scholarly journals Detection of ESKAPE pathogens and Clostridioides difficile in Simulated Skin Transmission Events with Metagenomic and Metatranscriptomic Sequencing

2021 ◽  
Author(s):  
Krista L. Ternus ◽  
Nicolette C. Keplinger ◽  
Anthony D. Kappell ◽  
Gene D. Godbold ◽  
Veena Palsikar ◽  
...  
Keyword(s):  
Microbial Community ◽  
Antimicrobial Resistance ◽  
Epidemiological Studies ◽  
Pathogen Transmission ◽  
Metagenomic Analysis ◽  
Indirect Transmission ◽  
Healthcare Settings ◽  
Clostridioides Difficile ◽  
Analysis Methods ◽  
Global Threat

1AbstractBackgroundAntimicrobial resistance is a significant global threat, posing major public health risks and economic costs to healthcare systems. Bacterial cultures are typically used to diagnose healthcare-acquired infections (HAI); however, culture-dependent methods provide limited presence/absence information and are not applicable to all pathogens. Next generation sequencing (NGS) has the capacity to detect a wide variety of pathogens, virulence elements, and antimicrobial resistance (AMR) signatures in healthcare settings without the need for culturing, but few research studies have explored how NGS could be used to detect viable human pathogen transmission events under different HAI-relevant scenarios.MethodsThe objective of this project was to assess the capability of NGS-based methods to detect the direct and indirect transmission of high priority healthcare-related pathogens. DNA was extracted and sequenced from a previously published study exploring pathogen transfer with simulated skin containing background microorganisms, which allowed for complementary culture and metagenomic analysis comparisons. RNA was also isolated from an additional set of samples to evaluate metatranscriptomic analysis methods at different concentrations.ResultsUsing various analysis methods and custom reference databases, both pathogenic and non-pathogenic members of the microbial community were taxonomically identified. Virulence and AMR genes known to reside within the community were also routinely detected. Ultimately, pathogen abundance within the overall microbial community played the largest role in successful taxonomic classification and gene identification.ConclusionsThese results illustrate the utility of metagenomic analysis in clinical settings or for epidemiological studies, but also highlight the limits associated with the detection and characterization of pathogens at low abundance in a microbial community.

scholarly journals Perspective of Pakistani Physicians towards Hospital Antimicrobial Stewardship Programs: A Multisite Exploratory Qualitative Study

2019 ◽  
Vol 16 (9) ◽  
pp. 1565 ◽  
Author(s):  
Khezar Hayat ◽  
Meagen Rosenthal ◽  
Ali Hassan Gillani ◽  
Panpan Zhai ◽  
Muhammad Majid Aziz ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Antimicrobial Stewardship ◽  
Tertiary Care ◽  
Public Hospitals ◽  
Teaching Hospitals ◽  
Antibiotic Prescribing ◽  
Healthcare Facilities ◽  
Healthcare Settings ◽  
Stewardship Program ◽  
Global Threat

Background: Antimicrobial resistance (AMR) is a global threat and the antimicrobial stewardship program (ASP) is a globally used tool to combat AMR. There is little information on the views among Pakistani physicians regarding AMR and the benefits of hospital antimicrobial stewardship implementation. This study was designed to explore the physicians’ views about ASP. Methods: Qualitative face-to-face and telephonic interviews were conducted by using purposive sampling method with 22 physicians working in seven tertiary care public hospitals of Punjab, Pakistan. All interviews were audio recorded and transcribed verbatim. Qualitative software was used, and a thematic analysis was conducted. Results: Three broad themes were identified: (1) the growing concern of antimicrobial resistance in Pakistan, (2) the role(s) of healthcare professionals in antibiotic prescribing, and (3) managing antibiotic resistance in hospitals. Inadequate resources, poor healthcare facilities, and insufficiently trained medical staff were the major hurdles in ASP implementation in Pakistan. Conclusions: Our study found a poor familiarity of hospital ASP among physicians working in public sector tertiary care teaching hospitals, and a number of distinct themes emerged during this study that could be helpful in establishing the concept of hospital ASP in Pakistan. Overall, physicians showed a positive attitude towards the enforcement of ASP in all healthcare settings, including teaching hospitals.

Recent Review on Subclass B1 Metallo-β-lactamases Inhibitors: Sword for Antimicrobial Resistance

2019 ◽  
Vol 20 (7) ◽  
pp. 756-762 ◽  
Author(s):  
Aditi Kaushik ◽  
Manish Kaushik ◽  
Viney Lather ◽  
J.S. Dua
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Antimicrobial Resistance ◽  
Global Health ◽  
Human Health ◽  
Microbial Pathogens ◽  
Present Review ◽  
Drug Molecules ◽  
Global Threat ◽  
Powerful Strategy

An emerging crisis of antibiotic resistance for microbial pathogens is alarming all the nations, posing a global threat to human health. The production of the metallo-β-lactamase enzyme is the most powerful strategy of bacteria to produce resistance. An efficient way to combat this global health threat is the development of broad/non-specific type of metallo-β-lactamase inhibitors, which can inhibit the different isoforms of the enzyme. Till date, there are no clinically active drugs against metallo- β-lactamase. The lack of efficient drug molecules against MBLs carrying bacteria requires continuous research efforts to overcome the problem of multidrug-resistance bacteria. The present review will discuss the clinically potent molecules against different variants of B1 metallo-β-lactamase.

scholarly journals Evaluating Metagenomic Analysis for Pathogen Transmission in Healthcare Settings

2020 ◽  
Vol 41 (S1) ◽  
pp. s224-s224
Author(s):  
Curt Hewitt ◽  
Katharina Weber ◽  
Danielle LeSassier ◽  
Anthony Kappell ◽  
Kathleen Schulte ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Dna Analysis ◽  
Pathogen Transmission ◽  
Species Level ◽  
Metagenomic Analysis ◽  
Skin Microbiome ◽  
Limited Information ◽  
Culture Methods ◽  
Data Set ◽  
Skin Contact

Background: The prevalence of healthcare-acquired infections (HAIs) and rising levels of antimicrobial resistance place a significant burden on modern healthcare systems. Cultures are typically used to track HAIs; however, culture methods provide limited information and are not applicable to all pathogens. Next-generation sequencing (NGS) can detect and characterize pathogens present within a sample, but few research studies have explored how NGS could be used to detect pathogen transmission events under HAI-relevant scenarios. The objective of this CDC-funded project was to evaluate and correlate sequencing approaches for pathogen transmission with standard culture-based analysis. Methods: We modeled pathogen transfer via hand contact using synthetic skin. These skin coupons were seeded with a community of commensal organisms to mimic the human skin microbiome. Pathogens were added at physiologically relevant high or low levels prior to skin-to-skin contact. The ESKAPE pathogens: E. faecium, S. aureus, K. pneumoniae, A. baumannii, P. aeruginosa, and Enterobacter spp plus C. difficile were employed because they are the most common antibiotic resistant HAIs. Pathogen transfer between skin coupons was measured following direct skin contact and fomite surface transmission. The effects of handwashing or fomite decontamination were also evaluated. Transferred pathogens were enumerated via culture to establish a robust data set against which DNA and RNA sequence analyses of the same samples could be compared. These data also provide a quantitative assessment of individual ESKAPE+C pathogen transfer rates in skin contact scenarios. Results: Metagenomic and metatranscriptomic analysis using custom analysis pipelines and reference databases successfully identified the commensal and pathogenic organisms present in each sample at the species level. This analysis also identified antibiotic resistance genes and plasmids. Metatranscriptomic analysis permitted not only gene identification but also confirmation of gene expression, a critical factor in the evaluation of antibiotic resistance. DNA analysis does not require cell viability, a key differentiator between sequencing and culturing reflected in simulated handwashing data. Sensitivity remains a key limitation of metagenomic analysis, as shown by the poor species identification and gene content characterization of pathogens present at low abundance within the simulated microbial community. Species level identification typically failed as ratios fell below 1:1,000 pathogen CFU:total community CFU. Conclusions: These findings demonstrate the strengths and weaknesses of NGS for molecular epidemiology. The data sets produced for this study are publicly available so they can be employed for future metagenomic benchmarking studies.Funding: NoneDisclosures: None

scholarly journals A Continuously Active Antimicrobial Surface Coating Reduces Bioburden in a Healthcare Setting

2020 ◽  
Vol 41 (S1) ◽  
pp. s439-s439
Author(s):  
Valerie Beck
Keyword(s):  
Surface Coating ◽  
Geometric Mean ◽  
Healthcare Setting ◽  
Aerobic Bacteria ◽  
Healthcare Settings ◽  
Additional Layer ◽  
Clostridioides Difficile ◽  
Sustained Reduction ◽  
Before And After ◽  
Healthcare Associated

Background: It is well known that contaminated surfaces contribute to the transmission of pathogens in healthcare settings, necessitating the need for antimicrobial strategies beyond routine cleaning with momentary disinfectants. A recent publication demonstrated that application of a novel, continuously active antimicrobial surface coating in ICUs resulted in the reduction of healthcare-associated infections. Objective: We determined the general microbial bioburden and incidence of relevant pathogens present in patient rooms at 2 metropolitan hospitals before and after application of a continuously active antimicrobial surface coating. Methods: A continuously active antimicrobial surface coating was applied to patient rooms in intensive care units (ICUs) twice over an 18-month period and in non-ICUs twice over a 6-month study period. The environmental bioburden was assessed 8–16 weeks after each treatment. A 100-cm2 area was swabbed from frequently touched areas in patient rooms: patient chair arm rest, bed rail, TV remote, and backsplash behind the sink. The total aerobic bacteria count was determined for each location by enumeration on tryptic soy agar (TSA); the geometric mean was used to compare bioburden before and after treatment. Each sample was also plated on selective agar for carbapenem-resistant Enterobacteriaceae (CRE), vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA), and Clostridioides difficile to determine whether pathogens were present. Pathogen incidence was calculated as the percentage of total sites positive for at least 1 of the 4 target organisms. Results: Before application of the antimicrobial coating, total aerobic bacteria counts in ICUs were >1,500 CFU/100 cm2, and at least 30% of the sites were positive for a target pathogen (ie, CRE, VRE, MRSA or C. difficile). In non-ICUs, the bioburden before treatment was at least 500 CFU/100 cm2, with >50% of sites being contaminated with a pathogen. After successive applications of the surface coating, total aerobic bacteria were reduced by >80% in the ICUs and >40% in the non-ICUs. Similarly, the incidence of pathogen-positive sites was reduced by at least 50% in both ICUs and non-ICUs. Conclusions: The use of a continuously active antimicrobial surface coating provides a significant (P < .01) and sustained reduction in aerobic bacteria while also reducing the occurrence of epidemiologically important pathogens on frequently touched surfaces in patient rooms. These findings support the use of novel antimicrobial technologies as an additional layer of protection against the transmission of potentially harmful bacteria from contaminated surfaces to patients.Funding: Allied BioScience provided Funding: for this study.Disclosures: Valerie Beck reports salary from Allied BioScience.

scholarly journals Molecular epidemiology and antimicrobial resistance of Clostridioides difficile in Germany, 2014–2019

2021 ◽  
Vol 311 (4) ◽  
pp. 151507
Author(s):  
Ahmed Mohamed Mostafa Abdrabou ◽  
Zia Ul Habib Bajwa ◽  
Alexander Halfmann ◽  
Alexander Mellmann ◽  
Anna Nimmesgern ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Molecular Epidemiology ◽  
Clostridioides Difficile

scholarly journals Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

Nature ◽  
2011 ◽  
Vol 480 (7377) ◽  
pp. 368-371 ◽  
Author(s):  
Rachel Mackelprang ◽  
Mark P. Waldrop ◽  
Kristen M. DeAngelis ◽  
Maude M. David ◽  
Krystle L. Chavarria ◽  
...  
Keyword(s):  
Microbial Community ◽  
Rapid Response ◽  
Metagenomic Analysis

scholarly journals Crumbling the Castle: Targeting DNABII Proteins for Collapsing Bacterial Biofilms as a Therapeutic Approach to Treat Disease and Combat Antimicrobial Resistance

Antibiotics ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 104
Author(s):  
James V. Rogers ◽  
Veronica L. Hall ◽  
Charles C. McOsker
Keyword(s):  
Antimicrobial Resistance ◽  
Bacterial Infections ◽  
Antimicrobial Agents ◽  
Defense Mechanism ◽  
Treatment Options ◽  
Bacterial Biofilms ◽  
Host Immune System ◽  
New Antibiotics ◽  
Financial Burdens ◽  
Global Threat

Antimicrobial resistance (AMR) is a concerning global threat that, if not addressed, could lead to increases in morbidity and mortality, coupled with societal and financial burdens. The emergence of AMR bacteria can be attributed, in part, to the decreased development of new antibiotics, increased misuse and overuse of existing antibiotics, and inadequate treatment options for biofilms formed during bacterial infections. Biofilms are complex microbiomes enshrouded in a self-produced extracellular polymeric substance (EPS) that is a primary defense mechanism of the resident microorganisms against antimicrobial agents and the host immune system. In addition to the physical protective EPS barrier, biofilm-resident bacteria exhibit tolerance mechanisms enabling persistence and the establishment of recurrent infections. As current antibiotics and therapeutics are becoming less effective in combating AMR, new innovative technologies are needed to address the growing AMR threat. This perspective article highlights such a product, CMTX-101, a humanized monoclonal antibody that targets a universal component of bacterial biofilms, leading to pathogen-agnostic rapid biofilm collapse and engaging three modes of action—the sensitization of bacteria to antibiotics, host immune enablement, and the suppression of site-specific tissue inflammation. CMTX-101 is a new tool used to enhance the effectiveness of existing, relatively inexpensive first-line antibiotics to fight infections while promoting antimicrobial stewardship.

scholarly journals StrainPro – a highly accurate Metagenomic strain-level profiling tool

2019 ◽  
Author(s):  
Hsin-Nan Lin ◽  
Yaw-Ling Lin ◽  
Wen-Lian Hsu
Keyword(s):  
Microbial Community ◽  
Relative Abundance ◽  
Taxonomic Diversity ◽  
Evaluation Study ◽  
Taxonomic Composition ◽  
Strain Level ◽  
Metagenomic Analysis ◽  
Reference Database ◽  
Analysis Tool ◽  
Analysis Tools

ABSTRACTCharacterizing the taxonomic diversity of a microbial community is very important to understand the roles of microorganisms. Next generation sequencing (NGS) provides great potential for investigation of a microbial community and leads to Metagenomic studies. NGS generates DNA fragment sequences directly from microorganism samples, and it requires analysis tools to identify microbial species (or taxonomic composition) and estimate their relative abundance in the studied community. However, only a few tools could achieve strain-level identification and most tools estimate the microbial abundances simply according to the read counts. An evaluation study on metagenomic analysis tools concludes that the predicted abundance differed significantly from the true abundance. In this study, we present StrainPro, a novel metagenomic analysis tool which is highly accurate both at characterizing microorganisms at strain-level and estimating their relative abundances. A unique feature of StrainPro is it identifies representative sequence segments from reference genomes. We generate three simulated datasets using known strain sequences and another three simulated datasets using unknown strain sequences. We compare the performance of StrainPro with seven existing tools. The results show that StrainPro not only identifies metagenomes with high precision and recall, but it is also highly robust even when the metagenomes are not included in the reference database. Moreover, StrainPro estimates the relative abundance with high accuracy. We demonstrate that there is a strong positive linear relationship between observed and predicted abundances.

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