Application of LAMP assay for detection of carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii complex in ICU admitted sepsis patients: A rapid and cost-effective diagnostic tool

Carbapenem-resistant significant members of Acinetobacter calcoaceticus-Acinetobacter baumannii (CR-SM-ACB) complex have emerged as an important cause of sepsis, especially in ICUs. This study demonstrates the application of loop-mediated-isothermal-amplification (LAMP) assay for detection of CR-SM-ACB-complex from patients with sepsis. Whole-blood and culture-broths(CB) collected from patients with culture-positive sepsis were subjected to LAMP and compared with PCR, and RealAmp. Vitek-2 system and conventional PCR results were used as confirmatory references. The sensitivity and specificity of LAMP(97 % & 100 %) and RealAmp(100 % & 100 %) for detection of CR-SM-ACB-complex from CB were better than PCR(87 % & 100 %). Diagnostic accuracy of LAMP, RealAmp, and PCR for detection of SM-ACB-complex from CB was 98.5 %, 100 %, and 88.5 % respectively. Turnaround time of Culture, LAMP, PCR, and RealAmp was 28-53, 6-20, 9-23, and 6-20hours, respectively. LAMP is a simple, inexpensive tool that can be applied directly to positive CB and may be customized to detect emerging pathogens and locally-prevalent resistance genes and to optimize antimicrobial use.

MALDI-TOF bacterial subtyping for rapid detection of biomarkers in Staphylococcus aureus from subclinical bovine mastitis

AIMS

This study aimed to evaluate matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) bacterial subtyping for the rapid detection of biomarkers in Staphylococcus aureus from subclinical bovine mastitis.

METHODS AND RESULTS

A total of 229 S. aureus isolates were obtained from milk samples collected from cows with subclinical mastitis using microbiological culture. Staphylococcus aureus isolates were also submitted to PCR analysis targeting the mecA and mecC genes, which are indicative of methicillin resistance. Confirmation of the species was achieved through MALDI-TOF MS analysis. To analyze antimicrobial resistance patterns, the MALDI BioTyper Compass Explorer and ClinProTools Bruker software were employed, and dendrograms were generated using Bionumerics software.

CONCLUSIONS

MALDI-TOF MS successfully identified S. aureus at the species level, but no methicillin resistance was observed. Moreover, spectral typing displayed limited similarity when compared to pulsed-field gel electrophoresis (PFGE).

Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria

Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.

Data-Driven Two-Stage Framework for Identification and Characterization of Different Antibiotic-Resistant Escherichia coli Isolates Based on Mass Spectrometry Data

In clinical microbiology, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) is frequently employed for rapid microbial identification. However, rapid identification of antimicrobial resistance (AMR) in Escherichia coli based on a large amount of MALDI-TOF MS data has not yet been reported. This may be because building a prediction model to cover all E. coli isolates would be challenging given the high diversity of the E. coli population. This study aimed to develop a MALDI-TOF MS-based, data-driven, two-stage framework for characterizing different AMRs in E. coli. Specifically, amoxicillin (AMC), ceftazidime (CAZ), ciprofloxacin (CIP), ceftriaxone (CRO), and cefuroxime (CXM) were used. In the first stage, we split the data into two groups based on informative peaks according to the importance of the random forest. In the second stage, prediction models were constructed using four different machine learning algorithms-logistic regression, support vector machine, random forest, and extreme gradient boosting (XGBoost). The findings demonstrate that XGBoost outperformed the other four machine learning models. The values of the area under the receiver operating characteristic curve were 0.62, 0.72, 0.87, 0.72, and 0.72 for AMC, CAZ, CIP, CRO, and CXM, respectively. This implies that a data-driven, two-stage framework could improve accuracy by approximately 2.8%. As a result, we developed AMR prediction models for E. coli using a data-driven two-stage framework, which is promising for assisting physicians in making decisions. Further, the analysis of informative peaks in future studies could potentially reveal new insights. IMPORTANCE Based on a large amount of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) clinical data, comprising 37,918 Escherichia coli isolates, a data-driven two-stage framework was established to evaluate the antimicrobial resistance of E. coli. Five antibiotics, including amoxicillin (AMC), ceftazidime (CAZ), ciprofloxacin (CIP), ceftriaxone (CRO), and cefuroxime (CXM), were considered for the two-stage model training, and the values of the area under the receiver operating characteristic curve (AUC) were 0.62 for AMC, 0.72 for CAZ, 0.87 for CIP, 0.72 for CRO, and 0.72 for CXM. Further investigations revealed that the informative peak m/z 9714 appeared with some important peaks at m/z 6809, m/z 7650, m/z 10534, and m/z 11783 for CIP and at m/z 6809, m/z 10475, and m/z 8447 for CAZ, CRO, and CXM. This framework has the potential to improve the accuracy by approximately 2.8%, indicating a promising potential for further research.

MALDI-TOF MS Approaches for the Identification of the Susceptibility of Extended-Spectrum β-Lactamases in Escherichia coli

The increase in multidrug-resistant microorganisms that produce extended-spectrum β-lactamases (ESBLs) and carbapenemases is a serious problem worldwide. Recently, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been used for the rapid detection of antibiotic-resistant bacteria. The objective of this study was to establish a method to detect ESBL-producing Escherichia coli by monitoring the hydrolyzation of cefotaxime (CTX) using MALDI-TOF MS. According to the ratio of the peak intensity of CTX and hydrolyzed-CTX-related compounds, the ESBL-producing strains could be clearly distinguished after 15 min of incubation. Moreover, the minimum inhibitory concentration (MIC) values for E. coli were 8 μg/mL and lower than 4 μg/mL, which could be distinguished after 30 min and 60 min of incubation, respectively. The enzymatic activity was determined using the difference in the signal intensity of the hydrolyzed CTX at 370 Da for the ESBL-producing strains incubated with or without clavulanate. The ESBL-producing strains with low enzymatic activity or bla_CTX-M genes could be detected by monitoring the hydrolyzed CTX. These results show that this method can rapidly detect high-sensitivity ESBL-producing E. coli.

The use of matrix-assisted laser desorption/ionization mass spectrometry in enzyme activity assays and its position in the context of other available methods

Activity assays are indispensable for studying biochemical properties of enzymes. The purposes of measuring activity are wide ranging from a simple detection of the presence of an enzyme to kinetic experiments evaluating the substrate specificity, reaction mechanisms, and susceptibility to inhibitors. Common activity assay methods include spectroscopy, electrochemical sensors, or liquid chromatography coupled with various detection techniques. This review focuses on the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a growing and modern alternative, which offers high speed of analysis, sensitivity, versatility, possibility of automation, and cost-effectiveness. It may reveal reaction intermediates, side products or measure more enzymes at once. The addition of an internal standard or calculating the ratios of the substrate and product peak intensities and areas overcome the inherent inhomogeneous distribution of analyte and matrix in the sample spot, which otherwise results in a poor reproducibility. Examples of the application of MALDI-TOF MS for assaying hydrolases (including peptidases and β-lactamases for antibiotic resistance tests) and other enzymes are provided. Concluding remarks summarize advantages and challenges coming from the present experience, and draw future perspectives such as a screening of large libraries of chemical compounds for their substrate or inhibitory properties towards enzymes.

MALDI-TOF MS Indirect Beta-Lactamase Detection in Ampicillin-Resistant Haemophilus influenzae

Rapid identification of beta-lactamase-producing strains of Haemophilus influenzae plays key role in diagnostics in clinical microbiology. Therefore, the aim of this study was the rapid determination of beta-lactamase's presence in H. influenzae isolates via indirect detection of degradation ampicillin products using MALDI-TOF MS. H. influenzae isolates were subjected to antibiotic resistance testing using disk diffusion and MIC methodologies. Beta-lactamase activity was tested using MALDI-TOF MS, and results were compared to spectral analysis of alkaline hydrolysis. Resistant and susceptible strains of H. influenzae were distinguished, and strains with a high MIC level were identified as beta-lactamase-producing. Results indicate that MALDI-TOF mass spectrometry is also suitable for the rapid identification of beta-lactamase-producing H. influenzae. This observation and confirmation can accelerate identification of beta-lactamase strains of H. influenzae in clinical microbiology, which can have an impact on health in general.

MALDI-TOF mass spectrometry rapid pathogen identification and outcomes of patients with bloodstream infection: A systematic review and meta-analysis

There was inconsistent evidence regarding the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for microorganism identification with/without antibiotic stewardship team (AST) and the clinical outcome of patients with bloodstream infections (BSI). In a systematic review and meta-analysis, we evaluated the effectiveness of rapid microbial identification by MALDI-TOF MS with and without AST on clinical outcomes. We searched PubMed and EMBASE databases from inception to 1 February 2022 to identify pre-post and parallel comparative studies that evaluated the use of MALDI-TOF MS for microorganism identification. Pooled effect estimates were derived using the random-effects model. Twenty-one studies with 14,515 patients were meta-analysed. Compared with conventional phenotypic methods, MALDI-TOF MS was associated with a 23% reduction in mortality (RR = 0.77; 95% CI: 0.66; 0.90; I2  = 35.9%; 13 studies); 5.07-h reduction in time to effective antibiotic therapy (95% CI: -5.83; -4.31; I2  = 95.7%); 22.86-h reduction in time to identify microorganisms (95% CI: -23.99; -21.74; I2  = 91.6%); 0.73-day reduction in hospital stay (95% CI: -1.30; -0.16; I2  = 53.1%); and US$4140 saving in direct hospitalization cost (95% CI: $-8166.75; $-113.60; I2  = 66.1%). No significant heterogeneity sources were found, and no statistical evidence for publication bias was found. Rapid pathogen identification by MALDI-TOF MS with or without AST was associated with reduced mortality and improved outcomes of BSI, and may be cost-effective among patients with BSI.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in the diagnosis of microorganisms

Microbiology culture is the gold standard method for identifying microorganisms. This identification protocol takes several days to complete. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that can identify different microorganisms quickly and accurately. The objective of this work was to evaluate the use of MALDI-TOF MS in the routine of clinical laboratories to identify microorganisms and to identify their resistance to antimicrobials. This study evaluated the relevance of the MALDI-TOF MS technique for microbiological diagnosis through a literature review. The authors found that MALDI-TOF MS can identify bacteria, fungi, viruses and parasites, even in blood cultures, and also serves to assess antimicrobial resistance. Thus, MALDI-TOF MS can become an indispensable tool in laboratory diagnosis.

Application of MALDI-TOF MS for identification of environmental bacteria: A review

Bacteria play a variety of roles in the environment. They maintain the balance in the ecosystem and provide different ecosystem services such as in biogeochemical cycling of nutrients, biodegradation of toxic pollutants, and others. Therefore, isolation and identification of different environmental bacteria are important to most environmental research. Due to the high cost and time associated with the conventional molecular techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained considerable attention for routine identification of bacteria. This review aims to provide an overview of the application of MALDI-TOF MS in various environmental studies through bibliometric analysis and literature review. The bibliometric analysis helped to understand the time-variable application of MALDI-TOF MS in various environmental studies. The categorical literature review covers various environmental studies comprising areas like ecology, food microbiology, environmental biotechnology, agriculture, and plant sciences, which show the application of the technique for identification and characterization of pollutant-degrading, plant-associated, disease-causing, soil-beneficial, and other environmental bacteria. Further research should focus on bridging the gap between the phylogenetic identity of bacteria and their specific environmental functions or metabolic traits that can help in rapid advancements in environmental research, thereby, improving time and cost savings.

LAP-MALDI MS coupled with machine learning: an ambient mass spectrometry approach for high-throughput diagnostics

Large-scale population screening for early and accurate detection of disease is a key objective for future diagnostics. Ideally, diagnostic tests that achieve this goal are also cost-effective, fast and easily adaptable to new diseases with the potential of multiplexing. Mass spectrometry (MS), particularly MALDI MS profiling, has been explored for many years in disease diagnostics, most successfully in clinical microbiology but less in early detection of diseases. Here, we present liquid atmospheric pressure (LAP)-MALDI MS profiling as a rapid, large-scale and cost-effective platform for disease analysis. Using this new platform, two different types of tests exemplify its potential in early disease diagnosis and response to therapy. First, it is shown that LAP-MALDI MS profiling detects bovine mastitis two days before its clinical manifestation with a sensitivity of up to 70% and a specificity of up to 100%. This highly accurate, pre-symptomatic detection is demonstrated by using a large set of milk samples collected weekly over six months from approximately 500 dairy cows. Second, the potential of LAP-MALDI MS in antimicrobial resistance (AMR) detection is shown by employing the same mass spectrometric setup and similarly simple sample preparation as for the early detection of mastitis.

Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters

Streptomyces species have attracted considerable interest as a reservoir of medically important secondary metabolites, which are even diverse and different between strains. Here, we reassess ten Streptomyces venezuelae strains by presenting the highly resolved classification, using 16S rRNA sequencing, MALDI-TOF MS protein profiling, and whole-genome sequencing. The results revealed that seven of the ten strains were misclassified as S. venezuelae species. Secondary metabolite biosynthetic gene cluster (smBGC) mining and targeted LC-MS/MS based metabolite screening of S. venezuelae and misclassified strains identified in total 59 secondary metabolites production. In addition, a comparison of pyrrolamide-type antibiotic BGCs of four misclassified strains, followed by functional genomics, revealed that athv28 is critical in the synthesis of the anthelvencin precursor, 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). Our findings illustrate the importance of the accurate classification and better utilization of misclassified Streptomyces strains to discover smBGCs and their secondary metabolite products.

Clinically Applicable System for Rapidly Predicting Enterococcus faecium Susceptibility to Vancomycin

Enterococcus faecium is a clinically important pathogen that can cause significant morbidity and death. In this study, we aimed to develop a machine learning (ML) algorithm-based rapid susceptibility method to distinguish vancomycin-resistant E. faecium (VREfm) and vancomycin-susceptible E. faecium (VSEfm) strains. A predictive model was developed and validated to distinguish VREfm and VSEfm strains by analyzing the matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) spectra of unique E. faecium isolates from different specimen types. The algorithm used 5,717 mass spectra, including 2,795 VREfm and 2,922 VSEfm mass spectra, and was externally validated with 2,280 mass spectra of isolates (1,222 VREfm and 1,058 VSEfm strains). A random forest-based algorithm demonstrated overall good classification performances for the isolates from the specimens, with mean accuracy, sensitivity, and specificity of 0.78, 0.79, and 0.77, respectively, with 10-fold cross-validation, timewise validation, and external validation. Furthermore, the algorithm provided rapid results, which would allow susceptibility prediction prior to the availability of phenotypic susceptibility results. In conclusion, an ML algorithm designed using mass spectra obtained from the routine workflow may be able to rapidly differentiate VREfm strains from VSEfm strains; however, susceptibility results must be confirmed by routine methods, given the demonstrated performance of the assay. IMPORTANCE A modified binning method was incorporated to cluster MS shifting ions into a set of representative peaks based on a large-scale MS data set of clinical VREfm and VSEfm isolates, including 2,795 VREfm and 2,922 VSEfm isolates. Predictions with the algorithm were significantly more accurate than empirical antibiotic use, the accuracy of which was 0.50, based on the local epidemiology. The algorithm improved the accuracy of antibiotic administration, compared to empirical antibiotic prescription. An ML algorithm designed using MALDI-TOF MS spectra obtained from the routine workflow accurately differentiated VREfm strains from VSEfm strains, especially in blood and sterile body fluid samples, and can be applied to facilitate the rapid and accurate clinical testing of pathogens.

Development of Loop-Mediated Isothermal Amplification Assay for Detection of Clinically Significant Members of Acinetobacter calcoaceticus-baumannii Complex and Associated Carbapenem Resistance

Background:Acinetobacter calcoaceticus–baumannii (ACB) complex has emerged as an important nosocomial pathogen and is associated with life-threatening infections, especially among ICU patients, including neonates. Carbapenem resistance in Acinetobacter baumannii has emerged globally and is commonly mediated by bla_OXA-23. Clinically significant infections with carbapenem-resistant Acinetobacter baumannii (CRAB) are a major concern since therapeutic options are limited and associated mortality is high. Early diagnosis of both the pathogen and resistance is important to initiate the optimal therapy and prevent selection of resistance. In the current study, a loop-mediated isothermal amplification (LAMP) assay was developed for rapid detection of the ACB complex and carbapenem resistance mediated by bla_OXA-23.

Methodology: Universal LAMP primers were designed for the detection of significant members of the ACB complex and carbapenem resistance targeting the ITS 16S–23S rRNA and bla_OXA-23 gene respectively. The optimal conditions for the LAMP assay were standardized for each primer set using standard ATCC strains. The sensitivity of the LAMP assay was assessed based on the limit of detection (LOD) using different DNA concentrations and colony counts. The specificity of LAMP was determined using the non-ACB complex and non-Acinetobacter species. The results of the LAMP assay were compared with those of polymerase chain reaction (PCR).

Results: The optimal temperature for the LAMP assay was 65°C, and the detection time varied with various primers designed. Using the ITS Ab1 primer, LODs of LAMP and PCR assays were 100 pg/μl and 1 ng/μl of DNA concentration and 10⁴ cfu/ml and 10⁸ cfu/ml of colony count, respectively. The LAMP assay was 10- and 10⁴-fold more sensitive than PCR using DNA concentration and colony count, respectively. The LAMP assay was found to be specific for clinically important ACB complex species.

Significance of the study: The LAMP assay can be applied for early detection of significant species of the ACB complex from clinical samples and their carbapenem-resistant variants. Depending on the emerging pathogen and locally prevalent resistance genes, the LAMP assay can be modified for detection of colonization or infection by various resistant bugs.

MALDI-TOF Mass Spectroscopy Applications in Clinical Microbiology

There is a range of proteomics methods to spot and analyze bacterial protein contents such as liquid chromatography-mass spectrometry (LC-MS), two-dimensional gel electrophoresis, and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS), which give comprehensive information about the microorganisms that may be helpful within the diagnosis and coverings of infections. Microorganism identification by mass spectrometry is predicted on identifying a characteristic spectrum of every species so matched with an outsized database within the instrument. MALDI-TOF MS is one of the diagnostic methods, which is a straightforward, quick, and precise technique, and is employed in microbial diagnostic laboratories these days and may replace other diagnostic methods. This method identifies various microorganisms such as bacteria, fungi, parasites, and viruses, which supply comprehensive information. One of the MALDI-TOF MS's crucial applications is bacteriology, which helps identify bacterial species, identify toxins, and study bacterial antibiotic resistance. By knowing these cases, we will act more effectively against bacterial infections.

Rapid Detection of Escherichia coli Antibiotic Susceptibility Using Live/Dead Spectrometry for Lytic Agents

Antibiotic resistance is a serious threat to public health. The empiric use of the wrong antibiotic occurs due to urgency in treatment combined with slow, culture-based diagnostic techniques. Inappropriate antibiotic choice can promote the development of antibiotic resistance. We investigated live/dead spectrometry using a fluorimeter (Optrode) as a rapid alternative to culture-based techniques through application of the LIVE/DEAD® BacLightTM Bacterial Viability Kit. Killing was detected by the Optrode in near real-time when Escherichia coli was treated with lytic antibiotics-ampicillin and polymyxin B-and stained with SYTO 9 and/or propidium iodide. Antibiotic concentration, bacterial growth phase, and treatment time used affected the efficacy of this detection method. Quantification methods of the lethal action and inhibitory action of the non-lytic antibiotics, ciprofloxacin and chloramphenicol, respectively, remain to be elucidated.

Modern trends in identification of causative agents in infective endocarditis

Advances in the diagnosis and treatment of patients with infectious endocarditis are limited by the high frequency of cases with an unknown etiology and imperfection of microbiological (cultural) methods. To overcome these problems new approaches to the identification of infectious endocarditis pathogens were introduced, which allowed achieving certain positive results. However, it should be noted that despite the wide variety of diagnostic tools currently used, there is no ideal method for etiological laboratory diagnosis of infectious endocarditis. The article discusses the features and place of immunochemical, molecular biological (MALDI-TOF MS, real-time PCR, sequencing, in situ fluorescence hybridization, metagenomic methods, etc.), immunohistochemical methods, and their advantages and limitations.

[Infective Endocarditis with Unknown Etiology: Possibilities of Conquering and Role of Microbiologistics]

Current infectious endocarditis (IE) is characterized by changes in its etiological and epidemiological profiles associated with increased incidence of IE of undetermined etiology. This requires a search for ways to enhance the effectivity of diagnosis. Microbiologistics along with high-tech methods becomes decisively important for identifying the pathogen by studying cultures of blood and tissues from the affected heart valve. This determines timely diagnosis and treatment to be introduced to medical practice as a component of personalized medicine. The article focuses on the validity and features of microbiological (cultural), immunochemical, and molecular biological [MALDI-TOF MS (matrix-activated laser desorption/ionization with time-of-flight mass spectrometry), polymerase chain reaction, sequencing] studies.

Towards the Identification of Antibiotic-Resistant Bacteria Causing Urinary Tract Infections Using Volatile Organic Compounds Analysis-A Pilot Study

Antibiotic resistance is an unprecedented threat to modern medicine. The analysis of volatile organic compounds (VOCs) from bacteria potentially offers a rapid way to determine antibiotic susceptibility in bacteria. This study aimed to find the optimal conditions to obtain the maximum number of VOCs detected which next allowed the assessment of differences in VOC profiles between susceptible and resistant isolates of Escherichia coli causing urinary tract infections. The analysis of VOCs in the headspace above the bacterial cultures allowed the distinguishing of resistant and susceptible bacteria based on the abundance of six VOCs with 85.7% overall accuracy. The results of this preliminary study are promising, and with development could lead to a practical, faster diagnostic method for use in routine microbiology.

Rapid detection of extended-spectrum β-Lactamases producers in Enterobacteriaceae using a calorimetry approach

AIM

To design and assess a novel protocol that employs isothermal titration calorimetry (ITC) for rapid detection of extended-spectrum β-lactamase (ESBL)-producers in clinical pathogens.

METHODS AND RESULTS

A total of 69 clinical Enterobacteriaceae isolates were examined in the new ESBL-ITC test by examining the heat profiles associated with enzyme hydrolysis of different substrates (imipenem, cefotaxime and clavulanic acid). The presence of β-lactamase genes in the bacteria tested was confirmed by PCR and DNA sequencing. Comparative analysis between ESBL-ITC and conventional minimum inhibitory concentrations (MIC)/combined disk method (CDM) showed high agreement between the two assays. However, the ESBL-ITC test had a remarkable advantage of providing testing result within 1 h, in comparison to the 32-48 h required by MIC/CDM.

CONCLUSIONS

The ESBL-ITC test developed in this work offers a new option for rapid and accurate detection of ESBL-producers.

SIGNIFICANCE AND IMPACT OF THE STUDY

Timely detection of ESBL-producers is vital to guide the decision-making process in clinical treatment as well as in hospital-infection control. The new ESBL-ITC test provides a rapid phenotypic assay that can be further adapted for clinical diagnosis of ESBL-producing pathogens.

Comparison of the next-generation sequencing (NGS) technology with culture methods in the diagnosis of bacterial and fungal infections

Background

Bacterial and fungal infections that caused by various kinds of pathogens are frequently-occurring disease all over the world. To overcome the shortcomings of traditional culture method, we have adapted next-generation sequencing (NGS) technology to identify pathogens.

Methods

In this study, clinical samples from 20 patients pre-diagnosed with bacterial and fungal infections in the Shanghai Pulmonary Hospital of Tongji University, China, were investigated retrospectively to compare the NGS with conventional "gold standard" culture methods.

Results

The detection rates of bacterial or fungal infections were 95.0% (19/20) by NGS and 60.0% (12/20) by culture method. There was a significant difference between the results of NGS and traditional culture method by using McNemar's χ² test (P=0.008).

Conclusions

NGS, as an emerging diagnostic technology, shows outstanding advantages in the diagnosis of bacterial and fungal infections, and optimizes the treatment of infectious diseases. The clinical application and future development of NGS technology are worthy of expectation.

Detection of beta-lactamase production in clinical Prevotella species by MALDI-TOF MS method

Penicillins, can be used in treatment of infections due to Prevotella species if they are susceptible to penicillin. Early and accurate preliminary detection of β-lactamase-producing isolates is crucial for treatment of infection. The aim of this study was to determine β-lactamase-producing Prevotella species by MALDI-TOF MS and screen them for the presence of cfxA gene, responsible for β-lactamase production. A total of 500 clinically relevant Prevotella isolates, collected from 13 countries for the previous European antibiotic resistance surveillance study, were tested. Susceptibility testing was performed against ampicillin and ampicillin/sulbactam by Etest methodology. EUCAST guidelines were used for susceptibility interpretations; the isolates with MIC value ≤ 0.5 for ampicillin were considered susceptible and >2 resistant. All Prevotella isolates, were tested for detection of β-lactamase activity by MALDI-TOF MS (Vitek® MS Research Use Only) system and the presence of the cfxA gene by PCR method. The susceptibility levels of the isolates to ampicillin/sulbactam and ampicillin were 99.6% and 43.4%, respectively. A total 59% of isolates presented β-lactamase activity and 60.8% were cfxA gene positive. Both these tests were positive for isolates in the resistant category. Additionally, >95% of the isolates (n = 65) which ampicillin MIC values ranged from >0.5 μg/mL to 2 μg/ml displayed β-lactamase activity. We also found that the MALDI-TOF MS-based β-lactamase assay delivers results in 2 h. We found a high concordance between the MALDI-TOF MS β-lactamase results in terms of cfxA β-lactamase gene presence. MALDI-TOF MS may serve as a simple and efficient alternative method of the existing phenotypic and PCR-based methods.

Escherichia coli as a carrier of tetracyclines and penicillins resistance in wild pheasant (Phasianus colchicus)

Wild animals like pheasant seem to be a good source of information about human activities. Therefore, the wild pheasants and relative stable appendix microcenosis were selected for antibiotic resistance testing. Penicillin resistance by MALDI-TOF Mass Spectrometry and tetracyclines resistance by genetic methods using specific primers were tested. Differences between tetracycline and penicillin resistance were detected. Results showed high prevalence of resistant Escherichia coli isolated from wild pheasant appendix. E. coli isolated from wild pheasant appendix carried plasmids for penicillins and tetracyclines resistance where they were responsible for enzymatic degradation of penicillin and carried genes for regulating efflux pumps for tetracyclines. Results showed that tetracyclines and penicillins resistance is widespread between wild pheasants with a carrier as Escherichia coli isolated from relative stable microcenosis of appendix.

Rapid qualitative antibiotic resistance characterization using VITEK MS

Development and standardization of simple, timely, and cost-effective antibiotic susceptibility assays are much needed to address the emergence of global resistance. The use of matrix-assisted laser desorption/ionization time of flight mass spectrometry is routine for bacterial identification. This study evaluated 2 assays using the VITEK MS for rapid detection and accurate differentiation of bacterial antibiotic susceptibility. We describe an extraction method and direct-on-target microdroplet growth assay (DOT-MGA). Non-susceptible and susceptible strains of Staphylococcus aureus, Enterococcus species, Escherichia coli, and Klebsiella pneumoniae were tested. The liquid extraction method and DOT-MGA proved to be reliable assays providing consistent differentiation between non-susceptible and susceptible strains. Results from this study support VITEK MS and these assays as rapid and accurate tools to augment traditional susceptibility testing. If implemented clinically, these assays can reduce the cost of patient care and the time to deliver critically needed treatment.

Rapid identification of microorganisms from positive blood cultures in pediatric patients by MALDI-TOF MS: Sepsityper kit versus short-term subculture

BACKGROUND AND AIM

The rapid diagnosis of bloodstream infection (BSI) often leads to better clinical outcomes. The present study was conducted to compare two rapid protocols (Sepsityper kit and short-term subculture) for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based identification of microorganisms from positive blood cultures in pediatric patients.

METHODS

This study was conducted between May 1, 2018, and April 30, 2019, at a tertiary children's hospital in eastern China. Only monomicrobial blood cultures included in this study were used to conduct the Sepsityper kit protocol and short-term subculture protocol at the same time.

RESULTS

In total, 115 monomicrobial blood cultures were included in this study. For the Sepsityper kit protocol, 85.2% and 64.3% of microorganisms were correctly identified to the genus (score ≥ 1.700) and species levels (score ≥ 2.000), respectively. For the short-term subculture protocol, 89.6% and 70.4% of microorganisms were correctly identified to the genus and species levels, respectively. At the genus level (P = .321) or the species level (P = .325), there was no significant difference between the Sepsityper kit protocol and the short-term subculture protocol. Moreover, the short-term subculture protocol exhibited similar performance between Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB) (the genus level: 93.7% (GPB) versus 87.9% (GNB), P = .518; the species level: 68.4% (GPB) versus 81.8% (GNB), P = .147). In addition, the Sepsityper kit protocol exhibited similar performance between GPB and GNB at the genus level (86.1% (GPB) versus 84.8% (GNB), P = 1.000). However, the Sepsityper kit protocol exhibited better performance in GNB at the species level (58.2% (GPB) versus 81.8% (GNB), P = .017). The rates of yeast-like fungi were correctly identified to the genus level (0.0%) or the species level (0.0%) for short-term subculture protocol were significantly lower than those of other microorganisms (the genus level: 92.0%, P = .001; the species level: 72.3%, P = .024). However, a similar result of identification was not found using the Sepsityper kit protocol (the genus level: P = .384; the species level: P = .599). In addition, the two rapid protocols both exhibited better performance at the genus level when the time to positivity (TTP) of blood cultures <19 h (the Sepsityper kit protocol: 91.8% (TTP < 19 h) versus 77.8% (TTP ≥ 19 h), P = .034; the short-term subculture protocol: 95.1% (TTP < 19 h) versus 83.3% (TTP ≥ 19 h), P = .040). In addition, the two rapid protocols both exhibited better performance at the species level when the TTP of blood cultures was <19 h (the Sepsityper kit protocol: 78.7% (TTP < 19 h) versus 48.1% (TTP ≥ 19 h), P = .000; the short-term subculture protocol: 83.6% (TTP < 19 h) versus 55.6% (TTP ≥ 19 h), P = .001).

CONCLUSION

The Sepsityper kit protocol and short-term subculture protocol are both reliable and rapid methods for the identification of most microorganisms from positive blood cultures in pediatric patients. The performance of these two rapid protocols is associated with the TTP of blood cultures.

Detection of carbapenem-resistant Klebsiella pneumoniae on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using supervised machine learning approach

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is emerging as a significant pathogen causing healthcare-associated infections. Matrix-assisted laser desorption/ionisation mass spectrometry time-of-flight mass spectrometry (MALDI-TOF MS) is used by clinical microbiology laboratories to address the need for rapid, cost-effective and accurate identification of microorganisms. We evaluated application of machine learning methods for differentiation of drug resistant bacteria from susceptible ones directly using the profile spectra of whole cells MALDI-TOF MS in 46 CRKP and 49 CSKP isolates.

METHODS

We developed a two-step strategy for data preprocessing consisting of peak matching and a feature selection step before supervised machine learning analysis. Subsequently, five machine learning algorithms were used for classification.

RESULTS

Random forest (RF) outperformed other four algorithms. Using RF algorithm, we correctly identified 93% of the CRKP and 100% of the CSKP isolates with an overall classification accuracy rate of 97% when 80 peaks were selected as input features.

CONCLUSIONS

We conclude that CRKPs can be differentiated from CSKPs through RF analysis. We used direct colony method, and only one spectrum for an isolate for analysis, without modification of current protocol. This allows the technique to be easily incorporated into clinical practice in the future.

Screening of biomarkers of drug resistance or virulence in ESCAPE pathogens by MALDI-TOF mass spectrometry

Rapid identification and characterisation of drug-resistant bacterial pathogens have an important role in diagnostic and antimicrobial stewardship. Response time in the diagnosis of not only the etiological agent but also in antimicrobial susceptibility results is of utmost importance in patient treatment. In this study, matrix-assisted laser desorption ionisation–time of flight (MALDI-TOF) mass spectrometry (MS) was used to screen for biomarkers of ESCAPE (vancomycin-resistant Enterococcus faecium, methicillin-resistant Staphylococcus aureus, hypervirulent NAP1/ribotype 027 Clostridioides [Clostridium] difficile, multidrug resistant Acinetobacter baumannii, multidrug resistant Pseudomonas aeruginosa, and carbapenem-resistant Enterobacteriaceae) pathogens to predict antimicrobial resistance or hypervirulence. Several biomarkers of drug-resistant genotypes in S. aureus, A. baumannii, P. aeruginosa, and K. pneumoniae, as well as hypervirulence in C. difficile, were detected. The fastest possible susceptibility testing with MALDI-TOF MS is simultaneous detection of a characteristic drug-resistant peak and species identification in the same spectra generated in routine processing. According to our approach, resistance or virulence biomarker peaks can be identified while performing routine microbiology analysis, and no additional assays nor prolonged incubation time is needed. Outstanding biomarker peaks detected in our study should be further analysed by additional methods to identify the specific proteins involved.

Detection and identification of a protein biomarker in antibiotic-resistant Escherichia coli using intact protein LC offline MALDI-MS and MS/MS

AIMS

The identification and differentiation of antibiotic-resistant bacteria by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) profiling remains a challenge due to the difficulty in detecting unique protein biomarkers associated with this trait. To expand the detectable proteome in antibiotic-resistant bacteria, we describe a method implementing offline LC protein separation/fractionation prior to MALDI-ToF-MS and top-down MALDI-ToF/ToF-MS (tandem MS or MS/MS) for the analysis of several antibiotic-resistant Escherichia coli isolates.

METHODS AND RESULTS

Coupling offline LC with MALDI-ToF-MS increased the number of detected protein signals in the typically analyzed mass regions (m/z 3000-20 000) by a factor of 13. Using the developed LC-MALDI-ToF-MS protocol in conjunction with supervised principal components analysis, we detected a protein biomarker at m/z 9355 which correlated to β-lactam resistance among the E. coli bacteria tested. Implementing a top-down MALDI-ToF/ToF-MS approach, the prefractionated protein biomarker was inferred as a DNA-binding HU protein, likely translated from the bla_CMY-2 gene (encoding AmpC-type β-lactamase) in the incompatibility plasmid complex A/C (IncA/C).

CONCLUSIONS

Our results demonstrate the utility of LC-MALDI-MS and MS/MS to extend the number of proteins detected and perform MALDI-accessible protein biomarker discovery in microorganisms.

SIGNIFICANCE AND IMPACT OF THE STUDY

This outcome is significant since it expands the detectable bacterial proteome via MALDI-ToF-MS.

MALDI-TOF Mass Spectrometry and Specific Biomarkers: Potential New Key for Swift Identification of Antimicrobial Resistance in Foodborne Pathogens

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is today the reference method for direct identification of microorganisms in diagnostic laboratories, as it is notably time- and cost-efficient. In the context of increasing cases of enteric diseases with emerging multi-drug resistance patterns, there is an urgent need to adopt an efficient workflow to characterize antimicrobial resistance (AMR). Current approaches, such as antibiograms, are time-consuming and directly impact the "patient-physician" workflow. Through this mini-review, we summarize how the detection of specific patterns by MALDI-TOF MS, as well as bioinformatics, become more and more essential in research, and how these approaches will help diagnostics in the future. Along the same lines, the idea to export more precise biomarker identification steps by MALDI-TOF(/TOF) MS data towards AMR identification pipelines is discussed. The study also critically points out that there is currently still a lack of research data and knowledge on different foodborne pathogens as well as several antibiotics families such as macrolides and quinolones, and many questions are still remaining. Finally, the innovative combination of whole-genome sequencing and MALDI-TOF MS could be soon the future for diagnosis of antimicrobial resistance in foodborne pathogens.

Rapid Discrimination of Methicillin-Resistant Staphylococcus aureus by MALDI-TOF MS

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious pathogen in clinical settings and early detection is critical. Here, we investigated the MRSA discrimination potential of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using 320 clinical S. aureus isolates obtained in 2005–2014 and 181 isolates obtained in 2018. We conducted polymerase chain reactions (PCR) for staphylococcal cassette chromosome mec (SCCmec) typing and MALDI-TOF MS to find specific markers for methicillin resistance. We identified 21 peaks with significant differences between MRSA and methicillin-susceptible S. aureus (MSSA), as determined by mecA and SCCmec types. Each specific peak was sufficient to discriminate MRSA. We developed two methods for simple discrimination according to these peaks. First, a decision tree for MRSA based on six MRSA-specific peaks, three MSSA-specific peaks, and two SCCmec type IV peaks showed a sensitivity of 96.5%. Second, simple discrimination based on four MRSA-specific peaks and one MSSA peak had a maximum sensitivity of 88.3%. The decision tree applied to 181 S. aureus isolates from 2018 had a sensitivity of 87.6%. In conclusion, we used specific peaks to develop sensitive MRSA identification methods. This rapid and easy MALDI-TOF MS approach can improve patient management.

Rapid detection of antibiotic resistance in positive blood cultures by MALDI-TOF MS and an automated and optimized MBT-ASTRA protocol for Escherichia coli and Klebsiella pneumoniae

Introduction: For fast and effective antibiotic therapy of serious infections like sepsis, it is crucial with rapid information about antibiotic susceptibility, especially in a time when the number of infections caused by multi resistant bacteria has escalated in the world.Methods: Here, we have used a semi-quantitative MALDI-TOF-MS based method for antibiotic resistance detection, MBT-ASTRA™, which is based on the comparison of growth rate of the bacteria cultivated with and without antibiotics. We demonstrate a new protocol where several parameters have been optimized and automated leading to reduced hands-on time and improved capacity to simultaneously analyse multiple clinical samples and antibiotics.Results: Ninety minutes of incubation at 37 °C with agitation was sufficient to differentiate the susceptible and resistant strains of E. coli and K. pneumoniae, for the antibiotics cefotaxime, meropenem and ciprofloxacin. In total, 841 positive blood culture analyses of 14 reference strains were performed. The overall sensitivity was 99%, specificity 99% and the accuracy 97%. The assay gave no errors for cefotaxime (n = 263) or meropenem (n = 289) for sensitive and resistant strains, whilst ciprofloxacin (n = 289) gave six (0.7%) major errors (false resistance) and four (0.5%) very major errors (false susceptibility). The intermediate strains showed a larger variety compared to the E-test MIC values.Conclusions: The hands-on time and the analysis time to detect antibiotic resistance of clinical blood samples can be substantially reduced and the sample capacity can be increased by using automation and this improved protocol.

Molecular analysis and epidemiological typing of Vancomycin-resistant Enterococcus outbreak strains

Outbreaks of multidrug resistant bacteria including vancomycin-resistant enterococci (VRE) in healthcare institutions are increasing in Norway, despite a low level of resistance compared to other European countries. In this study, we describe epidemiological relatedness of vancomycin-resistant Enterococcus faecium isolated during an outbreak at a Norwegian hospital in 2012–2013. During the outbreak, 9454 fecal samples were screened for VRE by culture and/or PCR. Isolates from 86 patients carrying the vanA resistance gene were characterized using pulsed-field gel electrophoresis (PFGE), MALDI-TOF mass spectrometry and single nucleotide polymorphism typing. PFGE revealed two main clusters, the first comprised 56 isolates related to an initial outbreak strain, and the second comprised 21 isolates originating from a later introduced strain, together causing two partly overlapping outbreaks. Nine isolates, including the index case were not related to the two outbreak clusters. In conclusion, the epidemiological analyses show that the outbreak was discovered by coincidence, and that infection control measures were successful. All typing methods identified the two outbreak clusters, and the experiment congruence between the MALDI-TOF and the PFGE clustering was 63.2%, with a strong correlation (r = 72.4%). Despite lower resolution compared to PFGE, MALDI-TOF may provide an efficient mean for real-time monitoring spread of infection.

New Microbiological Techniques in the Diagnosis of Bloodstream Infections

BACKGROUND

When a bloodstream infection is suspected, the preliminary and definitive results of culture-based microbiological testing arrive too late to have any influence on the initial choice of empirical antibiotic treatment.

METHODS

This review is based on pertinent publications retrieved by a selective search of the literature and on the authors' clinical and scientific experience.

RESULTS

A number of technical advances now enable more rapid microbiological diagnosis of bloodstream infections. DNA- based techniques for the direct detection of pathogenic organisms in whole blood have not yet become established in routine use because of various limitations. On the other hand, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become available for routine use in clinical laboratories and has markedly shortened the time to diagnosis after blood samples that have been cultured in automated blood-culture systems turn positive. Further developments of this technique now enable it to be used directly for blood cultures that have been flagged positive, as well as for subcultures that have been incubated for only a short time on a solid nutrient medium. The microbial biomass of the subculture can also be used in parallel for more rapid susceptibility testing with conventional methods, or, in future, with MALDI-TOF MS.

CONCLUSION

The potential of all of these new techniques will only be realizable in practice if they are optimally embedded in the diagnostic process and if sufficient attention is paid to pre-analytical issues, particularly storage and transport times.

Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification

Mass spectrometry has revolutionized the clinical microbiology field in America’s and Europe’s industrialized countries, for being a fast, reliable and inexpensive technique. Our study is based on the comparison of the performance of two commercial platforms, Microflex LT (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMérieux, Marcy l´Etoile, France) for the identification of unusual and hard-to-diagnose microorganisms in a Reference Laboratory in Argentina. During a four-month period (February–May 2018) the diagnostic efficiency and the concordance between both systems were assessed, and the results were compared with the polyphasic taxonomic identification of all isolates. The study included 265 isolates: 77 Gram-Negative Bacilli, 33 Gram-Positive Cocci, 40 Anaerobes, 35 Actinomycetales, 19 Fastidious Microorganisms and 61 Gram-Positive Bacilli. All procedures were practiced according to the manufacturer’s recommendations in each case by duplicate, and strictly in parallel. Other relevant factors, such as the utility of the recommended extraction protocols, reagent stability and connectivity were also evaluated. Both systems correctly identified the majority of the isolates to species and complex level (82%, 217/265). Vitex MS achieved a higher number of correct species-level identifications between the gram-positive microorganisms; however, it presented greater difficulty in the identification of non-fermenting bacilli and a higher number of incorrect identifications when the profile of the microorganism was not represented in the commercial database. Both platforms showed an excellent performance on the identification of anaerobic bacteria and fastidious species. Both systems enabled the fast and reliable identification of most of the tested isolates and were shown to be very practical for the user.

Sequencing-based methods and resources to study antimicrobial resistance

Antimicrobial resistance extracts high morbidity, mortality and economic costs yearly by rendering bacteria immune to antibiotics. Identifying and understanding antimicrobial resistance are imperative for clinical practice to treat resistant infections and for public health efforts to limit the spread of resistance. Technologies such as next-generation sequencing are expanding our abilities to detect and study antimicrobial resistance. This Review provides a detailed overview of antimicrobial resistance identification and characterization methods, from traditional antimicrobial susceptibility testing to recent deep-learning methods. We focus on sequencing-based resistance discovery and discuss tools and databases used in antimicrobial resistance studies.

Rapid antibiotic susceptibility testing from blood culture bottles with species agnostic real-time polymerase chain reaction

Development and implementation of rapid antimicrobial susceptibility testing is critical for guiding patient care and improving clinical outcomes, especially in cases of sepsis. One approach to reduce the time-to-answer for antimicrobial susceptibility is monitoring the inhibition of DNA production, as differences in DNA concentrations are more quickly impacted compared to optical density changes in traditional antimicrobial susceptibility testing. Here, we use real-time PCR to rapidly determine antimicrobial susceptibility after short incubations with antibiotic. Application of this assay to a collection of 144 isolates in mock blood culture, covering medically relevant pathogens displaying high rates of resistance, provided susceptibility data in under 4 hours. This assay provided categorical agreement with a reference method in 96.3% of cases across all species. Sequencing of a subset of PCR amplicons showed accurate genus level identification. Overall, implementation of this method could provide accurate susceptibility results with a reduced time-to-answer for a number of medically relevant bacteria commonly isolated from blood culture.

Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

Klebsiella pneumoniae and related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinical Klebsiella isolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinical Klebsiella strains were analyzed by WGS, FTIR, and MALDI-TOF MS. FTIR showed high discriminatory power in comparison to the WGS reference, whereas MALDI-TOF MS exhibited a low ability to type the isolates. MALDI-TOF mass spectra were further analyzed for peaks that showed high specificity for different Klebsiella species. Phylogenetic analysis revealed that the Klebsiella isolates comprised three different species: K. pneumoniae, K. variicola, and K. quasipneumoniae Genome analysis showed that MALDI-TOF MS can be used to distinguish K. pneumoniae from K. variicola due to shifts of certain mass peaks. The peaks were tentatively identified as three ribosomal proteins (S15p, L28p, L31p) and one stress response protein (YjbJ), which exhibit amino acid differences between the two species. Overall, FTIR has high discriminatory power to recognize the clonal relationship of isolates, thus representing a valuable tool for rapid outbreak analysis and for the detection of transmission events due to fast turnaround times and low costs per sample. Furthermore, specific amino acid substitutions allow the discrimination of K. pneumoniae and K. variicola by MALDI-TOF MS.

The Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogens Causing Sepsis

BACKGROUND

Sepsis is a life-threatening condition with high rates of morbidity and mortality; effective and appropriate antibiotic therapy is essential for ensuring patient improvement. To aid in the diagnosis of sepsis, blood cultures are drawn and sent to the microbiology laboratory for pathogen growth, identification, and susceptibility testing. The clinical microbiology laboratory can assist the medical team by providing timely identification of the pathogen(s) causing the bloodstream infection through the use of rapid diagnostic technology. One of these rapid diagnostic technologies, MALDI-TOF MS, has been proven to reduce the time required for appropriate antibiotic therapy when used to identify pathogens grown in culture. This technology has also been used to identify pathogens directly from the positive blood cultures with great success.

CONTENT

In this minireview, we summarize the different methods that have been developed to directly identify pathogens from positive blood cultures by use of MALDI-TOF MS and the effect of this technology on patient outcomes. Additionally, we touch on current research in the field, including the identification of antimicrobial resistance directly from positive blood cultures by MALDI-TOF MS.

SUMMARY

Rapid identification of pathogens is important in the survival of patients undergoing a septic event. MALDI-TOF MS technology has played an important role in rapid identification, which has led to a reduction in the time to appropriate antibiotic therapy and contributed to the improvement of patient outcomes. The high sensitivity and specificity of MALDI-TOF MS identification, in combination with MALDI-TOF's rapid function and reduced labor costs, make this technology an attractive choice for clinical laboratories.

Automated analysis of lipid drug-response markers by combined fast and high-resolution whole cell MALDI mass spectrometry biotyping

Recent advances in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry have enabled whole cell-MALDI mass spectrometry biotyping of drug-treated cultured cells for rapid monitoring of known abundant pharmacodynamic protein markers such as polyacetylated histones. In contrast, generic and automated analytical workflows for discovery of such pharmacodynamic markers, in particular lipid markers, and their use in cellular tests of drug-like compounds are still lacking. Here, we introduce such a workflow and demonstrate its utility for cellular drug-response monitoring of BCR-ABL tyrosine kinase inhibitors in K562 leukemia cells: First, low-molecular mass features indicating drug responses are computationally extracted from groups of MALDI-TOF mass spectra. Then, the lipids/metabolites corresponding to these features are identified by MALDI-Fourier transformation mass spectrometry. To demonstrate utility of the method, we identify the potassium adduct of phosphatidylcholine PC(36:1) as well as heme B, a marker for erythroid differentiation, as markers for a label-free MALDI MS-based test of cellular responses to BCR-ABL inhibitors. Taken together, these results suggest that MALDI-TOF mass spectrometry of lipids and other low molecular mass metabolites could support cell-based drug profiling.

Molecular Methods for Detection of Antimicrobial Resistance

The increase in bacteria harboring antimicrobial resistance (AMR) is a global problem because there is a paucity of antibiotics available to treat multidrug-resistant bacterial infections in humans and animals. Detection of AMR present in bacteria that may pose a threat to veterinary and public health is routinely performed using standardized phenotypic methods. Molecular methods are often used in addition to phenotypic methods but are set to replace them in many laboratories due to the greater speed and accuracy they provide in detecting the underlying genetic mechanism(s) for AMR. In this article we describe some of the common molecular methods currently used for detection of AMR genes. These include PCR, DNA microarray, whole-genome sequencing and metagenomics, and matrix-assisted laser desorption ionization-time of flight mass spectrometry. The strengths and weaknesses of these methods are discussed, especially in the context of implementing them for routine surveillance activities on a global scale for mitigating the risk posed by AMR worldwide. Based on current popularity and ease of use, PCR and single-isolate whole-genome sequencing seem irreplaceable.

MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives

The laboratory diagnosis of infections is based on pathogen identification and antimicrobial susceptibility determination. The gold standard of cultivation, isolation and susceptibility testing is a time-consuming procedure and in some cases this can be threatening for patients' outcome. In the current review the applications of mass spectrometry in pathogen identification and especially in detecting biomarkers of antimicrobial resistance are analyzed. MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry is a new technology that has revolutionized pathogen identification and has also proven to accelerate detection of antimicrobial resistance compared to the traditional antibiotic susceptibility tests (AST) as well as DNA amplification methodologies. The technology has incorporated up to know four different methodologies: (I) the detection of differences of mass spectra of susceptible and resistant isolates of a given microorganism using the classical strain typing methodology; (II) the analysis of bacterial induced hydrolysis of β-lactam antibiotics; (III) the detection of stable (non-radioactive) isotope-labeled amino acids; and (IV) the analysis of bacterial growth in the presence and absence of antibiotics using an internal standard. The implementation of MALDI-TOF methodologies has improved detection of resistance in aerobic, Gram-positive and Gram-negative bacteria, mycobacteria, anaerobic bacteria, fungi and viruses. The MALDI-TOF is an easy to use, rapid, reliable, economical, and environmentally friendly methodology. However, this technology needs further development of research protocols that will be validated for routine application.

Rapid and robust MALDI-TOF MS techniques for microbial identification: a brief overview of their diverse applications

in mass spectrometry have enabled the investigation of various biological systems by directly analyzing diverse sets of biomolecules (i.e., proteins, lipids, and carbohydrates), thus making a significant impact on the life sciences field. Over the past decade, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely utilized as a rapid and reliable method for the identification of microorganisms. MALDI-TOF MS has come into widespread use despite its relatively low resolving power (full width at half maximum, FWHM: < 5,000) and its incompatibility with tandem MS analysis, features with which other high-resolution mass spectrometers are equipped. Microbial identification is achieved by searching databases containing mass spectra of peptides and proteins extracted from microorganisms of interest, using scoring algorithms to match analyzed spectra with reference spectra. In this paper, we give a brief overview of the diverse applications of rapid and robust MALDI-TOF MS-based techniques for microbial identification in a variety of fields, such as clinical diagnosis and environmental and food monitoring. We also describe the fundamental principles of MALDI-TOF MS. The general specifications of the two major MS-based microbial identification systems available in the global market (BioTyper® and VITEK® MS Plus) and the distribution of these instruments in Republic of Korea are also discussed. The current review provides an understanding of this emerging microbial identification and classification technology and will help bacteriologists and cell biologists take advantage of this powerful technique.

In vitro antimicrobial susceptibility testing methods: agar dilution to 3D tissue-engineered models

In the field of orthopaedic surgery, bacterial invasion of implants and the resulting periprosthetic infections are a common and unresolved problem. Antimicrobial susceptibility testing methods help to define the optimal treatment and identify antimicrobial resistance. This review discusses proven gold-standard techniques and recently developed models for antimicrobial susceptibility testing, while also providing a future outlook. Conventional, gold-standard methods, such as broth microdilution, are still widely applied in clinical settings. Although recently developed methods based on microfluidics and microdroplets have shown advantages over conventional methods in terms of testing speed, safety and the potential to provide a deeper insight into resistance mechanisms, extensive validation is required to translate this research to clinical practice. Recent optical and mechanical methods are complex and expensive and, therefore, not immediately clinically applicable. Novel osteoblast infection and tissue models best resemble infections in vivo. However, the integration of biomaterials into these models remains challenging and they require a long tissue culture, making their rapid clinical implementation unlikely. A method applicable for both clinical and research environments is difficult to realise. With a continuous increase in antimicrobial resistance, there is an urgent need for methods that analyse recurrent infections to identify the optimal treatment approaches. Graphical abstract Timeline of published and partly applied antimicrobial susceptibility testing methods, listed according to their underlying mechanism, complexity and application in research or clinics.

Management of KPC-producing Klebsiella pneumoniae infections

BACKGROUND

Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (KPC-KP) has become one of the most important contemporary pathogens, especially in endemic areas.

AIMS

To provide practical suggestion for physicians dealing with the management of KPC-KP infections in critically ill patients, based on expert opinions.

SOURCES

PubMed search for relevant publications related to the management of KPC-KP infections.

CONTENTS

A panel of experts developed a list of 12 questions to be addressed. In view of the current lack of high-level evidence, they were asked to provide answers on the bases of their knowledge and experience in the field. The panel identified several key aspects to be addressed when dealing with KPC-KP in critically ill patients (preventing colonization in the patient, preventing infection in the colonized patient and colonization of his or her contacts, reducing mortality in the infected patient by rapidly diagnosing the causative agent and promptly adopting the best therapeutic strategy) and provided related suggestions that were based on the available observational literature and the experience of panel members.

IMPLICATIONS

Diagnostic technologies could speed up the diagnosis of KPC-KP infections. Combination treatment should be preferred to monotherapy in cases of severe infections. For non-critically ill patients without severe infections, results from randomized clinical trials are needed for ultimately weighing benefits and costs of using combinations rather than monotherapy. Multifaceted infection control interventions are needed to decrease the rates of colonization and cross-transmission of KPC-KP.

Semi-quantitative MALDI-TOF for antimicrobial susceptibility testing in Staphylococcus aureus

Antibiotic resistant bacterial infections are a significant problem in the healthcare setting, in many cases requiring the rapid administration of appropriate and effective antibiotic therapy. Diagnostic assays capable of quickly and accurately determining the pathogen resistance profile are therefore crucial to initiate or modify care. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a standard method for species identification in many clinical microbiology laboratories and is well positioned to be applied towards antimicrobial susceptibility testing. One recently reported approach utilizes semi-quantitative MALDI-TOF MS for growth rate analysis to provide a resistance profile independent of resistance mechanism. This method was previously successfully applied to Gram-negative pathogens and mycobacteria; here, we evaluated this method with the Gram-positive pathogen Staphylococcus aureus. Specifically, we used 35 strains of S. aureus and four antibiotics to optimize and test the assay, resulting in an overall accuracy rate of 95%. Application of the optimized assay also successfully determined susceptibility from mock blood cultures, allowing both species identification and resistance determination for all four antibiotics within 3 hours of blood culture positivity.