Detection of Fluoroquinolone Resistance Single-Nucleotide Polymorphisms in Neisseria gonorrhoeae gyrA and parC Using MALDI-TOF Mass Spectrometry

Predicting antimicrobial resistance in E. coli with discriminative position fused deep learning classifier

Escherichia coli (E. coli) has become a particular concern due to the increasing incidence of antimicrobial resistance (AMR) observed worldwide. Using machine learning (ML) to predict E. coli AMR is a more efficient method than traditional laboratory testing. However, further improvement in the predictive performance of existing models remains challenging. In this study, we collected 1937 high-quality whole genome sequencing (WGS) data from public databases with an antimicrobial resistance phenotype and modified the existing workflow by adding an attention mechanism to enable the modified workflow to focus more on core single nucleotide polymorphisms (SNPs) that may significantly lead to the development of AMR in E. coli. While comparing the model performance before and after adding the attention mechanism, we also performed a cross-comparison among the published models using random forest (RF), support vector machine (SVM), logistic regression (LR), and convolutional neural network (CNN). Our study demonstrates that the discriminative positional colors of Chaos Game Representation (CGR) images can selectively influence and highlight genome regions without prior knowledge, enhancing prediction accuracy. Furthermore, we developed an online tool (https://github.com/tjiaa/E.coli-ML/tree/main) for assisting clinicians in the rapid prediction of the AMR phenotype of E. coli and accelerating clinical decision-making.

Stable isotope labeling as a promising tool for rapid drug susceptibility testing in Neisseria gonorrhoeae

The world is heading towards an era of intractable and impending untreatable N. gonorrhoeae, thereby underlining the significance of rapid and accurate prediction of drug resistance as an indispensable need of the hour. In the present study, we optimized and evaluated a stable isotope labeling-based approach using the MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry) for rapid and reliable detection of ciprofloxacin and azithromycin resistance in N. gonorrhoeae. All the isolates were cultured under three varied condition setups viz. medium supplemented with normal lysine, heavy lysine (isotope), and heavy lysine along with the antibiotics (ciprofloxacin/azithromycin), respectively. After incubation, spectra were acquired using the MALDI-TOF MS which were further screened for unique patterns (media-specific spectra) to differentiate drug-susceptible and resistant isolates. The results of the stable isotope labeling assay were comparable to the results of phenotypic methods used for susceptibility testing.

Analysis of single nucleotide polymorphisms (SNPs) associated with antibiotic resistance genes in Chilean Piscirickettsia salmonis strains

The aetiological agent of Piscirickettsiosis is Piscirickettsia salmonis, a Gram-negative intracellular pathogen, and high doses of antibiotics have regularly been employed to treat this infection. Seven florfenicol and/or oxytetracycline resistance genes (tet pump, tetE, Tclor/flor, Tbcr, TfloR, ompF and mdtN) were identified in strains by in silico genome analyses. Later, the number of single nucleotide polymorphisms (SNPs) and its relationship with the resistance to these antibiotics were identified and analysed, using the original LF-89 strain as reference. Trials to determine and compare the minimum inhibitory concentration (MIC) of oxytetracycline and florfenicol in each strain, as well as to quantify the gPCR transcripts levels in the selected genes, were performed. Therefore, variations in the resistance to both antibiotics were observed, where the strain with fewer SNPs showed the highest susceptibility. Consistently, the in silico 3D analyses of proteins encoded by the selected genes revealed structural changes, evident in the sequences with the highest number of SNPs. These results showed that the bacterial resistance to oxytetracycline was mainly linked to the presence of SNPs in relevant sites, antibiotic resistance genes and an OmpF porin, leading to important changes in the protein structure.

[Proteomic applications in the Clinical Microbiology laboratory]

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is rapidly becoming a new routine resource in Clinical Microbiology laboratories. Its usefulness for bacterial identification is now generally accepted, although there is still some reluctance as regards specific bacterial groups and some other microorganisms, such as moulds. There are other potential applications of this technology in Clinical Microbiology, which are beginning to be developed. A review is presented on the current data on the identification of microorganisms, including the most problematic groups, such as mycobacteria, anaerobic bacteria and moulds. We also analyse its applications for direct sample identification, its impact on pathogenic characteristics of microorganisms, and its potential epidemiological applications. Finally, we review the studies published on its applications for determining antimicrobial susceptibility, and its applications on amplicons, instead of microorganism protein extracts.

Advances in mass spectrometry for the identification of pathogens

Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.

Analysis of the contribution of molecular mechanisms into formation of gonoccocal resistance to tetracycline

We applied complex genetic analysis for evaluation of tetracycline-resistance markers in 129 clinical strains of Neisseria gonorrhoeae from Central, Privolzhskii, and Siberian regions. For detection of mutations in rpsJ gene and MtrRCDE locus we first used minisequence reaction followed by identification of products by MALDI-TOF mass spectrometry. The incidence of detection of resistance markers among the analyzed strains were: tetM--3.1%, mutations in genes rpsJ--82.2%, penB--62.8%, and mtrR--54.3%. The analyzed genetic markers were not detected in 17.5% strains. tetM gene was detected in only 12.5% strains from the Central Region. No differences were revealed in regional distribution of other genotypes. Genotypes tetM(pres), rpsJ(mut), mtrR(mut), and rpsJ(mut), penB(mut), mtrR(mut) reliably predict tetracycline resistance. Microbiological and genetic testing of tetracycline resistance yielded similar results.

Direct evaluation of drug resistance parameters in gonococcus

We carried out complex genetic analysis of clinical samples containing N. gonorrhoeae DNA, the genotype and profile of drug resistance of this agent were evaluated. Changes in genes responsible for the formation of N. gonorrhoeae resistance to penicillins, fluoroquinolones, and spectinomycin were detected during minisequencing with subsequent MALDI-TOF mass spectrometry. The sensitivity of gonococcus was evaluated directly in the clinical sample without culturing.

Mass-spectrometry based minisequencing method for the rapid detection of drug resistance in Mycobacterium tuberculosis

A MALDI TOF MS based minisequencing method has been developed and applied for the analysis of rifampin (RIF)- and isoniazid (INH)-resistant M. tuberculosis strains. Eight genetic markers of RIF resistance-nucleotide polymorphisms located in RRDR of rpoB gene, and three of INH resistance including codon 315 of katG gene and -8 and -15 positions of the promoter region of fabG1-inhA operon were worked out. Based on the analysis of 100 M. tuberculosis strains collected from the Moscow region in 1997-2005 we deduced that 91% of RIF-resistant and 94% of INH-resistant strains can be identified using the technique suggested. The approach is rapid, reliable and allows to reveal the drug resistance of M. tuberculosis strains within 12 h after sample isolation.

Molecular characteristics of rifampicin- and isoniazid-resistant Mycobacterium tuberculosis isolates from the Russian Federation

OBJECTIVES

Three Mycobacterium tuberculosis genetic loci--rpoB and katG genes and the fabG1(mabA)-inhA operon promoter region--were studied to reveal the mutations associated with rifampicin and isoniazid resistance.

METHODS

Four hundred and twelve isolates of M. tuberculosis from different regions of the Russian Federation were collected during 1997-2005. A matrix-assisted laser-desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS)-based minisequencing method was used for the detection of mutations.

RESULTS

Thirteen different variants of single mutations in codons 533, 531, 526, 516, 513 and 511 of the rifampicin resistance-determining region of the rpoB gene as well as the TTG insertion in the 514a position were found among the rifampicin-resistant isolates. Single nucleotide substitutions in codons 531, 526 and 516 (64.8%, 10.3% and 7.7%, respectively) were the most prevalent mutations. Codon 526 was shown to be the most variable of all. No mutations were detected in rpoB genes for 29 (10.7%) of the rifampicin-resistant isolates. 76.9% of the isoniazid-resistant isolates carried single mutations in codon 315 of the katG gene. For another 12.9% of them, double mutations in the katG gene and the fabG1(mabA)-inhA promoter region were revealed. No mutations were detected in 8.2% of the isoniazid-resistant isolates.

CONCLUSIONS

Molecular analysis of the loci of rpoB and katG genes and the inhA promoter region of 412 M. tuberculosis clinical isolates from various parts of the Russian Federation was carried out. The new MALDI-TOF MS-based method may be used for rapid and accurate monitoring of the spread of drug resistance.