scholarly journals Shortage in Appropriate Diagnostics of Antimicrobial Resistance in Lebanese Clinical Settings: A Crisis Amplified by COVID-19 and Economic Collapse

Author(s):  
Marwan Osman ◽  
Dalal Kasir ◽  
Issmat I. Kassem ◽  
Monzer Hamze
2020 ◽  
Vol 66 (10) ◽  
pp. 1278-1289
Author(s):  
Eric M Ransom ◽  
Robert F Potter ◽  
Gautam Dantas ◽  
Carey-Ann D Burnham

Abstract Background Next-generation sequencing (NGS) technologies are being used to predict antimicrobial resistance. The field is evolving rapidly and transitioning out of the research setting into clinical use. Clinical laboratories are evaluating the accuracy and utility of genomic resistance prediction, including methods for NGS, downstream bioinformatic pipeline components, and the clinical settings in which this type of testing should be offered. Content We describe genomic sequencing as it pertains to predicting antimicrobial resistance in clinical isolates and samples. We elaborate on current methodologies and workflows to perform this testing and summarize the current state of genomic resistance prediction in clinical settings. To highlight this aspect, we include 3 medically relevant microorganism exemplars: Mycobacterium tuberculosis, Staphylococcus aureus, and Neisseria gonorrhoeae. Last, we discuss the future of genomic-based resistance detection in clinical microbiology laboratories. Summary Antimicrobial resistance prediction by genomic approaches is in its infancy for routine patient care. Genomic approaches have already added value to the current diagnostic testing landscape in specific circumstances and will play an increasingly important role in diagnostic microbiology. Future advancements will shorten turnaround time, reduce costs, and improve our analysis and interpretation of clinically actionable results.


Author(s):  
Fernanda Loayza ◽  
Jay P. Graham ◽  
Gabriel Trueba

Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a “highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem”. In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.


Processes ◽  
2019 ◽  
Vol 7 (12) ◽  
pp. 964 ◽  
Author(s):  
Karen Li ◽  
Joanna Zheng ◽  
Thomas Deng ◽  
James Peng ◽  
Dagmar Daniel ◽  
...  

The spread of antimicrobial resistance pathogens in humans has increasingly become an issue that threatens public health. While the NCBI Pathogen Detection Isolates Browser (NPDIB) database has been collecting clinical isolate samples over time for various countries, few studies have been done to identify genes and pathogens responsible for the antimicrobial resistance in clinical settings. This study conducted the first multivariate statistical analysis of the high-dimensional historical data from the NPDIB database for six different countries from majorly inhabited landmasses, including Australia, Brazil, China, South Africa, the UK, and the US. The similarities among different countries in terms of genes and pathogens were investigated to understand the potential avenues for antimicrobial-resistance gene spreading. The genes and pathogens that were closely involved in antimicrobial resistance were further studied temporally by plotting time profiles of their frequency to evaluate the trend of antimicrobial resistance. It was found that several of these significant genes (i.e., aph(3″)-Ib, aph(6)-Id, blaTEM-1, and qacEdelta1) are shared among all six countries studied. Based on the time profiles, a large number of genes and pathogens showed an increasing occurrence. The most shared pathogens responsible for carrying the most important genes in the six countries in the clinical setting were Acinetobacter baumannii, E. coli and Shigella, Klebsiella pneumoniae and Salmonella enterica. South Africa carried the least similar antimicrobial genes to the other countries in clinical isolates.


2019 ◽  
Vol 5 (3) ◽  
pp. 430-442 ◽  
Author(s):  
Richard M. Leggett ◽  
Cristina Alcon-Giner ◽  
Darren Heavens ◽  
Shabhonam Caim ◽  
Thomas C. Brook ◽  
...  

AbstractThe MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is, Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.


2017 ◽  
Vol 45 (6) ◽  
pp. 1768-1778 ◽  
Author(s):  
Dan Cui ◽  
Xinliang Liu ◽  
Peter Hawkey ◽  
Hao Li ◽  
Quan Wang ◽  
...  

We analyzed China’s current use of and microbial resistance to antibiotics, and possible means of reducing antimicrobial resistance. Interventions like executive orders within clinical settings and educational approach with vertical approaches rather than an integrated strategy to curb the use of antimicrobials remain limited. An underlying problem is the system of incentives that has resulted in the intensification of inappropriate use by health professionals and patients. There is an urgent need to explore the relationship between financial and non-financial incentives for providers and patients, to eliminate inappropriate incentives. China’s national health reforms have created an opportunity to contain inappropriate use of antibiotics through more comprehensive and integrated strategies. Containment of microbial resistance may be achieved by strengthening surveillance at national, regional and hospital levels; eliminating detrimental incentives within the health system; and changing prescribing behaviors to a wider health systems approach, to achieve long-term, equitable and sustainable results and coordinate stakeholders’ actions through transparent sharing of information.


2008 ◽  
Vol 11 (2) ◽  
pp. 56-60 ◽  
Author(s):  
Jill K. Duthie

Abstract Clinical supervisors in university based clinical settings are challenged by numerous tasks to promote the development of self-analysis and problem-solving skills of the clinical student (American Speech-Language-Hearing Association, ASHA, 1985). The Clinician Directed Hierarchy is a clinical training tool that assists the clinical teaching process by directing the student clinician’s focus to a specific level of intervention. At each of five levels of intervention, the clinician develops an understanding of the client’s speech/language target behaviors and matches clinical support accordingly. Additionally, principles and activities of generalization are highlighted for each intervention level. Preliminary findings suggest this is a useful training tool for university clinical settings. An essential goal of effective clinical supervision is the provision of support and guidance in the student clinician’s development of independent clinical skills (Larson, 2007). The student clinician is challenged with identifying client behaviors in the therapeutic process and learning to match his or her instructions, models, prompts, reinforcement, and use of stimuli appropriately according to the client’s needs. In addition, the student clinician must be aware of techniques in the intervention process that will promote generalization of new communication behaviors. Throughout the intervention process, clinicians are charged with identifying appropriate target behaviors, quantifying the progress of the client’s acquisition of the targets, and making adjustments within and between sessions as necessary. Central to the development of clinical skills is the feedback provided by the clinical supervisor (Brasseur, 1989; Moss, 2007). Particularly in the early stages of clinical skills development, the supervisor is challenged with addressing numerous aspects of clinical performance and awareness, while ensuring the client’s welfare (Moss). To address the management of clinician and client behaviors while developing an understanding of the clinical intervention process, the University of the Pacific has developed and begun to implement the Clinician Directed Hierarchy.


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