Proposed nomenclature or classification changes for bacteria of medical importance: taxonomic update 5

Janda, J. Michael

doi:10.1016/j.diagmicrobio.2020.115047

Cited by 14 publications

(7 citation statements)

References 71 publications

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“…Microbiology taxonomy is in flux and many bacterial species have been newly described or have changed the genus in recent years ( Janda, 2020 ). It is hardly possible for any diagnostic database to be up to date at every moment in time.…”

Section: Discussionmentioning

confidence: 99%

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Cuénod

Foucault²,

Pflüger³

et al. 2021

Front. Cell. Infect. Microbiol.

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BackgroundAn accurate and timely identification of bacterial species is critical in clinical diagnostics. Species identification allows a potential first adaptation of empiric antibiotic treatments before the resistance profile is available. Matrix assisted Laser Desorption Ionization Time of Flight mass spectrometry (MALDI-TOF MS) is a widely used method for bacterial species identification. However, important challenges in species identification remain. These arise from (i) incomplete databases, (ii) close relatedness of species of interest, and (iii) spectral quality, which is currently vaguely defined.MethodsWe selected 47 clinically relevant bacterial isolates from 39 species, which can be challenging to identify by MALDI-TOF MS. We measured these isolates under various analytical conditions on two MALDI-TOF MS systems. First, we identified spectral features, which were associated with correct species identification in three different databases. Considering these features, we then systematically compared spectra produced with three different sample preparation protocols. In addition, we varied quantities of bacterial colony material applied and bacterial colony age.ResultsWe identified (i) the number of ribosomal marker peaks detected, (ii) the median relative intensity of ribosomal marker peaks, (iii) the sum of the intensity of all detected peaks, (iv) a high measurement precision, and (v) reproducibility of peaks to act as good proxies of spectral quality. We found that using formic acid, measuring bacterial colonies at a young age, and frequently calibrating the MALDI-TOF MS device increase mass spectral quality. We further observed significant differences in spectral quality between different bacterial taxa and optimal measurement conditions vary per taxon.ConclusionWe identified and applied quality measures for MALDI-TOF MS and optimized spectral quality in routine settings. Phylogenetic marker peaks can be reproducibly detected and provide an increased resolution and the ability to distinguish between challenging species such as those within the Enterobacter cloacae complex, Burkholderia cepacia complex, or viridans streptococci.

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Section: Discussionmentioning

confidence: 99%

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Cuénod

Foucault²,

Pflüger³

et al. 2021

Front. Cell. Infect. Microbiol.

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“…In summary, communication of prokaryotic taxonomic changes (in clinically relevant fashion) to our clinical colleagues may tremendously impact the care of patients. While published resources, such as Journal of Clinical Microbiology and other compendia (3,(16)(17)(18)(19)(20)(21)(22)(23), have sought to provide such updates, additional on-line resources can be of assistance. One such service, LPSN (List of Prokaryotic Names with Standing in Nomenclature) (bacterio.net), does provide notations of whether a given taxonomic designation has been "validly" or "nonvalidly" named.…”

Section: Discussionmentioning

confidence: 99%

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019

Munson

Carroll

2021

J Clin Microbiol

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Knowledge of novel prokaryotic taxa discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae. Future efforts to ascertain clinical relevance for many of these changes may be augmented by a Document Development Committee that has been appointed by the Clinical and Laboratory Standards Institute.

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“…We took the Taylor et al list [9] as a starting point, and added year of description for each species, removed not validly described species (i.e. those not recognized by the ICNP) and checked for name changes using the 'List of Prokaryotic names with Standing in Nomenclature' (LPSN) (https://lpsn.dsmz.de/; accessed June-November 2021) [15], as well as taxonomic updates published in [17][18][19][20][21][22][23][24] (Fig. 1a).…”

Section: Search Strategymentioning

confidence: 99%

A comprehensive list of bacterial pathogens infecting humans

et al. 2022

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There exists an enormous diversity of bacteria capable of human infection, but no up-to-date, publicly accessible list is available. Combining a pragmatic definition of pathogenicity with an extensive search strategy, we report 1513 bacterial pathogens known to infect humans described pre-2021. Of these, 73 % were regarded as established (have infected at least three persons in three or more references) and 27 % as putative (fewer than three known cases). Pathogen species belong to 10 phyla and 24 classes scattered throughout the bacterial phylogeny. We show that new human pathogens are discovered at a rapid rate. Finally, we discuss how our results could be expanded to a database, which could provide a useful resource for microbiologists. Our list is freely available and archived on GitHub and Zenodo and we have provided walkthroughs to facilitate access and use.

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Proposed nomenclature or classification changes for bacteria of medical importance: taxonomic update 5

Cited by 14 publications

References 71 publications

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Factors Associated With MALDI-TOF Mass Spectral Quality of Species Identification in Clinical Routine Diagnostics

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019

A comprehensive list of bacterial pathogens infecting humans

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