The clinical utility of next-generation sequencing in the neonatal intensive care unit

Bloodstream infection is a life-threatening complication in critically ill patients. Multi-drug resistant bacteria or fungi may increase the risk of invasive infections in hospitalized children and are difficult to treat in intensive care units. The purpose of this study was to use metagenomic next-generation sequencing (mNGS) to understand the bloodstream microbiomes of children with suspected sepsis in a pediatric intensive care unit (PICU). mNGS were performed on microbial cell-free nucleic acid from 34 children admitted to PICU, and potentially pathogenic microbes were identified. The associations of serological inflammation indicators, lymphocyte subpopulations, and other clinical phenotypes were also examined. mNGS of blood samples from children in PICU revealed potential eukaryotic microbial pathogens. The abundance of Pneumocystis jirovecii was positively correlated with a decrease in total white blood cell count and immunodeficiency. Hospital-acquired pneumonia patients showed a significant increase in blood bacterial species richness compared with community-acquired pneumonia children. The abundance of bloodstream bacteria was positively correlated with serum procalcitonin level. Microbial genome sequences from potential pathogens were detected in the bloodstream of children with suspected sepsis in PICU, suggesting the presence of bloodstream infections in these children.

Download Full-text

Neonatal Metabolic Acidosis in the Neonatal Intensive Care Unit: What Are the Genetic Causes?

Frontiers in Pediatrics ◽

10.3389/fped.2021.727301 ◽

2021 ◽

Vol 9 ◽

Author(s):

Haiyan Ma ◽

Zezhong Tang ◽

Feifan Xiao ◽

Long Li ◽

Yangfang Li ◽

...

Keyword(s):

Intensive Care ◽

Metabolic Acidosis ◽

Next Generation Sequencing ◽

Neonatal Intensive Care ◽

Treatment Options ◽

Genetic Diseases ◽

Clinical Signs ◽

Next Generation ◽

Genetic Causes ◽

Generation Sequencing

Neonatal metabolic acidosis (NMA) is a common problem, particularly in critically ill patients in neonatal intensive care units (NICUs). Complex etiologies and atypical clinical signs make diagnosis difficult; thus, it is crucial to investigate the underlying causes of NMA rapidly and provide disorder-specific therapies. Our study aims to provide an overview of the genetic causes of NMA in patients from NICUs. We performed next-generation sequencing (NGS) on neonates with NMA from January 2016 to December 2019. Clinical features, genetic diagnoses, and their effects on clinical interventions were collected for analysis. In the 354 enrolled patients, 131 (37%) received genetic diagnoses; 95 (72.5%) of them were autosomal recessively inherited diseases. Two hundred and fifteen variants spanning 57 genes were classified as pathogenic (P) or likely pathogenic (LP) in 131 patients. The leading cause was metabolic disorders due to 35 genes found in 89 patients (68%). The other 42 NMA patients (32%) with 22 genes had malformations and renal, neuromuscular, and immune-hematological disorders. Seven genes (MMUT, MMACHC, CHD7, NPHS1, OTC, IVD, and PHOX2B) were noted in more than four patients, accounting for 48.9% (64/131) of the identified P/LP variants. Forty-six diagnosed patients with uncorrected NMA died or gave up. In conclusion, 37% of neonates with metabolic acidosis had genetic disorders. Next-generation sequencing should be considered when investigating the etiology of NMA in NICUs. Based on early molecular diagnoses, valuable treatment options can be provided for some genetic diseases to achieve better outcomes.

Download Full-text

Application of Next-Generation Sequencing for Genetic Diagnosis in Neonatal Intensive Care Units: Results of a Multicenter Study in China

Frontiers in Genetics ◽

10.3389/fgene.2020.565078 ◽

2020 ◽

Vol 11 ◽

Author(s):

Tianwen Zhu ◽

Xiaohui Gong ◽

Fei Bei ◽

Li Ma ◽

Yan Chen ◽

...

Keyword(s):

Intensive Care ◽

Next Generation Sequencing ◽

Intensive Care Units ◽

Multicenter Study ◽

Neonatal Intensive Care ◽

Genetic Diagnosis ◽

Neonatal Intensive Care Units ◽

Next Generation ◽

Generation Sequencing

Download Full-text

Clinical utility of endotracheal tube cultures from neonates in a Neonatal Intensive Care Unit: Completion of an audit cycle

Journal of Infection ◽

10.1016/j.jinf.2011.04.085 ◽

2011 ◽

Vol 63 (6) ◽

pp. e44-e45

Author(s):

Peter Yew ◽

Patricia O'Hare ◽

Gordon Yip ◽

Jonathan Boyd ◽

Richard Tubman ◽

...

Keyword(s):

Intensive Care Unit ◽

Intensive Care ◽

Neonatal Intensive Care Unit ◽

Endotracheal Tube ◽

Neonatal Intensive Care ◽

Clinical Utility ◽

Audit Cycle

Download Full-text

Serratia marcescensOutbreak in a Neonatal Intensive Care Unit: New Insights from Next-Generation Sequencing Applications

Journal of Clinical Microbiology ◽

10.1128/jcm.00235-18 ◽

2018 ◽

Vol 56 (9) ◽

Cited By ~ 11

Author(s):

Christine Martineau ◽

Xuejing Li ◽

Cindy Lalancette ◽

Thérèse Perreault ◽

Eric Fournier ◽

...

Keyword(s):

Antibiotic Resistance ◽

Intensive Care ◽

Next Generation Sequencing ◽

16S Rrna ◽

Neonatal Intensive Care ◽

Next Generation ◽

Content Type ◽

Outbreak Investigations ◽

Relative Abundances ◽

Generation Sequencing

ABSTRACTSerratia marcescensis an environmental bacterium that is commonly associated with outbreaks in neonatal intensive care units (NICUs). Investigations ofS. marcescensoutbreaks require efficient recovery and typing of clinical and environmental isolates. In this study, we investigated how the use of next-generation sequencing applications, such as bacterial whole-genome sequencing (WGS) and bacterial community profiling, could improveS. marcescensoutbreak investigations. Phylogenomic links and potential antibiotic resistance genes and plasmids inS. marcescensisolates were investigated using WGS, while bacterial communities and relative abundances ofSerratiain environmental samples were assessed using sequencing of bacterial phylogenetic marker genes (16S rRNA andgyrBgenes). Typing results obtained using WGS for the 10S. marcescensisolates recovered during a NICU outbreak investigation were highly consistent with those obtained using pulsed-field gel electrophoresis (PFGE), the current standard typing method for this bacterium. WGS also allowed the identification of genes associated with antibiotic resistance in all isolates, while no plasmids were detected. Sequencing of the 16S rRNA andgyrBgenes both showed greater relative abundances ofSerratiaat environmental sampling sites that were in close contact with infected babies. Much lower relative abundances ofSerratiawere observed following disinfection of a room, indicating that the protocol used was efficient. Variations in the bacterial community composition and structure following room disinfection and among sampling sites were also identified through 16S rRNA gene sequencing. Together, results from this study highlight the potential for next-generation sequencing tools to improve and to facilitate outbreak investigations.

Download Full-text

The Psychosocial Aspects of Feeding in the Neonatal Intensive Care Unit and Beyond

Perspectives of the ASHA Special Interest Groups ◽

10.1044/2019_persp-19-00097 ◽

2019 ◽

Vol 4 (6) ◽

pp. 1507-1515

Author(s):

Lauren L. Madhoun ◽

Robert Dempster

Keyword(s):

Intensive Care Unit ◽

Intensive Care ◽

Neonatal Intensive Care Unit ◽

Hospital Discharge ◽

Neonatal Intensive Care ◽

Oral Feeding ◽

Medical Attention ◽

Primary Role ◽

Speech Language Pathologists ◽

The Family

Purpose Feeding challenges are common for infants in the neonatal intensive care unit (NICU). While sufficient oral feeding is typically a goal during NICU admission, this can be a long and complicated process for both the infant and the family. Many of the stressors related to feeding persist long after hospital discharge, which results in the parents taking the primary role of navigating the infant's course to ensure continued feeding success. This is in addition to dealing with the psychological impact of having a child requiring increased medical attention and the need to continue to fulfill the demands at home. In this clinical focus article, we examine 3 main areas that impact psychosocial stress among parents with infants in the NICU and following discharge: parenting, feeding, and supports. Implications for speech-language pathologists working with these infants and their families are discussed. A case example is also included to describe the treatment course of an infant and her parents in the NICU and after graduation to demonstrate these points further. Conclusion Speech-language pathologists working with infants in the NICU and following hospital discharge must realize the family context and psychosocial considerations that impact feeding progression. Understanding these factors may improve parental engagement to more effectively tailor treatment approaches to meet the needs of the child and family.

Download Full-text