A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia

Asare, Paul Tetteh; Lee, Chi-Hsien; Hürlimann, Vera; Teo, Youzheng; Cuénod, Aline; Akduman, Nermin; Gekeler, Cordula; Afrizal, Afrizal; Corthesy, Myriam; Kohout, Claire; Thomas, Vincent; Wouters, Tomás de; Greub, Gilbert; Clavel, Thomas; Pamer, Eric G.; Egli, Adrian; Maier, Lisa; Vonaesch, Pascale

doi:10.3389/fmicb.2023.1104707

Cited by 8 publications

(5 citation statements)

References 37 publications

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“…To maintain the extensibility of the application, the HDF5 file panel was created by storing the averaged spectra of each dataset, their annotation, the parameters used and their intensity matrix. This module will be helpful for the future construction of a reference MS spectra database which will be used for specimen identification by spectral matching [43].…”

Section: Discussionmentioning

confidence: 99%

MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra

Ben Hamouda,

Estellon,

Himet

et al. 2024

Preprint

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In the early 2000s, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) emerged as a performant and relevant tool for identifying micro-organisms. Since then, it has become practically essential for identifying bacteria in microbiological diagnostic laboratories. In the last decade, it was successfully applied for arthropod identification allowing to distinguish vectors from non-vectors of infectious diseases. However, identification failures are not rare, hampering it widely use. Failure is generally attributed either to the absence of respective counter species MS spectra in the database, or to the insufficient quality of query MS spectra (i.e. lower intensity and diversity of MS peaks detected). To avoid matching errors due to non-compliant spectra, the development of a strategy for detecting and excluding outlier MS profiles became compulsory. To this end, we created MSProfileR, an R package leading to a bioinformatics tool through a simple installation, integrating the control quality system of MS spectra and an analysis pipeline including peak detection and MS spectra comparisons. MSProfileR can also add metadata concerning the sample that the spectra are derived from. MSProfileR has been developed in the R environment and offers a user-friendly web interface using the R Shiny framework. It is available on Microsoft Windows as a web browser application by simply navigation using the link of the package on the Github. MSProfileR is therefore accessible to non-computer specialists and is freely available to the scientific community. We evaluated MSProfileR using two datasets including exclusively MS spectra from arthropods. In addition to coherent sample classification, outlier MS spectra were detected in each dataset confirming the value of MSProfileR.

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Section: Discussionmentioning

confidence: 99%

MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra

Ben Hamouda,

Estellon,

Himet

et al. 2024

Preprint

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“…The species were inoculated from frozen stocks into liquid culture media and passaged twice (1:100) overnight to ensure robust growth. The purity and identity of the species was regularly verified via sequencing of the 16S rRNA gene and/or MALDI TOF mass spectrometry (MS) 45 .…”

Section: Discussionmentioning

confidence: 99%

Non-antibiotic drugs break colonization resistance against pathogenicGammaproteobacteria

Grießhammer,

de la Cuesta-Zuluaga,

Zahir

et al. 2023

Preprint

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SummaryNon-antibiotic drugs can alter the composition of the gut microbiome, with largely undefined implications for human health. Here we compared the susceptibility of commensal and pathogenic bacteria to non-antibiotic drugs and found that pathogens show higher drug resistance, which could favor their expansion after treatment. We then developed a model system to screen for drug-microbiome interactions that increase the risk of enteropathogenic infections. Approximately 35% of the >50 drugs we tested increased the abundance ofSalmonellaTyphimurium in synthetic and human stool-derived microbial communities. This was due to direct effects of non-antibiotics on individual commensals, altered microbial interactions within communities and the potential ofSalmonellato exploit different metabolic niches. Non-antibiotic drugs that favoredSalmonellaexpansionin vitroalso promoted other enteric pathogens and increasedSalmonellaloads in gnotobiotic and conventional mice. These findings may inform future strategies to control pathogen proliferation and to assess individual microbiota-drug-pathogen risks for infection.

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“…Each colony on the plate is treated with 1μl of 25% formic acid and subsequently with 1μl of α-Cyano-4-hydroxycinnamic (CHAC) matrix. After sample preparation, the plate is loaded into a Microflex MALDI-TOF instrument for spectra measurement (Bruker Daltonics) and subsequent identification [43].…”

Section: Methodsmentioning

confidence: 99%

Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation

Dommann,

Keiser,

Garneau

et al. 2024

Preprint

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Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challenging in vitro resulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.

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A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia

Cited by 8 publications

References 37 publications

MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra

MSProfileR: An Open-Source Software for Quality Control of MALDI-TOF Spectra

Non-antibiotic drugs break colonization resistance against pathogenicGammaproteobacteria

Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation

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