#7: Moving targets: Recent changes in bacterial taxonomy of relevance to pharmaceuticals and healthcare products

Advances in metagenomics and other culture-independent methods have led to many taxonomic classifications of bacteria (such as Clostridium difficile becoming Clostridioides difficile) and the rate of change is rapid. Interest in these changes cuts across different disciplines. In this article, I’ve taken a look at a few that will impact the pharmaceutical microbiologist and others who have concerns with cleanroom-associated bacteria and other organisms that might be encountered in the fields of pharmaceuticals and healthcare products.

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One question the reader may have is ‘why should we care?’ To an extent many reclassifications have no impact or they are far removed from how we assess cleanrooms. However, the accurate identification and reporting of significant bacteria is important for understanding potential sources of origin of contamination; for understanding patterns of relatedness (the ‘holistic’ dimension of contamination control); and to understand organisms that are possibly proving to be challenging to disinfectants.

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Micrococcus luteus and ‘friends’

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Some species of the human skin associated bacterium Micrococcus have been assessed as being closely related and a Micrococcus luteus group has been formed, based on studies utilising genome-sequencing techniques. This is of importance given that most surveys of cleanroom microbiota place M. luteus as the most common contaminant recovered, irrespective of the global location of the cleanroom. Micrococcus aloeverae, Micrococcus endophyticus , Micrococcus luteus and Micrococcus yunnanensis are phenotypically and genotypically closely related, and together comprise the M. luteus group.

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From Propionibacterium acnes to Cutibacterium acnes

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Propionibacterium acnes was reclassified in 2016 as Cutibacterium acnes. This organism has an association with the scalp and hair follicles, being found in particular abundance in sebaceous glands. There are three subspecies of C. acnes: C. acnes subsp. acnes; C. acnes subsp. defendens, and C. acnes subsp. elongatum. Where there is a degree of human intervention in Grade A and B, including C. acnes in the panel of organisms used to qualify the sterility test is a sensible move.

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The reclassification was part of a change that led to the genus Propionibacterium being

re-classified into three genera: Acidipropionibacterium, Cutibacterium, and Pseudopropionibacterium.

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Disinfectant efficacy testing: Enterobacter to Klebsiella

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The organism Enterobacter aerogenes is sometimes used in disinfectant efficacy testing as a representative Gram-negative bacterium. E. aerogenes was reclassified as Klebsiella

aerogenes following whole genome sequencing (WGS) in 2017.

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Skin deep: Mammaliicoccus

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Some of the common skin-associated Staphylococci have been placed in a new genus called Mammaliicoccus. Reclassification includes Staphylococcus sciuri and S. lentus. M. sciuri and M. lentus are positive for the presence of cytochrome oxidase using an oxidase test.

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Staphylococci-like

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Other Staphylococci have been reclassified in recent years through the development ton new genera as the results of DNA-DNA hybridisation. Stumbling across these may cause confusion and may be reassuring to know they are, from the cleanroom perspective, ‘staphs’.

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The newer genera are: Gemella, Macrococcus, Salinicoccus, Jeotgalicoccus, Salinicoccus, Aliicoccus, Abyssicoccus, Corticicoccus, and Auricoccus. These sit within the family Staphylococcaceae.

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A related change is with the assignment of Nosocomiicoccus as a member of the family Staphylococcaceae.

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Bacillus diversification

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The development of Bacillus species has been considerable across the past two decades. In the past couple of years six new genera of Bacillus species have emerged: Peribacillus, Cytobacillus, Mesobacillus, Neobacillus, Metabacillus, and Alkalihalobacillus.

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Other phylogenetically similar ‘Bacillus’ organisms are: Brevibacillus, Geobacillus, Lysinibacillus, Paenibacillus, Alicyclobacillus, Alkalicoccus, Aneurinibacillus, Gracilibacillus, Hydrogenibacillus, Sporosarcina, Ureibacillus, Solibacillus, and Virgibacillus.

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The fundamental concern for the contamination control specialist is that each member of the list is an endospore former.

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The above represent just a few examples of how microbial taxonomy continues to change at a very rapid rate in this era of molecular diagnostics including whole genome sequencing.

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Further reading:

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1.?????Oren A and Garrity GM. Notification that new names of prokaryotes, new combinations and new?taxonomic opinions have appeared in volume 66, part 11, of the IJSEM. Int J Syst Evol Microbiol. 2017;67(2):179-182

2.?????Fenwick AJ, Carroll KC. Practical problems when incorporating rapidly changing microbial taxonomy into clinical practice. Clinical Chemistry and Laboratory Medicine (CCLM). 2019;57(9):e238-e240

3.?????Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 70, part 10 of the IJSEM. Int J Syst Evol Microbiol. 2021;71(1)

4.?????E Munson, KC Carroll. An update on the novel genera and species and revised taxonomic status of bacterial organisms described in 2016 and 2017. J Clin Microbiol, 57 (2019), pp. e01181-e01218

5.?????A Oren, GM Garrity. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol, 68 (2018), pp. 2130-2133

6.?????CS Kraft, AJ McAdam, KC Carroll. A rose by any other name: practical updates on microbial nomenclature for clinical microbiology. J Clin Microbiol, 55 (2017), pp. 3-4