Article
Immunology
Weili Zhang, Siying Wu, Jin Deng, Quanfeng Liao, Ya Liu, Li Xiong, Ling Shu, Yu Yuan, Yuling Xiao, Ying Ma, Mei Kang, Dongdong Li, Yi Xie
Summary: The research investigated the changes in TAT before and after the adoption of TLA in the laboratory, revealing a significant reduction in TAT for CSF samples and improvements in TAT for other types of samples. Additionally, there was a significant decrease in the incidence of broth growth for pre-TLA compared to post-TLA.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Alberto Signoroni, Alessandro Ferrari, Stefano Lombardi, Mattia Savardi, Stefania Fontana, Karissa Culbreath
Summary: Full Laboratory Automation is changing work habits in clinical microbiology, and deep learning architectures are revolutionizing visual interpretation tasks. DeepColony is a multi-network system that can effectively interpret diagnostic bacterial culture plates in clinical microbiology, achieving presumptive pathogen identification.
NATURE COMMUNICATIONS
(2023)
Review
Microbiology
Dorina Timofte, Els M. Broens, Luca Guardabassi, Constanca Pomba, Fergus Allerton, John Ikonomopoulos, Gudrun Overesch, Peter Damborg
Summary: Clinical microbiology laboratories have an important role in guiding antimicrobial treatment, but there is a need for standardized training and harmonization of diagnostic procedures, particularly in veterinary clinical microbiology. The European Network for Optimization of Veterinary Antimicrobial Treatment (ENOVAT) aims to address these issues by working with experts to standardize laboratory methodologies and optimize veterinary antimicrobial treatment, potentially creating a template for international implementation.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Review
Microbiology
Liang Wang, Fen Li, Bin Gu, Pengfei Qu, Qinghua Liu, Junjiao Wang, Jiawei Tang, Shubin Cai, Qi Zhao, Zhong Ming
Summary: Studies suggest that reductionism does not provide a comprehensive understanding of complex systems like microbiota and related diseases. Microbes exist in complex communities, and with the development of metaomics techniques, a deeper understanding of the human microbiome from various perspectives can provide new insights and potential diagnostic biomarkers for human diseases. This mini-review explores the potential applications of metaomics techniques in clinical diagnoses, such as infectious diseases, and discusses the limitations of these techniques.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Amy L. Leber, Ellena Peterson, Jennifer Dien Bard
Summary: The COVID pandemic has highlighted the importance of laboratory medicine and the critical shortage of trained laboratory personnel. The need for laboratory professionals is expected to grow by 11% by 2030. Proposed actions to address this issue include increasing awareness of the medical laboratory science profession and providing more training opportunities. Recent survey data shows that 80% of microbiology laboratories have vacant positions due to a lack of qualified applicants.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Pediatrics
Jyotsna Bhattacharya, Ellen J. J. Silver, Einat Blumfield, Dominique M. M. Jan, Betsy C. C. Herold, David L. L. Goldman
Summary: In children with complicated appendicitis, rupture of the appendix leads to higher morbidity rates. Longer hospital stay is associated with more severe illness, including ICU stay, ileus, and multiple drainage procedures. The duration of symptoms prior to presentation is linked to a longer stay. The presence of abscess, right upper quadrant free fluid, and elevated C-reactive protein are independently associated with a longer stay.
FRONTIERS IN PEDIATRICS
(2022)
Article
Immunology
Antonella Mencacci, Giuseppe Vittorio De Socio, Eleonora Pirelli, Paola Bondi, Elio Cenci
Summary: Clinical diagnostic laboratories produce valuable information that needs to be clinically relevant, accurate, and timely. However, technological challenges and laboratory workflow practices can affect the timeliness and clinical value of diagnostics. This article explores how prioritizing patient-oriented approaches can optimize technology advances for improved patient care.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Infectious Diseases
Ernestina Gambrah, Alex Owusu-Ofori, Eno Biney, Chris Oppong, Susan E. Coffin
Summary: The study aimed to characterize antibiotic usage in the treatment of uncomplicated urinary tract infection in a Ghanaian Accident & Emergency ward, revealing high rates of improper usage.
Results showed that most patients with confirmed UTI had isolates that were not susceptible to antibiotics selected for empiric treatment, and only a small percentage of patients had their empiric regimen adjusted based on the sensitivity of the isolates.
It is suggested to establish hospital-wide guidelines to improve antibiotic utilization and patient outcomes by increasing the use of urine cultures and tailoring therapy in response to culture results.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Medical Laboratory Technology
KyungYi Kim, Sang-Guk Lee, Tae Hyun Kim, Sang Gyu Lee
Summary: This study analyzed the clinical and economic effectiveness of Total laboratory automation (TLA) and found that TLA significantly improves laboratory performance, has a relatively quick payback period, and can reduce total hospital expenses in the long term. Therefore, the capital investment for TLA adoption is considered worthwhile.
ANNALS OF LABORATORY MEDICINE
(2022)
Review
Immunology
Alicia G. Beukers, Frances Jenkins, Sebastiaan J. van Hal
Summary: Whole genome sequencing (WGS) is widely used in managing microbial outbreaks, but the current model of sending isolates to a central lab for sequencing has limitations. The slow rollout of WGS in clinical labs is due to the need for trained personnel and regulatory requirements. Onsite sequencing has benefits over centralized sequencing, allowing for collaboration with local infection control staff and rapid data analysis to understand transmission chains.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Review
Medicine, General & Internal
Wenjun Zhou, Limin Zou, Fenyong Zhu, Jie Yang
Summary: This paper mainly discusses how to implement daily biosafety protection measures in clinical microbiology laboratories during the COVID-19 epidemic to ensure the safe conduct of routine clinical microbiology testing. The potential risks of the laboratory are analyzed from the perspective of personal protection before, during, and after testing based on the microbiological and epidemiological characteristics of the novel coronavirus. Improved biosafety measures and optimized workflows are introduced to ensure the safety of medical staff and the smooth progress of daily work.
Article
Microbiology
Karissa Culbreath, Heather Piwonka, John Korver, Mir Noorbakhsh
Summary: This study is the first large, multicenter study in North America to report on the benefits derived from laboratory automation measured in full-time equivalents (FTE), FTE reallocation, productivity, cost per specimen, and cost avoidance. The results show that regardless of the size of the facility, improved efficiencies can be realized after implementation of full laboratory automation.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Review
Medical Laboratory Technology
Luis F. B. Porto, Carolina N. Franca, Carlos E. dos S. Ferreira
Summary: In the healthcare industry, there is strong pressure to reduce costs and scarcity of resources, requiring the development of an innovative model combining quality, sustainability, and increased access. Decision-making processes need cost assessments and alignment with institutional strategies to remain competitive in the global business environment.
CLINICAL LABORATORY
(2021)
Article
Microbiology
Zhongxiao Wang, Lei Zhang, Min Zhao, Ying Wang, Huihui Bai, Yufeng Wang, Can Rui, Chong Fan, Jiao Li, Na Li, Xinhuan Liu, Zitao Wang, Yanyan Si, Andrea Feng, Mingxuan Li, Qiongqiong Zhang, Zhe Yang, Mengdi Wang, Wei Wu, Yang Cao, Lin Qi, Xin Zeng, Li Geng, Ruifang An, Ping Li, Zhaohui Liu, Qiao Qiao, Weipei Zhu, Weike Mo, Qinping Liao, Wei Xu
Summary: A convolutional neural network model was developed to automatically identify and classify bacterial vaginosis Nugent scores from microscope images, outperforming human health care practitioners in terms of accuracy and stability.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Carlo Santoro, Sofia Babanova, Pierangela Cristiani, Kateryna Artyushkova, Plamen Atanassov, Alain Bergel, Orianna Bretschger, Robert K. Brown, Kayla Carpenter, Alessandra Colombo, Rachel Cortese, Benjamin Erable, Falk Harnisch, Mounika Kodali, Sujal Phadke, Sebastian Riedl, Luis F. M. Rosa, Uwe Schroeder
Summary: The cross-laboratory study on microbial fuel cells (MFC) demonstrated that enriched microbial consortia from different geographic locations can exhibit similar electrochemical output in MFCs. Despite the diversity of bacterial communities, all MFCs were able to achieve similar maximum power outputs and COD removal efficiencies, indicating the potential for developing common standards for MFCs.
Article
Microbiology
Daniel M. Webber, Meghan A. Wallace, Carey-Ann D. Burnham
Summary: By reducing the incubation time for disk diffusion testing from 24 hours to 6 hours, the turnaround time for antimicrobial susceptibility testing can be significantly improved without additional costs or equipment requirements.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Miranda J. Wallace, Sophonie Jean, Meghan A. Wallace, Carey-Ann D. Burnham, Gautam Dantas
Summary: This study demonstrates species-specific patterns in antimicrobial resistance within the Bacteroides fragilis group (BFG) by using comparative genomics, validating new strategies for species-level organism identification and phenotypic resistance prediction in a routine clinical laboratory setting. The research emphasizes the importance of understanding and managing anaerobic infections, as well as the need for further investigations into the molecular basis for species-specific resistance patterns.
Article
Microbiology
Sanjam S. Sawhney, Eric M. Ransom, Meghan A. Wallace, Patrick J. Reich, Gautam Dantas, Carey-Ann D. Burnham
Summary: In this study, researchers discovered a high prevalence of Staphylococcus aureus isolates exhibiting a borderline oxacillin resistance phenotype (BORSA) in their neonatal intensive care unit (NICU). They found that the current MRSA screening methods misclassified BORSA, and identified specific markers that can distinguish BORSA from methicillin-susceptible S. aureus (MSSA). The findings have implications for epidemiological reporting of MRSA rates and can help improve MRSA screening methods.
Article
Microbiology
Tanis C. Dingle, Dulini Gamage, Sara Gomez-Villegas, Blake M. Hanson, Jinnethe Reyes, April Abbott, Carey-Ann D. Burnham, Jennifer Dien Bard, Stephanie Fritz, William R. Miller, Lars F. Westblade, Barbara Zimmer, Cesar A. Arias, Susan Butler-Wu
Summary: This multicenter study evaluated the prevalence of the cefazolin inoculum effect (CzIE) in North American methicillin-susceptible Staphylococcus aureus (MSSA) isolates. The study found that the CzIE was present in 18.6% of MSSA isolates, with varying prevalence across different study sites. Furthermore, more CzIE-positive isolates had a cefazolin MIC of 1.0 μg/mL, while more CzIE-negative isolates had a MIC of 0.25 μg/mL.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Virology
Antonios Kritikos, Sophie Gabellon, Jean-Luc Pagani, Matteo Monti, Pierre-Yves Bochud, Oriol Manuel, Alix Coste, Gilbert Greub, Matthieu Perreau, Giuseppe Pantaleo, Antony Croxatto, Frederic Lamoth
Summary: This study assessed the correlation between the anti-SARS-CoV-2 serological response and COVID-19 outcome. The results showed that antibody titers gradually increased and were significantly higher in patients requiring invasive ventilation. Serum testing at admission may be a good predictor for identifying severe COVID-19 patients who will require invasive mechanical ventilation.
Review
Microbiology
Sophonie Jean, Miranda J. Wallace, Gautam Dantas, Carey-Ann D. Burnham
Summary: Bacteroides fragilis group (BFG) species are common members of the human microbiota, providing benefits to hosts but also causing infections. BFG bacteria are often resistant to commonly used antimicrobials, making treatment challenging. Whole-genome sequencing supports recent proposals for taxonomic reclassifications within the BFG. Species-level reporting and susceptibility testing are important for effective treatment of BFG infections.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Manon Rosselin, Guy Prod'hom, Gilbert Greub, Antony Croxatto
Summary: The study evaluated the reliability and speed of the QMAC-dRAST system in monobacterial blood cultures, showing high consistency in Enterobacterales, non-fermentative Gram-negative bacteria, staphylococci, and enterococci with low VME rates. Repeatability and reproducibility assays demonstrated the high reliability of AST results.
Article
Microbiology
Eric M. Ransom, Carey-Ann D. Burnham
Summary: The study shows that including anaerobic bottles in blood cultures can increase the detection rate of bacteria, especially for obligate anaerobes. Additionally, anaerobic bottles are advantageous for some facultative anaerobes.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Microbiology
Bejan Mahmud, Meghan A. Wallace, Kimberly A. Reske, Kelly Alvarado, Carol E. Muenks, David A. Rasmussen, Carey-Ann D. Burnham, Cristina Lanzas, Erik R. Dubberke, Gautam Dantas
Summary: ESBL-producing Escherichia coli is becoming increasingly prevalent, driven by the spread of ESBL-encoding plasmids. This study provides an in-depth genomic investigation of clinical ESBL-like E. coli isolates, revealing a comprehensive map of plasmid sharing across different boundaries. Through sequence-based network analysis, specific plasmid lineages responsible for disseminating major ESBLs have been identified. This work highlights the importance of plasmid-mediated spread in the dissemination of ESBLs and provides valuable insight into the factors underlying the increased prevalence of these genes in clinical settings.
Article
Microbiology
Nicole E. Putnam, Jung-Ho Youn, Meghan A. Wallace, Paul M. Luethy, Carey-Ann D. Burnham, Susan Butler-Wu, John P. Dekker, Anna F. Lau
Summary: The Streptococcus bovis group consists of seven species and subspecies, and definitive identification is important due to their association with various diseases. However, currently used identification platforms have limitations and inconsistencies.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Microbiology
Nicole J. Tarlton, Meghan A. Wallace, Robert F. Potter, Kailun Zhang, Gautam Dantas, Erik R. Dubberke, Carey-Ann D. Burnham, Melanie L. Yarbrough
Summary: In this study, a Morganella morganii isolate MMOR1 was found to be susceptible to third/ fourth-generation cephalosporins and intermediate to meropenem, but positive for NDM and IMP carbapenemases by NG-Test CARBA 5. Further investigation revealed the presence of blaIMP-27, which caused a false-positive NDM result in NG-Test CARBA 5, suggesting the limited stability of this assay in detecting IMP-27.
MICROBIOLOGY SPECTRUM
(2023)
Article
Public, Environmental & Occupational Health
Miguel A. Chavez, Satish Munigala, Carey-Ann D. Burnham, Melanie L. Yarbrough, Crystal Squires, Josephine Fox, Heather Gasama, Kevin Hsueh, David K. Warren
Summary: This study implemented two interventions, kits for sample collection improvement and an electronic order alert for appropriate indications of fungal blood cultures, to enhance utilization and contamination control at the institution. The results showed that the electronic order alert was associated with decreased utilization of fungal blood cultures without a decrease in positivity rate.
INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY
(2023)
Article
Microbiology
Luke Diorio-Toth, Meghan A. A. Wallace, Christopher W. W. Farnsworth, Bin Wang, Danish Gul, Jennie H. H. Kwon, Saadia Andleeb, Carey-Ann D. Burnham, Gautam Dantas
Summary: This study tracks the long-term colonization patterns of intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan using whole-genome sequencing. The analysis of 822 bacterial genomes reveals long-term contamination by opportunistic pathogens and transient appearance of other common pathogens. Bacteria recovered from the ICU have more antibiotic resistance genes in their genomes compared to matched community spaces.
Article
Microbiology
Vincent Vanat, Sebastien Aeby, Gilbert Greub
Summary: Ticks are important vectors for medical pathogens. This research found that zoological gardens in Switzerland have fewer ticks than surrounding areas, but the ticks in zoos are more likely to carry Chlamydia-like organisms compared to ticks in control areas.
Article
Medicine, General & Internal
Alix T. Coste, Adrian Egli, Jacques Schrenzel, Beatrice Nickel, Andrea Zbinden, Reto Lienhard, Alexis Dumoulin, Martin Risch, Gilbert Greub
Summary: The IVDR regulation poses a major challenge for diagnostic microbiology laboratories due to its complexity and risks. The emergence of new pathogens further complicates the regulation, negatively impacting the development of new diagnostic tests. Additionally, the regulation affects the availability and costs of diagnostic tests, posing a risk to public health.
