A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

The Use of Machine Learning for Image Analysis Artificial Intelligence in Clinical Microbiology

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 in toto as its output interpretation and examples include application of the Nugent score for diagnosing bacterial vaginosis and interpretation of urine cultures. The benefits, challenges, development, and implementation strategies of IAAI tools are explored. In conclusion, IAAI is beginning to impact the routine practice of clinical microbiology, and its use can enhance the efficiency and quality of clinical microbiology practice. Although the future of IAAI is promising, currently IAAI only augments human effort and is not a replacement for human expertise.

False positive congenital cytomegalovirus saliva screening results with an FDA-approved assay at two institutions

BACKGROUND

Congenital cytomegalovirus (CMV) infection is a significant cause of childhood hearing loss and developmental delay. Congenital CMV screening was implemented at two large hospital-affiliated laboratories using the FDA-approved Alethia CMV Assay Test System. In July 2022, an increase in suspected false-positive results was noted, leading to implementation of prospective quality management strategies.

METHODS

The Alethia assay was performed per manufacturer-provided instructions on saliva swab specimens. After discovery of possible elevated false-positive rates, all positive results were confirmed by repeat Alethia testing on the same specimen, orthogonal polymerase chain reaction (PCR) on the same specimen, and/or clinical adjudication. Additionally, root cause analyses were conducted to pinpoint the source of false-positive results.

RESULTS

At Cleveland Clinic (CCF), 696 saliva specimens were tested after initiation of the prospective quality management strategy, of which 36 (5.2%) were positive for CMV. Five of 36 (13.9%) were confirmed CMV positive by repeat Alethia testing and orthogonal PCR. Vanderbilt Medical Center (VUMC) tested 145 specimens, of which 11 (7.6%) were positive. Two of 11 (18.2%) confirmed as positive by orthogonal PCR or clinical adjudication. The remaining specimens (31 from CCF and 9 from VUMC) were negative for CMV by repeat Alethia and/or orthogonal PCR testing.

DISCUSSION

These findings suggest a false positive rate of 4.5-6.2%, higher than the 0.2% reported for this assay in FDA claims. Laboratories using Alethia CMV may consider prospective quality management to evaluate all positive results. False-positive results can lead to unnecessary follow-up care and testing, and decreased confidence in laboratory testing.

Multicenter Evaluation of the BIOFIRE Blood Culture Identification 2 Panel for Detection of Bacteria, Yeasts, and Antimicrobial Resistance Genes in Positive Blood Culture Samples

Diagnostic tools that can rapidly identify and characterize microbes growing in blood cultures are important components of clinical microbiology practice because they help to provide timely information that can be used to optimize patient management. This publication describes the bioMérieux BIOFIRE Blood Culture Identification 2 (BCID2) Panel clinical study that was submitted to the U.S. Food & Drug Administration. Results obtained with the BIOFIRE BCID2 Panel were compared to standard-of-care (SoC) results, sequencing results, PCR results, and reference laboratory antimicrobial susceptibility testing results to evaluate the accuracy of its performance. Results for 1,093 retrospectively and prospectively collected positive blood culture samples were initially enrolled, and 1,074 samples met the study criteria and were included in the final analyses. The BIOFIRE BCID2 Panel demonstrated an overall sensitivity of 98.9% (1,712/1,731) and an overall specificity of 99.6% (33,592/33,711) for Gram-positive bacteria, Gram-negative bacteria and yeast targets which the panel is designed to detect. One hundred eighteen off-panel organisms, which the BIOFIRE BCID2 Panel is not designed to detect, were identified by SoC in 10.6% (114/1,074) of samples. The BIOFIRE BCID2 Panel also demonstrated an overall positive percent agreement (PPA) of 97.9% (325/332) and an overall negative percent agreement (NPA) of 99.9% (2,465/2,767) for antimicrobial resistance determinants which the panel is designed to detect. The presence or absence of resistance markers in Enterobacterales correlated closely with phenotypic susceptibility and resistance. We conclude that the BIOFIRE BCID2 Panel produced accurate results in this clinical trial.

Urinalysis exhibits excellent predictive capacity for the absence of urinary tract infection

OBJECTIVES

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.

SUBJECTS AND 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

12,252 urinalyses were included. 41% 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%). 24% of patients not meeting the CUTI definition were still prescribed antibiotics. 22% 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.

CONCLUSIONS

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 pre-menopausal women.

142. Evaluation of Meropenem-Vaborbactam Susceptibility and Underlying Resistance Mechanisms among Clinical KPC-producing Klebsiella pneumoniae

Background

Meropenem-vaborbactam (MV) is the first carbapenem/β-lactamase inhibitor combination developed to restore meropenem susceptibility against KPC-producing carbapenem-resistant Enterobacterales(CRE). Vaborbactam (VAB) potently inhibits Ambler class A and C β-lactamases by reversible covalent binding of boronate to serine side chains of β-lactamases. Resistance to MV in non-metallo-β-lactamase (MBL) producing Klebsiella pneumoniae (KP) isolates has been described but remains rare. We sought to identify the major molecular mechanisms associated with MV resistance in KPC-producing KP (KPC-KP) isolates.

Methods

Clinical isolates with elevated MV MICs were identified by the consult service. Additional clinical isolates with mutations in ompK35 or ompK36 genes were selected from a historic database. Isolates with MBL or OXA-48-like genes were excluded. Controls were comprised of MV susceptible KPC-KP isolates. MICs determination was done using Sensititre automated broth microdilution (BMD) according to CLSI. VAB and avibactam concentrations were held at 8 µg/ml and 4 µg/ml, respectively. Whole genome sequencing (WGS) was performed on all isolates. Genome libraries were prepared using Illumina Nextera XT and sequencing was performed on MiSeq and MinION.

Results

A total 119 KPC-KP isolates were included in the study. All isolates were resistant to meropenem. Twenty-one KPC-KP with elevated MV MICs were identified. All MV resistant isolates harbored mutations in ompK36 genes. Glycine/aspartate (GD 134-135) insertion, premature stop codon in ompK36 genes, and concomitantly elevated blaKPC copy number were predominant among MV resistant isolates. No insertion elements in ompK36 gene promoter region were found. Two MV resistant isolates exhibited unique mutations in blaKPC and envZ genes. See table for WGS and MIC results. Table 1.Whole genome sequencing and MICs of MV resistant KPC-KP isolatesα: Truncated at nodes 14 and 76, partial genotype consistent with blaSHV-12WT: Wild type*: Premature stop codonGD: Duplication of Glycine (G134) and Aspartate (D135)FS: Frameshift mutationins: insertionMEM: meropenemMVB: meropenem-vaborbactamCZA: ceftazidime-avibactamCFD: cefiderocolN/A: not availableTable 2.Whole genome sequencing and MICs of MV susceptible KPC-KP isolates

Conclusion

MV resistant KPC-KP isolates were reliably analyzed using WGS to reveal the contribution of omp gene mutations and blaKPC copy number to this phenotype. Elevated MV MICs were additionally recognized among clinical isolates from a historic database preceding MV availability. In the absence of MBL production, caution remains warranted with the use of MV empirically against KPC-KP due to non-β-lactamase mediated resistance mechanisms.

Disclosures

Daniel D. Rhoads, M.D. PhD, Luminex: Advisor/Consultant|Talis Biomedical: Advisor/Consultant|Thermo Fisher: Advisor/Consultant Federico Perez, M.D., Accelerate: Grant/Research Support|Merck: Grant/Research Support|Pfizer: Grant/Research Support Robert A. Bonomo, MD, NIH VA: Grant/Research Support|VenatoRx Merck Wockhardt Cystic Fibrosis Foundation: Grant/Research Support.

1064. Intra-Host SARS-CoV-2 Evolution Dynamics

Background

Our understanding of SARS-CoV-2 evolution is limited. Most estimates arise from analysis of global databases populated with unrelated sequences and is currently estimated at ∼27.7 substitutions/genome/year. SARS-CoV-2 polymerase contains a proofreading function encoded by NSP-14 limiting change. Additionally, virus evolution may be influenced by patient comorbidity. Intra-host mutational rate (MR) during infection remain poorly studied.

Methods

To minimize effect of vaccination and/or natural immunity on MR analysis, paired samples from adults originating from the initial pandemic wave (3/17/2020 through 5/27/2020) were retrieved and analyzed at Cleveland Clinic. Viral genome analysis was performed using next generation sequencing, and mutations between paired samples were quantified at allele frequencies (AF) ≥ 0.1, ≥ 0.5 and ≥ 0.75 and compared. MR was calculated employing F81 and JC69 evolution­­­­ models and compared between isolates with (Δ NSP-14) and without (wildtype, wt) non-synonymous mutations in NSP-14 and by comorbidity.

Results

A total of 40 patients (80 sample pairs) were identified. Median interval between paired tests was 15 days [range 5-32]. The estimated MR by F81 modeling was 317.2 (95%CI 312.0-322.3), 54.6 (95%CI 52.5-56.7) and 45.1 (95%CI 43.1-47.0) substitutions/genome/year at AF of ≥0.1, ≥0.5, ≥0.75 respectively. Rates in ΔNSP-14 (n=13) vs wt (n=27) groups were 557.7 (95%CI 537.0-578.2) vs 193.1 (95%CI 187.1-199.1) p-value 0.001, 50.8 (95%CI 44.3-57.3) vs 56.3 (95%CI 53.1-59.4) p-value 0.144, and 31.0 (95%CI 25.9-36.1) vs 51.3 (95%CI 48.3-54.3) p- value < 0.001 at AF ≥0.1, ≥0.5, ≥0.75 respectively. Patients with immune comorbidities (n=6) had significantly higher MR of 137.6 (95%CI 114.6-160.5) vs 40.5 (95%CI 38.4-42.7) p-value < 0.001, and 113.7 (95%CI 92.8-134.5) vs 33.4 (95%CI 31.5-35.4) p-value < 0.001 at AF ≥0.5 and ≥0.75 respectively. Similar results were obtained when using the JC69 model.

Conclusion

Intra-host SARS-CoV-2 mutation rates are higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated MR at low AF. Immunosuppressed patients have elevated MR at higher AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.

Disclosures

Frank Esper, M.D, Johnson and Johnson: Advisor/Consultant Daniel D. Rhoads, M.D. PhD, Luminex: Advisor/Consultant|Talis Biomedical: Advisor/Consultant|Thermo Fisher: Advisor/Consultant.

Building the Model

CONTEXT.—

Machine learning (ML) allows for the analysis of massive quantities of high-dimensional clinical laboratory data, thereby revealing complex patterns and trends. Thus, ML can potentially improve the efficiency of clinical data interpretation and the practice of laboratory medicine. However, the risks of generating biased or unrepresentative models, which can lead to misleading clinical conclusions or overestimation of the model performance, should be recognized.

OBJECTIVES.—

To discuss the major components for creating ML models, including data collection, data preprocessing, model development, and model evaluation. We also highlight many of the challenges and pitfalls in developing ML models, which could result in misleading clinical impressions or inaccurate model performance, and provide suggestions and guidance on how to circumvent these challenges.

DATA SOURCES.—

The references for this review were identified through searches of the PubMed database, the US Food and Drug Administration white papers and guidelines, conference abstracts, and online preprints.

CONCLUSIONS.—

With the growing interest in developing and implementing ML models in clinical practice, laboratorians and clinicians need to be educated in order to collect sufficiently large and high-quality data, properly report the data set characteristics, and combine data from multiple institutions with proper normalization. They will also need to assess the reasons for missing values, determine the inclusion or exclusion of outliers, and evaluate the completeness of a data set. In addition, they require the necessary knowledge to select a suitable ML model for a specific clinical question and accurately evaluate the performance of the ML model, based on objective criteria. Domain-specific knowledge is critical in the entire workflow of developing ML models.

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

As Omicron Takes Hold and Other New Variants Arise, COVID-19 Testing Remains the Universally Agreed Tool to Effect Transition From Pandemic to Endemic State

The COVID-19 pandemic has caused more than 448 million cases and 6 million deaths worldwide to date. Omicron is now the dominant SARS-CoV-2 variant, making up more than 90% of cases in countries reporting sequencing data. As the pandemic continues into its third year, continued testing is a strategic and necessary tool for transitioning to an endemic state of COVID-19. Here, we address three critical topics pertaining to the transition from pandemic to endemic: defining the endemic state for COVID-19, highlighting the role of SARS-CoV-2 testing as endemicity is approached, and recommending parameters for SARS-CoV-2 testing once endemicity is reached. We argue for an approach that capitalizes on the current public health momentum to increase capacity for PCR-based testing and whole genome sequencing to monitor emerging infectious diseases. Strategic development and utilization of testing, including viral panels in addition to vaccination, can keep SARS-CoV-2 in a manageable endemic state and build a framework of preparedness for the next pandemic.

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1

Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ^® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing

Background

Pseudomonas aeruginosa is a persistent and difficult-to-treat pathogen in many patients, especially those with Cystic Fibrosis (CF). Herein, we describe a longitudinal analysis of a series of multidrug resistant (MDR) P. aeruginosa isolates recovered in a 17-month period, from a young female CF patient who underwent double lung transplantation. Our goal was to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence evolution over time.

Methods

Twenty-two sequential P. aeruginosa isolates were obtained within a 17-month period, before and after a double-lung transplant. At the end of the study period, antimicrobial susceptibility testing, whole genome sequencing (WGS), phylogenetic analyses and RNAseq were performed in order to understand the genetic basis of the observed resistance phenotypes, establish the genomic population diversity, and define the nature of sequence changes over time.

Results

The majority of isolates were resistant to almost all tested antibiotics. A phylogenetic reconstruction revealed 3 major clades representing a genotypically and phenotypically heterogeneous population. The pattern of mutation accumulation and variation of gene expression suggested that a group of closely related strains was present in the patient prior to transplantation and continued to change throughout the course of treatment. A trend toward accumulation of mutations over time was observed. Different mutations in the DNA mismatch repair gene mutL consistent with a hypermutator phenotype were observed in two clades. RNAseq performed on 12 representative isolates revealed substantial differences in the expression of genes associated with antibiotic resistance and virulence traits.

Conclusions

The overwhelming current practice in the clinical laboratories setting relies on obtaining a pure culture and reporting the antibiogram from a few isolated colonies to inform therapy decisions. Our analyses revealed significant underlying genomic heterogeneity and unpredictable evolutionary patterns that were independent of prior antibiotic treatment, highlighting the need for comprehensive sampling and population-level analysis when gathering microbiological data in the context of CF P. aeruginosa chronic infection. Our findings challenge the applicability of antimicrobial stewardship programs based on single-isolate resistance profiles for the selection of antibiotic regimens in chronic infections such as CF.

Teleclinical Microbiology: An Innovative Approach to Providing Web-Enabled Diagnostic Laboratory Services in Syria

OBJECTIVES

Telemedicine can compensate for the lack of health care specialists in response to protracted humanitarian crises. We sought to assess the usability of a teleclinical microbiology (TCM) program to provide diagnostic services in a hard-to-reach region of Syria.

METHODS

A semimobile station was equipped with conventional micrograph and macrograph digital imaging systems. An electronic platform (Telemicrobiology in Humanitarian Crises, TmHC) was created to facilitate sharing, interpreting, and storing the results. A pilot study was conducted to identify the bacterial species and antimicrobial susceptibility pattern of 74 urinary clinical isolates. An experience survey was conducted to capture the feedback of 8 participants in the program.

RESULTS

The TmHC platform (https://sdh.ngo/tmhc/) enabled systematic transmission of the laboratory records and co-interpretation of the results. The isolates were identified as Escherichia coli (n = 61), Klebsiella pneumoniae (n = 12), and Proteus mirabilis(n = 1). All the isolates were multidrug resistant. The performance of our TCM module was rated 4 (satisfying) and 5 (very satisfying) by 6 and 2 users, respectively. Data security of and cost-effectiveness were the main perceived concerns.

CONCLUSIONS

Although we encountered several context-related obstacles, our TCM program managed to reach a highly vulnerable population of 4 million people confined in the northwest region of Syria.

Deep Convolutional Neural Networks Implementation for the Analysis of Urine Culture

BACKGROUND

Urine culture images collected using bacteriology automation are currently interpreted by technologists during routine standard-of-care workflows. Machine learning may be able to improve the harmonization of and assist with these interpretations.

METHODS

A deep learning model, BacterioSight, was developed, trained, and tested on standard BD-Kiestra images of routine blood agar urine cultures from 2 different medical centers.

RESULTS

BacterioSight displayed performance on par with standard-of-care-trained technologist interpretations. BacterioSight accuracy ranged from 97% when compared to standard-of-care (single technologist) and reached 100% when compared to a consensus reached by a group of technologists (gold standard in this study). Variability in image interpretation by trained technologists was identified and annotation "fuzziness" was quantified and found to correlate with reduced confidence in BacterioSight interpretation. Intra-testing (training and testing performed within the same institution) performed well giving Area Under the Curve (AUC) ≥0.98 for negative and positive plates, whereas, cross-testing on images (trained on one institution's images and tested on images from another institution) showed decreased performance with AUC ≥0.90 for negative and positive plates.

CONCLUSIONS

Our study provides a roadmap on how BacterioSight or similar deep learning prototypes may be implemented to screen for microbial growth, flag difficult cases for multi-personnel review, or auto-verify a subset of cultures with high confidence. In addition, our results highlight image interpretation variability by trained technologist within an institution and globally across institutions. We propose a model in which deep learning can enhance patient care by identifying inherent sample annotation variability and improving personnel training.

133. ARGONAUT-III: Susceptibility of Carbapenem-resistant Klebsiellae to Cefepime-Taniborbactam

Background

Klebsiellae are Gram-negative pathogens responsible for serious nosocomial and community-acquired infections. Carbapenem resistance, both intrinsic and acquired, complicates therapy. Taniborbactam (formerly VNRX-5133; Fig 1) is a bicyclic boronate β-lactamase inhibitor (BLI) that inhibits all four Ambler classes of β-lactamase enzymes, both serine- and metallo-, with the notable exception of class B IMP β-lactamases. Taniborbactam is currently undergoing phase 3 clinical trials in combination with cefepime (FEP; Fig 1) as part of the β-lactam-BLI (BL-BLI) combination FEP-taniborbactam (FTB).

Figure 1. Structures of taniborbactam and cefepime. The β-lactamase inhibitor is in red and the β-lactam antibiotic is in black.

Methods

We determined the activity of FTB against 200 carbapenem-resistant Klebsiellae (CRK) strains collected as part of the Antibiotic Resistance Leadership Group (ARLG) Consortium on Resistance against Carbapenems in Klebsiella (CRACKLE) study. Among these strains, 193 expressed class A KPCs, one expressed a class B NDM, and six expressed class D OXA-48 or variants. Broth microdilution minimum inhibitory concentrations (MIC)s were determined using the ThermoFisher Sensititre system with custom assay panels. American Type Culture Collection strains were used for quality control. The susceptible-dose-dependent breakpoint for FEP was provisionally used for FTB, where taniborbactam was fixed at 4 µg/mL.

Results

Among the 200 Klebsiella strains tested, susceptibility for β-lactams alone ranged from 1% for ceftazidime (CAZ), 2.5% for meropenem, and 13.5% for FEP (Table 1). The addition of BLIs increased % susceptibility compared to BL alone to: 98% for CAZ-avibactam (CZA); 95.5% for MEM-vaborbactam (MVB); and 99.0% for FTB. MIC₅₀ and MIC₉₀ were in the susceptible and provisionally susceptible range for CZA and MVB, and in the provisionally susceptible range for FTB. Analyzing the CZA and MVB non-susceptible strains, 7 of 9 MVB non-susceptible strains and 2 of 4 CZA-resistant strains were provisionally susceptible to FTB.

Table 1. MIC50 and MIC90 values (μg/mL) and percent susceptibility for Klebsiella pneumoniae strains (n=200). AMK, amikacin; CST, colistin; CAZ, ceftazidime; CZA, ceftazidime-avibactam; FEP, cefepime; FTB, cefepime-taniborbactam; MEM, meropenem; MVB, meropenem-vaborbactam; TGC, tigecycline. * The breakpoint for CST is intermediate, as no susceptible breakpoint is available. ** The susceptible-dose-dependent breakpoint for FEP alone was provisionally applied to FTB, where taniborbactam was fixed at 4 μg/mL. Breakpoints from CLSI M100, 31st ed, 2021.

Conclusion

The addition of taniborbactam restored susceptibility to FEP in 99.0% of CRACKLE isolates studied, comparable to CZA and MVB. Taniborbactam also restored FEP activity against some MVB- and CZA-resistant strains. FTB may provide a promising therapy for CRK infections.

Disclosures

Robin Patel, MD, 1928 Diagnostics (Consultant)BioFire Diagnostics (Grant/Research Support)ContraFect Corporation (Grant/Research Support)Curetis (Consultant)Hylomorph AG (Grant/Research Support)IDSA (Other Financial or Material Support, Editor’s Stipend)Infectious Diseases Board Review Course (Other Financial or Material Support, Honoraria)Mammoth Biosciences (Consultant)NBME (Other Financial or Material Support, Honoraria)Netflix (Consultant)Next Gen Diagnostics (Consultant)PathoQuest (Consultant)PhAST (Consultant)Qvella (Consultant)Samsung (Other Financial or Material Support, Patent Royalties)Selux Diagnostics (Consultant)Shionogi & Co., Ltd. (Grant/Research Support)Specific Technologies (Consultant)TenNor Therapeutics Limited (Grant/Research Support)Torus Biosystems (Consultant)Up-to-Date (Other Financial or Material Support, Honoraria) Robin Patel, MD, BioFire (Individual(s) Involved: Self): Grant/Research Support; Contrafect (Individual(s) Involved: Self): Grant/Research Support; IDSA (Individual(s) Involved: Self): Editor’s stipend; NBME, Up-to-Date and the Infectious Diseases Board Review Course (Individual(s) Involved: Self): Honoraria; Netflix (Individual(s) Involved: Self): Consultant; TenNor Therapeutics Limited (Individual(s) Involved: Self): Grant/Research Support; to Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Selux Diagnostics, 1928 Diagnostics, PhAST, Torus Biosystems, Mammoth Biosciences and Qvella (Individual(s) Involved: Self): Consultant David van Duin, MD, PhD, Entasis (Advisor or Review Panel member)genentech (Advisor or Review Panel member)Karius (Advisor or Review Panel member)Merck (Grant/Research Support, Advisor or Review Panel member)Pfizer (Consultant, Advisor or Review Panel member)Qpex (Advisor or Review Panel member)Shionogi (Grant/Research Support, Scientific Research Study Investigator, Advisor or Review Panel member)Utility (Advisor or Review Panel member) Vance G. Fowler, Jr., MD, MHS, Achaogen (Consultant)Advanced Liquid Logics (Grant/Research Support)Affinergy (Consultant, Grant/Research Support)Affinium (Consultant)Akagera (Consultant)Allergan (Grant/Research Support)Amphliphi Biosciences (Consultant)Aridis (Consultant)Armata (Consultant)Basilea (Consultant, Grant/Research Support)Bayer (Consultant)C3J (Consultant)Cerexa (Consultant, Other Financial or Material Support, Educational fees)Contrafect (Consultant, Grant/Research Support)Debiopharm (Consultant, Other Financial or Material Support, Educational fees)Destiny (Consultant)Durata (Consultant, Other Financial or Material Support, educational fees)Genentech (Consultant, Grant/Research Support)Green Cross (Other Financial or Material Support, Educational fees)Integrated Biotherapeutics (Consultant)Janssen (Consultant, Grant/Research Support)Karius (Grant/Research Support)Locus (Grant/Research Support)Medical Biosurfaces (Grant/Research Support)Medicines Co. (Consultant)MedImmune (Consultant, Grant/Research Support)Merck (Grant/Research Support)NIH (Grant/Research Support)Novadigm (Consultant)Novartis (Consultant, Grant/Research Support)Pfizer (Grant/Research Support)Regeneron (Consultant, Grant/Research Support)sepsis diagnostics (Other Financial or Material Support, Pending patent for host gene expression signature diagnostic for sepsis.)Tetraphase (Consultant)Theravance (Consultant, Grant/Research Support, Other Financial or Material Support, Educational fees)Trius (Consultant)UpToDate (Other Financial or Material Support, Royalties)Valanbio (Consultant, Other Financial or Material Support, Stock options)xBiotech (Consultant) Daniel D. Rhoads, MD, Becton, Dickinson and Company (Grant/Research Support) Michael Jacobs, MBBS, Venatorx Pharmaceuticals, Inc. (Grant/Research Support) Focco van den Akker, PhD, Venatorx Pharmaceuticals, Inc. (Grant/Research Support) David A. Six, PhD, Venatorx Pharmaceuticals, Inc. (Employee) Greg Moeck, PhD, Venatorx Pharmaceuticals, Inc. (Employee) Krisztina M. Papp-Wallace, Ph.D., Merck & Co., Inc. (Grant/Research Support)Spero Therapeutics, Inc. (Grant/Research Support)Venatorx Pharmaceuticals, Inc. (Grant/Research Support)Wockhardt Ltd. (Other Financial or Material Support, Research Collaborator) Robert A. Bonomo, MD, entasis (Research Grant or Support)Merck (Grant/Research Support)NIH (Grant/Research Support)VA Merit Award (Grant/Research Support)VenatoRx (Grant/Research Support)

1063. ARGONAUT-V: Susceptibility of Multidrug-Resistant (MDR) Pseudomonas aeruginosa to Cefepime-Taniborbactam

Background

P. aeruginosa is a Gram-negative pathogen responsible for many serious infections. MDR, both intrinsic and acquired, presents major clinical challenges. Taniborbactam (formerly VNRX-5133; Fig 1) is a β-lactamase inhibitor (BLI) characterized as a bicyclic boronate, uniquely possessing activity toward all four Ambler classes of β-lactamases, both serine and metallo, with the exception of class B IMP β-lactamases. The β-lactam-BLI (BL-BLI) combination cefepime-taniborbactam (FTB; Fig 1) is currently in phase 3 clinical trials.

Structures of taniborbactam and cefepime. The β-lactamase inhibitor is in red and the β-lactam antibiotic is in black.

Methods

The activity of FTB was tested against 197 well-characterized clinical P. aeruginosa isolates that were part of PRIMERS (Platforms for Rapid Identification of MDR-Gram-negative bacteria and Evaluation of Resistance Studies). Nearly 58% of these strains were reported as carbapenem-non-susceptible. Porin changes, efflux pumps, and/or the presence of acquired class A or class B carbapenemases were previously reported. Broth microdilution minimum inhibitory concentrations (MICs) were determined by CLSI M07 Ed. 11 methods with custom Sensititre frozen panels and interpreted using CLSI M100 Ed. 30 breakpoints. American Type Culture Collection strains were used for quality control. FEP breakpoints were provisionally used for FTB, where taniborbactam was fixed at 4 µg/mL.

Results

Percent susceptibility to BL agents alone was 45.2% for imipenem (IPM), 55.8% for meropenem (MEM), 60.9% for ceftazidime (CAZ), and 67.0% for FEP. The addition of BLI to BL increased % susceptibility for MEM-vaborbactam (MVB), 56.9%; ceftolozane-tazobactam (C/T), 77.7%, CAZ-avibactam (CZA), 79.7%, and FTB, 82.7%. MIC₅₀s were in the susceptible range for all drugs except IPM, which was intermediate, and all MIC₉₀s were in the resistant range (Table 1). Taniborbactam reduced FEP MIC by 2-fold in 32% of isolates and ≥ 4-fold in 13% of isolates. Against carbapenem-non-susceptible strains, % susceptibilities were: FTB, 68.5%, CZA, 63.0%, C/T, 59.3%; and MVB, 21.3% (Table 2).

MIC50 and MIC90 values (µg/mL) and percent susceptibility (%S) for all P. aeruginosa strains (n=197). AMK, amikacin; ATM, aztreonam; C/T, ceftolozane-tazobactam; CAZ, ceftazidime; CZA, ceftazidime-avibactam; FEP, cefepime; FTB, cefepime-taniborbactam; IPM, imipenem; MEM, meropenem; MVB, meropenem-vaborbactam; TZP, piperacillin-tazobactam; TOB, tobramycin. *The breakpoints for FEP and MEM alone were provisionally applied to FTB and MVB, respectively. Tazobactam, avibactam, and taniborbactam were fixed at 4 µg/mL, while vaborbactam was fixed at 8 µg/mL. Breakpoints from CLSI M100, 31st ed, 2021.

MIC50 and MIC90 values (µg/mL) and percent susceptibility (%S) for the subset of carbapenem-non-susceptible P. aeruginosa strains (n=108). AMK, amikacin; ATM, aztreonam; C/T, ceftolozane-tazobactam; CAZ, ceftazidime; CZA, ceftazidime-avibactam; FEP, cefepime; FTB, cefepime-taniborbactam; IPM, imipenem; MEM, meropenem; MVB, meropenem-vaborbactam; TZP, piperacillin-tazobactam; TOB, tobramycin. *The breakpoints for FEP and MEM alone were provisionally applied to FTB and MVB, respectively. Tazobactam, avibactam, and taniborbactam were fixed at 4 µg/mL, while vaborbactam was fixed at 8 µg/mL. Breakpoints from CLSI M100, 31st ed, 2021.

Conclusion

Compared to MVB, CZA, and C/T, FTB demonstrated the greatest activity against the 197 P. aeruginosa strains tested, including many carbapenem-non-susceptible strains. Pending completion of clinical development, FTB may be a promising therapeutic option for MDR P. aeruginosa infections.

Disclosures

Robin Patel, MD, 1928 Diagnostics (Consultant)BioFire Diagnostics (Grant/Research Support)ContraFect Corporation (Grant/Research Support)Curetis (Consultant)Hylomorph AG (Grant/Research Support)IDSA (Other Financial or Material Support, Editor’s Stipend)Infectious Diseases Board Review Course (Other Financial or Material Support, Honoraria)Mammoth Biosciences (Consultant)NBME (Other Financial or Material Support, Honoraria)Netflix (Consultant)Next Gen Diagnostics (Consultant)PathoQuest (Consultant)PhAST (Consultant)Qvella (Consultant)Samsung (Other Financial or Material Support, Patent Royalties)Selux Diagnostics (Consultant)Shionogi & Co., Ltd. (Grant/Research Support)Specific Technologies (Consultant)TenNor Therapeutics Limited (Grant/Research Support)Torus Biosystems (Consultant)Up-to-Date (Other Financial or Material Support, Honoraria) Robin Patel, MD, BioFire (Individual(s) Involved: Self): Grant/Research Support; Contrafect (Individual(s) Involved: Self): Grant/Research Support; IDSA (Individual(s) Involved: Self): Editor’s stipend; NBME, Up-to-Date and the Infectious Diseases Board Review Course (Individual(s) Involved: Self): Honoraria; Netflix (Individual(s) Involved: Self): Consultant; TenNor Therapeutics Limited (Individual(s) Involved: Self): Grant/Research Support; to Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Selux Diagnostics, 1928 Diagnostics, PhAST, Torus Biosystems, Mammoth Biosciences and Qvella (Individual(s) Involved: Self): Consultant David van Duin, MD, PhD, Entasis (Advisor or Review Panel member)genentech (Advisor or Review Panel member)Karius (Advisor or Review Panel member)Merck (Grant/Research Support, Advisor or Review Panel member)Pfizer (Consultant, Advisor or Review Panel member)Qpex (Advisor or Review Panel member)Shionogi (Grant/Research Support, Scientific Research Study Investigator, Advisor or Review Panel member)Utility (Advisor or Review Panel member) Vance G. Fowler, Jr., MD, MHS, Achaogen (Consultant)Advanced Liquid Logics (Grant/Research Support)Affinergy (Consultant, Grant/Research Support)Affinium (Consultant)Akagera (Consultant)Allergan (Grant/Research Support)Amphliphi Biosciences (Consultant)Aridis (Consultant)Armata (Consultant)Basilea (Consultant, Grant/Research Support)Bayer (Consultant)C3J (Consultant)Cerexa (Consultant, Other Financial or Material Support, Educational fees)Contrafect (Consultant, Grant/Research Support)Debiopharm (Consultant, Other Financial or Material Support, Educational fees)Destiny (Consultant)Durata (Consultant, Other Financial or Material Support, educational fees)Genentech (Consultant, Grant/Research Support)Green Cross (Other Financial or Material Support, Educational fees)Integrated Biotherapeutics (Consultant)Janssen (Consultant, Grant/Research Support)Karius (Grant/Research Support)Locus (Grant/Research Support)Medical Biosurfaces (Grant/Research Support)Medicines Co. (Consultant)MedImmune (Consultant, Grant/Research Support)Merck (Grant/Research Support)NIH (Grant/Research Support)Novadigm (Consultant)Novartis (Consultant, Grant/Research Support)Pfizer (Grant/Research Support)Regeneron (Consultant, Grant/Research Support)sepsis diagnostics (Other Financial or Material Support, Pending patent for host gene expression signature diagnostic for sepsis.)Tetraphase (Consultant)Theravance (Consultant, Grant/Research Support, Other Financial or Material Support, Educational fees)Trius (Consultant)UpToDate (Other Financial or Material Support, Royalties)Valanbio (Consultant, Other Financial or Material Support, Stock options)xBiotech (Consultant) Daniel D. Rhoads, MD, Becton, Dickinson and Company (Grant/Research Support) Michael Jacobs, MBBS, Venatorx Pharmaceuticals, Inc. (Grant/Research Support) Focco van den Akker, PhD, Venatorx Pharmaceuticals, Inc. (Grant/Research Support) David A. Six, PhD, Venatorx Pharmaceuticals, Inc. (Employee) Greg Moeck, PhD, Venatorx Pharmaceuticals, Inc. (Employee) Krisztina M. Papp-Wallace, Ph.D., Merck & Co., Inc. (Grant/Research Support)Spero Therapeutics, Inc. (Grant/Research Support)Venatorx Pharmaceuticals, Inc. (Grant/Research Support)Wockhardt Ltd. (Other Financial or Material Support, Research Collaborator) Robert A. Bonomo, MD, entasis (Research Grant or Support)Merck (Grant/Research Support)NIH (Grant/Research Support)VA Merit Award (Grant/Research Support)VenatoRx (Grant/Research Support)

1055. ARGONAUT-IV: Susceptibility of Carbapenem-resistant Klebsiellae to Ceftibuten/VNRX-5236

Background

Carbapenem resistance in Klebsiellae spp. arises through mutational and acquired mechanisms and is considered an “urgent threat” by the CDC. VNRX-5236 is a bicyclic boronate β-lactamase inhibitor (BLI) that combines oral bioavailability (via etzadroxil prodrug VNRX-7145; Figure 1) and activity against all three Ambler classes of serine β-lactamases. VNRX-7145 is currently in development with the oral cephalosporin, ceftibuten (CTB) (Figure 1).

Figure 1. Structures of VNRX-7145, VNRX-5236, and ceftibuten. The β-lactamase inhibitors are in red and the β-lactam antibiotic is in black.

Methods

The activity of CTB/VNRX-5236 against 200 carbapenem-resistant Klebsiellae from the Consortium on Resistance against Carbapenems in Klebsiella (CRACKLE) was assessed in this study. Among these, 193 expressed class A KPC enzymes, one expressed a class B NDM enzyme, and six expressed a class D OXA-48 or variant enzyme. Minimum inhibitory concentrations (MIC) were determined by broth microdilution (CLSI M07 Ed. 11) using the ThermoFisher Sensititre system with custom assay panels. MICs were interpreted using CLSI M100 Ed. 30, except the EUCAST breakpoint for CTB (S≤1 µg/mL) was used for CTB and was applied for comparative purposes to CTB/VNRX-5236 MICs where VNRX-5236 was fixed at 4 µg/mL. American Type Culture Collection strains were used for quality control.

Results

92.5% of stains studied in this CRACKLE collection were provisionally susceptible to CTB/VNRX-5236. In comparison, strains were 95.5% and 98% susceptible to meropenem-vaborbactam (MVB) and ceftazidime-avibactam (CZA), respectively. MIC₅₀s were in the susceptible range for CZA, MVB, and CTB/VNRX-5236; and resistant for CTB, ceftazidime (CAZ) and meropenem (MEM). MIC₉₀s were in the susceptible range for CZA, MVB, and CTB/VNRX-5236 and resistant range for CAZ, MEM, and CTB (Table 1). One of four CZA-resistant and three of nine MVB non-susceptible strains were provisionally susceptible to CTB/VNRX-5236.

MIC50 and MIC90 values (µg/mL) and percent susceptibility for Klebsiella pneumoniae strains (n=200). AMK, amikacin; CST, colistin; CAZ, ceftazidime; CZA, ceftazidime-avibactam; FEP, cefepime; MEM, meropenem; MVB, meropenem-vaborbactam; CTB, ceftibuten; TGC, tigecycline. * The breakpoint for CST is intermediate, as no susceptible breakpoint is available. ** The CTB breakpoint is valid only for urinary tract isolates. *** The breakpoint for CTB was provisionally used for CTB/VNRX-5236, where VNRX-5236 was fixed at 4 µg/mL.

Conclusion

The addition of VNRX-5236 enhanced the activity of CTB against the 200 Klebsiella isolates tested, reaching a total of 92.5% susceptibility. The prodrug (VNRX-7145) allows for oral administration, making it a potential option for step-down therapy. Importantly, VNRX-5236 has a broader spectrum of activity than existing oral BLIs, opening new treatment options for resistant infections as a key addition to the existing antibiotic arsenal.

Disclosures

Robin Patel, MD, 1928 Diagnostics (Consultant)BioFire Diagnostics (Grant/Research Support)ContraFect Corporation (Grant/Research Support)Curetis (Consultant)Hylomorph AG (Grant/Research Support)IDSA (Other Financial or Material Support, Editor’s Stipend)Infectious Diseases Board Review Course (Other Financial or Material Support, Honoraria)Mammoth Biosciences (Consultant)NBME (Other Financial or Material Support, Honoraria)Netflix (Consultant)Next Gen Diagnostics (Consultant)PathoQuest (Consultant)PhAST (Consultant)Qvella (Consultant)Samsung (Other Financial or Material Support, Patent Royalties)Selux Diagnostics (Consultant)Shionogi & Co., Ltd. (Grant/Research Support)Specific Technologies (Consultant)TenNor Therapeutics Limited (Grant/Research Support)Torus Biosystems (Consultant)Up-to-Date (Other Financial or Material Support, Honoraria) Robin Patel, MD, BioFire (Individual(s) Involved: Self): Grant/Research Support; Contrafect (Individual(s) Involved: Self): Grant/Research Support; IDSA (Individual(s) Involved: Self): Editor’s stipend; NBME, Up-to-Date and the Infectious Diseases Board Review Course (Individual(s) Involved: Self): Honoraria; Netflix (Individual(s) Involved: Self): Consultant; TenNor Therapeutics Limited (Individual(s) Involved: Self): Grant/Research Support; to Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Selux Diagnostics, 1928 Diagnostics, PhAST, Torus Biosystems, Mammoth Biosciences and Qvella (Individual(s) Involved: Self): Consultant David van Duin, MD, PhD, Entasis (Advisor or Review Panel member)genentech (Advisor or Review Panel member)Karius (Advisor or Review Panel member)Merck (Grant/Research Support, Advisor or Review Panel member)Pfizer (Consultant, Advisor or Review Panel member)Qpex (Advisor or Review Panel member)Shionogi (Grant/Research Support, Scientific Research Study Investigator, Advisor or Review Panel member)Utility (Advisor or Review Panel member) Vance G. Fowler, Jr., MD, MHS, Achaogen (Consultant)Advanced Liquid Logics (Grant/Research Support)Affinergy (Consultant, Grant/Research Support)Affinium (Consultant)Akagera (Consultant)Allergan (Grant/Research Support)Amphliphi Biosciences (Consultant)Aridis (Consultant)Armata (Consultant)Basilea (Consultant, Grant/Research Support)Bayer (Consultant)C3J (Consultant)Cerexa (Consultant, Other Financial or Material Support, Educational fees)Contrafect (Consultant, Grant/Research Support)Debiopharm (Consultant, Other Financial or Material Support, Educational fees)Destiny (Consultant)Durata (Consultant, Other Financial or Material Support, educational fees)Genentech (Consultant, Grant/Research Support)Green Cross (Other Financial or Material Support, Educational fees)Integrated Biotherapeutics (Consultant)Janssen (Consultant, Grant/Research Support)Karius (Grant/Research Support)Locus (Grant/Research Support)Medical Biosurfaces (Grant/Research Support)Medicines Co. (Consultant)MedImmune (Consultant, Grant/Research Support)Merck (Grant/Research Support)NIH (Grant/Research Support)Novadigm (Consultant)Novartis (Consultant, Grant/Research Support)Pfizer (Grant/Research Support)Regeneron (Consultant, Grant/Research Support)sepsis diagnostics (Other Financial or Material Support, Pending patent for host gene expression signature diagnostic for sepsis.)Tetraphase (Consultant)Theravance (Consultant, Grant/Research Support, Other Financial or Material Support, Educational fees)Trius (Consultant)UpToDate (Other Financial or Material Support, Royalties)Valanbio (Consultant, Other Financial or Material Support, Stock options)xBiotech (Consultant) Daniel D. Rhoads, MD, Becton, Dickinson and Company (Grant/Research Support) Michael Jacobs, MBBS, Venatorx Pharmaceuticals, Inc. (Grant/Research Support) Focco van den Akker, PhD, Venatorx Pharmaceuticals, Inc. (Grant/Research Support) David A. Six, PhD, Venatorx Pharmaceuticals, Inc. (Employee) Greg Moeck, PhD, Venatorx Pharmaceuticals, Inc. (Employee) Krisztina M. Papp-Wallace, Ph.D., Merck & Co., Inc. (Grant/Research Support)Spero Therapeutics, Inc. (Grant/Research Support)Venatorx Pharmaceuticals, Inc. (Grant/Research Support)Wockhardt Ltd. (Other Financial or Material Support, Research Collaborator) Robert A. Bonomo, MD, entasis (Research Grant or Support)Merck (Grant/Research Support)NIH (Grant/Research Support)VA Merit Award (Grant/Research Support)VenatoRx (Grant/Research Support)

Clinical and Infection Prevention Applications of SARS-CoV-2 Genotyping: An IDSA/ASM Consensus Review Document

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with >2 million genomes sequenced at this writing. The rise of more transmissible variants of concern that affect vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, clinical reporting for laboratories, and emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretell a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.

Artificial Intelligence and Mapping a New Direction in Laboratory Medicine: A Review

BACKGROUND

Modern artificial intelligence (AI) and machine learning (ML) methods are now capable of completing tasks with performance characteristics that are comparable to those of expert human operators. As a result, many areas throughout healthcare are incorporating these technologies, including in vitro diagnostics and, more broadly, laboratory medicine. However, there are limited literature reviews of the landscape, likely future, and challenges of the application of AI/ML in laboratory medicine.

CONTENT

In this review, we begin with a brief introduction to AI and its subfield of ML. The ensuing sections describe ML systems that are currently in clinical laboratory practice or are being proposed for such use in recent literature, ML systems that use laboratory data outside the clinical laboratory, challenges to the adoption of ML, and future opportunities for ML in laboratory medicine.

SUMMARY

AI and ML have and will continue to influence the practice and scope of laboratory medicine dramatically. This has been made possible by advancements in modern computing and the widespread digitization of health information. These technologies are being rapidly developed and described, but in comparison, their implementation thus far has been modest. To spur the implementation of reliable and sophisticated ML-based technologies, we need to establish best practices further and improve our information system and communication infrastructure. The participation of the clinical laboratory community is essential to ensure that laboratory data are sufficiently available and incorporated conscientiously into robust, safe, and clinically effective ML-supported clinical diagnostics.

The truth about SARS-CoV-2 cycle threshold values is rarely pure and never simple

Nucleic acid amplification tests (NAATs) are the reference standard methods for SARS-CoV-2 detection because of their high analytical sensitivity and specificity. Many NAATs, which use reverse-transcription real-time PCR (RT-PCR), are clinically validated, technically validated, and authorized by the U.S. Food & Drug Administration (FDA) to be interpreted qualitatively as "detected" (positive for SARS-CoV-2 RNA) or "not detected" (negative for SARS-CoV-2 RNA). As of this writing there are over 250 SARS-CoV-2 molecular diagnostic tests that have obtained emergency use authorization from the FDA. The primary results generated by RT-PCR are fluorescent light emissions; serial detection of this fluorescence is plotted and the amplification curves visualized. Positive or negative interpretation depends on whether or not the curve exceeds a specified signal threshold. Part of the resulting process includes determination of the number of cycles needed before the fluorescent signal crosses this threshold (Ct value). In general, the more viral RNA in the initial specimen, the fewer the number of amplification cycles required to generate a positive signal; thus, the lower the Ct value, the higher the viral burden in the primary sample. Though all current SARS-CoV-2 NAATs are authorized only for qualitative interpretation, as of 10 December 2020, the FDA explicitly states that the Ct value results may be reported by the clinical laboratory in addition to the qualitative interpretation. Throughout the pandemic, many scientists, physicians, politicians, and public citizens have attempted to emphasize the importance (or unimportance) of certain pandemic-related interventions, mitigation strategies, the disease itself, and testing approaches. Some have advocated that a specific variable is most important in a testing approach and should be maximized to the potential detriment of the others: analytical sensitivity and specificity, cost, turnaround time, sample type, or accessibility of collection. If the truth was obvious, then there would be little debate, but the debate has been important and earnest. As Oscar Wilde wrote, "The truth is rarely pure and never simple." We suggest that this quote describes the current situation on the debate over the relevance of Ct values, and we will explore the clinical utility of quantitative SARS-CoV-2 testing here.

Recent advances in rapid antimicrobial susceptibility testing systems

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.

Interlaboratory Agreement of Anti-Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Serologic Assays in the Expedited College of American Pathologists Proficiency Testing Program

CONTEXT.—

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently emerged, currently pandemic virus, and the etiologic agent of coronavirus disease 2019 (COVID-19). Clinical testing for antibodies to SARS-CoV-2 has rapidly become widespread, but data regarding the interlaboratory performance of these serologic assays are limited.

OBJECTIVE.—

To describe the development and initial results of the College of American Pathologists (CAP) SARS-CoV-2 Serology Survey.

DESIGN.—

Members from the CAP Microbiology and Diagnostic Immunology and Flow Cytometry Committees formed a working group to support development of a new proficiency testing survey for anti-SARS-CoV-2 antibody assays. Supplemental questions in the survey assessed the state of SARS-CoV-2 serologic testing among participating laboratories as of July 2020. Results were analyzed for agreement by immunoglobulin (Ig) isotype tested, assay manufacturer, and methodology.

RESULTS.—

A total of 4125 qualitative results were received from 1110 laboratories participating in the first survey. Qualitative agreement for assays measuring anti-SARS-CoV-2 total antibodies or IgG was greater than 90% for all 3 samples in the survey. Qualitative agreement for IgM and IgA for the negative sample was greater than 95%, but lacked consensus for the other 2 samples.

CONCLUSIONS.—

These initial data suggest overall excellent agreement and comparable performance for most qualitative anti-SARS-CoV-2 IgG and total antibody assays across all participating clinical laboratories, regardless of specific target antigen or assay methodology.

Monitoring Ceftazidime-Avibactam and Aztreonam Concentrations in the Treatment of a Bloodstream Infection Caused by a Multidrug-Resistant Enterobacter sp. Carrying Both Klebsiella pneumoniae Carbapenemase-4 and New Delhi Metallo-β-Lactamase-1

In an infection with an Enterobacter sp. isolate producing Klebsiella pneumoniae Carbapenemase-4 and New Delhi Metallo-β-Lactamase-1 in the United States, recognition of the molecular basis of carbapenem resistance allowed for successful treatment by combining ceftazidime-avibactam and aztreonam. Antimicrobial synergy testing and therapeutic drug monitoring assessed treatment adequacy.

Asymptomatic Patient Testing After 10:1 Pooling Using the Xpert Xpress SARS-CoV-2 Assay

Objectives

Pool testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) preserves testing resources at the risk of missing specimens through specimen dilution.

Methods

To determine whether SARS-CoV-2 specimens would be missed after 10:1 pooling, we identified 10 specimens with midrange (ie, 25-34 cycles) and 10 with late (ie, >34-45 cycles) crossing threshold (Ct) values and tested these both neat and after 10:1 pooling. Final test results and Ct changes were compared.

Results

Overall, 17 of 20 specimens that contained SARS-CoV-2 were detected after 10:1 pooling with the Xpert Xpress SARS-CoV-2 Assay (Cepheid), rendering an 85% positive percentage of agreement. All 10 of 10 specimens with an undiluted Ct in the mid-Ct range were detected after 10:1 pooling, in contrast to 7 of 10 with an undiluted Ct in the late-Ct range. The overall Ct difference between the neat testing and the 10:1 pool was 2.9 cycles for the N2 gene target and 3 cycles for the E gene target. The N2 gene reaction was more sensitive than the E gene reaction, detecting 16 of 20 positive specimens after 10:1 pooling compared with 9 of 20 specimens.

Conclusions

An 85% positive percentage of agreement was achieved, with only specimens with low viral loads being missed following 10:1 pooling. The average impact on both reverse transcription polymerase chain reactions within this assay was about 3 cycles.

Home testing for COVID-19: Benefits and limitations

The home test kits for detecting SARS-CoV-2 infection with Food and Drug Administration emergency use authorization primarily use either isothermal nucleic acid amplification or antigen detection, and each test has advantages and limitations in terms of sensitivity and specificity, cost, results reporting, and results turnaround time. In clinical studies, these tests provide accurate positive results in symptomatic individuals, although negative results are less accurate. There are also accuracy concerns for positive results in asymptomatic individuals. These factors have implications for their clinical interpretation and use.

Diatoms: A novel cause of granulomatous inflammation of the head and neck

OBJECTIVE

We report the first 4 cases of intraoral nonnecrotizing granulomatous foreign body reactions to diatoms, plausibly as a result of exogenous material introduced following iatrogenic or traumatic injury.

STUDY DESIGN

Clinical and histopathologic findings of 4 intraoral cases of nonnecrotizing granulomatous foreign body reaction to diatoms, single-celled algae belonging to the taxonomic phylum Bacillariophyta, are reported.

RESULTS

The lesions presented either in the jaws or in the soft tissue overlying the alveolar bone, in some instances mimicking an inflammatory lesion of odontogenic etiology. Microscopically, the lesions presented as nonnecrotizing granulomatous inflammation associated with either spherical and radially symmetric or rectangular and bilaterally symmetric diatomaceous foreign material.

CONCLUSION

The diagnosis of a diatom-associated foreign body reaction necessitates familiarization with the histopathologic features of these organisms to accurately characterize the nature of such lesions.

Variability in the Laboratory Measurement of Cytokines

CONTEXT.—

The measurement of cytokines in clinical laboratories is becoming an increasingly routine part of immune monitoring when administering biologic and cell-based immunotherapies and also for clinical assessment of inflammatory conditions. While a number of commercial assays and platforms are available for cytokine measurement, there is currently little standardization among these analytical methods.

OBJECTIVE.—

To characterize the variability and comparability among cytokine testing platforms that are commonly used in clinical laboratories.

DESIGN.—

We analyzed data for 4 cytokines (interleukin [IL]-1, IL-6, IL-8, and tumor necrosis factor-alpha [TNF-α]) from 6 College of American Pathologists cytokine surveys administered from 2015 to 2018. Analyses interrogated variability between testing methods and variability within each laboratory across the mailings.

RESULTS.—

Significant variability was noted across methods with analysis of IL-1 showing the least variability and IL-6, IL-8, and TNF-α varying between methods to a greater extent. Intralab variability was also significant with TNF-α measurements again showing the greatest variability.

CONCLUSIONS.—

This retrospective analysis of College of American Pathologists proficiency testing data for cytokine measurement is the largest method comparison to date, and this study provides a description of the variation of cytokine measurement across methods, across laboratories, and within laboratories. Serial monitoring of cytokines should preferentially be performed by the same method within the same laboratory.

Diagnosis of prion diseases by RT-QuIC results in improved surveillance

OBJECTIVE

To present the National Prion Disease Pathology Surveillance Center's (NPDPSC's) experience using CSF real-time quaking-induced conversion (RT-QuIC) as a diagnostic test, to examine factors associated with false-negative RT-QuIC results, and to investigate the impact of RT-QuICs on prion disease surveillance.

METHODS

Between May 2015 and April 2018, the NPDPSC received 10,498 CSF specimens that were included in the study. Sensitivity and specificity analyses were performed on 567 autopsy-verified cases. Prion disease type, demographic characteristics, specimen color, and time variables were examined for association with RT-QuIC results. The effect of including positive RT-QuIC cases in prion disease surveillance was examined.

RESULTS

The diagnostic sensitivity and specificity of RT-QuIC across all prion diseases were 90.3% and 98.5%, respectively. Diagnostic sensitivity was lower for fatal familial insomnia, Gerstmann-Sträussler-Scheinker disease, sporadic fatal insomnia, variably protease sensitive prionopathy, and the VV1 and MM2 subtypes of sporadic Creutzfeldt-Jakob disease. Individuals with prion disease and negative RT-QuIC results were younger and had lower tau levels and nonelevated 14-3-3 levels compared to RT-QuIC-positive cases. Sensitivity was high throughout the disease course. Some cases that initially tested RT-QuIC negative had a subsequent specimen test positive. Including positive RT-QuIC cases in surveillance statistics increased laboratory-based case ascertainment of prion disease by 90% over autopsy alone.

CONCLUSIONS

RT-QuIC has high sensitivity and specificity for diagnosing prion diseases. Sensitivity limitations are associated with prion disease type, age, and related CSF diagnostic results. RT-QuIC greatly improves laboratory-based prion disease ascertainment for surveillance purposes.

CLASSIFICATION OF EVIDENCE

This study provides Class III evidence that second-generation RT-QuIC identifies prion disease with a sensitivity of 90.3% and specificity of 98.5% among patients being screened for these diseases due to concerning symptoms.

Computer Vision and Artificial Intelligence Are Emerging Diagnostic Tools for the Clinical Microbiologist

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.

Feasibility of Remote Assessment of Human Prion Diseases for Research and Surveillance

BACKGROUND

Prion disease research and surveillance can be challenging due to the disease's difficulty to diagnose, rapid progression, and geographic dispersion. Improving accessibility through teleneurology could improve the ability to conduct these activities.

OBJECTIVES

The aim of this study was to determine the feasibility of conducting teleneurology assessments for research and surveillance of prion diseases.

METHOD

Participants were offered in-person visit, medical record review, or teleneurology assessment. Standardized histories and assessments evaluating cognition, functional ability, and neuropsychiatric symptoms were collected. Data regarding participants' satisfaction with teleneurology were collected.

RESULTS

From April 2017 to July 2018, the study received 114 referrals. 45 and 5 participants consented for the teleneurology and medical record review arms of the study, respectively. 29 subjects participated in at least one teleneurology visit. Participants expressed satisfaction with teleneurology and found it easy to participate. Some aspects of the examination were hindered or interrupted due to technological reasons.

CONCLUSIONS

We demonstrate the feasibility and preference of teleneurology as a modality in which subjects with prion disease can partake in clinical research. Technological aspects sometimes interfered with research assessments.

635. Genomic Evolution and Progression of Antimicrobial Resistance in a Series of Extensively Drug-Resistant Pseudomonas aeruginosa (XDR-Pa) Isolates from a Cystic Fibrosis Lung Transplant Recipient

Background

Chronic respiratory infection due to extensively drug-resistant Pseudomonas aeruginosa (XDR-Pa) is a significant cause of mortality in cystic fibrosis (CF) patients. The CF respiratory anatomy, chronic antibiotic use, and PA colonization creates a milieu for high evolutionary pressure and genetic diversity. We sought to explore the progression of antibiotic resistance and genome evolution of XDR-Pa in a longitudinal series of isolates collected from an18-year-old CF patient who underwent lung transplantation.

Methods

Consecutive respiratory isolates were collected from December 2016 to March 2018. Standard disk diffusion methods were used to evaluate antimicrobial susceptibility. Whole-genome sequencing (WGS) data were obtained on an Illumina NextSeq and assembled. Variants were identified using the GATK HaplotypeCaller and their functional impact was determined using snpEff. Maximum likelihood phylogenetic trees were constructed using MEGA and BEAST. Panther was used to test for enrichment of Gene Ontology functional categories among mutated genes.

Results

Phylogenetic analysis of complete genome sequences showed that 18 isolates formed a monophyletic group. Analysis using BEAST showed that genomes shared a common ancestor that was present prior to transplant. Over 300 single nucleotide variants and small insertion-deletion mutations were found, in comparison with a reconstruction of the ancestral sequence (Figure 1). Shared patterns of antibiotic susceptibility profiles were largely concordant with phylogenetic clustering and trended toward a decrease in susceptibility over time. Two different frameshift mutations in the DNA mismatch repair gene mutL were found in 15 genomes and these exhibited an increased rate of transition to transversion mutations, consistent with a hypermutator phenotype.

Conclusion

WGS of XDR-Pa identified variations in antibiotic resistance and virulence genes. Changes in mutL likely accelerated the accumulation of mutations. Multiple related sub-groups of strains appear to have been circulating prior to transplant and continued to diverge during the treatment period. Correlating antibiotic pressure, susceptibility profiles, and WGS in XDR-Pa from a single patient reveals the clinical impact of genomic evolution in CF.

Disclosures

All authors: No reported disclosures.

1358. A Novel Rapidly Growing Mycobacteria (RGM) Species Causing Soft Tissue and Orthopedic Hardware Infection After Trauma

Background

The widespread use of molecular techniques has resulted in increasing numbers of newly characterized rapidly growing mycobacteria (RGM). Many RGM cause soft tissue and orthopedic hardware infection, particularly after trauma. RGM species identification remains challenging with few genetic differences between species.

Methods

We describe a case involving RGM. We report results of matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (Bruker Biotyper), sequencing of rpoB, erm(39), and 16S rRNA genes, and antibiotic susceptibility testing (AST). We review previous reports describing similar RGM infections.

Results

A 58-year-old male sustained multiple fractures and right thigh compartment syndrome after a motorcycle accident. He underwent fasciotomy and multi-stage surgical fixations. 3 months later, he had wound dehiscence, purulence and multiple fluid collections of his right leg and knee requiring surgical drainage and removal of orthopedic hardware. After 4 days, acid-fast bacilli grew on routine bacterial culture media. MALDI-TOF identified the isolate as Mycobacterium mageritense. In contrast, sequencing of 16S rRNA (100% identity) and erm(39) (> 99% identity) identified the isolate as Mycobacterium houstonense; erm(39) only had 80% similarity with Mycobacterium fortuitum. Sequencing of rpoB showed a 19 bp difference with the M. houstonense type strain, and showed similarity to M. fortuitum (97.64%) than M. houstonense (97.45%). AST demonstrated resistance to clarithromycin only. After initial treatment with imipenem, ciprofloxacin, and doxycycline, definite therapy with ciprofloxacin and doxycycline was successful. In the literature, we found one case each of M. mageritense and M. houstonense infection after trauma.

Conclusion

This case highlights the importance of RGM other than M. fortuitum as a cause of soft tissue and orthopedic hardware infections, and illustrates the difficulty of identifying them to the species level. Sequencing of erm(39) and 16S rRNA gene identified the isolate as M. houstonense, but the larger difference (>2.5%) in rpoB sequence suggests a novel species. Further characterization is underway. Efforts to determine RGM species and antibiotic susceptibility give important insight into diagnosis and management.

Disclosures

All authors: No reported disclosures.

610. Meropenem-vaborbactam (MV) In Vitro Activity Against Carbapenem-Resistant Klebsiella pneumoniae (CRKP) Isolates with Outer Membrane Porin Gene Mutations

Background

Vaborbactam is a cyclic boronic acid β-lactamase inhibitor (BLI) developed to potently inhibit Ambler class A&C enzymes, including KPC carbapenemases. Metallo-β-lactamases (MBL) and some Class D oxacillinases (OXA) are not inactivated by vaborbactam. Meropenem-vaborbactam (MV) was recently approved for the treatment of carbapenem-resistant Enterobacteriaceae complicated urinary tract infections. Recent studies have identified outer membrane porin (Ompk35 and -36) mutations in Klebsiella pneumoniae (KP) as a mechanism of decreased susceptibility to MV. We evaluated the activity of MV against a historical cohort of KP clinical isolates with these porin gene mutations.

Methods

WGS of carbapenem-resistant KP clinical isolates was performed and those harboring mutations in Ompk35 or Ompk36 were selected for testing. Strain KP ATCC BAA-1705 was used as a positive control. Meropenem and MV minimum inhibitory concentrations (MIC) were determined by broth microdilution (BMD) in custom 96-well plates (ThermoFisher Scientific) with a constant 8 µg/mL vaborbactam concentration. The MIC of ceftazidime–avibactam (CZA) was determined by standard BMD reference methods and interpreted according to CLSI criteria.

Results

A total of 105 KP isolates with either partial or complete mutations in outer membrane porin genes were included in the analysis. All isolates were resistant to Meropenem. The median MV MIC was 0.03 µg/mL (range, 0.015 to >16 µg/mL). Eleven isolates (10.4%) were resistant to MV. Sixteen additional isolates (16.1%) demonstrated higher than expected MV MICs ranging from 1 to 4 µg/mL. Only 1/11 resistant isolates harbored a gene for MBL production. Gene mutations in bla_KPC were not detected. See Table 1 for characteristics of resistant isolates.

Conclusion

Resistance and decreased susceptibility to MV is demonstrated in a historical cohort of KP clinical isolates dating back to 2013. WGS reliably identifies porin variants secondary to gene mutations in Ompk35 and Ompk36 as the underlying mechanism of decreased susceptibility. CZA appears to retain activity against these isolates. Caution should be exercised regarding the empiric use of MV against increasingly resistant KP as a result of non-β-lactamase-mediated mechanisms.

Disclosures

All authors: No reported disclosures.

651. Multi-Center Evaluation of the BioFire® FilmArray® Blood Culture Identification 2 Panel for the Detection of Microorganisms and Resistance Markers in Positive Blood Cultures

Background

The BioFire® FilmArray® Blood Culture Identification 2 (BCID2) Panel is a diagnostic test that provides results for 26 bacterial, 7 fungal pathogens and 10 antimicrobial resistance (AMR) genes from positive blood culture (PBC) specimens in about an hour. The BCID2 Panel builds upon the existing BCID Panel with several additional assays that include Candida auris and an expanded AMR gene menu that provides methicillin-resistant Staphylococcus aureus (MRSA) results plus detection for mcr-1, carbapenem resistance, and ESBL. Here, we summarize studies conducted to establish clinical performance using an Investigational Use Only version of the BCID2 Panel.

Methods

Three studies were performed. The first involves prospective collection and testing of an expected ~1,000 residual PBCs at 7 US and 2 EU sites, which began in October 2018 and will conclude in June 2019. BCID2 Panel performance is compared with reference methods of microbial culture as well as PCR/sequencing for AMR genes. In addition, BCID2 Panel MRSA results are compared with the FDA-cleared Xpert MRSA/SA BC system (Cepheid, Inc). Relevant bacterial isolates recovered from PBCs are also evaluated by various phenotypic antimicrobial susceptibility testing (AST) methods. The prospective evaluation is supplemented with a second study that involves testing of ~300 pre-selected, archived PBCs containing rare organisms. The third study includes over 500 seeded blood cultures containing very rare organisms with an evaluation of co-spiked samples.

Results

With over 1,200 samples tested to date (out of an anticipated 1,800 total), the BCID2 Panel has demonstrated an overall sensitivity of >98% and specificity of >99% for identification of microorganisms compared with culture. Concordance between the BCID2 Panel and the Xpert MRSA/SA BC test is >99% for identification of MRSA. Evaluation of BCID2 Panel AMR gene detection relative to AST and PCR is ongoing.

Conclusion

The FilmArray® BCID2 Panel appears to be a sensitive, specific, and robust test for rapid detection of microorganisms and MRSA in PBCs. With the use of this comprehensive test, improved antimicrobial stewardship is anticipated.

Disclosures

All authors: No reported disclosures

A Practical Primer on Prion Pathology

Prion diseases comprise a group of transmissible degenerative encephalopathies resulting from propagation of a misfolded cellular protein of uncertain function. As is generally the case with rare diseases, lack of institutional experience compromises individual familiarity with the varying, and apparently protean, manifestations of prion diseases, both clinically and pathologically. Coupled with the documented transmissibility of these diseases both within and between species, the Centers for Disease Control and Prevention (CDC) has established the National Prion Disease Pathology Surveillance Center to both aid with diagnosis of prion disease and to survey the United States for evidence of zoonotic transmission. We have assembled this primer with the hope that our accumulated experience will enable the neuropathological community to help the CDC "save lives and protect people."

Sensitivity of Cerebrospinal Fluid Cytology for the Diagnosis of Cryptococcal Infections: A 21-Year Single-Institution Retrospective Review

Objectives

Cryptococcal meningoencephalitis is the most common fungal infection of the central nervous system diagnosed by cerebrospinal fluid cytology (CSF) studies. Existing literature suggests that routine CSF cytomorphologic evaluations are exquisitely specific; however, less is known about their sensitivity.

Methods

An electronic record review of the cytopathology and microbiology files was conducted for the 21-year interval from January 1, 1995, through December 31, 2015.

Results

In 21 years, 12,584 CSF samples were processed in the laboratory. Of these, 24 (0.2%) were reported positive for cryptococcal organisms by light microscopy, and 129 CSF fungal cultures were positive for Cryptococcus species. All cotested specimens with positive cytology results were positive on culture (15 specimens, 100% specificity). Twenty-four samples with positive culture results were negative by CSF cytology (sensitivity 39%).

Conclusions

When culture is used as a gold standard, CSF cytology is 100% specific and 39% sensitive, with a positive predictive value of 100% and a negative predictive value of 99.8%.

ARGONAUT-I: Activity of Cefiderocol (S-649266), a Siderophore Cephalosporin, against Gram-Negative Bacteria, Including Carbapenem-Resistant Nonfermenters and Enterobacteriaceae with Defined Extended-Spectrum β-Lactamases and Carbapenemases

The activity of the siderophore cephalosporin cefiderocol is targeted against carbapenem-resistant Gram-negative bacteria. In this study, the activity of cefiderocol against characterized carbapenem-resistant Acinetobacter baumannii complex, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Enterobacteriaceae strains was determined by microdilution in iron-depleted Mueller-Hinton broth. The MIC90s against A. baumannii, S. maltophilia, and P. aeruginosa were 1, 0.25, and 0.5 mg/liter, respectively. Against Enterobacteriaceae, the MIC90 was 1 mg/liter for the group harboring OXA-48-like, 2 mg/liter for the group harboring KPC-3, and 8 mg/liter for the group harboring TEM/SHV ESBL, NDM, and KPC-2.

1351. In vitro Activity of Cefiderocol (S-649266), a Siderophore Cephalosporin, Against Enterobacteriaceae With Defined Extended-Spectrum Β-Lactamases and Carbapenemases

Background

Cefiderocol is a novel siderophore cephalosporin targeted for activity against carbapenem and multidrug-resistant Gram-negative species, including extended-spectrum β-lactamase (ESBL) and carbapenemase-producing strains. The Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae (CRACKLE) is a federally funded, prospective multi-center consortium of 20 hospitals from nine US healthcare systems to track carbapenem-resistant Enterobacteriaceae.

Methods

Minimum inhibitory concentrations (MICs) of cefiderocol and meropenem were determined by broth microdilution according to current CLSI guidelines. Cefiderocol was tested in iron-depleted cation-adjusted Mueller–Hinton (MH) broth, meropenem was tested in cation-adjusted MH broth. Cefiderocol MICs were read as the first drug well in which the growth was significantly reduced (i.e., a button of &lt;1 mm or light/faint turbidity) relative to the growth observed in the growth control well containing the same medium. Trailing endpoints were disregarded. Isolates tested included 35 Escherichia coli, five Enterobacter/Citrobacter group, and 794 Klebsiella pneumoniae. Isolates had characterized β-lactamases including TEM, SHV, and CTX-M ESBLs and KPC, NDM, and OXA carbapenemases.

Results

Cefiderocol MICs ranged from ≤0.03 to &gt;64 mg/L, with overall MIC50 of 0.5 mg/L and MIC90 of 4 mg/L (table). MIC90 value (≤0.03 mg/L) was lowest against isolates with no ESBLs or carbapenemases. MIC90 was 1 mg/L for OXA and TEM/SHV groups, 2–4 mg/L for KPC-3 groups and 8 mg/L for NDM and KPC-2 groups.

Conclusion

Compared with isolates without ESBLs and carbapenemases, cefiderocol shows higher MICs against isolates with ESBLs, including TEM, SHV, and CTX-M and carbapenemases including KPC, NDM, and OXA. The clinical utility of cefiderocol against ESBL and carbapenemase-producing Enterobacteriaceae is dependent on the pharmacokinetic and pharmacodynamic properties of cefiderocol.

Disclosures

M. R. Jacobs, Achaogen: Investigator, Research grant. Shionogi: Investigator, Research grant. S. S. Richter, bioMerieux: Grant Investigator, Research grant. BD Diagnostics: Grant Investigator, Research grant. Roche: Grant Investigator, Research grant. Hologic: Grant Investigator, Research grant. Diasorin: Grant Investigator, Research grant. Accelerate: Grant Investigator, Research grant. Biofire: Grant Investigator, Research grant. D. Van Duin, Shionogi: Scientific Advisor, Consulting fee. achaogen: Scientific Advisor, Consulting fee. Allergan: Scientific Advisor, Consulting fee. Astellas: Scientific Advisor, Consulting fee. Neumedicine: Consultant, Consulting fee. T2 Biosystems: Scientific Advisor, Consulting fee. Roche: Scientific Advisor, Consulting fee.

1348. In vitro Activity of Plazomicin, a Next-Generation Aminoglycoside, Against Carbapenemase-Producing Klebsiella pneumoniae

Background

Methods

Results

Conclusion

Disclosures

Screening and Diagnosis of Monoclonal Gammopathies: An International Survey of Laboratory Practice

Context.—

Serum tests used for the screening and diagnosis of monoclonal gammopathies include serum protein electrophoresis (SPE; agarose gel or capillary zone), immunofixation (IFE) and immunosubtraction capillary electrophoresis, serum free light chains, quantitative immunoglobulins, and heavy/light–chain combinations. Urine protein electrophoresis and urine IFE may also be used to identify Bence-Jones proteinuria.

Objective.—

To assess current laboratory practice for monoclonal gammopathy testing.

Design.—

In April 2016, a voluntary questionnaire was distributed to 923 laboratories participating in a protein electrophoresis proficiency testing survey.

Results.—

Seven hundred seventy-four laboratories from 38 countries and regions completed the questionnaire (83.9% response rate; 774 of 923). The majority of participants (68.6%; 520 of 758) used agarose gel electrophoresis as their SPE method, whereas 31.4% (238 of 758) used capillary zone electrophoresis. The most common test approaches used in screening were SPE with reflex to IFE/immunosubtraction capillary electrophoresis (39.3%; 299 of 760); SPE only (19.1%; 145 of 760); SPE and IFE or immunosubtraction capillary electrophoresis (13.9%; 106 of 760); and SPE with IFE, serum free light chain, and quantitative immunoglobulins (11.8%; 90 of 760). Only 39.8% (305 of 767) of laboratories offered panel testing for ordering convenience. Although SPE was used by most laboratories in diagnosing new cases of myeloma, when laboratories reported the primary test used to follow patients with monoclonal gammopathy, only 55.7% (403 of 724) chose SPE, with the next most common selections being IFE (18.9%; 137 of 724), serum free light chain (11.7%; 85 of 724), and immunosubtraction capillary electrophoresis (2.1%; 15 of 724).

Conclusions.—

Ordering and testing practices for the screening and diagnosis of monoclonal gammopathy vary widely across laboratories. Improving utilization management and report content, as well as recognition and development of laboratory-directed testing guidelines, may serve to enhance the clinical value of testing.

Detection of Pseudomonas aeruginosa biomarkers from thermally injured mice in situ using imaging mass spectrometry

Monitoring patients with burn wounds for infection is standard practice because failure to rapidly and specifically identify a pathogen can result in poor clinical outcomes, including death. Therefore, a method that facilitates detection and identification of pathogens in situ within minutes of biopsy would be a significant benefit to clinicians. Mass spectrometry is rapidly becoming a standard tool in clinical settings, capable of identifying specific pathogens from complex samples. Imaging mass spectrometry (IMS) expands the information content by enabling spatial resolution of biomarkers in tissue samples as in histology, without the need for specific stains/antibodies. Herein, a murine model of thermal injury was used to study infection of burn tissue by Pseudomonas aeruginosa. This is the first use of IMS to detect P. aeruginosa infection in situ from thermally injured tissue. Multiple molecular features could be spatially resolved to infected or uninfected tissue. This demonstrates the potential use of IMS in a clinical setting to aid doctors in identifying both presence and species of pathogens in tissue.

The cytopathology of Actinomyces, Nocardia, and their mimickers

Nocardia species and Actinomyces species are 2 of the most commonly diagnosed filamentous bacteria in routine cytopathology practice. These genera share many overlapping cytomorphologic features, including their thin, beaded, branching, Gram-positive, GMS-positive filamentous structures that fragment at their peripheries into bacillary- and coccoid-appearing forms. Features that help distinguish between these 2 microorganisms include the width of their filamentous structures, the angles at which they branch, and their ability or lack thereof to retain a modified acid-fast stain. In addition to cytomorphologic overlap, overlap in clinical presentation is frequent with pulmonary and mucocutaneous presentations seen in both. Differentiating between Nocardia and Actinomyces is essential because patients with these infections require different approaches to medical management. Both antibiotic susceptibilities and the need for early surgical intervention as part of the treatment plan vary greatly among these 2 groups. This review focuses on the clinical presentation, cytomorphology and staining characteristics that can be useful in identifying and distinguishing between Nocardia and Actinomyces infections, as well as their mimickers.

Interactive effects of temperature and dietary supplementation of arginine or guanidinoacetic acid on nutritional and physiological responses in male broiler chickens

1. The aim of this experiment was to study the interactive effect of rearing temperature and dietary supplementation of arginine (Arg) or guanidinoacetic acid (GAA) on performance, gut morphology and ascites indices in broiler chickens raised under the same condition in the first 2 weeks and then reared under normal (23-26°C) or subnormal (17°C) ambient temperatures for the next 3 weeks. 2. This experiment was conducted as a split plot with 900 Ross 308 male broiler chicks that were allocated to two houses (as main plots); each consisted of 5 treatments (as sub-plots) with 6 replicates of 15 birds. The 5 diets were (1) control, (2) control + 0.60 g/kg GAA, (3) control + 1.20 g/kg GAA, (4) control + 0.86 g/kg Arg and (5) control + 1.72 g/kg Arg. 3. Feed intake (0-35 d) of birds fed on a diet containing 1.2 g GAA/kg and reared under normal temperature was reduced compared to control fed birds. Birds fed on a diet containing 1.72 g/kg Arg and reared under subnormal temperature had higher weight gain compared to those fed on control or GAA-added diets in overall study period. 4. Supplementation of diets with Arg alleviated the adverse effect of cold stress as reflected by reduction in blood haematocrit (41% vs. 37%), and right ventricle to total ventricle ratio (0.28 vs. 0.25) at 35 d of age. Addition of Arg to the diet of birds reared under cold stress resulted in a higher jejunal villus surface area compared to those fed on control or GAA-added diets. 5. Findings of this study revealed that Arg or GAA supplementation of diets did not affect performance of birds under normal temperatures, but Arg supplementation of the diet significantly alleviated the adverse effect of cold stress on performance, gut development and ascites syndrome. In addition, GAA supplementation at 1.2 g/kg improved jejunal villus surface area in birds raised under subnormal temperature.