Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey
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ABSTRACT:
PROVIDER: PRJEB76591 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13258649.fastq.gz | Fastqsanger.gz | |||
| ERR13258650.fastq.gz | Fastqsanger.gz | |||
| ERR13258651.fastq.gz | Fastqsanger.gz | |||
| ERR13258652.fastq.gz | Fastqsanger.gz | |||
| ERR13258654.fastq.gz | Fastqsanger.gz |
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Project description:Pichia kudriavzevii causes life-threatening infections in immune compromised hosts including hospitalized neonates. This pathogen is resistant to fluconazole while uncommon, strains resistant to multiple antifungal drugs voriconazole, amphotericin B and echinocandins have been reported in healthcare environments. Understanding how P. kudriavzevii spread, persist, and adapt to healthcare settings could help us develop better management strategies. In this study, whole genome sequencing identifies multiple outbreaks of bloodstream infections caused by P. kudriavzevii in a single neonatal intensive care unit (NICU) over five years. Interestingly, two genetically diverse clusters of P. kudriavzevii population showed frequent loss of heterozygosity (LOH) events between two temporal samples. The first outbreak cluster (during 2015-16) showed LOH at chromosomes 1, 4 and 5 and the other outbreak cluster (year 2020) exhibited marked LOH at chromosome 2. The circulation of two separate strain clusters of P. kudriavzevii suggests nosocomial transmission in the NICU in different time periods. Further, to evaluate the gene expression difference between isolates from two clusters, we compared the transcriptomic profiles of three isolates of cluster I and II and exhibiting distinct fluconazole MICs. While no difference was found at the azole target gene ERG11 or the ATP-binding cassette (ABC) transporter genes, differences in transcript abundance were found between the two isolates in genes coding for cell division and filamentation, repressor of ABC gene, FCR1 and ERG5 gene involved in ergosterol biosynthesis pathway. Our study indicates significant diversity, persistence, and rapid evolution of P. kudriavzevii within a single NICU.
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Project description:In the last decade, Candida krusei has caused multiple outbreaks of candidemia in Neonatal Intensive Care Units (NICUs) in low-and middle-income countries such as Brazil, India, and South Africa. In India, C. krusei ranks as the sixth cause of candidemia in adult ICUs. Additionally, sporadic outbreaks of nosocomial candidemia in the NICUs are widely reported from India. However, the genetic population of C. krusei causing outbreaks remain largely unknown. In the present study, we used whole genome sequencing to examine the genetic structure of C. krusei population causing candidemia spanning a period of five years (2015-20) in a single NICU in Delhi, India. Further, to evaluate the mechanisms of azole antifungal resistance in C. krusei, we compare the transcriptomic profiles of fluconazole susceptible (FLU-S) and resistant (FLU-R) isolates. Transcriptomic assay was performed in logarithmically growing C. krusei clinical isolates 123/P/19 and 1390/P/18 strains. STAR aligner v.2.5.2b was used to sequence the trimmed reads with the specified reference genome of P. kudriavzevii to determine the unique gene hit counts. A total of 178 genes were differentially expressed by at least 1.5-fold in 1390/P/18 as compared to 123/P/19 isolate. Principal component analysis (PCA) of normalized read counts also depicted almost similar transcriptomic profile between the two C. krusei strains with 53 % variance at principal component 1. Out of 178 differentially expressed genes, 72 were up-regulated and 106 were down-regulated in 1390/P/18 strain compared to 123/P/19 strain. Functionally, genes associated with transport (n=10), mitogen activated protein kinase signaling (MAPK; n=8), transcription factors (TF; n=6) and ergosterol biosynthesis (n=3) were expressed differentially.
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Project description:Background. The Staphylococcus capitis NRCS-A strain has emerged as a global cause of late-onset sepsis associated with outbreaks in neonatal intensive care units (NICUs) whose transmission is incompletely understood.Methods. Demographic and clinical data for 45 neonates with S. capitis and 90 with other coagulase-negative staphylococci (CoNS) isolated from sterile sites were reviewed, and clinical significance was determined. S. capitis isolated from 27 neonates at 2 hospitals between 2017 and 2022 underwent long-read (ONT) (n=27) and short-read (Illumina) sequencing (n=18). These sequences were compared with S. capitis sequenced from blood culture isolates from other adult and paediatric patients in the same hospitals (n=6), S. capitis isolated from surface swabs (found in 5/150 samples), rectal swabs (in 2/69 samples) in NICU patients and NICU environmental samples (in 5/114 samples). Reads from all samples were mapped to a hybrid assembly of a local sterile site strain, forming a complete UK NRCS-A reference genome, for outbreak analysis and comparison with 826 other S. capitis from the UK and Germany.Results. S. capitis bacteraemia was associated with increased length of NICU stay at sampling (median day 22 vs day 12 for other CoNS isolated; P=0.05). A phylogeny of sequenced S. capitis revealed a cluster comprised of 25/27 neonatal sterile site isolates and 3/5 superficial, 2/2 rectal and 1/5 environmental isolates. No isolates from other wards belonged to this cluster. Phylogenetic comparison with published sequences confirmed that the cluster was NRCS-A outbreak strain but found a relatively high genomic diversity (mean pairwise distance of 84.9 SNPs) and an estimated NRCS-A S. capitis molecular clock of 5.1 SNPs/genome/year (95% credibility interval 4.3-5.9). The presence of S. capitis in superficial cultures did not correlate with neonatal bacteraemia, but both neonates with rectal NRCS-A S. capitis carriage identified also experienced S. capitis bacteraemia.Conclusions. S. capitis bacteraemia occurred in patients with longer NICU admission than other CoNS. Genomic analysis confirms clinically significant infections with the NRCS-A S. capitis strain, distinct from non-NICU clinical samples. Multiple introductions of S. capitis, rather than prolonged environmental persistence, were seen over 5 years of infections.
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Project description:Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.
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Project description:An atypical pattern of neonatal sepsis, characterized by persistent positive blood culture despite effective antimicrobial therapy, has been correlated with adverse outcomes. However, previous studies focused only on coagulate-negative staphylococcus infection.All episodes of persistent bloodstream infection (BSI), defined as 3 or more consecutive positive blood cultures with the same bacterial species, at least two of them 48 hours apart, during a single sepsis episode, were enrolled over an 8-year period in a tertiary level neonatal intensive care unit. These cases were compared with all non-persistent BSI during the same period.We identified 81 episodes of persistent BSI (8.5% of all neonatal late-onset sepsis) in 74 infants, caused by gram-positive pathogens (n=38, 46.9%), gram-negative pathogens (n=21, 25.9%), fungus (n=20, 24.7%) and polymicrobial bacteremia (n=2, 2.5%). Persistent BSI does not differ from non-persistent BSI in most clinical characteristics and patient demographics, but tends to have a prolonged septic course, longer duration of feeding intolerance and more frequent requirement of blood transfusions. No difference was observed for death attributable to infection (9.8% vs. 6.5%), but neonates with persistent BSI had significantly higher rates of infectious complications (29.6% vs. 9.2%, P < 0.001), death from all causes (21.6% vs. 11.7%, P = 0.025), and duration of hospitalization among survivors [median (interquartile range): 80.0 (52.5-117.5) vs. 64.0 (40.0-96.0) days, P = 0.005] than those without persistent BSI.Although persistent BSI does not contribute directly to increased mortality, the associated morbidities, infectious complications and prolonged septic courses highlight the importance of aggressive treatment to optimize outcomes.
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