Acinetobacter baumannii Genomic Sequence-Based Core Genome Multilocus Sequence Typing Using Ridom SeqSphere+ and Antimicrobial Susceptibility Prediction in ARESdb.

Whole-genome sequencing (WGS) is rapidly replacing traditional typing methods for the investigation of infectious disease outbreaks. Additionally, WGS data are being used to predict phenotypic antimicrobial susceptibility. Acinetobacter baumannii, which is often multidrug-resistant, is a significant culprit in outbreaks in health care settings. A well-characterized collection of A. baumannii was studied using core genome multilocus sequence typing (cgMLST). Seventy-two isolates previously typed by PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) provided by the Antimicrobial Resistance Leadership Group (ARLG) were analyzed using a clinical microbiology laboratory developed workflow for cgMLST with genomic susceptibility prediction performed using the ARESdb platform. Previously performed PCR/ESI-MS correlated with cgMLST using relatedness thresholds of allelic differences of ≤9 and ≤200 allelic differences in 78 and 94% of isolates, respectively. Categorical agreement between genotypic and phenotypic antimicrobial susceptibility across a panel of 11 commonly used drugs was 89%, with minor, major, and very major error rates of 8%, 11%, and 1%, respectively.

Modifiable Risk Factors for the Emergence of Ceftolozane-tazobactam Resistance.

BACKGROUND: Ceftolozane-tazobactam (TOL-TAZ) affords broad coverage against Pseudomonas aeruginosa. Regrettably, TOL-TAZ resistance has been reported. We sought to identify modifiable risk factors that may reduce the emergence of TOL-TAZ resistance. METHODS: Twenty-eight consecutive patients infected with carbapenem-resistant P. aeruginosa isolates susceptible to TOL-TAZ, treated with ≥72 hours of TOL-TAZ , and with P. aeruginosa isolates available both before and after TOL-TAZ exposure between January 2018 and December 2019 in Baltimore, Maryland, were included. Cases were defined as patients with at least a 4-fold increase in P. aeruginosa TOL-TAZ MICs after exposure to TOL-TAZ. Independent risk factors for the emergence of TOL-TAZ resistance comparing cases and controls were investigated using logistic regression. Whole genome sequencing of paired isolates was used to identify mechanisms of resistance that emerged during TOL-TAZ therapy. RESULTS: Fourteen patients (50%) had P. aeruginosa isolates which developed at least a 4-fold increase in TOL-TAZ MICs(ie, cases). Cases were more likely to have inadequate source control (29% vs 0%, P = .04) and were less likely to receive TOL-TAZ as an extended 3-hour infusion (0% vs 29%; P = .04). Eighty-six percent of index isolates susceptible to ceftazidime-avibactam (CAZ-AVI) had subsequent P. aeruginosa isolates with high-level resistance to CAZ-AVI, after TOL-TAZ exposure and without any CAZ-AVI exposure. Common mutations identified in TOL-TAZ resistant isolates involved AmpC, a known binding site for both ceftolozane and ceftazidime, and DNA polymerase. CONCLUSIONS: Due to our small sample size, our results remain exploratory but forewarn of the potential emergence of TOL-TAZ resistance during therapy and suggest extending TOL-TAZ infusions may be protective. Larger studies are needed to investigate this association.

Core Genome Multilocus Sequence Typing and Prediction of Antimicrobial Susceptibility Using Whole-Genome Sequences of Escherichia coli Bloodstream Infection Isolates.

In total, 50 Escherichia coli bloodstream isolates from the clinical laboratory and 12 E. coli isolates referred for pulsed-field gel electrophoresis (PFGE) were sequenced, assessed for clonality using core genome multilocus sequence typing (cgMLST), and evaluated for genomic susceptibility predictions using ARESdb. Results of sequence typing using whole-genome sequencing (WGS)-based MLST and sequence type (ST)-specific PCR were identical. Overall categorical agreement between genotypic (ARESdb) and phenotypic susceptibility testing for 62 isolates and 11 antimicrobial agents was 91%. Among the referred isolates, high major error rates were found for ceftazidime, cefepime, and piperacillin-tazobactam.

Multicenter Evaluation of the Unyvero Platform for Testing Bronchoalveolar Lavage Fluid.

Bronchoalveolar lavage (BAL) culture is a standard, though time-consuming, approach for identifying microorganisms in patients with severe lower respiratory tract (LRT) infections. The sensitivity of BAL culture is relatively low, and prior antimicrobial therapy decreases the sensitivity further, leading to overuse of empirical antibiotics. The Unyvero LRT BAL Application (Curetis GmbH, Germany) is a multiplex molecular panel that detects 19 bacteria, 10 antibiotic resistance markers, and a fungus, Pneumocystis jirovecii, in BAL fluid in ∼4.5 h. Its performance was evaluated using 1,016 prospectively collected and 392 archived specimens from 11 clinical trial sites in the United States. Overall positive and negative percent agreements with culture results for identification of bacteria that grow in routine cultures were 93.4% and 98.3%, respectively, with additional potential pathogens identified by Unyvero in 21.7% of prospectively collected specimens. For detection of P. jirovecii, the positive percent agreement with standard testing was 87.5%. Antibiotic resistance marker results were compared to standard antibiotic susceptibility test results to determine positive predictive values (PPVs). PPVs ranged from 80 to 100%, based on the microorganism and specific resistance marker(s). The Unyvero LRT BAL Application provides accurate detection of common agents of bacterial pneumonia and of P. jirovecii The sensitivity and rapidity of this panel suggest significant clinical value for choosing appropriate antibiotics and for antibiotic stewardship.

Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates.

High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data. Heterogeneity, sensitivity and precision were evaluated by reference-independent and reference-dependent benchmarking using 846 Gram-negative clinical isolates. Interestingly, the majority of predicted sequences were tool-specific, resulting in a pronounced heterogeneity across tools for the reference-independent assessment. In the reference-dependent assessment, sensitivity and precision values were found to substantially vary between tools and across taxa, with cBar exhibiting the highest median sensitivity (87.45%) but a low median precision (27.05%). Furthermore, integrating the individual tools into an ensemble approach showed increased sensitivity (95.55%) while reducing the precision (25.62%). CBar and plasmidSPAdes exhibited the strongest concordance with respect to identified antibiotic resistance factors. Moreover, false-positive plasmid predictions typically contained only few antibiotic resistance factors. In conclusion, while high degrees of heterogeneity and variation in sensitivity and precision were observed across the different tools and taxa, existing tools are valuable for investigating the plasmid-borne resistome. Nevertheless, additional studies on representative clinical data sets will be necessary to translate in silico plasmid prediction approaches from research to clinical application.

A high leukocyte count and administration of hydrocortisone hamper PCR-based diagnostics for bloodstream infections.

Bloodstream infections (BSIs) require an accurate and fast identification of causative pathogens. Molecular diagnostics, in particular polymerase chain reaction (PCR)-based approaches for BSI diagnostics directly from whole blood, suffer from limitations such as inhibition leading to invalid results. In this retrospective study, we analyzed 23 parameters for their potential interference with LightCycler SeptiFast PCR tests (n = 2167) routinely performed at our institution. The overall inhibition rate was 9.1%. Test date, type of ward, procalcitonin levels, high leukocyte counts, and absolute neutrophil count were significantly associated with inhibition. For a subset (n = 448), cut-off values for leukocyte counts of < 5700 cells/µL and ≥ 26,900 cells/µL were significantly associated with a low (5%) and high (67%) inhibition risk. For patients with a moderate to high leukocyte count (5700-26,900 cells/µL), the additional administration of hydrocortisone significantly increased the inhibition risk. Furthermore, freezing of blood samples prior to DNA extraction and SF testing appeared to neutralize inhibitory factors. It remains to be investigated whether other molecular diagnostic tests are susceptible to similar inhibiting parameters.

Species Identification and Antibiotic Resistance Prediction by Analysis of Whole-Genome Sequence Data by Use of ARESdb: an Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial.

Whole-genome sequencing (WGS) is now routinely performed in clinical microbiology laboratories to assess isolate relatedness. With appropriately developed analytics, the same data can be used for prediction of antimicrobial susceptibility. We assessed WGS data for identification using open-source tools and antibiotic susceptibility testing (AST) prediction using ARESdb compared to matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) identification and broth microdilution phenotypic susceptibility testing on clinical isolates from a multicenter clinical trial of the FDA-cleared Unyvero lower respiratory tract infection (LRTI) application (Curetis). For the trial, more than 2,000 patient samples were collected from intensive care units across nine hospitals and tested for LRTI. The isolate subset used in this study included 620 clinical isolates originating from 455 LRTI culture-positive patient samples. Isolates were sequenced using the Illumina Nextera XT protocol and FASTQ files with raw reads uploaded to the ARESdb cloud platform (ares-genetics.cloud; released for research use in 2020). The platform combines Ares Genetics' proprietary database ARESdb with state-of-the-art bioinformatics tools and curated public data. For identification, WGS showed 99 and 93% concordance with MALDI-TOF MS at the genus and species levels, respectively. WGS-predicted susceptibility showed 89% categorical agreement with phenotypic susceptibility across a total of 129 species-compound pairs analyzed, with categorical agreement exceeding 90% in 78 species-compound pairs and reaching 100% in 32. Results of this study add to the growing body of literature showing that, with improvement of analytics, WGS data could be used to predict antimicrobial susceptibility.

Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review.

BACKGROUND: Antimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. Appropriate treatment of infectious diseases with the right antibiotics reduces the spread of antibiotic resistance. Today, clinical practice relies on molecular and PCR techniques for pathogen identification and culture-based antibiotic susceptibility testing (AST). Recently, WGS has started to transform clinical microbiology, enabling prediction of resistance phenotypes from genotypes and allowing for more informed treatment decisions. WGS-based AST (WGS-AST) depends on the detection of AMR markers in sequenced isolates and therefore requires AMR reference databases. The completeness and quality of these databases are material to increase WGS-AST performance. METHODS: We present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. We used the public databases CARD and ResFinder with a final dataset of 2587 isolates across five clinically relevant pathogens from PATRIC and NDARO, public repositories of antibiotic-resistant bacterial isolates. RESULTS: CARD and ResFinder WGS-AST performance had an overall balanced accuracy of 0.52 (±0.12) and 0.66 (±0.18), respectively. Major error rates were higher in CARD (42.68%) than ResFinder (25.06%). However, CARD showed almost no very major errors (1.17%) compared with ResFinder (4.42%). CONCLUSIONS: We show that AMR databases need further expansion, improved marker annotations per antibiotic rather than per antibiotic class and validated multivariate marker panels to achieve clinical utility, e.g. in order to meet performance requirements such as provided by the FDA for clinical microbiology diagnostic testing.

Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs.

The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, our analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, we designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction. MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, our predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them.

Epigenome-Wide Association Study Identifies Cardiac Gene Patterning and a Novel Class of Biomarkers for Heart Failure.

BACKGROUND: Biochemical DNA modification resembles a crucial regulatory layer among genetic information, environmental factors, and the transcriptome. To identify epigenetic susceptibility regions and novel biomarkers linked to myocardial dysfunction and heart failure, we performed the first multi-omics study in myocardial tissue and blood of patients with dilated cardiomyopathy and controls. METHODS: Infinium human methylation 450 was used for high-density epigenome-wide mapping of DNA methylation in left-ventricular biopsies and whole peripheral blood of living probands. RNA deep sequencing was performed on the same samples in parallel. Whole-genome sequencing of all patients allowed exclusion of promiscuous genotype-induced methylation calls. RESULTS: In the screening stage, we detected 59 epigenetic loci that are significantly associated with dilated cardiomyopathy (false discovery corrected P≤0.05), with 3 of them reaching epigenome-wide significance at P≤5×10-8. Twenty-seven (46%) of these loci could be replicated in independent cohorts, underlining the role of epigenetic regulation of key cardiac transcription regulators. Using a staged multi-omics study design, we link a subset of 517 epigenetic loci with dilated cardiomyopathy and cardiac gene expression. Furthermore, we identified distinct epigenetic methylation patterns that are conserved across tissues, rendering these CpGs novel epigenetic biomarkers for heart failure. CONCLUSIONS: The present study provides to our knowledge the first epigenome-wide association study in living patients with heart failure using a multi-omics approach.

Intact cell mass spectrometry as a progress tracking tool for batch and fed-batch fermentation processes.

Penicillin production during a fermentation process using industrial strains of Penicillium chrysogenum is a research topic permanently discussed since the accidental discovery of the antibiotic. Intact cell mass spectrometry (ICMS) can be a fast and novel monitoring tool for the fermentation progress during penicillin V production in a nearly real-time fashion. This method is already used for the characterization of microorganisms and the differentiation of fungal strains; therefore, the application of ICMS to samples directly harvested from a fermenter is a promising possibility to get fast information about the progress of fungal growth. After the optimization of the ICMS method to penicillin V fermentation broth samples, the obtained ICMS data were evaluated by hierarchical cluster analysis or an in-house software solution written especially for ICMS data comparison. Growth stages of a batch and fed-batch fermentation of Penicillium chrysogenum are differentiated by one of those statistical approaches. The application of two matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) instruments in the linear positive ion mode from different vendors demonstrated the universal applicability of the developed ICMS method. The base for a fast and easy-to-use method for monitoring the fermentation progress of P. chrysogenum is created with this ICMS method developed especially for fermentation broth samples.

Combining light microscopy, dielectric spectroscopy, MALDI intact cell mass spectrometry, FTIR spectromicroscopy and multivariate data mining for morphological and physiological bioprocess characterization of filamentous organisms.

Along with productivity and physiology, morphological growth behavior is the key parameter in bioprocess design for filamentous fungi. Lacking tools for fast, reliable and efficient analysis however, fungal morphology is still commonly tackled by empirical trial-and-error techniques during strain selection and process development procedures. Bridging the gap, this work presents a comprehensive analytical approach for morphological analysis combining automated high-throughput microscopy, multi-frequency dielectric spectroscopy, MALDI intact cell mass spectrometry and FTIR spectromicroscopy. Industrial fed-batch production processes were investigated in fully instrumented, automated bioreactors using the model system Penicillium chrysogenum. Physiological process characterization was based on the determination of specific conversion rates as scale-independent parameters. Conventional light microscopic morphological analysis was based on holistic determination of time series for more than 30 morphological parameters and their frequency distributions over the respective parameter range by automated high-throughput light microscopy. Characteristic protein patterns enriched in specific morphological and physiological states were further obtained by MALDI intact cell mass spectrometry. Spatial resolution of molecular biomass composition was facilitated by FTIR spectromicroscopy. Real-time in situ monitoring of morphological process behavior was achieved by linking multi-frequency dielectric spectroscopy with above outlined off-line methods. Data integration of complementing orthogonal techniques for morphological and physiological analysis together with multivariate modeling of interdependencies between morphology, physiology and process parameters facilitated complete bioprocess characterization. The suggested approach will thus help understanding morphological and physiological behavior and, in turn, allow to control and optimize those complex processes.

Reagent-free monitoring of multiple clinically relevant parameters in human blood plasma using a mid-infrared quantum cascade laser based sensor system.

We present a semi-automated point-of-care (POC) sensor approach for the simultaneous and reagent-free determination of clinically relevant parameters in blood plasma. The portable sensor system performed direct mid-infrared (MIR) transmission measurements of blood plasma samples using a broadly tunable external-cavity quantum cascade laser source with high spectral power density. This enabled the use of a flow cell with a long path length (165 µm) which resulted in high signal-to-noise ratios and a rugged system, insensitive to clogging. Multivariate calibration models were built using well established Partial-Least-Squares (PLS) regression analysis. Selection of spectral pre-processing procedures was optimized by an automated evaluation algorithm. Several analytes, including glucose, lactate, triglycerides, cholesterol, total protein as well as albumin, were successfully quantified in routinely taken blood plasma samples from 67 critically ill patients. Although relying on a spectral range from 1030 cm(-1) to 1230 cm(-1), which is optimal for glucose and lactate but rather unusual for protein analysis, it was possible to selectively determine the albumin and total protein concentrations with sufficient accuracy for POC application.

A novel method for fast and statistically verified morphological characterization of filamentous fungi.

Along with productivity and physiology, morphological growth behavior is the key parameter in bioprocess design for filamentous fungi. Despite complex interactions between fungal morphology, broth viscosity, mixing kinetics, transport characteristics and process productivity, morphology is still commonly tackled only by empirical trial-and-error techniques during strain selection and process development procedures. In fact, morphological growth characteristics are investigated by computational analysis of only a limited number of pre-selected microscopic images or via manual evaluation of images, which causes biased results and does not allow any automation or high-throughput quantification. To overcome the lack of tools for fast, reliable and quantitative morphological analysis, this work introduces a method enabling statistically verified quantification of fungal morphology in accordance with Quality by Design principles. The novel, high-throughput method presented here interlinks fully automated recording of microscopic images with a newly developed evaluation approach reducing the need for manual intervention to a minimum. Validity of results is ensured by concomitantly testing the acquired sample for representativeness by statistical inference via bootstrap analysis. The novel approach for statistical verification can be equally applied as control logic to automatically proceed with morphological analysis of a consecutive sample once user defined acceptance criteria are met. Hence, analysis time can be reduced to an absolute minimum. The quantitative potential of the developed methodology is demonstrated by characterizing the morphological growth behavior of two industrial Penicillium chrysogenum production strains in batch cultivation.

Switching industrial production processes from complex to defined media: method development and case study using the example of Penicillium chrysogenum.

BACKGROUND: Filamentous fungi are versatile cell factories and widely used for the production of antibiotics, organic acids, enzymes and other industrially relevant compounds at large scale. As a fact, industrial production processes employing filamentous fungi are commonly based on complex raw materials. However, considerable lot-to-lot variability of complex media ingredients not only demands for exhaustive incoming components inspection and quality control, but unavoidably affects process stability and performance. Thus, switching bioprocesses from complex to defined media is highly desirable. RESULTS: This study presents a strategy for strain characterization of filamentous fungi on partly complex media using redundant mass balancing techniques. Applying the suggested method, interdependencies between specific biomass and side-product formation rates, production of fructooligosaccharides, specific complex media component uptake rates and fungal strains were revealed. A 2-fold increase of the overall penicillin space time yield and a 3-fold increase in the maximum specific penicillin formation rate were reached in defined media compared to complex media. CONCLUSIONS: The newly developed methodology enabled fast characterization of two different industrial Penicillium chrysogenum candidate strains on complex media based on specific complex media component uptake kinetics and identification of the most promising strain for switching the process from complex to defined conditions. Characterization at different complex/defined media ratios using only a limited number of analytical methods allowed maximizing the overall industrial objectives of increasing both, method throughput and the generation of scientific process understanding.

Core Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates.

Over the past decade, whole-genome sequencing (WGS) has overtaken traditional bacterial typing methods for studies of genetic relatedness. Further, WGS data generated during epidemiologic studies can be used in other clinically relevant bioinformatic applications, such as antibiotic resistance prediction. Using commercially available software tools, the relatedness of 38 clinical isolates of multidrug-resistant Pseudomonas aeruginosa was defined by two core genome multilocus sequence typing (cgMLST) methods, and the WGS data of each isolate was analyzed to predict antibiotic susceptibility to nine antibacterial agents. The WGS typing and resistance prediction data were compared with pulsed-field gel electrophoresis (PFGE) and phenotypic antibiotic susceptibility results, respectively. Simpson's Diversity Index and adjusted Wallace pairwise assessments of the three typing methods showed nearly identical discriminatory power. Antibiotic resistance prediction using a trained analytical pipeline examined 342 bacterial-drug combinations with an overall categorical agreement of 92.4% and very major, major, and minor error rates of 3.6, 4.1, and 4.1%, respectively. IMPORTANCE Multidrug-resistant Pseudomonas aeruginosa isolates are a serious public health concern due to their resistance to nearly all or all of the available antibiotics, including carbapenems. Utilizing molecular approaches in conjunction with antibiotic susceptibility prediction software warrants investigation for use in the clinical laboratory workflow. These molecular tools coupled with antibiotic resistance prediction tools offer the opportunity to overcome the extended turnaround time and technical challenges of phenotypic susceptibility testing.

Defining Baseline Mechanisms of Cefiderocol Resistance in the Enterobacterales.

The objective of this study was to identify putative mechanisms contributing to baseline cefiderocol resistance among carbapenem-resistant Enterobacterales (CRE). We evaluated 56 clinical CRE isolates with no previous exposure to cefiderocol. Cefiderocol and comparator agent minimum inhibitory concentrations (MICs) were determined by broth microdilution. Short-read and/or long-read whole genome sequencing was pursued. Cefiderocol nonwild type (NWT; i.e., MICs ≥4 mg/L) CRE were compared with species-specific reference genomes and with cefiderocol wild type (WT) CRE isolates to identify genes or missense mutations, potentially contributing to elevated cefiderocol MICs. A total of 14 (25%) CRE isolates met cefiderocol NWT criteria. Of the 14 NWT isolates, various ß-lactamases (e.g., carbapenemases in Klebsiella pneumoniae and AmpC ß-lactamases in Enterobacter cloacae complex) in combination with permeability defects were associated with a ≥ 80% positive predictive value in identifying NWT isolates. Unique mutations in the sensor kinase gene baeS were identified among NWT isolates. Cefiderocol NWT isolates were more likely to be resistant to colistin than WT isolates (29% vs. 0%). Our findings suggest that no consistent antimicrobial resistance markers contribute to baseline cefiderocol resistance in CRE isolates and, rather, cefiderocol resistance results from a combination of heterogeneous mechanisms.

Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data.

Antimicrobial resistance prediction from whole genome sequencing data (WGS) is an emerging application of machine learning, promising to improve antimicrobial resistance surveillance and outbreak monitoring. Despite significant reductions in sequencing cost, the availability and sampling diversity of WGS data with matched antimicrobial susceptibility testing (AST) profiles required for training of WGS-AST prediction models remains limited. Best practice machine learning techniques are required to ensure trained models generalize to independent data for optimal predictive performance. Limited data restricts the choice of machine learning training and evaluation methods and can result in overestimation of model performance. We demonstrate that the widely used random k-fold cross-validation method is ill-suited for application to small bacterial genomics datasets and offer an alternative cross-validation method based on genomic distance. We benchmarked three machine learning architectures previously applied to the WGS-AST problem on a set of 8,704 genome assemblies from five clinically relevant pathogens across 77 species-compound combinations collated from public databases. We show that individual models can be effectively ensembled to improve model performance. By combining models via stacked generalization with cross-validation, a model ensembling technique suitable for small datasets, we improved average sensitivity and specificity of individual models by 1.77% and 3.20%, respectively. Furthermore, stacked models exhibited improved robustness and were thus less prone to outlier performance drops than individual component models. In this study, we highlight best practice techniques for antimicrobial resistance prediction from WGS data and introduce the combination of genome distance aware cross-validation and stacked generalization for robust and accurate WGS-AST.

Cefiderocol Activity Against Clinical Pseudomonas aeruginosa Isolates Exhibiting Ceftolozane-Tazobactam Resistance.

BACKGROUND: Mutations in the AmpC-AmpR region are associated with treatment-emergent ceftolozane-tazobactam (TOL-TAZ) and ceftazidime-avibactam (CAZ-AVI) resistance. We sought to determine if these mutations impact susceptibility to the novel cephalosporin-siderophore compound cefiderocol. METHODS: Thirty-two paired isolates from 16 patients with index P. aeruginosa isolates susceptible to TOL-TAZ and subsequent P. aeruginosa isolates available after TOL-TAZ exposure from January 2019 to December 2020 were included. TOL-TAZ, CAZ-AVI, imipenem-relebactam (IMI-REL), and cefiderocol minimum inhibitory concentrations (MICs) were determined using broth microdilution. Whole-genome sequencing of paired isolates was used to identify mechanisms of resistance to cefiderocol that emerged, focusing on putative mechanisms of resistance to cefiderocol or earlier siderophore-antibiotic conjugates based on the previously published literature. RESULTS: Analyzing the 16 pairs of P. aeruginosa isolates, ≥4-fold increases in cefiderocol MICs occurred in 4 of 16 isolates. Cefiderocol nonsusceptibility criteria were met for only 1 of the 4 isolates, using Clinical and Laboratory Standards Institute criteria. Specific mechanisms identified included the following: AmpC E247K (2 isolates), MexR A66V and L57D (1 isolate each), and AmpD G116D (1 isolate) substitutions. For both isolates with AmpC E247K mutations, ≥4-fold MIC increases occurred for both TOL-TAZ and CAZ-AVI, while a ≥4-fold reduction in IMI-REL MICs was observed. CONCLUSIONS: Our findings suggest that alterations in the target binding sites of P. aeruginosa-derived AmpC ß-lactamases have the potential to reduce the activity of 3 of 4 novel ß-lactams (ie, ceftolozane-tazobactam, ceftazidime-avibactam, and cefiderocol) and potentially increase susceptibility to imipenem-relebactam. These findings are in need of validation in a larger cohort.

Genomic and Phenotypic Analysis of Linezolid-Resistant Staphylococcus epidermidis in a Tertiary Hospital in Innsbruck, Austria.

Whole genome sequencing is a useful tool to monitor the spread of resistance mechanisms in bacteria. In this retrospective study, we investigated genetic resistance mechanisms, sequence types (ST) and respective phenotypes of linezolid-resistant Staphylococcus epidermidis (LRSE, n = 129) recovered from a cohort of patients receiving or not receiving linezolid within a tertiary hospital in Innsbruck, Austria. Hereby, the point mutation G2603U in the 23S rRNA (n = 91) was the major resistance mechanism followed by the presence of plasmid-derived cfr (n = 30). The majority of LRSE isolates were ST2 strains, followed by ST5. LRSE isolates expressed a high resistance level to linezolid with a minimal inhibitory concentration of ≥256 mg/L (n = 83) in most isolates, particularly in strains carrying the cfr gene (p < 0.001). Linezolid usage was the most prominent (but not the only) trigger for the development of linezolid resistance. However, administration of linezolid was not associated with a specific resistance mechanism. Restriction of linezolid usage and the monitoring of plasmid-derived cfr in LRSE are potential key steps to reduce linezolid resistance and its transmission to more pathogenic Gram-positive bacteria.