MALDI-TOF MS protein fingerprinting of mixed samples

Sample preparation and culture condition effects on MALDI-TOF MS identification of bacteria: A review

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI-TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI-TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements.

Genomic Features and Molecular Function of a Novel Stress-Tolerant Bacillus halotolerans Strain Isolated from an Extreme Environment

Simple Summary

The Qinghai–Tibet Plateau is known as the “third pole of the world”. Due to the extreme geographical location, Qinghai–Tibet Plateau has unique ecosystems characterized by oxygen deficiency, low temperature, high salinity and alkalinity. We carried out the current study to explore the excellent extremophilic Bacillus strains via potential stress resistance as well as biocontrol properties in the Qinghai–Tibet Plateau. We found a Bacillus halotolerans strain with a promising ability to withstand harsh environments and which also exhibits an optimistic biocontrol activity against plant pathogens. We revealed the whole genome sequencing and its taxonomic position and elucidated its molecular functions that were responsible for enhancing stress tolerance as well as suppressing plant pathogens at the genetic level. Lastly, we identified this strain harbored the specific genes associated with stresses resistance, biocontrol function, and can be used as a biological agent in the agriculture field.

Abstract

Due to its topographical position and climatic conditions, the Qinghai–Tibet Plateau possesses abundant microorganism resources. The extremophilic strain KKD1 isolated from Hoh Xil possesses strong stress tolerance, enabling it to propagate under high salinity (13%) and alkalinity (pH 10.0) conditions. In addition, KKD1 exhibits promising biocontrol activity against plant pathogens. To further explore these traits at the genomic level, we performed whole-genome sequencing and analysis. The taxonomic identification according to the average nucleotide identity based on BLAST revealed that KKD1 belongs to Bacillus halotolerans. Genetic screening of KKD1 revealed that its stress resistance mechanism depends on osmotic equilibrium, membrane transportation, and the regulation of ion balance under salt and alkaline stress. The expression of genes involved in these pathways was analyzed using real-time quantitative PCR. The presence of different gene clusters encoding antimicrobial secondary metabolites indicated the various pathways by which KKD1 suppresses phytopathogenic growth. Moreover, the lipopeptides surfactin and fengycin were identified as being significant antifungal components of KKD1. Through comparative genomics analysis, we noticed that KKD1 harbored specific genes involved in stress resistance and biocontrol, thus providing a new perspective on the genomic features of the extremophilic Bacillus species.

Detection of Intrinsically Resistant Candida in Mixed Samples by MALDI TOF-MS and a Modified Naïve Bayesian Classifier

MALDI-TOF MS is one of the major methods for clinical fungal identification, but it is currently only suitable for pure cultures of isolated strains. However, multiple fungal coinfections might occur in clinical practice. Some fungi involved in coinfection, such as Candida krusei and Candida auris, are intrinsically resistant to certain drugs. Identifying intrinsically resistant fungi from coinfected mixed cultures is extremely important for clinical treatment because different treatment options would be pursued accordingly. In this study, we counted the peaks of various species generated by Bruker Daltonik MALDI Biotyper software and accordingly constructed a modified naïve Bayesian classifier to analyze the presence of C. krusei and C. auris in simulated mixed samples. When reasonable parameters were fixed, the modified naïve Bayesian classifier effectively identified C. krusei and C. auris in the mixed samples (sensitivity 93.52%, specificity 92.5%). Our method not only provides a viable solution for identifying the two highlighted intrinsically resistant Candida species but also provides a case for the use of MALDI-TOF MS for analyzing coinfections of other species.

Detection of SARS-CoV-2 Infection in Human Nasopharyngeal Samples by Combining MALDI-TOF MS and Artificial Intelligence

The high infectivity of SARS-CoV-2 makes it essential to develop a rapid and accurate diagnostic test so that carriers can be isolated at an early stage. Viral RNA in nasopharyngeal samples by RT-PCR is currently considered the reference method although it is not recognized as a strong gold standard due to certain drawbacks. Here we develop a methodology combining the analysis of from human nasopharyngeal (NP) samples by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with the use of machine learning (ML). A total of 236 NP samples collected in two different viral transport media were analyzed with minimal sample preparation and the subsequent mass spectra data was used to build different ML models with two different techniques. The best model showed high performance in terms of accuracy, sensitivity and specificity, in all cases reaching values higher than 90%. Our results suggest that the analysis of NP samples by MALDI-TOF MS and ML is a simple, safe, fast and economic diagnostic test for COVID-19.

Rapid direct detection of pathogens for diagnosis of joint infections by MALDI-TOF MS after liquid enrichment in the BacT/Alert blood culture system

Pathogen identification is a critical step during diagnosis of infectious diseases. Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF-MS) has become the gold standard for identification of microorganisms cultured on solid media in microbiology laboratories. Direct identification of microbes from liquid specimen, circumventing the need for the additional overnight cultivation step, has been successfully established for blood culture, urine and liquor. Here, we evaluate the ability of MALDI-TOF MS for direct identification of pathogens in synovial fluid after liquid enrichment in BacT/Alert blood culture bottles. Influence of synovial specimen quality on direct species identification with the MALDI BioTyper/Sepsityper was tested with samples inoculated from pretested native synovia with concomitant inoculation of blood or pus, or highly viscous fluid. Here, we achieved >90% concordance with culture on solid medium, and only mixed-species samples posed significant problems. Performance in routine diagnostics was tested prospectively on bottles inoculated by treating physicians on ward. There, we achieved >70% concordance with culture on solid media. The major contributors to test failure were the absence of a measurable mass signal and mixed-specimen samples. The Sepsityper workflow worked well on samples derived from BacT/Alert blood culture bottles inoculated with synovial fluid, giving concordant results to identification from solid media. Host remnant material in the inoculum, such as blood or pus, had no detrimental effect on identification score values of the BioTyper system after processing with the Sepsityper workflow, and neither had the initial viscosity of the synovial sample.