scholarly journals Influence of the Incubator as Direct Patient Environment on Bacterial Colonization of Neonates

2021 ◽  
Vol 9 (12) ◽  
pp. 2533
Author(s):  
Isabel Lange ◽  
Birgit Edel ◽  
Kristin Dawczynski ◽  
Hans Proquitté ◽  
Mathias W. Pletz ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neonatal Intensive Care ◽  
Low Birthweight ◽  
Bacterial Colonization ◽  
Bacterial Species ◽  
Neonatal Intensive Care Units ◽  
Whole Genome ◽  
Very Low Birthweight Infants ◽  
Healthcare Associated

Background: Preventing healthcare-associated infections (HAI) in neonatal intensive care units is a challenge of highest priority. For further insight into the incubator as direct patient environment and potential source for contamination, we present data correlating microbiological samples of very low birthweight infants in the form of colonization results of surveillance screenings with samples of their associated incubator in this study. Methods: Samples were taken via rectal and throat swabs of neonates as well as Polywipe® sponges for the incubator. If the same bacterial species was found in corresponding neonate and incubator samples, whole genome sequencing via Illumina technology was performed. Results: 52 microbiological species matches were found, and 30 matches were sequenced where we found 26 clonal pairs (12 E. faecalis, 10 S. aureus, 2 E. coli, 1 E. cloacae, and 1 E. faecium). Conclusion: The combinations of measurements of weekly screenings swabs, probing of surfaces with Polywipes®, and whole genome sequencing showed transmissions of microorganism and risk for potential non-physiological colonization of neonatal infants.

scholarly journals 1212. Whole Genome Sequencing for High-Resolution Methicillin-Resistant Staphylococcus aureus Outbreaks Tracing in Neonatal Intensive Care Units and In silico Resistance and Virulence Markers Detection

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S367-S367
Author(s):  
Geraldine Durand ◽  
Fabien Javerliat ◽  
Michele Bes ◽  
Frédéric Laurent ◽  
Francois Vandenesch ◽  
...  
Keyword(s):  
Intensive Care ◽  
High Resolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
In Silico ◽  
Neonatal Intensive Care ◽  
Neonatal Intensive Care Units ◽  
Whole Genome ◽  
Virulence Markers ◽  
Main Cluster

Abstract Background The French National Reference Center for Staphylococci used whole genome sequencing (WGS) to investigate outbreaks due to a virulent MRSA clone containing the toxic shock syndrome toxin-1 (TSST-1+, sequence type 5, Geraldine clone) increasingly reported in neonatal intensive care units (ICUs). Methods We analyzed 48 isolates previously characterized by spa typing: 31 isolates from outbreak 1 (infected or colonized patients, healthcare workers carriage and environment), 12 isolates from four distinct outbreaks (2, 3, 4, and 5) that occurred in geographically independent neonatal ICUs, and five sporadic strains. We performed WGS using a de novo assembly approach to perform comparisons between isolates (EpiSeq®, bioMérieux). A phylogenetic analysis was constructed by comparing single nucleotide variations (SNVs) in 2020 core-genes using a cutoff of 40 SNVs for defining isolates belonging to the same transmission cluster. We detected in silico resistance and virulence markers using the same bioinformatic pipeline. Results For outbreak 1, 25/31 isolates with two distinct but related spa types t002 and t111 were highly related (<13 SNVs), suggesting the transmission of the same strain; 6/31 isolates were genetically distinct (>80 SNVs) from the previous cluster of 25 isolates suggesting their origin from separate sources. Interestingly the three isolates of outbreak 2 with a spa t111 differed by less than 22 SNVs from the main cluster of the 25 isolates of outbreak 1. This suggested origin from the same transmission cluster. The other three outbreaks showing respectively a spa t002 for outbreak 3 and outbreak 4 and a spa t045 for outbreak 5 were not affiliated to the main cluster of outbreak 1. The isolates carry numerous virulence factors (including TSST-1) and resistance markers confering a peculiar antibiotic resistance profile to the Geraldine clone. Conclusion WGS provides the resolution power to reveal unsuspected transmission events not indicated by conventional methods (different spa type). Based on its high resolution WGS is an all in one tool for epidemiology, virulence and resistance analysis. It really transforms outbreak management and infection control practice for an early response and should replace conventional methods for detection of MRSA transmission. Disclosures G. Durand, bioMérieux: Employee, Salary. F. Javerliat, bioMérieux: Employee, Salary.

scholarly journals Rapid Whole-Genome Sequencing for Genetic Disease Diagnosis in Neonatal Intensive Care Units

2012 ◽  
Vol 4 (154) ◽  
pp. 154ra135-154ra135 ◽  
Author(s):  
C. J. Saunders ◽  
N. A. Miller ◽  
S. E. Soden ◽  
D. L. Dinwiddie ◽  
A. Noll ◽  
...  
Keyword(s):  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Intensive Care Units ◽  
Genome Sequencing ◽  
Genetic Disease ◽  
Neonatal Intensive Care ◽  
Disease Diagnosis ◽  
Neonatal Intensive Care Units ◽  
Whole Genome

scholarly journals A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kathy E. Raven ◽  
Sophia T. Girgis ◽  
Asha Akram ◽  
Beth Blane ◽  
Danielle Leek ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Dna Extraction ◽  
Genome Sequencing ◽  
Clinical Microbiology ◽  
Bacterial Species ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Library Preparation ◽  
Simultaneous Processing ◽  
Antimicrobial Resistance Gene

AbstractWhole-genome sequencing is likely to become increasingly used by local clinical microbiology laboratories, where sequencing volume is low compared with national reference laboratories. Here, we describe a universal protocol for simultaneous DNA extraction and sequencing of numerous different bacterial species, allowing mixed species sequence runs to meet variable laboratory demand. We assembled test panels representing 20 clinically relevant bacterial species. The DNA extraction process used the QIAamp mini DNA kit, to which different combinations of reagents were added. Thereafter, a common protocol was used for library preparation and sequencing. The addition of lysostaphin, lysozyme or buffer ATL (a tissue lysis buffer) alone did not produce sufficient DNA for library preparation across the species tested. By contrast, lysozyme plus lysostaphin produced sufficient DNA across all 20 species. DNA from 15 of 20 species could be extracted from a 24-h culture plate, while the remainder required 48–72 h. The process demonstrated 100% reproducibility. Sequencing of the resulting DNA was used to recapitulate previous findings for species, outbreak detection, antimicrobial resistance gene detection and capsular type. This single protocol for simultaneous processing and sequencing of multiple bacterial species supports low volume and rapid turnaround time by local clinical microbiology laboratories.

Identifying Genetic Determinants of Atopic Dermatitis and Bacterial Colonization Using Whole Genome Sequencing

2015 ◽  
Vol 135 (2) ◽  
pp. AB391 ◽  
Author(s):  
Rasika A. Mathias ◽  
Sameer Chavan ◽  
Kruthika R. Iyer ◽  
Nicholas M. Rafaels ◽  
Meher Boorgula ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Colonization ◽  
Whole Genome ◽  
Genetic Determinants

scholarly journals Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements—identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland

BMJ Open ◽  
2018 ◽  
Vol 8 (2) ◽  
pp. e021823 ◽  
Author(s):  
Tanja Stadler ◽  
Dominik Meinel ◽  
Lisandra Aguilar-Bultet ◽  
Jana S Huisman ◽  
Ruth Schindler ◽  
...  
Keyword(s):  
Observational Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Mobile Genetic Elements ◽  
University Hospital ◽  
Whole Genome ◽  
Hospital Acquired Infections ◽  
Genetic Elements ◽  
Hospital Acquired

IntroductionExtended-spectrum beta-lactamases (ESBL)-producing Enterobacteriaceae were first described in relation with hospital-acquired infections. In the 2000s, the epidemiology of ESBL-producing organisms changed as especially ESBL-producingEscherichia coliwas increasingly described as an important cause of community-acquired infections, supporting the hypothesis that in more recent years ESBL-producing Enterobacteriaceae have probably been imported into hospitals rather than vice versa. Transmission of ESBL-producing Enterobacteriaceae is complicated by ESBL genes being encoded on self-transmissible plasmids, which can be exchanged among the same and different bacterial species. The aim of this research project is to quantify hospital-wide transmission of ESBL-producing Enterobacteriaceae on both the level of bacterial species and the mobile genetic elements and to determine if hospital-acquired infections caused by ESBL producers are related to strains and mobile genetic elements predominantly circulating in the community or in the healthcare setting. This distinction is critical in prevention since the former emphasises the urgent need to establish or reinforce antibiotic stewardship programmes, and the latter would call for more rigorous infection control.Methods and analysisThis protocol presents an observational study that will be performed at the University Hospital Basel and in the city of Basel, Switzerland. ESBL-producing Enterobacteriaceae will be collected from any specimens obtained by routine clinical practice or by active screening in both inpatient and outpatient settings, as well as from wastewater samples and foodstuffs, both collected monthly over a 12-month period for analyses by whole genome sequencing. Bacterial chromosomal, plasmid and ESBL-gene sequences will be compared within the cohort to determine genetic relatedness and migration between humans and their environment.Ethics and disseminationThis study has been approved by the local ethics committee (Ethikkommission Nordwest-und Zentralschweiz) as a quality control project (Project-ID 2017–00100). The results of this study will be published in peer-reviewed medical journals, communicated to participants, the general public and all relevant stakeholders.

scholarly journals Are Many Patients Diagnosed With Healthcare-associated Clostridioides difficile Infections Colonized With the Infecting Strain on Admission?

2019 ◽  
Vol 69 (10) ◽  
pp. 1801-1804 ◽  
Author(s):  
Melany Gonzalez-Orta ◽  
Carlos Saldana ◽  
Yilen Ng-Wong ◽  
Jennifer Cadnum ◽  
Annette Jencson ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Acute Care ◽  
Genome Sequencing ◽  
Acute Care Hospital ◽  
Whole Genome ◽  
Care Hospital ◽  
Clostridioides Difficile ◽  
Healthcare Associated

Abstract In a cohort of 480 patients admitted to an acute care hospital, 68 (14%) had positive perirectal cultures for toxigenic Clostridioides difficile on admission. Of the 11 patients (2%) diagnosed with healthcare-associated C. difficile infections, 3 (27%) had genetically related admission and infection isolates, based on whole-genome sequencing.

scholarly journals Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm

2020 ◽  
Vol 8 (6) ◽  
pp. 855 ◽  
Author(s):  
Alexandra Irrgang ◽  
Natalie Pauly ◽  
Bernd-Alois Tenhagen ◽  
Mirjam Grobbel ◽  
Annemarie Kaesbohrer ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Multidrug Resistant ◽  
Meat Production ◽  
Whole Genome ◽  
Phenotypic Resistance ◽  
Long Read ◽  
Pig Farm ◽  
Human Infections

Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans to non-human reservoirs (i.e., environment, animals, food). In Germany, the occurrence of CPE in livestock and food has been systematically monitored since 2016. In the 2019 monitoring, an OXA-48-producing E. coli (19-AB01443) was recovered from a fecal sample of a fattening pig. Phenotypic resistance was confirmed by broth microdilution and further characterized by PFGE, conjugation, and combined short-/long-read whole genome sequencing. This is the first detection of this resistance determinant in samples from German meat production. Molecular characterization and whole-genome sequencing revealed that the blaOXA-48 gene was located on a common pOXA-48 plasmid-prototype. This plasmid-type seems to be globally distributed among various bacterial species, but it was frequently associated with clinical Klebsiella spp. isolates. Currently, the route of introduction of this plasmid/isolate combination into the German pig production is unknown. We speculate that due to its strong correlation with human isolates a transmission from humans to livestock has occurred.

scholarly journals Application of combined genomic and transfer analyses to identify factors mediating regional spread of antibiotic resistant bacterial lineages

2020 ◽  
Author(s):  
Joyce Wang ◽  
Betsy Foxman ◽  
Ali Pirani ◽  
Zena Lapp ◽  
Lona Mody ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Patient Characteristics ◽  
Patient Transfer ◽  
Whole Genome ◽  
Nursing Facilities ◽  
Antibiotic Resistant ◽  
Patient Level ◽  
Healthcare Associated

ABSTRACTBackgroundPatients entering nursing facilities (NFs) are frequently colonized with antibiotic resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission we applied whole-genome sequencing to track the spread of four ARO species across regional NFs and evaluated patient-level characteristics and transfer acute-care hospitals (ACHs) as risk factors for colonization.Methods584 patients from six NFs were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm) and ciprofloxacin-resistant Escherichia coli (CipREc) colonization. Genomic analysis was performed to quantify ARO spread between NFs and compared to patient-transfer networks. The association between admission colonization and patient-level variables and recent ACH exposures was examined using multivariable regression models.ResultsThe majority of ARO isolates across study sites belonged to major healthcare-associated lineages: MRSA (ST5;N=89/117); VREfc (ST6;N=68/75); CipREc (ST131; N=58/64), and VREfm (clade A; N=129/129). While the genomic similarity of strains between NF pairs was associated with overlap in their feeder ACHs (Spearman’s rho=0.44-0.75, p<0.05 for MRSA, VREfc and CipREc), limited phylogenetic clustering by either ACH or NF supported regional endemicity. Significant predictors for ARO colonization on NF admission included lower functional status (adjusted odds ratio [aOR]>1 for all four AROs) and recent exposure to glycopeptides (aOR>2 for VREfm, VREfc and MRSA) or 3rd/4th-generation cephalosporins (aOR>2 for MRSA and VREfm). Transfer from specific ACHs was an independent risk factor for only one ARO/ACH pair (VREfm/ACH19, aOR=2.48[1.06-5.83]).ConclusionIn this region, healthcare-associated ARO lineages are endemic among connected NFs and ACHs, making patient characteristics more informative of NF admission colonization risk than exposure to specific ACHs.SummaryUsing a combination of whole-genome sequencing, patient transfer and clinical data, we discerned the dissemination of four high-priority antibiotic-resistant organisms (ARO) in the regional healthcare network, and epidemiolocal drivers underlying the high ARO importation rate into regional nursing facilities.

Use of whole-genome sequencing to detect an outbreak of Malassezia pachydermatis infection and colonization in a neonatal intensive care unit—California, 2015–2016

2020 ◽  
Vol 41 (7) ◽  
pp. 851-853 ◽  
Author(s):  
Nancy A. Chow ◽  
Raymond Chinn ◽  
Alice Pong ◽  
Kerry Schultz ◽  
Janice Kim ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Intensive Care ◽  
Neonatal Intensive Care Unit ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neonatal Intensive Care ◽  
Infection Prevention ◽  
Whole Genome ◽  
Prevention Measures ◽  
Malassezia Pachydermatis

AbstractWhole-genome sequencing confirmed the presence of a Malassezia pachydermatis outbreak among neonates in a neonatal intensive care unit. This technology supports the importance of adhering to infection prevention measures.

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