scholarly journals Complete Genome Assemblies of Three Highly Prevalent, Toxigenic Clostridioides difficile Strains Causing Health Care-Associated Infections in Australia

2021 ◽  
Vol 10 (31) ◽  
Author(s):  
Keeley O’Grady ◽  
Thomas V. Riley ◽  
Daniel R. Knight
Keyword(s):  
Health Care ◽  
Gastrointestinal Illness ◽  
High Quality ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Hybrid Genome ◽  
Life Threatening ◽  
Health Care Associated Infections ◽  
Genome Assemblies ◽  
Reference Genomes

Clostridioides difficile infection (CDI) is the leading cause of life-threatening health care-related gastrointestinal illness worldwide. Phylogenetically appropriate closed reference genomes are essential for studies of C. difficile transmission and evolution. Here, we provide high-quality complete hybrid genome assemblies for the three most prevalent C. difficile strains causing CDI in Australia.

scholarly journals Increased Clinical Specificity with Ultrasensitive Detection of Clostridioides difficile Toxins: Reduction of Overdiagnosis Compared to Nucleic Acid Amplification Tests

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
Johanna Sandlund ◽  
Joel Estis ◽  
Phoebe Katzenbach ◽  
Niamh Nolan ◽  
Kirstie Hinson ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Patient Outcomes ◽  
Single Molecule ◽  
Clinical Performance ◽  
Neutralization Assay ◽  
Nucleic Acid Amplification ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Health Care Associated Infections ◽  
Stool Specimens

ABSTRACT Clostridioides difficile infection (CDI) is one of the most common health care-associated infections, resulting in significant morbidity, mortality, and economic burden. Diagnosis of CDI relies on the assessment of clinical presentation and laboratory tests. We evaluated the clinical performance of ultrasensitive single-molecule counting technology for detection of C. difficile toxins A and B. Stool specimens from 298 patients with suspected CDI were tested with the nucleic acid amplification test (NAAT; BD MAX Cdiff assay or Xpert C. difficile assay) and Singulex Clarity C. diff toxins A/B assay. Specimens with discordant results were tested with the cell cytotoxicity neutralization assay (CCNA), and the results were correlated with disease severity and outcome. There were 64 NAAT-positive and 234 NAAT-negative samples. Of the 32 NAAT+/Clarity− and 4 NAAT−/Clarity+ samples, there were 26 CCNA− and 4 CCNA− samples, respectively. CDI relapse was more common in NAAT+/toxin+ patients than in NAAT+/toxin− and NAAT−/toxin− patients. The clinical specificity of Clarity and NAAT was 97.4% and 89.0%, respectively, and overdiagnosis was more than three times more common in NAAT+/toxin− than in NAAT+/toxin+ patients. The Clarity assay was superior to NAATs for the diagnosis of CDI, by reducing overdiagnosis and thereby increasing clinical specificity, and the presence of toxins was associated with negative patient outcomes.

scholarly journals Emerging Chryseobacterium indologenes Infection in Indian Neonatal Intensive Care Units: A Case Report

Antibiotics ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 109 ◽  
Author(s):  
Rishika Mehta ◽  
Ashish Pathak
Keyword(s):  
Health Care ◽  
Intensive Care ◽  
Intensive Care Units ◽  
Neonatal Intensive Care ◽  
Multidrug Resistant ◽  
Neonatal Intensive Care Units ◽  
Indwelling Catheters ◽  
Chryseobacterium Indologenes ◽  
Life Threatening ◽  
Health Care Associated Infections

Antibiotic-resistant pathogens and nosocomial infections constitute common and serious problems for neonates admitted to neonatal intensive care units worldwide. Chryseobacterium indologenes is a non-lactose-fermenting, gram-negative, health care-associated pathogen (HCAP). It is ubiquitous and intrinsically resistant to several antibiotics. Despite its low virulence, C. indologenes has been widely reported to cause life-threatening infections. Patients on chronic immunosuppressant drugs, harboring invasive devices and indwelling catheters become the nidus for C. indologenes. Typically, C. indologenes causes major health care-associated infections such as pneumonia, empyema, pyelonephritis, cystitis, peritonitis, meningitis, and bacteremia in patients harboring central venous catheters. Management of C. indologenes infection in neonates is not adequately documented owing to underreporting, particularly in India. Because of its multidrug resistance and the scant availability of data from the literature, the effective empirical treatment of C. indologenes is challenging. We present an uncommon case of bacteremia caused by C. indologenes in a preterm newborn baby with moderate respiratory distress syndrome who was successfully treated. We also provide a review of infections in the neonatal age group. Henceforth, in neonates receiving treatments involving invasive equipment use and long-term antibiotic therapy, multidrug resistant C. indologenes should be considered an HCAP.

scholarly journals Clinical and Molecular Characterization of Invasive Heteroresistant Vancomycin-Intermediate Staphylococcus aureus Infections in Korean Hospitals

2015 ◽  
Vol 54 (3) ◽  
pp. 760-763 ◽  
Author(s):  
Eu Suk Kim ◽  
In-Gyu Bae ◽  
Jeong Eun Cho ◽  
Yun Jung Choi ◽  
Il-Hwan Kim ◽  
...  
Keyword(s):  
Health Care ◽  
Staphylococcus Aureus ◽  
Molecular Characterization ◽  
Sequence Type ◽  
Content Type ◽  
Health Care Associated Infections ◽  
Persistent Bacteremia

Invasive heteroresistant vancomycin-intermediateStaphylococcus aureus(h-VISA) isolates were identified and characterized in 10 Korean hospitals from July 2009 to June 2011. The prevalence of h-VISA infections was 3.3% (42/1,289). Most (41/42) were health care-associated infections caused by strains belonging to sequence type 5. Cases of persistent bacteremia were frequent (17/42), and 30-day mortality was high (16/40).

scholarly journals Whole genome data from Curtobacterium flaccumfaciens pv. flaccumfaciens strains associated with tan spot of mungbean and soybean reveal diverse plasmid profiles

2021 ◽  
Author(s):  
Niloofar Vaghefi ◽  
Dante Adorada ◽  
Lauren Huth ◽  
Lisa A Kelly ◽  
Barsha Poudel ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Population Genomics ◽  
Tan Spot ◽  
Glycoside Hydrolases ◽  
High Quality ◽  
Host Association ◽  
Genome Data ◽  
Pathogenic Variability ◽  
Genome Assemblies ◽  
Reference Genomes

Despite the substantial economic impact of Curtobacterium flaccumfaciens pv. flaccumfaciens (Cff) on legume productions worldwide, the genetic basis of its pathogenicity and potential host association is poorly understood. The production of high-quality reference genome assemblies of Cff strains associated with different hosts sheds light on the genetic basis of its pathogenic variability and host association. Moreover, the study of recent outbreaks of bacterial wilt and microevolution of the pathogen in Australia requires access to high-quality, reference genomes that are sufficiently closely related to the population being studied within Australia. We provide the first genome assemblies of Cff strains associated with mungbean and soybean, which revealed high variability in their plasmid composition. The analysis of Cff genomes revealed an extensive suite of carbohydrate-active enzymes potentially associated with pathogenicity, including four carbohydrate esterases, 50 glycoside hydrolases, 23 glycosyl transferases, and a polysaccharide lyase. We also identified 11 serine peptidases, three of which were located within a linear plasmid, pCff119. These high-quality assemblies and annotations will provide a foundation for population genomics studies of Cff in Australia and for answering fundamental questions regarding pathogenicity factors and adaptation of Cff to various hosts worldwide, and, at a broader scale, contribute to unravelling genomic features of Gram-positive, xylem-inhabiting bacterial pathogens.

scholarly journals Hybrid Genome Assemblies of Marine Bacteria Isolated from the Sponge Sycon capricorn

2021 ◽  
Vol 10 (43) ◽  
Author(s):  
Oliver L. Mead ◽  
Erin E. Hahn ◽  
Maja A. Adamska
Keyword(s):  
Marine Bacteria ◽  
Bacterial Species ◽  
Content Type ◽  
Microbial Genomes ◽  
Calcareous Sponge ◽  
Hybrid Genome ◽  
Whole Genomes ◽  
Complex Relationships ◽  
Genome Assemblies

Sponges have complex relationships with bacteria, the roles of which include food, important components of the holobiont, pathogens, and accidentally accumulated elements of the environment. Consequently, sponges are reservoirs of microbial genomes and novel compounds. Therefore, we isolated and sequenced the whole genomes of bacterial species from the calcareous sponge Sycon capricorn .

scholarly journals Decolonization in Prevention of Health Care-Associated Infections

2016 ◽  
Vol 29 (2) ◽  
pp. 201-222 ◽  
Author(s):  
Edward J. Septimus ◽  
Marin L. Schweizer
Keyword(s):  
Health Care ◽  
Sodium Hypochlorite ◽  
Povidone Iodine ◽  
Tea Tree Oil ◽  
Gram Negative ◽  
Content Type ◽  
Tea Tree ◽  
Increased Risk ◽  
Health Care Associated Infections ◽  
Gram Negative Organisms

SUMMARYColonization with health care-associated pathogens such asStaphylococcus aureus, enterococci, Gram-negative organisms, andClostridium difficileis associated with increased risk of infection. Decolonization is an evidence-based intervention that can be used to prevent health care-associated infections (HAIs). This review evaluates agents used for nasal topical decolonization, topical (e.g., skin) decolonization, oral decolonization, and selective digestive or oropharyngeal decontamination. Although the majority of studies performed to date have focused onS. aureusdecolonization, there is increasing interest in how to apply decolonization strategies to reduce infections due to Gram-negative organisms, especially those that are multidrug resistant. Nasal topical decolonization agents reviewed include mupirocin, bacitracin, retapamulin, povidone-iodine, alcohol-based nasal antiseptic, tea tree oil, photodynamic therapy, omiganan pentahydrochloride, and lysostaphin. Mupirocin is still the gold standard agent forS. aureusnasal decolonization, but there is concern about mupirocin resistance, and alternative agents are needed. Of the other nasal decolonization agents, large clinical trials are still needed to evaluate the effectiveness of retapamulin, povidone-iodine, alcohol-based nasal antiseptic, tea tree oil, omiganan pentahydrochloride, and lysostaphin. Given inferior outcomes and increased risk of allergic dermatitis, the use of bacitracin-containing compounds cannot be recommended as a decolonization strategy. Topical decolonization agents reviewed included chlorhexidine gluconate (CHG), hexachlorophane, povidone-iodine, triclosan, and sodium hypochlorite. Of these, CHG is the skin decolonization agent that has the strongest evidence base, and sodium hypochlorite can also be recommended. CHG is associated with prevention of infections due to Gram-positive and Gram-negative organisms as well asCandida. Conversely, triclosan use is discouraged, and topical decolonization with hexachlorophane and povidone-iodine cannot be recommended at this time. There is also evidence to support use of selective digestive decontamination and selective oropharyngeal decontamination, but additional studies are needed to assess resistance to these agents, especially selection for resistance among Gram-negative organisms. The strongest evidence for decolonization is for use among surgical patients as a strategy to prevent surgical site infections.

Patient value co-creation in online health communities

2015 ◽  
Vol 26 (1) ◽  
pp. 72-96 ◽  
Author(s):  
Jing Zhao ◽  
Tao Wang ◽  
Xiucheng Fan
Keyword(s):  
Health Care ◽  
Social Identity ◽  
Care Service ◽  
Health Care Service ◽  
Content Type ◽  
Mediation Analyses ◽  
Online Health Communities ◽  
Life Threatening ◽  
Health Communities ◽  
Patient Value

Purpose – Patient value co-creation represents a key research priority and an essential determinant of health care service outcomes. Yet few studies empirically examine the factors that motivate patients to participate actively in value co-creation. The purpose of this paper is to seek to identify the motivators of such activities in online health communities (OHC) and examine their specific and unique effects. Design/methodology/approach – A netnographic study helps identify the motivators that drive patients’ value co-creation activities in OHCs. The combination of these results with social identity theories suggest the hypotheses; mediation analyses test the hypothesized model with data collected from eight OHCs that address both life-threatening and non-life-threatening illnesses. Findings – The netnographic results show that social identity drives patients’ value co-creation activities. Interactions among OHC members and the cognitive resources of the OHC both contribute to the development of its social identity. Furthermore, benevolence trust, shared vision, and shared language determine how likely an OHC member is to identify with a particular OHC, which further influences his or her value co-creation activities in that OHC. Originality/value – Although value co-creation is critical to the health care sector, few studies examine antecedents of patient value co-creation empirically. This study represents an initial attempt to do so by combining innovative netnographic analyses with mediation analyses.

scholarly journals Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Richard A. Stanton ◽  
Gillian McAllister ◽  
Jonathan B. Daniels ◽  
Erin Breaker ◽  
Nicholas Vlachos ◽  
...  
Keyword(s):  
Health Care ◽  
Pseudomonas Aeruginosa ◽  
Multilocus Sequence Typing ◽  
Core Genome ◽  
Health Care Environment ◽  
Content Type ◽  
Health Care Associated Infections ◽  
Opportunistic Human Pathogen ◽  
The Stability ◽  
Core Genes

ABSTRACT Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.

scholarly journals Towards complete and error-free genome assemblies of all vertebrate species

Nature ◽  
2021 ◽  
Vol 592 (7856) ◽  
pp. 737-746 ◽  
Author(s):  
Arang Rhie ◽  
Shane A. McCarthy ◽  
Olivier Fedrigo ◽  
Joana Damas ◽  
Giulio Formenti ◽  
...  
Keyword(s):  
Cost Effective ◽  
Lessons Learned ◽  
Vertebrate Species ◽  
High Quality ◽  
Protein Coding ◽  
Sequencing Technologies ◽  
Long Read ◽  
Genome Assemblies ◽  
Assembly Error ◽  
Reference Genomes

AbstractHigh-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

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