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 Coproduction of KPC-18 and VIM-1 Carbapenemases by Enterobacter cloacae: Implications for Newer β-Lactam–β-Lactamase Inhibitor Combinations

2015 ◽  
Vol 54 (3) ◽  
pp. 791-794 ◽  
Author(s):  
Gina K. Thomson ◽  
James W. Snyder ◽  
Christi L. McElheny ◽  
Kenneth S. Thomson ◽  
Yohei Doi
Keyword(s):  
Acute Care ◽  
Genome Sequencing ◽  
Acute Care Hospital ◽  
Enterobacter Cloacae ◽  
Sequence Type ◽  
Whole Genome ◽  
Care Hospital ◽  
Content Type ◽  
Lactamase Inhibitor

Enterobacter cloacaestrain G6809 with reduced susceptibility to carbapenems was identified from a patient in a long-term acute care hospital in Kentucky. G6809 belonged to sequence type (ST) 88 and carried two carbapenemase genes,blaKPC-18andblaVIM-1. Whole-genome sequencing localizedblaKPC-18to the chromosome andblaVIM-1to a 58-kb plasmid. The strain was highly resistant to ceftazidime-avibactam. Insidious coproduction of metallo-β-lactamase with KPC-type carbapenemase has implications for the use of next-generation β-lactam–β-lactamase inhibitor combinations.

scholarly journals Anin silicosurvey ofClostridioides difficileextrachromosomal elements

2019 ◽  
Author(s):  
Bastian Hornung ◽  
Ed J. Kuijper ◽  
Wiep Klaas Smits
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
In Silico ◽  
Sequence Data ◽  
Whole Genome ◽  
Clostridioides Difficile ◽  
Extrachromosomal Elements ◽  
European Nucleotide Archive ◽  
Healthcare Associated ◽  
Systematic Identification

AbstractThe gram-positive enteropathogenClostridioides difficileis the major cause of healthcare associated diarrhoea and is also an important cause of community-acquired infectious diarrhoea. Considering the burden of the disease, many studies have employed whole genome sequencing to identify factors that contribute to virulence and pathogenesis. Though extrachromosomal elements such as plasmids are important for these processes in other bacteria, the few characterized plasmids ofC. difficilehave no relevant functions assigned and no systematic identification of plasmids has been carried out to date. Here, we perform anin silicoanalysis of publicly available sequence data, to show that ∼13% of allC. difficilestrains contain extrachromosomal elements, with 1-6 elements per strain. Our approach identifies known plasmids (e.g. pCD6, pCD630 and cloning plasmids) and 6 novel putative plasmid families. Our study shows that plasmids are abundant and may encode functions that are relevant forC. difficilephysiology. The newly identified plasmids may also form the basis for the construction of novel cloning plasmids forC. difficilethat are compatible with existing tools.RepositoriesThe assembled circular type plasmids have been deposited at the European Nucleotide Archive (ENA) under accession numbers ERZ940801 and ERZ940803-ERZ940808.

scholarly journals 531. Practical and Evidence-Based Considerations for Implementation of Bacterial Whole-Genome Sequencing Within Longitudinal Infection Control Practice

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S255-S255
Author(s):  
Donald S Chen ◽  
Moira Quinn ◽  
Rita M Sussner ◽  
Guiqing Wang ◽  
John T Fallon ◽  
...  
Keyword(s):  
Infection Control ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tertiary Care ◽  
False Negative ◽  
Lessons Learned ◽  
Evidence Based ◽  
Guidance Document ◽  
Whole Genome ◽  
Care Hospital

Abstract Background Whole-genome sequencing (WGS) of bacteria is becoming a routine tool within microbiology, yet its utility to help guide infection control (IC) practice longitudinally is underexplored. As with any technology adopted in the hospital, the integration of WGS into IC practice must be carefully managed and considered. We qualitatively report an evidence-based implementation workflow that considers WGS to help proactively guide IC professionals during investigation of infectious outbreaks. Methods We built upon lessons learned in an ongoing surveillance effort at a tertiary care hospital—utilizing retrospective WGS data within the Philips IntelliSpace Epidemiology system—to understand facilitators and barriers to the use of bacterial WGS longitudinally to inform IC workflow. Our team established a 9-month workgroup to study the practical aspects of implementing WGS in routine IC practice. From expert opinion collected via the workgroup, in addition to evidence from the literature, a workflow guidance document and checklist were codified. New ideas included incorporating education to promote the establishment of an IC triage process. Results Facilitators to implementation included ability to display genomic relatedness alongside relevant patient data to enable clinical actionability, ability to pivot time and resources rapidly when infections are a pseudo outbreak (false positive) or missed outbreak (false negative), opportunities for nuanced staff education, and willingness to be a first-of-kind adopter. Barriers were communication of genomic concepts to IC professionals and relevant institutional stakeholders, maintaining sharable notes of active investigations to promote data-sharing practices, and timing and review of relevant interventions into the facility workflow. Strategies to address these issues are considered. Conclusion This study provides a novel framework for adaptation of existing IC workflow strategies to leverage the utility of bacterial WGS, and it presents a schema to effectively engage relevant stakeholders, based on an analysis of the unique challenges inherent within IC practice. It also offers an innovative model for the development and implementation of IC workflows to account for, and adapt to, site-specific conditions. Disclosures All authors: No reported disclosures.

scholarly journals 2440. Using a geospatially explicit agent-based model of a regional healthcare network to assess varied antibiotic risk on Clostridioides difficile infection incidence

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S843-S844
Author(s):  
Sarah Rhea ◽  
Kasey Jones ◽  
Georgiy Bobashev ◽  
Breda Munoz ◽  
James Rineer ◽  
...  
Keyword(s):  
Acute Care ◽  
Acute Care Hospital ◽  
Care Hospital ◽  
Healthcare Facilities ◽  
Agent Based ◽  
Healthcare Network ◽  
Clostridioides Difficile ◽  
Unit Increase ◽  
Clostridioides Difficile Infection ◽  
The Impact

Abstract Background Different antibiotic classes are associated with different Clostridioides difficile infection (CDI) risk. The impact of varied antibiotic risk on CDI incidence can be explored using agent-based models (ABMs). ABMs can simulate complete systems (e.g., regional healthcare networks) comprised of discrete, unique agents (e.g., patients) which can be represented using a synthetic population, or model-generated representation of the population. We used an ABM of a North Carolina (NC) regional healthcare network to assess the impact of increasing antibiotic risk ratios (RRs) across network locations on healthcare-associated (HA) and community-associated (CA) CDI incidence. Methods The ABM describes CDI acquisition and patient movement across 14 network locations (i.e., nodes) (11 short-term acute care hospitals, 1 long-term acute care hospital, 1 nursing home, and the community). We used a sample of 2 million synthetic NC residents as ABM microdata. We updated agent states (i.e., location, antibiotic exposure, C. difficile colonization, CDI status) daily. We applied antibiotic RRs of 1, 5, 8.9 (original model RR), 15, and 20 to agents across the network to simulate varied risk corresponding to different antibiotic classes. We determined network HA-CDI and CA-CDI incidence and percent mean change for each RR. Results In this simulation study, HA-CDI incidence increased with increasing antibiotic risk, ranging from 11.3 to 81.4 HA-CDI cases/100,000 person-years for antibiotic RRs of 1 to 20, respectively. On average, the per unit increase in antibiotic RR was 33% for HA-CDI and 6% for CA-CDI (figure). Conclusion We used a geospatially explicit ABM to simulate increasing antibiotic risk, corresponding to different antibiotic classes, and to explore the impact on CDI incidence. The per unit increase in antibiotic risk was greater for HA-CDI than CA-CDI due to the higher probability of receiving antibiotics and higher concentration of agents with other CDI risk factors in the healthcare facilities of the ABM. These types of analyses, which demonstrate the interconnectedness of network healthcare facilities and the associated community served by the network, might help inform targeted antibiotic stewardship efforts in certain network locations. Disclosures All authors: No reported disclosures.

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.

scholarly journals 740. Elucidation of the Mode of Clostridioides difficile Transmission Based on One Health Approach

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S468-S468
Author(s):  
Sadako Yoshizawa ◽  
Tomoka Sawa ◽  
Kohji Komori ◽  
Masakazu Sasaki ◽  
Nobuaki Mori ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
One Health ◽  
Companion Animals ◽  
Living Environment ◽  
Animal Origin ◽  
Toxin Gene ◽  
Whole Genome ◽  
Mlst Analysis ◽  
Clostridioides Difficile

Abstract Background Community-onset Clostridioides difficile (C. difficile) infection (CACDI) has been increasing in recent years. To explore the transmission route of CACDI, we performed the whole-genome sequencing of C. difficile isolated from CACDI patients and compared it to the isolates from livestock, companion animals, and soil. Methods From October 2020 until April 2021, fecal specimens of cattle, poultry, swine, felines, canines, CACDI patients, their families, and soil from the CACDI patients' living environment were applied for isolation of C.difficile. Whole-genome sequencing of C. difficile was performed on the MiSeq system (Illumina). Using the draft genome obtained from these analyses, the house-keeping gene (tpi), MLST, toxin genes (tcdA, tcdB, cdtA, cdtB), and resistance genes (gyrA, gyrB, rpoA, rpoB, rpoC) were comprehensively analyzed. Results As of March 31, 2021, 275 specimens were collected. Forty-five fecal specimens of companion animal origin (23 feline and 22 canines) were collected and the positive rate of C.difficile was 28.9% (2 felines, 11 canines). In MLST analysis, ST 15 (4 strains), ST 26 (2 strains), ST 42, ST 3, ST 28, ST 100, and ST 185 were detected in canines, and ST 203 and ST 297 strains were detected in felines. Samples of livestock origin were collected from 135 cattle, 41 poultries, and 20 swine. The detection rate in cattle was 11%, toxin-gene positivity was 60%. MLST analysis of 9 strains revealed ST 11 (5 strains), ST 2, ST 15, ST 58, and ST 101. No isolates were found from poultry or swine. Patient-derived strains of CACDI were collected from 14 patients at 2 sites. MLST analysis revealed ST42, ST37, ST100, and ST203(two isolates, respectively), ST 224, ST 81, ST 28, and ST 47. 2 isolates were unclassifiable. One case was a healthy 1-year-old girl, whose family revealed no isolation of C.difficile. Impressively, the soil in the parks (A and B) related to the child detected C.difficile from 4/4 samples (toxin-gene positivity; 75%) in Park A and 1/4 samples (toxin-gene positive) in Park B. MLST analysis demonstrated ST 42, the same as that in the affected child and core-genome single-nucleotide polymorphisms(SNPs) analysis suggested closely related strain. Conclusion Our results suggest one health approach is fundamental to prevent the transmission of C.difficile. Disclosures All Authors: No reported disclosures

scholarly journals 1186. Decreased Laboratory-Identified Clostridioides difficile Infections with Implementation of an Electronic Hand Hygiene Monitoring System in a Long-Term Acute Care Hospital Decreased Laboratory-Identified Clostridioides difficile Infections with Implementation of an Electronic Hand Hygiene Monitoring System in a Long-Term Acute Care Hospital

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S425-S425
Author(s):  
Maureen Banks ◽  
Andrew Phillips ◽  
Keith Chin ◽  
Lou Ann Bruno-Murtha
Keyword(s):  
Data Collection ◽  
Hand Hygiene ◽  
Monitoring System ◽  
Acute Care ◽  
Acute Care Hospital ◽  
Care Hospital ◽  
Intervention Period ◽  
Environmental Cleaning ◽  
Clostridioides Difficile

Abstract Background Hand hygiene (HH) is the cornerstone of infection prevention and improved compliance has been associated with reduced healthcare-associated infections (HAIs). However, traditional methods for HH data collection have limitations and may not accurately reflect true compliance. We sought to evaluate whether an electronic hand hygiene monitoring system (HHMS) can improve data collection, compliance, and reduce HAIs. Methods A HHMS was implemented as part of a pilot at a single facility in June 2018 for all healthcare workers (HCWs) who entered patient rooms. The system prompted HCWs to perform HH with an audible and visual reminder emitted from a badge if a HH event had not been registered within specific timeframes of entering or exiting a patient room. The system captured compliance with preferential handwashing (soap and water) for at least 15 seconds upon exit of Clostridioides difficile (C. difficile) designated rooms. All HH data were collected by the HHMS. Hand hygiene compliance and HAI data were compared for the pre-intervention (June 2017-May 2018) and intervention periods (July 2018-March 2019). No changes were made to environmental cleaning protocols or compliance monitoring, nor in antibiotic stewardship practices. Results HH compliance by direct observation in the pre-intervention period was 91% (1,612 observations). HH compliance with the HHMS during the intervention period was 97% (2,778,402 observations). The mean monthly HH opportunities recorded during the pre-intervention period was 134, while the HHMS captured 308,711, a greater than 2,300-fold increase. The incidence of healthcare facility-onset C. difficile infections (HO-CDI) pre-intervention was 9.60 per 10,000 patient-days (41 GDH+/Toxin+ laboratory-identified [labID] events/42,726 patient-days). With the HHMS, HO-CDI decreased 70% (P = 0.0003) to 2.89 per 10,000 patient-days (9 labID events/31,169 patient-days). No policy changes in environmental cleaning of high-touch surfaces were made or observed during the pilot. Conclusion The use of an HHMS facilitated more comprehensive HH data and improved compliance. The preliminary findings also support an association between more robust HH compliance data and a significant decrease in toxin-producing CDI. Disclosures All authors: No reported disclosures.

scholarly journals Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains

2019 ◽  
Vol 6 (2) ◽  
Author(s):  
Bradley T Endres ◽  
Khurshida Begum ◽  
Hua Sun ◽  
Seth T Walk ◽  
Ali Memariani ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
The United States ◽  
Whole Genome Sequence ◽  
Snp Analysis ◽  
Whole Genome ◽  
Ribotype 027 ◽  
Clostridioides Difficile

Abstract Background The epidemic Clostridioides difficile ribotype 027 strain resulted from the dissemination of 2 separate fluoroquinolone-resistant lineages: FQR1 and FQR2. Both lineages were reported to originate in North America; however, confirmatory large-scale investigations of C difficile ribotype 027 epidemiology using whole genome sequencing has not been undertaken in the United States. Methods Whole genome sequencing and single-nucleotide polymorphism (SNP) analysis was performed on 76 clinical ribotype 027 isolates obtained from hospitalized patients in Texas with C difficile infection and compared with 32 previously sequenced worldwide strains. Maximum-likelihood phylogeny based on a set of core genome SNPs was used to construct phylogenetic trees investigating strain macro- and microevolution. Bayesian phylogenetic and phylogeographic analyses were used to incorporate temporal and geographic variables with the SNP strain analysis. Results Whole genome sequence analysis identified 2841 SNPs including 900 nonsynonymous mutations, 1404 synonymous substitutions, and 537 intergenic changes. Phylogenetic analysis separated the strains into 2 prominent groups, which grossly differed by 28 SNPs: the FQR1 and FQR2 lineages. Five isolates were identified as pre-epidemic strains. Phylogeny demonstrated unique clustering and resistance genes in Texas strains indicating that spatiotemporal bias has defined the microevolution of ribotype 027 genetics. Conclusions Clostridioides difficile ribotype 027 lineages emerged earlier than previously reported, coinciding with increased use of fluoroquinolones. Both FQR1 and FQR2 ribotype 027 epidemic lineages are present in Texas, but they have evolved geographically to represent region-specific public health threats.

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