rose: heart failure (13.9%-34.4%), pulmonary vascular disease (1.2%-7.1%), valvular heart disease (5.0%-9.8%), and renal failure (7.1%-19.6%; P<0.001 for all). As compared with those with primary cardiac diagnoses, elderly CICU patients with primary noncardiac diagnoses had higher rates of noncardiac procedure use and risk-adjusted in-hospital mortality (P<0.001 for all). Risk-adjusted in-hospital mortality declined slightly in the overall cohort from 9.3% to 8.9% (P<0.001).ConclusionsMore than half of all elderly patients with a CICU stay across the United States now have primary noncardiac diagnoses at discharge. These patients receive different types of care and have worse outcomes than patients with primary cardiac diagnoses. Our work has important implications for the development of appropriate training and staffing models for the future critical care workforce.

Dataset Information

Surface microbes in the neonatal intensive care unit: changes with routine cleaning and over time.

Publications

Surface microbes in the neonatal intensive care unit: changes with routine cleaning and over time.

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