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Kritikos A, Prod'hom G, Jacot D, Croxatto A, Greub G. The Impact of Laboratory Automation on the Time to Urine Microbiological Results: A Five-Year Retrospective Study. Diagnostics (Basel) 2024; 14:1392. [PMID: 39001282 PMCID: PMC11240889 DOI: 10.3390/diagnostics14131392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Total laboratory automation (TLA) is a valuable component of microbiology laboratories and a growing number of publications suggest the potential impact of automation in terms of analysis standardization, streaking quality, and the turnaround time (TAT). The aim of this project was to perform a detailed investigation of the impact of TLA on the workflow of commonly treated specimens such as urine. This is a retrospective observational study comparing two time periods (pre TLA versus post TLA) for urine specimen culture processing. A total of 35,864 urine specimens were plated during the pre-TLA period and 47,283 were plated during the post-TLA period. The median time from streaking to identification decreased from 22.3 h pre TLA to 21.4 h post TLA (p < 0.001), and the median time from streaking to final validation of the report decreased from 24.3 h pre TLA to 23 h post TLA (p < 0.001). Further analysis revealed that the observed differences in TAT were mainly driven by the contaminated and positive samples. Our findings demonstrate that TLA has the potential to decrease turnaround times of samples in a laboratory. Nevertheless, changes in laboratory workflow (such as extended opening hours for plate reading and antibiotic susceptibility testing or decreased incubation times) might further maximize the efficiency of TLA and optimize TATs.
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Affiliation(s)
- Antonios Kritikos
- Institute of Microbiology, Lausanne University Hospital (CHUV), University of Lausanne, 1005 Lausanne, Switzerland
- Unité d'Infectiologie, Département de Médecine, Hôpital de Fribourg HFR, 1752 Villars-sur-Glâne, Switzerland
| | - Guy Prod'hom
- Institute of Microbiology, Lausanne University Hospital (CHUV), University of Lausanne, 1005 Lausanne, Switzerland
| | - Damien Jacot
- Institute of Microbiology, Lausanne University Hospital (CHUV), University of Lausanne, 1005 Lausanne, Switzerland
| | - Antony Croxatto
- Institute of Microbiology, Lausanne University Hospital (CHUV), University of Lausanne, 1005 Lausanne, Switzerland
- ADMED Microbiology, 2000 La Chaux-de-Fonds, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital (CHUV), University of Lausanne, 1005 Lausanne, Switzerland
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Trigueiro G, Oliveira C, Rodrigues A, Seabra S, Pinto R, Bala Y, Gutiérrez Granado M, Vallejo S, Gonzalez V, Cardoso C. Conversion of a classical microbiology laboratory to a total automation laboratory enhanced by the application of lean principles. Microbiol Spectr 2024; 12:e0215323. [PMID: 38230933 PMCID: PMC10846136 DOI: 10.1128/spectrum.02153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/03/2023] [Indexed: 01/18/2024] Open
Abstract
Laboratory automation in microbiology improves productivity and reduces sample turnaround times (TATs). However, its full potential can be unlocked through the optimization of workflows by adopting lean principles. This study aimed to explore the relative impact of laboratory automation and continuous improvement events (CIEs) on productivity and TATs. Laboratory automation took place in November 2020 and consisted of the introduction of WASPLab and VITEK MS systems. CIEs were run in May and September 2021. Before the conversion, the laboratory processed about ~492 samples on weekdays and had 10 full-time equivalent (FTE) staff for a productivity of 49 samples/FTE/day. In March 2021, after laboratory automation, the caseload went up to ~621 while the FTEs decreased to 8.5, accounting for productivity improvement to 73 samples/FTE/day. The hypothetical productivity went up to 110 samples/FTE/day following CIEs, meaning that the laboratory could at that point deal with a caseload increase to ~935 with unchanged FTEs. Laboratory conversion also led to an improvement in TATs for all sample types. For vaginal swabs and urine samples, median TATs decreased from 70.3 h [interquartile range (IQR): 63.5-93.1] and 73.7 h (IQR: 35.6-50.7) to 48.2 h (IQR: 44.8-67.7) and 40.0 h (IQR: 35.6-50.7), respectively. Automation alone was responsible for 37.2% and 75.8% of TAT reduction, respectively, while the remaining reduction of 62.8% and 24.2%, respectively, was achieved due to CIEs. The laboratory reached productivity and TAT goals predefined by the management after CIEs. In conclusion, automation substantially improved productivity and TATs, while the subsequent implementation of lean management further unlocked the potential of laboratory automation.IMPORTANCEIn this study, we combined total laboratory automation with lean management to show that appropriate laboratory work organization enhanced the benefit of the automation and substantially contributed to productivity improvements. Globally, the rapid availability of accurate results in the setting of a clinical microbiology laboratory is part of patient-centered approaches to treat infections and helps the implementation of antibiotic stewardship programs backed by the World Health Organization. Locally, from the point of view of laboratory management, it is important to find ways of maximizing the benefits of the use of technology, as total laboratory automation is an expensive investment.
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Affiliation(s)
- Graça Trigueiro
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Carlos Oliveira
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Alexandra Rodrigues
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Sofia Seabra
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Rui Pinto
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Yohann Bala
- Global Medical Affairs, bioMérieux, Marcy L’Etoile, France
| | | | - Sandra Vallejo
- Lab Consultancy, bioMérieux, bioMérieux SA, Lisbon, Portugal
| | | | - Carlos Cardoso
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
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Vanstokstraeten R, Demuyser T, Piérard D, Wybo I, Blockeel C, Mackens S. Culturomics in Unraveling the Upper Female Reproductive Tract Microbiota. Semin Reprod Med 2023; 41:151-159. [PMID: 38101449 DOI: 10.1055/s-0043-1777758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
In recent years, the study of the human microbiome has surged, shedding light on potential connections between microbiome composition and various diseases. One specific area of intense interest within this research is the female reproductive tract, as it holds the potential to influence the process of embryo implantation. Advanced sequencing technologies have delivered unprecedented insights into the microbial communities, also known as microbiota, residing in the female reproductive tract. However, their efficacy encounters significant challenges when analyzing low-biomass microbiota, such as those present in the endometrium. These molecular techniques are susceptible to contamination from laboratory reagents and extraction kits, leading to sequencing bias that can significantly alter the perceived taxonomy of a sample. Consequently, investigating the microbiota of the upper female reproductive tract necessitates the exploration of alternative methods. In this context, the current review delves into the application of culturomics in unraveling the upper female reproductive tract microbiota. While culturomics holds value in research, its transition to routine clinical practice appears remote, at least in the foreseeable future.
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Affiliation(s)
- Robin Vanstokstraeten
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
- AIMS Lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Shari Mackens
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
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Mencacci A, De Socio GV, Pirelli E, Bondi P, Cenci E. Laboratory automation, informatics, and artificial intelligence: current and future perspectives in clinical microbiology. Front Cell Infect Microbiol 2023; 13:1188684. [PMID: 37441239 PMCID: PMC10333692 DOI: 10.3389/fcimb.2023.1188684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Clinical diagnostic laboratories produce one product-information-and for this to be valuable, the information must be clinically relevant, accurate, and timely. Although diagnostic information can clearly improve patient outcomes and decrease healthcare costs, technological challenges and laboratory workflow practices affect the timeliness and clinical value of diagnostics. This article will examine how prioritizing laboratory practices in a patient-oriented approach can be used to optimize technology advances for improved patient care.
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Affiliation(s)
- Antonella Mencacci
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
- Microbiology, Perugia General Hospital, Perugia, Italy
| | | | - Eleonora Pirelli
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Paola Bondi
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Elio Cenci
- Microbiology and Clinical Microbiology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
- Microbiology, Perugia General Hospital, Perugia, Italy
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Vanstokstraeten R, Mackens S, Callewaert E, Blotwijk S, Emmerechts K, Crombé F, Soetens O, Wybo I, Vandoorslaer K, Mostert L, De Geyter D, Muyldermans A, Blockeel C, Piérard D, Demuyser T. Culturomics to Investigate the Endometrial Microbiome: Proof-of-Concept. Int J Mol Sci 2022; 23:12212. [PMID: 36293066 PMCID: PMC9602868 DOI: 10.3390/ijms232012212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/03/2022] [Accepted: 10/09/2022] [Indexed: 08/29/2023] Open
Abstract
The microbiome of the reproductive tract has been associated with (sub)fertility and it has been suggested that dysbiosis reduces success rates and pregnancy outcomes. The endometrial microbiome is of particular interest given the potential impact on the embryo implantation. To date, all endometrial microbiome studies have applied a metagenomics approach. A sequencing-based technique, however, has its limitations, more specifically in adequately exploring low-biomass settings, such as intra-uterine/endometrial samples. In this proof-of-concept study, we demonstrate the applicability of culturomics, a high-throughput culturing approach, to investigate the endometrial microbiome. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy, as part of their routine work-up at Brussels IVF, were included after their informed consent. Biopsies were used to culture microbiota for up to 30 days in multiple aerobic and anaerobic conditions. Subsequent WASPLab®-assisted culturomics enabled a standardized methodology. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA sequencing was applied to identify all of bacterial and fungal isolates. Eighty-three bacterial and two fungal species were identified. The detected species were in concordance with previously published metagenomics-based endometrial microbiota analyses as 77 (91%) of them belonged to previously described genera. Nevertheless, highlighting the added value of culturomics to identify most isolates at the species level, 53 (62.4%) of the identified species were described in the endometrial microbiota for the first time. This study shows the applicability and added value of WASPLab®-assisted culturomics to investigate the low biomass endometrial microbiome at a species level.
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Affiliation(s)
- Robin Vanstokstraeten
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Shari Mackens
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ellen Callewaert
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Susanne Blotwijk
- Biostatistics and Medical Informatics Research Group (BISI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Kristof Emmerechts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Florence Crombé
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Laurence Mostert
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Deborah De Geyter
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Astrid Muyldermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
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Antonios K, Croxatto A, Culbreath K. Current State of Laboratory Automation in Clinical Microbiology Laboratory. Clin Chem 2021; 68:99-114. [PMID: 34969105 DOI: 10.1093/clinchem/hvab242] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/15/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Although it has been 30 years since the first automation systems were introduced in the microbiology laboratory, total laboratory automation (TLA) has only recently been recognized as a valuable component of the laboratory. A growing number of publications illustrate the potential impact of automation. TLA can improve standardization, increase laboratory efficiency, increase workplace safety, and reduce long-term costs. CONTENT This review provides a preview of the current state of automation in clinical microbiology and covers the main developments during the last years. We describe the available hardware systems (that range from single function devices to multifunction workstations) and the challenging alterations on workflow and organization of the laboratory that have to be implemented to optimize automation. SUMMARY Despite the many advantages in efficiency, productivity, and timeliness that automation offers, it is not without new and unique challenges. For every advantage that laboratory automation provides, there are similar challenges that a laboratory must face. Change management strategies should be used to lead to a successful implementation. TLA represents, moreover, a substantial initial investment. Nevertheless, if properly approached, there are a number of important benefits that can be achieved through implementation of automation in the clinical microbiology laboratory. Future developments in the field of automation will likely focus on image analysis and artificial intelligence improvements. Patient care, however, should remain the epicenter of all future directions and there will always be a need for clinical microbiology expertise to interpret the complex clinical and laboratory information.
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Affiliation(s)
- Kritikos Antonios
- University of Lausanne, Institute of Microbiology, Lausanne, Switzerland
| | - Antony Croxatto
- University of Lausanne, Institute of Microbiology, Lausanne, Switzerland
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Gao J, Chen Q, Peng Y, Jiang N, Shi Y, Ying C. Copan Walk Away Specimen Processor (WASP) Automated System for Pathogen Detection in Female Reproductive Tract Specimens. Front Cell Infect Microbiol 2021; 11:770367. [PMID: 34869072 PMCID: PMC8635742 DOI: 10.3389/fcimb.2021.770367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Objective Automation is increasingly being applied in clinical laboratories; however, preanalytical processing for microbiology tests and screening is still largely performed using manual methods owing to the complex procedures involved. To promote automation of clinical microbiology laboratories, it is important to assess the performance of automated systems for different specimen types separately. Therefore, the aim of this study was to explore the potential clinical application of the Copan Walk Away Specimen Processor (WASP) automated preanalytical microbiology processing system in the detection of pathogens in female reproductive tract specimens and its feasibility in optimizing diagnostic procedures. Methods Female reproductive tract specimens collected from pregnant women at their first obstetric check-up were inoculated into culture media using the Copan WASP automated specimen processing system and were also cultured using a conventional manual inoculation method. After 48 h of culture, the growth of colonies was observed, and the types of bacteria, number of colonies, and efficiency in isolating single colonies were compared between the automated and manual groups. The specimens collected from the WASP system using the Copan-ESwab sample collection tubes were further analyzed for the presence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Ureaplasmaurealyticum (UU) via fluorescence quantitative polymerase chain reaction (qPCR) and an immunochromatographic assay to investigate the feasibility of this method in optimizing detection of these common pathogens of the female reproductive tract. Results Compared with the manual culture method, the Copan WASP microbiology automation system detected fewer bacterial types (P<0.001) and bacterial colonies (P<0.001) but had a higher detection rate of single colonies (P<0.001). There was no significant difference in the detection rates of common pathogens encountered in clinical obstetrics and gynecology, including group B Streptococcus (GBS) (P=0.575) and Candida (P=0.917), between the two methods. Specimens collected in the Copan-ESwab tubes could be used for screening of GBS and CT via fluorescence-based qPCR but not with immunochromatography. However, UU and NG were not detected in any sample with either method; thus, further validation is required to determine the feasibility of the Copan system for screening these pathogens. Conclusion The Copan WASP microbiology automation system could facilitate the optimization of diagnostic procedures for detecting common pathogens of the female reproductive system, thereby reducing associated costs.
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Affiliation(s)
- Jing Gao
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Qiujing Chen
- Institute of Cardiovascular Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiqian Peng
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Nanyan Jiang
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Youhao Shi
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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Subcutaneous tissue disinfection significantly reduces Cutibacterium acnes burden in primary open shoulder surgery. J Shoulder Elbow Surg 2021; 30:1537-1543. [PMID: 33421560 DOI: 10.1016/j.jse.2020.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 02/01/2023]
Abstract
BACKGROUND Cutibacterium acnes is one of the major pathogens responsible for infection after shoulder surgery. Surgical dissection of the dermis may expose C acnes from sebum-producing hair follicles. Because of contact with the surgeon's gloves and instruments, further spread occurs throughout the surgical field. The purpose of this study was to determine whether subcutaneous tissue disinfection could reduce the C acnes culture rate in primary open shoulder surgery. METHODS All patients eligible for primary open shoulder surgery by a deltopectoral approach were prospectively enrolled in our 2-arm, randomized, single-blinded clinical trial. In all patients, a skin swab of the operative field was taken prior to standard surgical skin preparation. After exposure of the deltoid fascia, the disinfection group received an additional preparation of the subcutaneous layer with povidone-iodine solution. Once the proximal humerus was completely exposed, 5 swabs from different sites were taken for microbiological examination according to a strict specimen collection protocol. All cultures were incubated in aerobic and anaerobic conditions for 14 days. RESULTS Between February and December 2019, 108 patients were enrolled in the 2 groups: treatment (n = 70) and control (n = 38). The 2 groups did not show any significant difference in terms of sex, age, body mass index, or occurrence of diabetes. The subcutaneous disinfection protocol significantly reduced the positive culture rate of the operating field for all germs combined (P = .036) and specifically for C acnes (P = .013). The reduction of positive swabs for C acnes was significant for the surgeon's gloves (P = .041), as well as the retractors (P = .007). CONCLUSION Disinfection of the subcutaneous tissue significantly reduced the C acnes culture rate during primary open shoulder surgery. We highly recommend this simple step as an adjunct to the current surgical practice to limit iatrogenic contamination of the surgical field. Future studies may observe a reduction in postoperative shoulder infection owing to this practice.
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Wang Z, Zhang L, Zhao M, Wang Y, Bai H, Wang Y, Rui C, Fan C, Li J, Li N, Liu X, Wang Z, Si Y, Feng A, Li M, Zhang Q, Yang Z, Wang M, Wu W, Cao Y, Qi L, Zeng X, Geng L, An R, Li P, Liu Z, Qiao Q, Zhu W, Mo W, Liao Q, Xu W. Deep Neural Networks Offer Morphologic Classification and Diagnosis of Bacterial Vaginosis. J Clin Microbiol 2021; 59:e02236-20. [PMID: 33148709 PMCID: PMC8111127 DOI: 10.1128/jcm.02236-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/01/2020] [Indexed: 11/20/2022] Open
Abstract
Bacterial vaginosis (BV) is caused by the excessive and imbalanced growth of bacteria in vagina, affecting 30 to 50% of women. Gram staining followed by Nugent scoring based on bacterial morphotypes under the microscope is considered the gold standard for BV diagnosis; this method is often labor-intensive and time-consuming, and results vary from person to person. We developed and optimized a convolutional neural network (CNN) model and evaluated its ability to automatically identify and classify three categories of Nugent scores from microscope images. The CNN model was first established with a panel of microscopic images with Nugent scores determined by experts. The model was trained by minimizing the cross-entropy loss function and optimized by using a momentum optimizer. The separate test sets of images collected from three hospitals were evaluated by the CNN model. The CNN model consisted of 25 convolutional layers, 2 pooling layers, and a fully connected layer. The model obtained 82.4% sensitivity and 96.6% specificity with the 5,815 validation images when altered vaginal flora and BV were considered the positive samples, which was better than the rates achieved by top-level technologists and obstetricians in China. The capability of our model for generalization was so strong that it exhibited 75.1% accuracy in three categories of Nugent scores on the independent test set of 1,082 images, which was 6.6% higher than the average of three technologists, who are hold bachelor's degrees in medicine and are qualified to make diagnostic decisions. When three technologists ran one specimen in triplicate, the precision of three categories of Nugent scores was 54.0%. One hundred three samples diagnosed by two technologists on different days showed a repeatability of 90.3%. The CNN model outperformed human health care practitioners in terms of accuracy and stability for three categories of Nugent score diagnosis. The deep learning model may offer translational applications in automating diagnosis of bacterial vaginosis with proper supporting hardware.
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Affiliation(s)
- Zhongxiao Wang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
| | - Lei Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Min Zhao
- Peking University First Hospital, Beijing, China
| | - Ying Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Huihui Bai
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Yufeng Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Can Rui
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Chong Fan
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jiao Li
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Na Li
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xinhuan Liu
- Peking University Third Hospital, Beijing, China
| | - Zitao Wang
- The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yanyan Si
- Binzhou Medical University Hospital, Binzhou, China
| | - Andrea Feng
- Beijing HarMoniCare Women's and Children's Hospital, Beijing, China
| | - Mingxuan Li
- Suzhou Turing Microbial Technologies Co., Ltd., Suzhou, China
- Beijing Turing Microbial Technologies Co., Ltd., Beijing, China
| | - Qiongqiong Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
- School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Zhe Yang
- Department of Physics, Tsinghua University, Beijing, China
| | - Mengdi Wang
- Department of Operations Research and Financial Engineering, Princeton University, Princeton, New Jersey, USA
| | - Wei Wu
- Suzhou Turing Microbial Technologies Co., Ltd., Suzhou, China
- Beijing Turing Microbial Technologies Co., Ltd., Beijing, China
| | - Yang Cao
- Suzhou Turing Microbial Technologies Co., Ltd., Suzhou, China
- Beijing Turing Microbial Technologies Co., Ltd., Beijing, China
| | - Lin Qi
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xin Zeng
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Li Geng
- Peking University Third Hospital, Beijing, China
| | - Ruifang An
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ping Li
- Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhaohui Liu
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Qiao Qiao
- The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Weipei Zhu
- The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Weike Mo
- Suzhou Turing Microbial Technologies Co., Ltd., Suzhou, China
- Beijing Turing Microbial Technologies Co., Ltd., Beijing, China
- Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Qinping Liao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
- School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Wei Xu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China
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Yue P, Zhou M, Zhang L, Yang Q, Song H, Xu Z, Zhang G, Xie X, Xu Y. Clinical Performance of BD Kiestra InoqulA Automated System in a Chinese Tertiary Hospital. Infect Drug Resist 2020; 13:941-947. [PMID: 32280250 PMCID: PMC7132006 DOI: 10.2147/idr.s245173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/10/2020] [Indexed: 11/25/2022] Open
Abstract
Background The aim of this study was to evaluate the clinical performance of the BD Kiestra InoqulA automated specimen processing system with commonly encountered clinical microbiology specimens. Materials and Methods Four types of clinical specimens (sputum, urine, normally sterile body fluids, and feces) were inoculated onto relevant agar plates using a manual method and the BD Kiestra automated system. The number of isolated pathogen species, number of isolated single colonies and uniformity of plate streaking were calculated and compared between two methods. Results Significantly more isolated colonies were observed on plates inoculated by InoqulA for all specimen types and media with the exception of sputum specimens inoculated onto chocolate agar with vancomycin (P =0.076) and urine onto China blue agar (P =0.856). The quality of plate streaking was also better with InoqulA for all specimen types and media with the exception of urine specimens (P =1.000) and sterile body fluids (P =0.56) inoculated onto China blue agar. Conclusion This is the first evaluation study of InoqulA with 4 types of clinical specimens in China. It focused on the effect of streaking plates automatically with the magnetic bead. Inoculation of clinical specimens with the BD Kiestra InoqulA system is superior to the manual method for recovery of single colonies and the overall quality of semi-quantitative plate streaking.
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Affiliation(s)
- Pinli Yue
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Lintao Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Hongmei Song
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Zhipeng Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Ge Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Xiuli Xie
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Yingchun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
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11
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Vandenberg O, Durand G, Hallin M, Diefenbach A, Gant V, Murray P, Kozlakidis Z, van Belkum A. Consolidation of Clinical Microbiology Laboratories and Introduction of Transformative Technologies. Clin Microbiol Rev 2020; 33:e00057-19. [PMID: 32102900 PMCID: PMC7048017 DOI: 10.1128/cmr.00057-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clinical microbiology is experiencing revolutionary advances in the deployment of molecular, genome sequencing-based, and mass spectrometry-driven detection, identification, and characterization assays. Laboratory automation and the linkage of information systems for big(ger) data management, including artificial intelligence (AI) approaches, also are being introduced. The initial optimism associated with these developments has now entered a more reality-driven phase of reflection on the significant challenges, complexities, and health care benefits posed by these innovations. With this in mind, the ongoing process of clinical laboratory consolidation, covering large geographical regions, represents an opportunity for the efficient and cost-effective introduction of new laboratory technologies and improvements in translational research and development. This will further define and generate the mandatory infrastructure used in validation and implementation of newer high-throughput diagnostic approaches. Effective, structured access to large numbers of well-documented biobanked biological materials from networked laboratories will release countless opportunities for clinical and scientific infectious disease research and will generate positive health care impacts. We describe why consolidation of clinical microbiology laboratories will generate quality benefits for many, if not most, aspects of the services separate institutions already provided individually. We also define the important role of innovative and large-scale diagnostic platforms. Such platforms lend themselves particularly well to computational (AI)-driven genomics and bioinformatics applications. These and other diagnostic innovations will allow for better infectious disease detection, surveillance, and prevention with novel translational research and optimized (diagnostic) product and service development opportunities as key results.
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Affiliation(s)
- Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
| | - Géraldine Durand
- bioMérieux, Microbiology Research and Development, La Balme Les Grottes, France
| | - Marie Hallin
- Department of Microbiology, LHUB-ULB, Groupement Hospitalier Universitaire de Bruxelles (GHUB), Université Libre de Bruxelles, Brussels, Belgium
| | - Andreas Diefenbach
- Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Labor Berlin, Charité-Vivantes GmbH, Berlin, Germany
| | - Vanya Gant
- Department of Clinical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Patrick Murray
- BD Life Sciences Integrated Diagnostic Solutions, Scientific Affairs, Sparks, Maryland, USA
| | - Zisis Kozlakidis
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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12
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Cheng CWR, Ong CH, Chan DSG. Impact of BD Kiestra InoqulA streaking patterns on colony isolation and turnaround time of methicillin-resistant Staphylococcus aureus and carbapenem-resistant Enterobacterale surveillance samples. Clin Microbiol Infect 2020; 26:1201-1206. [PMID: 31935564 DOI: 10.1016/j.cmi.2020.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To determine if using alternative streaking patterns on the BD Kiestra InoqulA can impact colony isolation and improve turnaround time (TAT) of methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacterales (CRE) screening samples. METHODS A total of 1571 positive MRSA screening samples were studied, of which 755 screening plates were streaked by the standard pattern (4-Quadrant uniform S200) and 816 plates were streaked by an alternative pattern (Zigzag 3.5-1 S200). A total of 424 CRE-positive screening samples were studied, of which 211 screening plates were streaked by the standard pattern (Zigzag 2.5-1 inoc S200) and 213 plates were streaked by an alternative customized pattern (Zigzag 3.5-1 vertstreak s200). RESULTS There was a reduction in the number of MRSA screening plates with insufficient isolated colonies for confirmatory testing from 75 plates (9.9%) when using the standard pattern to 18 plates (2.2%) when using the alternative streaking pattern. MRSA cases with a TAT above 36 hours also reduced significantly from 144 (19.1%) to 20 (2.4%). The number of CRE screening plates with insufficient colonies for same-day confirmatory testing reduced from 16 (7.6%) when using the standard pattern to two plates (1.1%) when using the alternative customized pattern. CRE cases with a TAT above 36 hours also reduced from 16 (7.6%) to seven (3.3%). CONCLUSIONS The change in streaking patterns resulted in more plates with sufficient isolated colonies as well as reduced man-hours and materials required to perform subculture of mixed colonies and overall improvements in TAT.
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Affiliation(s)
- C W R Cheng
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, Singapore.
| | - C H Ong
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, Singapore
| | - D S G Chan
- Department of Laboratory Medicine, Ng Teng Fong General Hospital, Singapore
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Abstract
The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory. After reviewing this chapter, the reader will be able to:List key considerations for specimen collection for microbiology testing. Discuss the advantages and limitations of automation in the clinical microbiology laboratory. Describe the evolution of microorganism identification methods. Discuss the benefits and limitations of molecular microbiology point-of-care testing. Summarize currently available multiplex molecular microbiology testing options.
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14
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Faron ML, Buchan BW, Samra H, Ledeboer NA. Evaluation of WASPLab Software To Automatically Read chromID CPS Elite Agar for Reporting of Urine Cultures. J Clin Microbiol 2019; 58:e00540-19. [PMID: 31694967 PMCID: PMC6935927 DOI: 10.1128/jcm.00540-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 10/26/2019] [Indexed: 11/20/2022] Open
Abstract
Urine cultures are among the most common specimens received by clinical laboratories and generate a major share of the laboratory workload. Chromogenic agar can expedite culture results, but technologist review is still needed. In this study, we evaluated the ability of the WASPLab software to interpret urine specimens plated onto chromID CPS Elite (CPSE) agar. Urine specimens submitted for bacterial culture were plated onto CPSE agar with a 1-μl loop using the WASP. Each plate was imaged after 0 and 18 h of incubation, and colonies were enumerated by color using the WASPLab software and a technologist's reading from a high-definition (HD) monitor. The results were reported as negative if <10 colonies/plate were detected. Laboratory information system (LIS) time stamps were used to measure the time to result. A total of 1,581 urine cultures were tested. The sensitivity and specificity of the software were 99.8% and 68.5%, respectively, which included 2 manual-positive/automation-negative (MP/AN) results and 170 manual-negative/automation-positive (MN/AP) results. Of the 170 MN/AP specimens, 116 were caused by microcolonies missed by the technologist. The remaining MN/AP results were caused by either count differences near the 10-colony threshold (n = 43) or count differences of >50 CFU (n = 11). The use of both CPSE agar and the WASPLab software improved the time to result for urine culture, reducing the average time to result by 4 h 42 min for negative specimens and 3 h 28 min for positive specimens compared to that with standard-of-care testing. These data demonstrate that the use of CPSE agar and automated plate reading has the potential to improve turnaround time while maintaining high sensitivity and reducing urine culture workload.
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Affiliation(s)
| | - Blake W Buchan
- Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin, USA
| | - Hasan Samra
- Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nathan A Ledeboer
- Medical College of Wisconsin, Milwaukee, Wisconsin, USA
- Wisconsin Diagnostic Laboratories, Milwaukee, Wisconsin, USA
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16
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Cherkaoui A, Renzi G, Vuilleumier N, Schrenzel J. Copan WASPLab automation significantly reduces incubation times and allows earlier culture readings. Clin Microbiol Infect 2019; 25:1430.e5-1430.e12. [PMID: 30986560 DOI: 10.1016/j.cmi.2019.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
Abstract
OBJECTIVE The aim was to evaluate whether laboratory automation (inoculation and automated incubation combined with timely defined high-resolution digital imaging) may help reduce the time required to obtain reliable culture analysis results. METHODS We compared the results obtained by WASPLab automation against WASP-based automated inoculation coupled to conventional incubation and manual diagnostic on 1294 clinical samples (483 for the derivation set and 811 for the independent validation set) that included urine, genital tract and non-sterile site specimens, as well as ESwabs for screening of methicillin-resistant Staphylococcus aureus (MRSA), methicillin-sensitive Staphylococcus aureus (MSSA), extended-spectrum beta-lactamases (ESBLs) and carbapenemase-producing Enterobacteriaceae (CPE). We used sequential routine specimens referred to the bacteriology laboratory at Geneva University Hospitals between October 2018 and March 2019. RESULTS The detection sensitivity of MRSA and MSSA at 18 hr on WASPLab was 100% (95% confidence interval [CI], 94.48-100.00%). The detection sensitivity of ESBL and CPE at 16 hr on WASPLab was 100% (95% confidence interval [CI], 94.87% to 100.00%). For urine specimens, the similarity was 79% (295/375) between 18 hr and 24 hr of incubation on WASPLab. For genital tract and non-sterile site specimens, the similarity between 16 hr and 28 hr of incubation on WASPLab were 26% (72/281) and 77% (123/159) respectively. Thus, 28 hr was defined as the final incubation time on WASPLab for genital tract and non-sterile site specimens. CONCLUSIONS The results of this study show that WASPLab automation enables a reduction of the culture reading time for all specimens tested without affecting performances. Implementing the established and duly validated incubation times will allow appropriate laboratory workflows for improved efficiency to be built.
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Affiliation(s)
- A Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.
| | - G Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland
| | - N Vuilleumier
- Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland; Division of Laboratory Medicine, Department of Medical Specialities, Faculty of Medicine, Geneva, Switzerland
| | - J Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland; Genomic Research Laboratory, Division of Infectious Diseases, Department of Medical Specialities, Faculty of Medicine, Geneva, Switzerland
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17
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Bailey AL, Ledeboer N, Burnham CAD. Clinical Microbiology Is Growing Up: The Total Laboratory Automation Revolution. Clin Chem 2018; 65:634-643. [PMID: 30518664 DOI: 10.1373/clinchem.2017.274522] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/28/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Historically, culture-based microbiology laboratory testing has relied on manual methods, and automated methods (such as those that have revolutionized clinical chemistry and hematology over the past several decades) were largely absent from the clinical microbiology laboratory. However, an increased demand for microbiology testing and standardization of sample-collection devices for microbiology culture, as well as a dwindling supply of microbiology technologists, has driven the adoption of automated methods for culture-based laboratory testing in clinical microbiology. CONTENT We describe systems currently enabling total laboratory automation (TLA) for culture-based microbiology testing. We describe the general components of a microbiology automation system and the various functions of these instruments. We then introduce the 2 most widely used systems currently on the market: Becton Dickinson's Kiestra TLA and Copan's WASPLab. We discuss the impact of TLA on metrics such as turnaround time and recovery of microorganisms, providing a review of the current literature and perspectives from laboratory directors, managers, and technical staff. Finally, we provide an outlook for future advances in TLA for microbiology with a focus on artificial intelligence for automated culture interpretation. SUMMARY TLA is playing an increasingly important role in clinical microbiology. Although challenges remain, TLA has great potential to affect laboratory efficiency, turnaround time, and the overall quality of culture-based microbiology testing.
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Affiliation(s)
- Adam L Bailey
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Nathan Ledeboer
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO;
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Fihman V, Bleunven SC, Le Glaunec JM, Maillebuau F, De Rochebouet I, Nebbad-Lechani B, Desroches M, Decousser JW. Are bacterial culture quantifications reliable? Comparative performance of the WASP automated inoculation instrument in the era of ISO 15189 accreditation. J Med Microbiol 2018; 67:1581-1588. [DOI: 10.1099/jmm.0.000847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- V. Fihman
- 2EA Dynamyc, Université Paris Est Créteil– Ecole Vétérinaire de Maison Alfort, F-94000 Créteil, France
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
| | - S. C. Bleunven
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
- 3Laboratoire de Microbiologie-Hygiène, Centre Hospitalier Intercommunal de Villeneuve-Saint-Georges, F-94195 Villeneuve-Saint-Georges, France
| | - J. M. Le Glaunec
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
| | - F. Maillebuau
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
| | - I. De Rochebouet
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
| | - B. Nebbad-Lechani
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
| | - M. Desroches
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
- 4INSERM, UMR 1137, IAME, Faculté De Médecine, Site Xavier Bichat, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - J. W. Decousser
- 1Unité de Bactériologie-Hygiène, Département de Virologie, Bactériologie-Hygiène, Parasitologie-Mycologie, Unité Transversale de Traitement des Infections, Hôpitaux Universitaires Henri Mondor, DHU 'Virus, Immunité et Cancers', Assistance Publique – Hôpitaux de Paris, F-94000 Créteil, France
- 4INSERM, UMR 1137, IAME, Faculté De Médecine, Site Xavier Bichat, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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Bloemberg GV, Braun-Kiewnick A, Tedrup J, Meijerink C, Durer E, Ritter C, Keller PM, Hombach M. Evaluation of the AID carbapenemase line probe assay for rapid detection and identification of carbapenemase genes in Gram-negative bacilli. J Antimicrob Chemother 2018; 72:1948-1954. [PMID: 28402500 DOI: 10.1093/jac/dkx100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/06/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives This study evaluated the AID carbapenemase line probe assay (LPA) for the detection and identification of carbapenem resistance genes in Enterobacteriaceae and other Gram-negative bacilli (GNB) using bacterial cultures and DNA extracts directly from patient urine samples. Methods The AID carbapenemase LPA detects 13 different carbapenemase genes. Test probe accuracy was verified for using clinical Enterobacteriaceae isolates harbouring bla KPC , bla VIM , bla NDM , bla GIM , bla AIM , bla SPM , bla IMP and bla OXA-48 and a well-characterized set of Escherichia coli DH5α strains transformed with the vector plasmid pUC57- kan harbouring bla BIC , bla SIM , bla DIM , bla IMI-3 , bla IMI-1 and bla NMC-A . Sensitivity and specificity was determined by testing 151 clinical GNB strains previously characterized for the production of carbapenemase activity and carbapenemase genes. Direct detection of carbapenemase genes using the LPA was determined using 299 clinical urine specimens. Analytical sensitivity for detection in urine was determined by testing serial dilutions of bla KPC and bla NDM in clinical Klebsiella pneumoniae strains. Results All carbapenemase gene probes showed 100% accuracy without cross-reactions. Sensitivity and specificity of the LPA using clinical isolates was 100% for each. Analytical sensitivity for detection of bla KPC and bla NDM in urine was 10 1 -10 2 cfu. The LPA detected carbapenemase genes in 20 urines, which were confirmed in 12 samples by conventional multiplex PCR. Remarkably, 0 of the 20 urines grew carbapenemase-suspicious GNB applying EUCAST recommendations. Conclusions The AID carbapenemase LPA is an accurate, sensitive and easy-to-use test for the detection and identification of carbapenemase genes, which can readily be implemented in any diagnostic laboratory.
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Affiliation(s)
- Guido V Bloemberg
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Andrea Braun-Kiewnick
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Jan Tedrup
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Carla Meijerink
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Elena Durer
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Claudia Ritter
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Peter M Keller
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Michael Hombach
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
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