1. Automation in Clinical Microbiology

Paul P. Bourbeaua and Nathan A. Ledeboerb

ABSTRACT

Historically, the trend toward automation in clinical pathology laboratories has largely bypassed the clinical microbiology laboratory. In this article, we review the historical impediments to automation in the microbiology laboratory and offer insight into the reasons why we believe that we are on the cusp of a dramatic change that will sweep a wave of automation into clinical microbiology laboratories. We review the currently available specimen-processing instruments as well as the total laboratory automation solutions. Lastly, we outline the types of studies that will need to be performed to fully assess the benefits of automation in microbiology laboratories.

Journal of Clinical Microbiology. June 2013 vol. 51 no. 6 1658-1665

Of the primary drivers of automation, standardization of identification methods to matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) and the adoption of liquid microbiology specimen transport have allowed microbiology laboratories to simplify collection and identification systems, creating a work flow that can be optimized with automation.

HISTORICAL IMPEDIMENTS TO
AUTOMATION IN MICROBIOLOGY

Microbiology is too complex to automate

No machine can replace a human in the microbiology laboratory

Automation is too expensive for microbiology laboratories

Microbiology laboratories are too small to automate.

WINDS OF CHANGE

Industry changes. Overall testing volumes are increasing 10 to 15% per year , driven in part by an aging population, testing innovations, infection control demands, and the growing challenges resulting from detection and identification of multidrug-resistant microorganisms. Consolidation of laboratories, particularly for microbiology testing, continues to increase. Larger laboratories have a greater potential to benefit from lab automation than smaller laboratories. Today, in most laboratories, plate reading is primarily a first-shift activity.

Personnel shortages. Fewer students are choosing medical technology as a career than occurred a generation ago.

Quality issues.

Demand by clinicians for new tests continues to grow, not just in total numbers but also for the types (width and breath) of testing being performed.

ABSTRACT

Automated chemistry laboratories dependent on robotic processes are the standard in both academic and large community hospital settings. Diagnostic microbiology manufacturers are betting that robotics will be used for specimen processing, plate reading, and organism identification in the near future. These systems are highly complex and have large footprints and hefty price tags. However, they are touted as being more efficient, rapid, and accurate than standard processes. Hospital administrators may be swayed to institute these new systems because of the promise of the need for fewer skilled workers, higher throughput, and greater efficiency. They also may be swayed by the fact that workers with the requisite clinical microbiology skills are becoming more difficult to find, and this technology should allow fewer skilled workers to handle larger numbers of cultures

Automated microbiology: not ready for prime time. Clinical microbiology laboratory automation lags behind its chemistry and hematology counterparts. The microbiology lab harbors odiferous incubators. The tests are manual, and results are available in days instead of minutes. MALDI-TOF, the newest technology, still relies on incubation and isolated colonies. The most revolutionary technology in the clinical microbiology laboratory has been automated direct specimen real-time PCR, and even it has limitations.

Microbiology is primed for a breakthrough in automation. Ideally, this breakthrough should reduce labor costs and decrease the historically slow microbiology turnaround time (TAT).

 A combination of robotic arms and fingers manipulates specimens and plates. Conveyors send the inoculated plates to smart incubators. Pipettes or loops make Gram stain slides. After incubation, the systems read and digitize colony growth and may even pick colonies for susceptibility testing or MALDI-TOF.

The makers of the BD Kiestra, the Copan WASP, and the bioMérieux FMLA (full microbiology lab automation).

Total laboratory automation (TLA): cheaper in the long run.

 Still require plate reading by a microbiologist.

The estimated cost of an automated specimen processor is $125,000 to $350,000.

The cost of a complete TLA system is estimated to be into the millions of dollars.

Conclusions.

Automation is not the only solution for staffing shortages in microbiology.

Technical innovation should move away from culture-based approaches toward rapid, non-culture-dependent microbiology. These instruments are within the reach of most clinical microbiology laboratories due to their small size and relative ease of use. They allow smaller labs to be early adopters of efficient technologies, to improve patient care, and to increase revenue without large investments.

The current TLA instruments are simply too large, too expensive, and unnecessarily complicated, and they have too many shortcomings to be a sound investment for most medium- to small-size laboratories.

 Most of their claimed advantages remain poorly substantiated to date.

In summary, the current TLA systems have essentially automated 20th century classic microbiology. Similarly to the way cell phones allowed some underdeveloped countries to bypass telephone poles and go straight to cell towers, TLA should involve some sort of transformative, disruptive, truly revolutionary technology that we have not yet imagined.

2. DI TRUYỀN KHÁNG THUỐC CỦA VI KHUẨN ĐƯỜNG RUỘT

Theo chiều dọc ( nhiễm sắc thể, c): AmpC: kháng cephalosporin thế hệ 1 ,2,3.

Theo chiều ngang (plasmid, p): ESBL ( Extended Spectrum Beta-lactamse): kháng cephalosporin thế hệ 1,2,3,4. Nhạy imipenem.

3. Tình hình lậu cầu kháng thuốc

Neisseria gonorrhoeae Antimicrobial Susceptibility Surveillance - The Gonococcal Isolate Surveillance Project, 27 Sites, United States, 2014 MMWR July 14, 2016.

Nghiên cứu khảo sát tính kháng thuốc của NG do GISP thực hiện (Gonococcal Isolate Surveillance Project) tại 27 thành phố của Hoa Kỳ.

Trong số 5093 chủng NG được phân lập vào năm 2014 thì có 25,3% kháng tetracycline, 19,2% kháng ciprofloxacin, và 16,2% kháng penicillin.

Giảm nhạy cảm với azithromycin (Azi-RS) (khi nồng độ ức chế tối [MIC] ≥2,0 µg/mL) tăng từ 0,6% năm 2013 lên 2,5% năm 2014. Các chủng giảm nhạy cảm Azi-RS không giảm nhạy cảm đồng thời với cefixime hoặc ceftriaxone.

Tần suất giảm nhạy cảm cefixime Cfx-RS (MIC ≥0,25 µg/mL) tăng từ 0,1% năm 2006 lên 1,4% năm 2010 và 2011, giảm còn 0,4% năm 2013, và tăng lại 0.8% năm 2014.

Giảm nhạy cảm ceftriaxone Cro-RS (MIC ≥0,125 µg/mL) tăng từ 0,1% năm 2008 lên 0.4% năm 2011 và giảm còn 0.1% năm 2013 và 2014. Tỷ lệ NG kháng thuốc ở MSM cao hơn ở MSW.

Tổng kết KSĐ lậu 6 tháng đầu năm 2016 tại Bệnh viện Da liễu TPHCM vs CDC 2014

4. PCR LẬU

Khuyến cáo về các xét nghiệm chẩn đoán CT và NG đang lưu hành được đưa ra vào năm 2014 dưới sự phối hợp của 4 tổ chức của Hoa Kỳ là CDC, FDA, Centers for Medicaid Services (CMS) và Association of Public Health Laboratories (APHL) trên cơ sở phân tích và tổng hợp y học chứng cứ Medline database trong 6 năm từ 2008-2014.

Có 5 nhà sản xuất được FDA công nhận cho thử nghiệm NAAT để tìm CT và NG tại Hoa kỳ, bao gồm Abbott RealTime m2000 CT/NG (Abbott Molecular), Amplicor and cobas CT/NG test (Roche Molecular Diagnostics); Aptima, (Hologic/Gen-Probe); BD ProbeTec ET and Qx (Becton Dickinson), và Xpert CT/NG Assay (Cepheid).

Papp JR, Schachter J, Gaydos C, et al. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae. MMWR Recomm Rep 2014;63(No. RR-02).