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  1. Article ; Online: Stenotrophomonas maltophilia Susceptibility Testing Challenges and Strategies.

    Rhoads, Daniel D

    Journal of clinical microbiology

    2021  Volume 59, Issue 9, Page(s) e0109421

    Abstract: Stenotrophomonas maltophilia is intrinsically resistant to many beta-lactam antibiotics, including carbapenems, and is resistant to aminoglycosides, which limits the therapeutic repertoire for managing S. maltophilia infections. Additionally, employing ... ...

    Abstract Stenotrophomonas maltophilia is intrinsically resistant to many beta-lactam antibiotics, including carbapenems, and is resistant to aminoglycosides, which limits the therapeutic repertoire for managing S. maltophilia infections. Additionally, employing automated
    MeSH term(s) Aminoglycosides ; Anti-Bacterial Agents/pharmacology ; Carbapenems ; Gram-Negative Bacterial Infections/drug therapy ; Humans ; Microbial Sensitivity Tests ; Stenotrophomonas maltophilia
    Chemical Substances Aminoglycosides ; Anti-Bacterial Agents ; Carbapenems
    Language English
    Publishing date 2021-08-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.01094-21
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  2. Article ; Online: Computer Vision and Artificial Intelligence Are Emerging Diagnostic Tools for the Clinical Microbiologist.

    Rhoads, Daniel D

    Journal of clinical microbiology

    2020  Volume 58, Issue 6

    Abstract: Artificial intelligence (AI) is increasingly becoming an important component of clinical microbiology informatics. Researchers, microbiologists, laboratorians, and diagnosticians are interested in AI-based testing because these solutions have the ... ...

    Abstract Artificial intelligence (AI) is increasingly becoming an important component of clinical microbiology informatics. Researchers, microbiologists, laboratorians, and diagnosticians are interested in AI-based testing because these solutions have the potential to improve a test's turnaround time, quality, and cost. A study by Mathison et al. used computer vision AI (B. A. Mathison, J. L. Kohan, J. F. Walker, R. B. Smith, et al., J Clin Microbiol 58:e02053-19, 2020, https://doi.org/10.1128/JCM.02053-19), but additional opportunities for AI applications exist within the clinical microbiology laboratory. Large data sets within clinical microbiology that are amenable to the development of AI diagnostics include genomic information from isolated bacteria, metagenomic microbial findings from primary specimens, mass spectra captured from cultured bacterial isolates, and large digital images, which is the medium that Mathison et al. chose to use. AI in general and computer vision in specific are emerging tools that clinical microbiologists need to study, develop, and implement in order to improve clinical microbiology.
    MeSH term(s) Artificial Intelligence ; Clinical Laboratory Services ; Computers ; Laboratories ; Neural Networks, Computer
    Language English
    Publishing date 2020-05-26
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.00511-20
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  3. Article ; Online: Meningococcal Urethritis: Old and New.

    Burns, Bethany L / Rhoads, Daniel D

    Journal of clinical microbiology

    2022  Volume 60, Issue 11, Page(s) e0057522

    Abstract: Neisseria meningitidis is a common commensal bacterium found in the respiratory tract, but it can also cause severe, invasive disease. Vaccines have been employed which have been successful in helping to prevent invasive disease caused by encapsulated N. ...

    Abstract Neisseria meningitidis is a common commensal bacterium found in the respiratory tract, but it can also cause severe, invasive disease. Vaccines have been employed which have been successful in helping to prevent invasive disease caused by encapsulated N. meningitidis from the A, C, W, Y, and B serogroups. Currently, nonencapsulated N. meningitidis groups are more common commensals in the population than in the prevaccine era. One emerging nonencapsulated group of bacteria is the U.S. N. meningitidis urethritis clade (US_NmUC), which can cause meningococcal urethritis in men. US_NmUC has unique genotypic and phenotypic features that may increase its fitness in the male urethra. It is diagnostically challenging to identify and distinguish meningococcal urethritis from Neisseria gonorrhoeae, as the clinical presentation and microbiological findings are overlapping. In this review, the history of meningococcal urethritis, emergence of US_NmUC, laboratory diagnosis, and clinical treatment are all explored.
    MeSH term(s) Male ; Humans ; Urethritis/diagnosis ; Urethritis/microbiology ; Neisseria meningitidis ; Neisseria gonorrhoeae ; Serogroup ; Urethra/microbiology ; Meningococcal Infections/microbiology
    Language English
    Publishing date 2022-08-15
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.00575-22
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  4. Article ; Online: Diagnostic stewardship for urinary tract infection: A snapshot of the expert guidance.

    Werneburg, Glenn T / Rhoads, Daniel D

    Cleveland Clinic journal of medicine

    2022  Volume 89, Issue 10, Page(s) 581–587

    Abstract: The urine culture, the cornerstone for laboratory diagnosis of urinary tract infection (UTI), is associated with a high frequency of false-positive and false-negative results, and its diagnostic threshold is debated. Urine culture takes days to result, ... ...

    Abstract The urine culture, the cornerstone for laboratory diagnosis of urinary tract infection (UTI), is associated with a high frequency of false-positive and false-negative results, and its diagnostic threshold is debated. Urine culture takes days to result, and antibiotics are often initiated while awaiting final culture readings. Further, asymptomatic bacteriuria-the presence of bacteria in urine in the absence of UTI symptoms-generally does not warrant treatment. The authors review current expert guidance on the use of urine culture, including approaches to ordering, processing, and reporting of urine cultures, with the goal of reducing unnecessary antibiotic use and misdiagnosis of UTI.
    MeSH term(s) Anti-Bacterial Agents/therapeutic use ; Bacteriuria/diagnosis ; Bacteriuria/drug therapy ; Bacteriuria/microbiology ; Humans ; Urinalysis/methods ; Urinary Tract Infections/diagnosis ; Urinary Tract Infections/drug therapy
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2022-10-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639116-3
    ISSN 1939-2869 ; 0891-1150
    ISSN (online) 1939-2869
    ISSN 0891-1150
    DOI 10.3949/ccjm.89a.22008
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  5. Article ; Online: The Use of Machine Learning for Image Analysis Artificial Intelligence in Clinical Microbiology.

    Burns, Bethany L / Rhoads, Daniel D / Misra, Anisha

    Journal of clinical microbiology

    2023  Volume 61, Issue 9, Page(s) e0233621

    Abstract: The growing transition to digital microbiology in clinical laboratories creates the opportunity to interpret images using software. Software analysis tools can be designed to use human-curated knowledge and expert rules, but more novel artificial ... ...

    Abstract The growing transition to digital microbiology in clinical laboratories creates the opportunity to interpret images using software. Software analysis tools can be designed to use human-curated knowledge and expert rules, but more novel artificial intelligence (AI) approaches such as machine learning (ML) are being integrated into clinical microbiology practice. These image analysis AI (IAAI) tools are beginning to penetrate routine clinical microbiology practice, and their scope and impact on routine clinical microbiology practice will continue to grow. This review separates the IAAI applications into 2 broad classification categories: (i) rare event detection/classification or (ii) score-based/categorical classification. Rare event detection can be used for screening purposes or for final identification of a microbe including microscopic detection of mycobacteria in a primary specimen, detection of bacterial colonies growing on nutrient agar, or detection of parasites in a stool preparation or blood smear. Score-based image analysis can be applied to a scoring system that classifies images
    MeSH term(s) Female ; Humans ; Artificial Intelligence ; Machine Learning ; Software ; Image Processing, Computer-Assisted ; Urinalysis
    Language English
    Publishing date 2023-07-03
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/jcm.02336-21
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  6. Article ; Online: The Truth about SARS-CoV-2 Cycle Threshold Values Is Rarely Pure and Never Simple.

    Rhoads, Daniel D / Pinsky, Benjamin A

    Clinical chemistry

    2021  Volume 68, Issue 1, Page(s) 16–18

    MeSH term(s) COVID-19/diagnosis ; Humans ; RNA, Viral ; Real-Time Polymerase Chain Reaction ; SARS-CoV-2/isolation & purification ; Viral Load
    Chemical Substances RNA, Viral
    Language English
    Publishing date 2021-07-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 80102-1
    ISSN 1530-8561 ; 0009-9147
    ISSN (online) 1530-8561
    ISSN 0009-9147
    DOI 10.1093/clinchem/hvab146
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  7. Article ; Online: Lowering the Barriers to Routine Whole-Genome Sequencing of Bacteria in the Clinical Microbiology Laboratory.

    Rhoads, Daniel D

    Journal of clinical microbiology

    2018  Volume 56, Issue 9

    Abstract: Whole-genome sequencing of bacterial isolates is increasingly being used to predict antibacterial susceptibility and resistance. Mason and coauthors describe the phenotypic susceptibility interpretations of more than 1, ... ...

    Abstract Whole-genome sequencing of bacterial isolates is increasingly being used to predict antibacterial susceptibility and resistance. Mason and coauthors describe the phenotypic susceptibility interpretations of more than 1,300
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Bacteria/genetics ; Bacteria/isolation & purification ; Communicable Diseases/diagnosis ; Communicable Diseases/microbiology ; Computational Biology ; Diagnostic Tests, Routine/economics ; Diagnostic Tests, Routine/methods ; Drug Resistance, Bacterial/drug effects ; Drug Resistance, Bacterial/genetics ; Genome, Bacterial/genetics ; Genotype ; Humans ; Laboratories/economics ; Laboratories/standards ; Phenotype ; Sequence Analysis, DNA ; Software ; Time Factors
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2018-08-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 390499-4
    ISSN 1098-660X ; 0095-1137
    ISSN (online) 1098-660X
    ISSN 0095-1137
    DOI 10.1128/JCM.00813-18
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  8. Article: Commentary: Improving the Efficiency of the Ova and Parasite Examination Using Cloud-Based Image Analysis.

    Rhoads, Daniel D

    Journal of pathology informatics

    2017  Volume 8, Page(s) 49

    Language English
    Publishing date 2017-12-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2579241-6
    ISSN 2153-3539 ; 2229-5089
    ISSN (online) 2153-3539
    ISSN 2229-5089
    DOI 10.4103/jpi.jpi_63_17
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  9. Article ; Online: Recent advances in rapid antimicrobial susceptibility testing systems.

    Jacobs, Michael R / Colson, Jordan D / Rhoads, Daniel D

    Expert review of molecular diagnostics

    2021  Volume 21, Issue 6, Page(s) 563–578

    Abstract: Introduction: Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged.: Areas covered: Advances in rapid phenotypic and molecular-based AST ... ...

    Abstract Introduction: Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged.
    Areas covered: Advances in rapid phenotypic and molecular-based AST systems.
    Expert opinion: AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Anti-Infective Agents/pharmacology ; Anti-Infective Agents/therapeutic use ; Bacteria/genetics ; Humans ; Microbial Sensitivity Tests ; beta-Lactamases/genetics
    Chemical Substances Anti-Bacterial Agents ; Anti-Infective Agents ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2021-05-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2112530-2
    ISSN 1744-8352 ; 1473-7159
    ISSN (online) 1744-8352
    ISSN 1473-7159
    DOI 10.1080/14737159.2021.1924679
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  10. Article ; Online: Urinalysis Exhibits Excellent Predictive Capacity for the Absence of Urinary Tract Infection.

    Werneburg, Glenn T / Lewis, Kevin C / Vasavada, Sandip P / Wood, Hadley M / Goldman, Howard B / Shoskes, Daniel A / Li, Ina / Rhoads, Daniel D

    Urology

    2023  Volume 175, Page(s) 101–106

    Abstract: Objective: To assess predictive value of urinalysis for negative urine culture and absence of urinary tract infection, re-evaluate the microbial growth threshold for positive urine culture result, and describe antimicrobial resistance features. Urine ... ...

    Abstract Objective: To assess predictive value of urinalysis for negative urine culture and absence of urinary tract infection, re-evaluate the microbial growth threshold for positive urine culture result, and describe antimicrobial resistance features. Urine culture is associated with 27% of U.S. hospitalizations, and unnecessary antibiotic prescription is a main antibiotic resistance contributor.
    Methods: Urinalyses with urine culture from women ages 18-49 from 2013 to 2020 were studied. Clinically diagnosed urinary tract infection (CUTI) was defined as (1) uropathogen growth, (2) documented diagnosis of urinary tract infection, and (3) antibiotic prescription. Sensitivity, specificity, and diagnostic predictive values were used to assess urinalysis performance in predicting isolation of a uropathogen by culture and in detection of CUTI.
    Results: Total 12,252 urinalyses were included. Forty-one percent of urinalyses were associated with positive urine culture and 1287 (10.5%) with CUTI. Negative urinalysis exhibited high predictive accuracy for negative urine culture (specificity 90.3%, PPV 87.3%) and absence of CUTI (specificity 92.2%, PPV 97.4%). Twenty-four percent of patients not meeting the CUTI definition were still prescribed antibiotics. Twenty-two percent of cultures associated with CUTI exhibited growth less than 100,000 CFU/mL. Escherichia coli was implemented as causing 70% of CUTIs, and 4.2% of these produced an extended spectrum beta-lactamase.
    Conclusion: Negative urinalysis exhibits high predictive accuracy for absence of CUTI. A reporting threshold of 10,000 CFU/mL is more clinically appropriate than a 100,000 CFU/mL cutpoint. Reflex culture based on urinalysis results could complement clinical judgement and improve laboratory and antibiotic stewardship in premenopausal women.
    MeSH term(s) Humans ; Female ; Urinary Tract Infections/diagnosis ; Urinary Tract Infections/drug therapy ; Urinalysis/methods ; Anti-Bacterial Agents/therapeutic use ; Escherichia coli
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-03-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 192062-5
    ISSN 1527-9995 ; 0090-4295
    ISSN (online) 1527-9995
    ISSN 0090-4295
    DOI 10.1016/j.urology.2023.02.028
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