Outbreak of Dirkmeia churashimaensis Fungemia in a Neonatal Intensive Care Unit, India.
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ABSTRACT:
SUBMITTER: Chowdhary A
PROVIDER: S-EPMC7101094 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Lodderomyces elongisporus is a recently emerging yeast pathogen predominantly reported in adult patients who had immunosuppression and/or intravenous access devices. Here, we report a fungemia outbreak caused by L. elongisporus in a neonatal intensive care unit (NICU) in Delhi, India, from September 2021 to February 2022. All 10 neonates had low birthweight, and nine of the patients survived after amphotericin B treatment. Whole-genome sequence analyses of the patient isolates as well as those from other sources in India grouped them into two clusters: one cluster consists of isolates exclusively from stored apples and the other cluster includes isolates from patients, clinical environments, and stored apples. All outbreak strains from patients were closely related to each other and showed highly similar heterozygosity patterns across all 11 major scaffolds. While overall very similar, strains from the inanimate environment of the same neonatal intensive care unit showed loss of heterozygosity at scaffold 2 (NW_001813676) compared to the patient strains. Interestingly, evidence for recombination was found in all samples. All clinical strains were susceptible to 10 tested antifungal drugs, and comparisons with strains with high fluconazole MICs derived from the surface of stored apples revealed significant genome divergence between the clinical and apple surface strains, including 119 nonsynonymous single nucleotide polymorphisms (SNPs) in 24 triazole resistance-related genes previously found in other Candida spp. Together, our results indicate significant diversity, recombination, and persistence in the hospital setting and a high rate of evolution in this emerging yeast pathogen. IMPORTANCE Lodderomyces elongisporus was initially considered a teleomorph of Candida parapsilosis. However, DNA sequence analyses revealed it as a distinctive species. Invasive infections due to L. elongisporus have been reported globally. We report an outbreak of fungemia due to L. elongisporus in a NICU affecting 10 preterm, low-birthweight neonates during a period of 6 months. The outbreak investigation identified two environmental sites, the railing and the temperature panel of the neonate open care warmer, harboring L. elongisporus. Whole-genome sequencing confirmed that the neonate isolates were closely related to each other whereas strains from the inanimate clinical environment were related to clinical strains but showed a marked loss of heterozygosity. Further, L. elongisporus strains recovered previously from the surface of stored apples showed high fluconazole MICs and alterations in triazole resistance-related genes. Genome-wide SNP comparisons revealed recombination as an important source for genomic diversity during adaptation of L. elongisporus to different environments.
| S-EPMC10294660 | biostudies-literature
Project description:AimTo investigate the frequency, etiology, and current management strategies for diarrhea in newborn.MethodsRetrospective, nationwide study involving 5801 subjects observed in neonatal intensive care units during 3 years. The main anamnesis and demographic characteristics, etiology and characteristics of diarrhea, nutritional and therapeutic management, clinical outcomes were evaluated.ResultsThirty-nine cases of diarrhea (36 acute, 3 chronic) were identified. The occurrence rate of diarrhea was 6.72 per 1000 hospitalized newborn. Etiology was defined in 29 of 39 newborn (74.3%): food allergy (20.5%), gastrointestinal infections (17.9%), antibiotic-associated diarrhea (12.8%), congenital defects of ion transport (5.1%), withdrawal syndrome (5.1%), Hirschsprung's disease (2.5%), parenteral diarrhea (2.5%), cystic fibrosis (2.5%), and metabolic disorders (2.5%). Three patients died due to complications related to diarrhea (7.7%). In 19 of 39 patients (48.7%), rehydration was performed exclusively by the enteral route.ConclusionDiarrhea in neonates is a challenging clinical condition due to the possible heterogeneous etiologies and severe outcomes. Specific guidelines are advocated in order to optimize management of diarrhea in this particular setting.
| S-EPMC2880780 | biostudies-literature
Project description:Infectious diseases outbreaks are a cause of significant morbidity and mortality among hospitalized patients. Infants admitted to the neonatal intensive care unit (NICU) are particularly vulnerable to infectious complications during hospitalization. Thus, rapid recognition of and response to outbreaks in the NICU is essential. At Rush University Medical Center, whole-genome sequencing (WGS) has been utilized since early 2016 as an adjunctive method for outbreak investigations. The use of WGS and potential lessons learned are illustrated for 3 different NICU outbreak investigations involving methicillin-resistant Staphylococcus aureus (MRSA), group B Streptococcus (GBS), and Serratia marcescens. WGS has contributed to the understanding of the epidemiology of outbreaks in our NICU, and it has also provided further insight in settings of unusual diseases or when lower-resolution typing methods have been inadequate. WGS has emerged as the new gold standard for evaluating strain relatedness. As barriers to implementation are overcome, WGS has the potential to transform outbreak investigation in healthcare settings.
| S-EPMC9495531 | biostudies-literature
Project description:Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak.Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools.The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters.The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates.
| S-EPMC4594962 | biostudies-literature
Project description:Our aim was to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routinely used in the microbiology laboratory for bacterial identification, for bacterial typing in the setting of extended spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KP) outbreak in the neonatal intensive care unit (NICU). Isolates from a 2011 outbreak in the NICU were retrieved from frozen stocks and analyzed by MALDI-TOF. The MALDI typing was compared with core genome multilocus sequence typing (cg-MLST). MALDI typing divided the 33 outbreak isolates into 2 clones: sequence type (ST)-290 and 405. These results were in complete agreement with cg-MLST results. The differentiation of the outbreak isolates into two clones correlated with the patients' location in the NICU, but also with their place of residence.Conclusion: Here, we show that MALDI-TOF MS, which has been integrated into the microbiology laboratory workflow for microbial species identification, can be secondarily used for epidemiological typing at no added cost. What is Known: • Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now routinely used in the microbiology laboratory for bacterial identification What is New: • MALDI typing was used for outbreak investigation in the NICU and divided the outbreak isolates into two clones • MALDI-TOF MS may be secondarily used for epidemiological typing at no added cost.
| S-EPMC7283987 | biostudies-literature
Project description:Coagulase-negative staphylococci (CoNS) have become the leading cause of bloodstream infections (BSIs) in intensive care units (ICUs), particularly in premature neonates. Vancomycin-intermediate heteroresistant CoNS (hVICoNS) have been identified as sources of BSIs worldwide, and their potential to emerge as significant pathogens in the neonatal ICU (NICU) remains uncertain. This study describes the molecular epidemiology of an outbreak of vancomycin-heteroresistant (hV) Staphylococcus epidermidis central-line-associated BSI (CLABSI) in a single tertiary care NICU and compares it to a second tertiary care NICU that had not been associated with an outbreak. Between November 2009 and April 2014, 119 S. epidermidis CLABSIs were identified in two tertiary care NICUs in Quebec, Canada. Decreased vancomycin susceptibility was identified in about 88% of all collected strains using Etest methods. However, discrepancies were found according to the Etest and population analysis profiling-area under the concentration-time curve (PAP-AUC) methods used. All strains were susceptible to linezolid, and a few isolates were nonsusceptible to daptomycin. Great genetic diversity was observed within the collection, with 31 pulsed-field gel electrophoresis (PFGE) patterns identified. The outbreak strains were all determined to be heteroresistant to vancomycin and were polyclonal. The study identified two major clones, PFGE patterns E and G, which were found in both NICUs across the 5-year study period. This suggests the persistence of highly successful clones that are well adapted to the hospital environment. hV S. epidermidis seems more common than currently realized in the NICU, and certain hV S. epidermidis clones can become endemic to the NICU. The reservoirs for these clones remain unknown at this time, and identification of the reservoirs is needed to better understand the impact of hV S. epidermidis in the NICU and to inform infection prevention strategies. In addition, there is a need to investigate and validate hV determination protocols for different species of CoNS.
| S-EPMC5038295 | biostudies-literature
Project description:We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference.
| S-EPMC7021795 | biostudies-literature
Project description:Serratia marcescens is an environmental bacterium that is commonly associated with outbreaks in neonatal intensive care units (NICUs). Investigations of S. marcescens outbreaks 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 improve S. marcescens outbreak investigations. Phylogenomic links and potential antibiotic resistance genes and plasmids in S. marcescens isolates were investigated using WGS, while bacterial communities and relative abundances of Serratia in environmental samples were assessed using sequencing of bacterial phylogenetic marker genes (16S rRNA and gyrB genes). Typing results obtained using WGS for the 10 S. marcescens isolates 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 and gyrB genes both showed greater relative abundances of Serratia at environmental sampling sites that were in close contact with infected babies. Much lower relative abundances of Serratia were 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.
| S-EPMC6113457 | biostudies-literature
Project description:BACKGROUND:Variation in healthcare delivery and outcomes in neonatal intensive care units (NICUs) may be partly explained by differences in safety culture. OBJECTIVE:To describe NICU care giver assessments of safety culture, explore variability within and between NICUs on safety culture domains, and test for association with care giver characteristics. METHODS:NICU care givers in 12 hospitals were surveyed using the Safety Attitudes Questionnaire (SAQ), which has six scales: teamwork climate, safety climate, job satisfaction, stress recognition, perception of management and working conditions. Scale means, SDs and percent positives (percent agreement) were calculated for each NICU. RESULTS:There was substantial variation in safety culture domains among NICUs. Composite mean score across the six domains ranged from 56.3 to 77.8 on a 100-point scale and NICUs in the top four NICUs were significantly different from the bottom four (p<0.001). Across the six domains, respondent assessments varied widely, but were least positive on perceptions of management (3%-80% positive; mean 33.3%) and stress recognition (18%-61% positive; mean 41.3%). Comparisons of SAQ scale scores between NICUs and a previously published adult ICU cohort generally revealed higher scores for NICUs. Composite scores for physicians were 8.2 (p=0.04) and 9.5 (p=0.02) points higher than for nurses and ancillary personnel. CONCLUSION:There is significant variation and scope for improvement in safety culture among these NICUs. The NICU variation was similar to variation in adult ICUs, but NICU scores were generally higher. Future studies should validate whether safety culture measured with the SAQ correlates with clinical and operational outcomes in NICUs.
| S-EPMC3845658 | biostudies-literature