Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential.

The 2009 H1N1 pandemic (pdm09) lineage of influenza A virus (IAV) crosses interspecies barriers with frequent human-to-swine spillovers each year. These spillovers reassort and drift within swine populations, leading to genetically and antigenically novel IAV that represent a zoonotic threat. We quantified interspecies transmission of the pdm09 lineage, persistence in swine, and identified how evolution in swine impacted zoonotic risk. Human and swine pdm09 case counts between 2010 and 2020 were correlated and human pdm09 burden and circulation directly impacted the detection of pdm09 in pigs. However, there was a relative absence of pdm09 circulation in humans during the 2020-21 season that was not reflected in swine. During the 2020-21 season, most swine pdm09 detections originated from human-to-swine spillovers from the 2018-19 and 2019-20 seasons that persisted in swine. We identified contemporary swine pdm09 representatives of each persistent spillover and quantified cross-reactivity between human seasonal H1 vaccine strains and the swine strains using a panel of monovalent ferret antisera in hemagglutination inhibition (HI) assays. The swine pdm09s had variable antigenic reactivity to vaccine antisera, but each swine pdm09 clade exhibited significant reduction in cross-reactivity to one or more of the human seasonal vaccine strains. Further supporting zoonotic risk, we showed phylogenetic evidence for 17 swine-to-human transmission events of pdm09 from 2010 to 2021, 11 of which were not previously classified as variants, with each of the zoonotic cases associated with persistent circulation of pdm09 in pigs. These data demonstrate that reverse-zoonoses and evolution of pdm09 in swine results in viruses that are capable of zoonotic transmission and represent a potential pandemic threat.

Phylogenetic diversity statistics for all clades in a phylogeny.

The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem. Other descriptive statistics, such as the minimum PD, average PD, and standard deviation of PD, can provide invaluable insight into the distribution of PD across a phylogeny (relative to a fixed value of k). However, there has been limited or no research on computing these statistics, especially when required for each clade in a phylogeny, enabling direct comparisons of PD between clades. We introduce efficient algorithms for computing PD and the associated descriptive statistics for a given phylogeny and each of its clades. In simulation studies, we demonstrate the ability of our algorithms to analyze large-scale phylogenies with applications in ecology and evolutionary biology. The software is available at https://github.com/flu-crew/PD_stats.

PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny.

The use of next-generation sequencing technology has enabled phylogenetic studies with hundreds of thousands of taxa. Such large-scale phylogenies have become a critical component in genomic epidemiology in pathogens such as SARS-CoV-2 and influenza A virus. However, detailed phenotypic characterization of pathogens or generating a computationally tractable dataset for detailed phylogenetic analyses requires objective subsampling of taxa. To address this need, we propose parnas, an objective and flexible algorithm to sample and select taxa that best represent observed diversity by solving a generalized k-medoids problem on a phylogenetic tree. parnas solves this problem efficiently and exactly by novel optimizations and adapting algorithms from operations research. For more nuanced selections, taxa can be weighted with metadata or genetic sequence parameters, and the pool of potential representatives can be user-constrained. Motivated by influenza A virus genomic surveillance and vaccine design, parnas can be applied to identify representative taxa that optimally cover the diversity in a phylogeny within a specified distance radius. We demonstrated that parnas is more efficient and flexible than existing approaches. To demonstrate its utility, we applied parnas to 1) quantify SARS-CoV-2 genetic diversity over time, 2) select representative influenza A virus in swine genes derived from over 5 years of genomic surveillance data, and 3) identify gaps in H3N2 human influenza A virus vaccine coverage. We suggest that our method, through the objective selection of representatives in a phylogeny, provides criteria for quantifying genetic diversity that has application in the the rational design of multivalent vaccines and genomic epidemiology. PARNAS is available at https://github.com/flu-crew/parnas.

RF-Net 2: fast inference of virus reassortment and hybridization networks.

MOTIVATION: A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method called RF-Net for accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens. RESULTS: Here, we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, called Fast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. In addition, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical IAV evolutionary analyses. AVAILABILITY AND IMPLEMENTATION: RF-Net 2 is available at https://github.com/flu-crew/rf-net-2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model.

MOTIVATION: The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. This has motivated an extensive body of work on phylogenetic methods that are statistically consistent under MSC. One such particularly popular method is ASTRAL, a quartet-based species tree inference method. Novel studies suggest that ASTRAL also performs well when given multi-locus gene trees in simulation studies. Further, Legried et al. recently demonstrated that ASTRAL is statistically consistent under the gene duplication and loss model (GDL). GDL is prevalent in evolutionary histories and is the first core process in the powerful duplication-loss-coalescence evolutionary model (DLCoal) by Rasmussen and Kellis. RESULTS: In this work, we prove that ASTRAL is statistically consistent under the general DLCoal model. Therefore, our result supports the empirical evidence from the simulation-based studies. More broadly, we prove that the quartet-based inference approach is statistically consistent under DLCoal. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cyclodextrin-assisted surface-enhanced Raman spectroscopy: a critical review.

Numerous approaches have been proposed to overcome the intrinsically low selectivity of surface-enhanced Raman spectroscopy (SERS), and the modification of SERS substrates with diverse recognition molecules is one of such approaches. In contrast to the use of antibodies, aptamers, and molecularly imprinted polymers, application of cyclodextrins (CDs) is still developing with less than 100 papers since 1993. Therefore, the main goal of this review is the critical analysis of all available papers on the use of CDs in SERS analysis, including physicochemical studies of CD complexation and the effect of CD presence on the Raman enhancement. The results of the review reveal that there is controversial information about CD efficiency and further experimental investigations have to be done in order to estimate the real potential of CDs in SERS-based analysis.

Thermodynamic Study of Formamidinium Lead Iodide (CH5N2PbI3) from 5 to 357 K.

In the present study, the molar heat capacity of solid formamidinium lead iodide (CH5N2PbI3) was measured over the temperature range from 5 to 357 K using a precise automated adiabatic calorimeter. In the above temperature interval, three distinct phase transitions were found in ranges from 49 to 56 K, from 110 to 178 K, and from 264 to 277 K. The standard thermodynamic functions of the studied perovskite, namely the heat capacity C°p(T), enthalpy [H0(T) - H0(0)], entropy S0(T), and [G°(T) - H°(0)]/T, were calculated for the temperature range from 0 to 345 K based on the experimental data. Herein, the results are discussed and compared with those available in the literature as measured by nonclassical methods.

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it.

MOTIVATION: The evolution of complexity is one of the most fascinating and challenging problems in modern biology, and tracing the evolution of complex traits is an open problem. In bacteria, operons and gene blocks provide a model of tractable evolutionary complexity at the genomic level. Gene blocks are structures of co-located genes with related functions, and operons are gene blocks whose genes are co-transcribed on a single mRNA molecule. The genes in operons and gene blocks typically work together in the same system or molecular complex. Previously, we proposed a method that explains the evolution of orthologous gene blocks (orthoblocks) as a combination of a small set of events that take place in vertical evolution from common ancestors. A heuristic method was proposed to solve this problem. However, no study was done to identify the complexity of the problem. RESULTS: Here, we establish that finding the homologous gene block problem is NP-hard and APX-hard. We have developed a greedy algorithm that runs in polynomial time and guarantees an O(ln⁡n) approximation. In addition, we formalize our problem as an integer linear program problem and solve it using the PuLP package and the standard CPLEX algorithm. Our exploration of several candidate operons reveals that our new method provides more optimal results than the results from the heuristic approach, and is significantly faster. AVAILABILITY AND IMPLEMENTATION: The software and data accompanying this paper are available under the GPLv3 and CC0 license respectively on: https://github.com/nguyenngochuy91/Relevant-Operon.

Thermodynamic Properties of the First-Generation Hybrid Dendrimer with "Carbosilane Core/Phenylene Shell" Structure.

The molar heat capacity of the first-generation hybrid dendrimer with a "carbosilane core/phenylene shell" structure was measured for the first time in the temperature range T = 6-600 K using a precise adiabatic vacuum calorimeter and DSC. In the above temperature interval, the glass transition of the studied compound was observed, and its thermodynamic characteristics were determined. The standard thermodynamic functions (the enthalpy, the entropy, and the Gibbs energy) of the hybrid dendrimer were calculated over the range from T = 0 to 600 K using the experimentally determined heat capacity. The standard entropy of formation of the investigated dendrimer was evaluated at T = 298.15 K. The obtained thermodynamic properties of the studied hybrid dendrimer were compared and discussed with the literature data for some of the first-generation organosilicon and pyridylphenylene dendrimers.

Exact median-tree inference for unrooted reconciliation costs.

BACKGROUND: Solving median tree problems under tree reconciliation costs is a classic and well-studied approach for inferring species trees from collections of discordant gene trees. These problems are NP-hard, and therefore are, in practice, typically addressed by local search heuristics. So far, however, such heuristics lack any provable correctness or precision. Further, even for small phylogenetic studies, it has been demonstrated that local search heuristics may only provide sub-optimal solutions. Obviating such heuristic uncertainties are exact dynamic programming solutions that allow solving tree reconciliation problems for smaller phylogenetic studies. Despite these promises, such exact solutions are only suitable for credibly rooted input gene trees, which constitute only a tiny fraction of the readily available gene trees. Standard gene tree inference approaches provide only unrooted gene trees and accurately rooting such trees is often difficult, if not impossible. RESULTS: Here, we describe complex dynamic programming solutions that represent the first nonnaïve exact solutions for solving the tree reconciliation problems for unrooted input gene trees. Further, we show that the asymptotic runtime of the proposed solutions does not increase when compared to the most time-efficient dynamic programming solutions for rooted input trees. CONCLUSIONS: In an experimental evaluation, we demonstrate that the described solutions for unrooted gene trees are, like the solutions for rooted input gene trees, suitable for smaller phylogenetic studies. Finally, for the first time, we study the accuracy of classic local search heuristics for unrooted tree reconciliation problems.

Determination of methotrexate in spiked human urine using SERS-active sorbent.

This report is dedicated to determination of anticancer drug methotrexate (MTX) in human urine using surface-enhanced Raman spectroscopy (SERS). Aluminum oxide loaded with silver nanoparticles (AO-Ag) was proposed as SERS-active sorbent and used for solid-phase extraction (SPE) of the analyte and its SERS-based determination (SPE-SERS protocol). MTX has strong SERS signal only in alkaline media that challenges its determination in urine due to strong background signal caused by creatinine. The application of SPE step enables to purify and concentrate the analyte making MTX determination possible. Also, the application of the same material for SPE pretreatment and SERS analysis enables to simplify and speed-up the protocol. The protocol was developed and tested using artificially spiked samples of human urine collected during different time of day to account deviating composition of the urine matrix. The use of dilution step of the analyte-containing urine was proposed prior SPE-SERS protocol to reduce the difference between morning-time- and daytime-collected urine achieving maximal reliability of the analysis. Additional physicochemical study was performed to estimate an influence of the primary intrinsic urine components (salts, urea, creatinine) and their mixtures on the analytical signal. Final protocol enables MTX determination in human urine within 20-300 µg mL-1 range of concentrations with satisfactory precision (11-19% RSD), accuracy (97-104% apparent recovery), and limit of detection (4.2 µg mL-1). Accounting that the analysis requires less than 15 min and portable Raman spectrometer, the protocol seems to be promising for therapeutic drug monitoring in hospitals to identify poor MTX clearance in a timely manner and minimize adverse effects of therapy. Graphical Abstract.

Optical sensors for determination of biogenic amines in food.

This review presents the state-of-the-art of optical sensors for determination of biogenic amines (BAs) in food by publications covering about the last 10 years. Interest in the development of rapid and preferably on-site methods for quantification of BAs is based on their important role in implementation and regulation of various physiological processes. At the same time, BAs can develop in different kinds of food by fermentation processes or microbial activity or arise due to contamination, which induces toxicological risks and food poisoning and causes serious health issues. Therefore, various optical chemosensor systems have been devised that are easy to assemble and fast responding and low-cost analytical tools. If amenable to on-site analysis, they are an attractive alternative to existing instrumental analytical methods used for BA determination in food. Hence, also portable sensor systems or dipstick sensors are described based on various probes that typically enable signal readouts such as photometry, reflectometry, luminescence, surface-enhanced Raman spectroscopy, or ellipsometry. The quantification of BAs in real food samples and the design of the sensors are highlighted and the analytical figures of merit are compared. Future instrumental trends for BA sensing point to the use of cell phone-based fully automated optical evaluation and devices that could even comprise microfluidic micro total analysis systems.

Sample pretreatment and SERS-based detection of ceftriaxone in urine.

The aim of the work is the development of the procedure for ceftriaxone (antibiotic drug of cephalosporin class) detection in urine using surface-enhanced Raman spectroscopy (SERS). Hydroxylamine stabilized silver nanoparticles were used as SERS-active material. Additional urine pretreatment steps were developed in order to eliminate the influence of creatinine on the ceftriaxone SERS signal. These steps include adjusting of the sample pH to alkaline value (pH 13) and purification of the sample using silica gel column chromatography. Alkali pH increases SERS signal of ceftriaxone, while silica gel separates the analyte from creatinine-the main admixture in urine which provides inappropriate SERS signal background. Additionally, it was found that total protein content up to 0.2 mg/mL (upper level for urine of healthy person) and pH deviation of initial urine do not influence on SERS signal of ceftriaxone. The proposed detection procedure enables fast (~ 10 min) determination of ceftriaxone in artificially spiked urine samples within 5 to 500 µg/mL range of concentrations which matches the range of the drug concentrations in urine after injection of therapeutically required dosages. Limits of detection (3σ) and quantification (10σ) were found to be 0.4 and 2.0 µg/mL, correspondingly. Graphical abstract Application of urine pretreatment enables the purification of target analyte from intrinsic urine components and improves SERS-based detection of ceftriaxone (antibiotic drug).

SERS detection of ceftriaxone and sulfadimethoxine using copper nanoparticles temporally protected by porous calcium carbonate.

The authors describe a new composite based on SERS-active copper nanoparticles (CuNPs; 10 ± 2 nm) incorporated into calcium carbonate microspheres (CaCO3-CuNPs; 3.4 ± 0.3 µm). The CaCO3 coating acts as a temporal protector of CuNPs against oxidation. Incorporated CuNPs have significantly improved stability during storage and a month-long shelf lifetime. The composite was used for SERS detection of rhodamine 6G and two antibacterial drugs (ceftriaxone and sulfadimethoxine). Two analytical formats, one with and one without solid phase extraction, are introduced to demonstrate the flexibility of the method. Both formats imply the dissolution of CaCO3 matrix before SERS analysis to release CuNP used as SERS substrate. The study of the influence of pH value and acid nature on the SERS signal demonstrated that HCl is the most efficient candidate to release the CuNPs. Sensitivity (expressed as LOD) is shown to be improved by more than one order when solid phase extraction is used. The average SERS enhancement factor is 10^7 which makes the material efficiency comparable to the one of silver nanoparticles. The LOD (<5 µM), precision (RSDs between 20 and 24% at LOD levels), and trueness (apparent recoveries 84-113%) for the two antibiotics (ceftriaxone and sulfadimethoxine) make the method quite useful for quantitative analysis and therapeutic drug monitoring at physiologically relevant concentrations. Graphical abstract A composite with temporally stable copper nanoparticles was synthesized, studied, and used for SERS detection of two antibacterial drugs. The analytical efficiency of the composite was found appropriate for quantitative analysis due to Raman enhancement comparable with silver nanostructures.

Betulin-3,28-diphosphate. Physico-Chemical Properties and In Vitro Biological Activity Experiments.

Betulin-3,28-diphosphate (BDP) obtained by phosphorylation of betulin using POCl3 has two main structural forms-BDP-1 and BDP-2-which differ in ethanol solubility, melting point, FTIR spectra, thermoanalytical characteristics and biological activity. Betulin-3,28-diphosphate and its sodium salt (Na-BDP) were characterized using 13C and 31P-NMR spectra, powder XRD experiments, as well as differential scanning calorimetry (DSC) and thermogravimetric analysis (TG) methods. The exo-effects at 193 ± 8 °C for ethanol soluble BDP-1 samples (-19.7 ± 0.2 kJ∙mol-1) were about three times less than for ethanol insoluble BDP-2 samples f (-70.5 ± 0.7 kJ∙mol-1). The DSC curves of Na-BDP-1 and Na-BDP-2 characterized the endo-effects having a maximum at 95⁻112 °C. Water-soluble Na-BDP-1 was obtained as needle-like crystals, unlike poorly crystalline Na-BDP-2, whereas BDP-1 and BDP-2 aged with time and were isolated as amorphous substances. In vitro experiments on rats showed that compared to the control, Na-BDP-1 increased catalase and SOD activity and improved energy metabolism more effectively than Na-BDP-2.

Standard Thermodynamic Functions of Tripeptides N-Formyl-l-methionyl-l-leucyl-l-phenylalaninol and N-Formyl-l-methionyl-l-leucyl-l-phenylalanine Methyl Ester.

The heat capacities of tripeptides N-formyl-l-methionyl-l-leucyl-l-phenylalaninol (N-f-MLF-OH) and N-formyl-l-methionyl-l-leucyl-l-phenylalanine methyl ester (N-f-MLF-OMe) were measured by precision adiabatic vacuum calorimetry over the temperature range from T = (6 to 350) K. The tripeptides were stable over this temperature range, and no phase change, transformation, association, or thermal decomposition was observed. The standard thermodynamic functions: molar heat capacity Cp,m, enthalpy H(T) - H(0), entropy S(T), and Gibbs energy G(T) - H(0) of peptides were calculated over the range from T = (0 to 350) K. The low-temperature (T ≤ 50 K) heat capacities dependencies were analyzed using the Debye's and the multifractal theories. The standard entropies of formation of peptides at T = 298.15 K were calculated.

SERS as a tool for determination of structurally related compounds: The case of sulfanilamide class antibiotics.

Analysis of real objects based on surface-enhanced Raman spectroscopy (SERS) often utilizes new SERS substrates and/or complex analysis procedures, and they are optimized for only the determination of a single analyte. Moreover, analysis simplicity and selectivity are often sacrificed for maximum (sometimes unnecessary) sensitivity. Consequently, this trend limits the versatility of SERS analysis and complicates its practical implementation. Thus, we have developed a universal, but simple SERS assay suitable for the determination of structurally related antibiotics (five representatives of the sulfanilamide class) in complex objects (human urine and saliva). The assay involves only mixing of acidified analyzed solution with co-activating agent (polydiallyldimethylammonium chloride - PDDA) and SERS substrate (standard colloidal silver nanoparticles). Acidification promotes the generation of SERS spectra with maximum similarity and intensity, which is explained by the favorable enhancement of the protonated sulfanilamide moiety (a structurally similar part of the studied antibiotics) as a result of its strong electrostatic interaction with the SERS-active surface. Meanwhile, the addition of PDDA improves analysis selectivity by reducing background signal from body fluids, enabling to simplify sample pretreatment (dilution for urine; mucin removal and dilution for saliva). Therefore, the assay allows for rapid (≤10 min), precise, and accurate class-specific determination of sulfanilamides within concentration ranges suitable for non-invasive therapeutic drug monitoring in urine (40-600 µM) and saliva (10-30 µM). We also believe that thorough investigation of structurally related analytes and accompanying effects (e.g., high spectral similarity) is a promising direction to improve the understanding of SERS in general and expand its capabilities as an analytical tool.

Asymmetric Cluster-Based Measures for Comparative Phylogenetics.

Phylogenetic inference and reconstruction methods generate hypotheses on evolutionary history. Competing inference methods are frequently used, and the evaluation of the generated hypotheses is achieved using tree comparison costs. The Robinson-Foulds (RF) distance is a widely used cost to compare the topology of two trees, but this cost is sensitive to tree error and can overestimate tree differences. To overcome this limitation, a refined version of the RF distance called the Cluster Affinity (CA) distance was introduced. However, CA distances are symmetric and cannot compare different types of trees. These asymmetric comparisons occur when gene trees are compared with species trees, when disparate datasets are integrated into a supertree, or when tree comparison measures are used to infer a phylogenetic network. In this study, we introduce a relaxation of the original Affinity distance to compare heterogeneous trees called the asymmetric CA cost. We also develop a biologically interpretable cost, the Cluster Support cost that normalizes by cluster size across gene trees. The characteristics of these costs are similar to the symmetric CA cost. We describe efficient algorithms, derive the exact diameters, and use these to standardize the cost to be applicable in practice. These costs provide objective, fine-scale, and biologically interpretable values that can assess differences and similarities between phylogenetic trees.

New surface-enhanced Raman scattering platforms: composite calcium carbonate microspheres coated with astralen and silver nanoparticles.

Surface-enhanced Raman scattering (SERS) microspectroscopy is a very promising label-free, noncontact, and nondestructive method for real-time monitoring of extracellular matrix (ECM) development and cell integration in scaffolds for tissue engineering. Here, we prepare a new type of micrometer-sized SERS substrate, core-shell microparticles composed of solid carbonate core coated with silver nanoparticles and polyhedral multishell fullerene-like structure, astralen. Astralen has been assembled with polyallylamine hydrochloride (PAH) by the layer-by-layer manner followed by Ag nanoparticle formation by means of a silver mirror reaction, giving the final structure of composite particles CaCO3(PAH/astralen)x/Ag, where x = 1-3. The components of the microparticle carry multiple functionalities: (i) an easy identification by Raman imaging (photostable astralen) and (ii) SERS due to a rough surface of Ag nanoparticles. A combination of Ag and astralen nanoparticles provides an enhancement of astralen Raman signal by more than 1 order of magnitude. Raman signals of commonly used scaffold components such as polylactide and polyvinyl alcohol as well as ECM component (hyaluronic acid) are significantly enhanced. Thus, we demonstrate that new mechanically robust and easily detectable (by astralen signal or optically) core-shell microspheres based on biocompatible CaCO3 can be used as SERS platform. Particle design opens many future perspectives for fabrication of SERS platforms with multiple functions for biomedical applications, for example, for theranostic.

Cyclodextrin-assisted SERS determination of fluoroquinolone antibiotics in urine and blood plasma.

This paper describes the use of cyclodextrins (CDs) to improve the determination of fluoroquinolone antibiotics in human body fluids using surface-enhanced Raman spectroscopy (SERS). CDs were used to (i) prepare the CD-SERS substrate (synthesis and stabilization of silver nanoparticles), (ii) increase the sensitivity of the assay by enhancing the interaction between analyte molecules and the substrate, and (iii) improve the analysis accuracy by reducing the interaction between the substrate and endogenous components of body fluids. Two native CDs (α-CD and ß-CD) and two of their derivatives with hydroxypropyl groups were tested, and the best results were obtained with CD-SERS substrate prepared using native ß-CD. The CD-SERS assay has been developed and optimized for the determination of commonly used and structurally related fluoroquinolones (ciprofloxacin, norfloxacin, pefloxacin, and levofloxacin) in urine and blood plasma samples. Importantly, the non-significant difference in the interaction of the CD-modified SERS substrate with various fluoroquinolones has been successfully used to develop a versatile assay suitable for the analyte-class-specific analysis. Calibration plots were obtained for concentration ranges suitable for the determination of the antibiotics in urine (50-500 µg mL-1) and blood plasma (1-6 µg mL-1). The following figures of merit were obtained (for urine and blood plasma, respectively): RSD values are ≤15% and ≤23%, LOD values are 2.9-5.8 and 0.05-0.34 µg mL-1, recovery ranges are 96-105% and 91-111%. In addition, the influence of excessive concentrations of some main endogenous components of the body fluids on the analytical signal was studied. This step was used to evaluate possible limitations of the assay associated with the deviation of the composition of the body fluid matrix. Therefore, accounting for the short analysis time (≤15 min) and the use of a portable Raman spectrometer, the proposed assay can be suggested for therapeutic drug monitoring in hospitals.