WGS for Bacterial Identification and Susceptibility Testing in the Clinical Lab

2021 ◽  
pp. 25-44
Author(s):  
Sophia Vourli ◽  
Fanourios Kontos ◽  
Spyridon Pournaras
Keyword(s):  
Susceptibility Testing ◽  
Bacterial Identification

scholarly journals Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing

2017 ◽  
Vol 22 (6) ◽  
pp. 585-608 ◽  
Author(s):  
Yiyan Li ◽  
Xing Yang ◽  
Weian Zhao
Keyword(s):  
Antibiotic Susceptibility ◽  
Susceptibility Testing ◽  
Point Of Care ◽  
Single Cells ◽  
Turnaround Time ◽  
Resistant Bacteria ◽  
Representative Point ◽  
Antibiotic Susceptibility Testing ◽  
Bacterial Identification ◽  
Automated Systems

Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.

scholarly journals Clinical and Financial Benefits of Rapid Bacterial Identification and Antimicrobial Susceptibility Testing

1999 ◽  
Vol 37 (5) ◽  
pp. 1415-1418 ◽  
Author(s):  
Joan Barenfanger ◽  
Cheryl Drake ◽  
Gail Kacich
Keyword(s):  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Average Length ◽  
Antimicrobial Susceptibility Testing ◽  
Variable Cost ◽  
Bacterial Identification ◽  
Time Period ◽  
Normal Manner ◽  
Financial Benefits ◽  
Evening Shift

To assess the expected clinical and financial benefits of rapid reporting of microbiology results, we compared patients whose cultured samples were processed in the normal manner to patients whose samples were processed more rapidly due to a minor change in work flow. For the samples tested in the rapid-reporting time period, the vast majority of bacterial identification and antimicrobial susceptibility testing (AST) results were verified with the Vitek system on the same day that they were available. This time period was called rapid AST (RAST). For RAST, a technologist on the evening shift verified the data that became available during that shift. For the control time period, cultures were processed in the normal manner (normal AST [NAST]), which did not include evening-shift verification. For NAST, the results for approximately half of the cultures were verified on the first day that the result was available. The average turnaround time for the reporting of AST results was 39.2 h for RAST and 44.4 h for NAST (5.2 h faster for RAST [P = 0.001]). Subsequently, physicians were able to initiate appropriate antimicrobial therapy sooner for patients whose samples were tested as part of RAST (P = 0.006). The mortality rates were 7.9 and 9.6% for patients whose samples were tested as part of RAST and NAST, respectively (P = 0.45). The average length of stay was 10.7 days per patient for RAST and 12.6 days for NAST, a difference of 2.0 days less for RAST (P = 0.006). The average variable cost was $4,927 per patient for RAST and $6,677 for NAST, a difference of $1,750 less per patient for RAST (P = 0.001). This results in over $4 million in savings in variable costs per year in our hospital.

scholarly journals External Quality Assessment of Bacterial Identification and Antimicrobial Susceptibility Testing in African National Public Health Laboratories, 2011–2016

2019 ◽  
Vol 4 (4) ◽  
pp. 144 ◽  
Author(s):  
Olga Perovic ◽  
Ali A. Yahaya ◽  
Crystal Viljoen ◽  
Jean-Bosco Ndihokubwayo ◽  
Marshagne Smith ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
External Quality Assessment ◽  
Antimicrobial Susceptibility Testing ◽  
Bacterial Identification ◽  
African Region ◽  
External Quality ◽  
Bacterial Diseases ◽  
National Public Health

Background: In 2002, the World Health Organization (WHO) launched a regional microbiology external quality assessment (EQA) programme for national public health laboratories in the African region, initially targeting priority epidemic-prone bacterial diseases, and later including other common bacterial pathogens. Objectives: The aim of this study was to analyse the efficacy of an EQA programme as a laboratory quality system evaluation tool. Methods: We analysed the proficiency of laboratories’ performance of bacterial identification and antimicrobial susceptibility testing (AST) for the period 2011–2016. The National Institute for Communicable Diseases of South Africa provided technical coordination following an agreement with WHO, and supplied EQA samples of selected bacterial organisms for microscopy (Gram stain), identification, and antimicrobial susceptibility testing (AST). National public health laboratories, as well as laboratories involved in the Invasive Bacterial Diseases Surveillance Network, were enrolled by the WHO Regional Office for Africa to participate in the EQA programme. We analysed participants’ results of 41 surveys, which included the following organisms sent as challenges: Streptococcus pneumonia, Haemophilus influenzae, Neisseria meningitidis, Salmonella Typhi, Salmonella Enteritidis, Shigella flexneri, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus anginosus, Enterococcus faecium, Serratia marcescens, Acinetobacter baumannii, and Enterobacter cloacae. Results: Eighty-one laboratories from 45 countries participated. Overall, 76% of participants obtained acceptable scores for identification, but a substantial proportion of AST scores were not in the acceptable range. Of 663 assessed AST responses, only 42% had acceptable scores. Conclusion: In the African Region, implementation of diagnostic stewardship in clinical bacteriology is generally suboptimal. This report illustrates that AST is poorly done compared to microscopy and identification. It is critically important to make the case for implementation of quality assurance in AST, as it is the cornerstone of antimicrobial resistance surveillance reporting and implementation of the Global Antimicrobial Resistance Surveillance System.

scholarly journals A simple blood-culture bacterial pellet preparation for faster accurate direct bacterial identification and antibiotic susceptibility testing with the VITEK 2 system

2013 ◽  
Vol 62 (5) ◽  
pp. 773-777 ◽  
Author(s):  
Guy Prod’hom ◽  
Christian Durussel ◽  
Gilbert Greub
Keyword(s):  
Ammonium Chloride ◽  
Antibiotic Susceptibility ◽  
Susceptibility Testing ◽  
Blood Cultures ◽  
Correct Identification ◽  
Antibiotic Susceptibility Testing ◽  
Bacterial Identification ◽  
Lower Accuracy ◽  
Direct Inoculation ◽  
Vitek 2

An ammonium chloride procedure was used to prepare a bacterial pellet from positive blood cultures, which was used for direct inoculation of VITEK 2 cards. Correct identification reached 99 % for Enterobacteriaceae and 74 % for staphylococci. For antibiotic susceptibility testing, very major and major errors were 0.1 and 0.3 % for Enterobacteriaceae, and 0.7 and 0.1 % for staphylococci, respectively. Thus, bacterial pellets prepared with ammonium chloride allow direct inoculation of VITEK cards with excellent accuracy for Enterobacteriaceae and a lower accuracy for staphylococci.

A Rapid Procedure for Bacterial Identification and Antimicrobial Susceptibility Testing Directly from Positive Blood Cultures

The Analyst ◽  
2021 ◽  
Author(s):  
Bo Sun ◽  
Weili Hong ◽  
Pu Wang ◽  
Guang-Hui Zheng ◽  
Xixiong Kang ◽  
...  
Keyword(s):  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
Blood Cultures ◽  
Antimicrobial Susceptibility Testing ◽  
Bacterial Identification ◽  
Rapid Procedure

There is an urgent need to develop a rapid procedure that can rapidly identify and obtain antimicrobial susceptibility testing (AST) results directly from positive blood cultures. Here, we report a...

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