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PubMed2026

Stenotrophomonas maltophilia in the Antimicrobial Resistance Era: Species-Complex Taxonomy, Pathogenesis, Evolving Therapeutic Priorities, and Genomic Surveillance.

Stenotrophomonas maltophilia is a globally distributed, aerobic, non-fermenting Gram-negative bacillus increasingly recognized as an opportunistic pathogen in hospitalized and immunocompromised patients. Clinical interpretation is challenging because respiratory and device-associated isolates may represent colonization, polymicrobial infection, or true invasive disease. Recent genomic studies further suggest that organisms historically identified as S. maltophilia comprise a genetically diverse species complex, with implications for epidemiology, virulence, resistance surveillance, and susceptibility testing. Treatment is difficult because of biofilm formation, persistence in water-associated healthcare reservoirs, and intrinsic or acquired resistance mediated by L1 and L2 β-lactamases, multidrug efflux pumps, reduced permeability, mobile resistance determinants, and biofilm-associated tolerance. Current IDSA guidance identifies cefiderocol monotherapy as the preferred treatment for invasive S. maltophilia infection, whereas aztreonam-avibactam and agents such as trimethoprim-sulfamethoxazole, levofloxacin, and minocycline occupy alternative or combination-based roles. Nevertheless, the therapeutic evidence base remains uneven, and clinical decisions should integrate infection severity, source control, susceptibility findings, pharmacokinetic/pharmacodynamic (PK/PD) exposure, toxicity, infection site, and host-related factors. This review summarizes advances in taxonomy, epidemiology, pathogenesis, diagnostics, resistance, treatment, infection prevention, and genomic surveillance, and highlights the need for standardized identification, validated breakpoints, prospective comparative-effectiveness studies, and pragmatic or adaptive trial designs.

L1 β-lactamase↗
PubMed1979

[Immunological characteristics of the protein antigens of the family Neisseriaceae. II. The importance of an immunochemical analysis of the protein complexes for a study of taxonomy problems].

The study of antigenic interrelations in the family Neisseriaceae resulted in the isolation of 2 main immunologically separated variants of protein complexes: the first variant was characteristic of nonpathogenic and pathogenic species of the genus Neisseria as well as of 7 taxonomically undefined Neisseria species (N. lactamicus, N. cuniculi, N. ellongata, N. ovis, N. animalis, N. cinerea, N. canis) and Gemella haemolysans; the second variant was represented by the genera Branhamella and Acinetobacter. N. caviae and 3 out of 14 Neisseria strains of undefined species had no common antigens with the genera Neisseria and Branhamella. The importance of the immunotyping of protein complexes for studying the problems connected with the taxonomy of the family Neisseriaceae was considered.

Antigens, Bacterial↗
PubMed1975

Arenavirus taxonomy: a review.

Despite a late beginning, the construction of the arenavirus taxon and its placement in the scheme of the International Committee on Taxonomy of Viruses has now been completed. The bringing together of the member viruses has already provided valuable indications of promising laboratory and field study approaches; in the future this classification will contribute further to our understanding of the natural history and disease processes of the human pathogens of the group.

Arboviruses↗
PubMed1979

[Nosology, epidemiology and bacteriological taxonomy: salmonella infections as an example (author's transl)].

Salmonella infections are discussed as an example of the interdependence of the classification of infectious diseases on the one hand and the taxonomy of bacteria on the other. The term paratyphoid was first created as a name for a disease but was later turned into a common name for the cause and then refined into a specific epitheton of a species of bacteria. It was difficult to create terms for pathology as long as a reliable differentiation of related species of bacteria was not possible, so both a typhoid and an enteric form of paratyphoid fever were referred to, superimposing the clinical differentiation of typhoid fevers and food poisoning (enteritis infectiosa). Epidemiology and bacteriology cannot expect their classifications to determine the classification of bacteria on the level of genus and subgenus, but systematic bacteriology should not conserve or create species and subspecies that are unnecessary for applied medical bacteriology. The needs of epidemiology usually require identification and determination of serovar, biovar and phagovar of the individual strain, but for pathology it is important to classify series of strains on the basis of certain combinations of serovars, biovars, and phagovars as special forms.

Humans↗
PubMedDate not supplied

[Numerical taxonomy and employment of the computer in diagnostic medical microbiology (author's transl)].

The institution is proposed of a expert committee to study and introduce new methods to allow a better diffusion of numerical taxonomy among clinical bacteriologists. Computers are nowadays rather diffuse devices that can contribute to bring order in the field of the classification of microorganisms and to introduce new keys for the identification of isolates from pathological materials.

Bacteria↗
PubMed1978

Gas-liquid-chromatography of trimethylsilyl derivatives from whole cell methanolysates of Leptospira : preliminary evaluation of its applicability to the taxonomy of the genus.

Gas-liquid-chromatography of trimethylsilyl derivatives from whole cell methanolysates was investigated as a supplmentary means for taxonomical classification within the genus Leptospira. Reproducibility of this technique was assessed through the peak height variations occurring in chromatograms of strain Patoc 1, serotype patoc, when samples either from the same or different batches of culture were used. From each chromatogram seven peaks were selected. Their heights were measured and calculated as percent values of the seven peaks total height. The values of relative standard deviation reported show that the reproducibility of this technique lies within the usual limits of biological methods. Four out of seven different serotypes analyzed gave elution patterns dissimilar enough to allow a clear distinction among them by the simple visual examination. Differentiation of the other three had to be done comparing the relative heights of the seven selected peaks. One not yet classified new strain was submitted to this technique; results seemed to confirm available serological information about it. Data reported encourage further research in order to evaluate the potential of GLC as an useful aid in the taxonomy of genus Leptospira.

Chromatography, Gas↗
PubMedDate not supplied

[Thermotolerance of the Candida. Relationships with ecology, pathology and taxonomy (author's transl)].

An investigation on the maximum temperature of growth is reported on 477 strains of Candida, 23 species and 1 variety, including species actually not identied as Candida, but well known under that generic name in medical and veterinary mycology. C. pseudotropicalis is the most thermotolerante species (49 degrees), C. albicans coming only in second position (42 degrees -48 degrees); the less thermotolerante species is C. humicola (29 degrees), but the less thermotolerante strain is a C. sake (26 degrees -32 degrees). The relationships between the maximum temperature of growth and the ecology, the pathology and the taxonomy are discuted. In the group C. krusei a linkage between the maximum temperature and the utilisation of a sugar has been established, auguring a more close relation between the thermic characteristic and the enzymologic equipment of a yeast.

Candida↗
PubMed1976

Methodologic problems of common terminology, measurement, and classification. 11. Modifications and new approaches to taxonomy in long-term care: advantages and limitations of the ICD.

The primary advantage of an internationally accepted classification of diseases is that data from different countries and parts of the world can be compared and even pooled. Two basic conditions have to be fulfilled if the classification is to be used by a heterogeneous group of users and the data are to be compared: there must exist significant agreement on the content of categories, and the categories must be used in the agreed sense. A brief description is given of a WHO project that has attempted to satisfy these two conditions in the field of mental disorders. Additionally, taxonomy in long-term care requires that a classification should 1) be multiaxial and include certain nondisease as well as disease factors that affect treatment and outcome; 2) be a classification of individuals rather than of diseases and reflect the presence of multiple conditions and degrees of severity; 3) allow linkage of episodes of illness and care in the same individual; 4) be suitable for use by nonmedical personnel, who often play a decisive role in long-term care; and 5) be accompanied by glossaries giving operational terms suitable for reliability and validity tests.

Classification↗
PubMed2026

Two Saccharopolyspora isolates from archaeological excavation sites: polyphasic taxonomy, biosynthetic potential, bioactivity profiling and description of Saccharopolyspora antiqui sp. nov.

Archaeological excavation sites represent underexplored microbial habitats with the potential to recover taxonomically and biotechnologically valuable actinomycetes. In this study, two Saccharopolyspora strains, 5N708T and 5N102, were isolated from soil samples collected from the Gaziantep-Doliche-Dülük and Bitlis-Ahlat-Selçuklu Cemetery archaeological excavation sites in Türkiye. A polyphasic taxonomic approach, including 16S rRNA gene sequencing, phylogenetic and phylogenomic analyses, average nucleotide identity, digital DNA-DNA hybridization, phenotypic characterization, and chemotaxonomic analyses, showed that strain 5N708T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora antiqui sp. nov. is proposed, whereas strain 5N102 was assigned to Saccharopolyspora elongata. Both isolates were further evaluated for their antimicrobial, antioxidant, and cytotoxic activities, and their biosynthetic potential was investigated by genome mining. Both strains showed activity against Staphylococcus aureus, with strain 5N708T producing the larger inhibition zone. Strain 5N102 exhibited markedly stronger antioxidant activity than strain 5N708T in radical scavenging, ferric reducing antioxidant power, and reducing power assays. In contrast, strain 5N708T showed more promising cytotoxic activity, with relative selectivity toward MIA PaCa-2 pancreatic cancer cells compared with HEK293 cells after prolonged incubation. Genome mining revealed multiple biosynthetic gene clusters in both isolates, supporting their capacity to produce secondary metabolites. These findings indicate that archaeological soils are promising reservoirs of taxonomically novel and biologically active Saccharopolyspora strains.

Saccharopolyspora↗
PubMed2022

Revisiting Papillomavirus Taxonomy: A Proposal for Updating the Current Classification in Line with Evolutionary Evidence.

Papillomaviruses infect a wide array of animal hosts and are responsible for roughly 5% of all human cancers. Comparative genomics between different virus types belonging to specific taxonomic groupings (e.g., species, and genera) has the potential to illuminate physiological differences between viruses with different biological outcomes. Likewise, extrapolation of features between related viruses can be very powerful but requires a solid foundation supporting the evolutionary relationships between viruses. The current papillomavirus classification system is based on pairwise sequence identity. However, with the advent of metagenomics as facilitated by high-throughput sequencing and molecular tools of enriching circular DNA molecules using rolling circle amplification, there has been a dramatic increase in the described diversity of this viral family. Not surprisingly, this resulted in a dramatic increase in absolute number of viral types (i.e., sequences sharing <90% L1 gene pairwise identity). Many of these novel viruses are the sole member of a novel species within a novel genus (i.e., singletons), highlighting that we have only scratched the surface of papillomavirus diversity. I will discuss how this increase in observed sequence diversity complicates papillomavirus classification. I will propose a potential solution to these issues by explicitly basing the species and genera classification on the evolutionary history of these viruses based on the core viral proteins (E1, E2, and L1) of papillomaviruses. This strategy means that it is possible that a virus identified as the closest neighbor based on the E1, E2, L1 phylogenetic tree, is not the closest neighbor based on L1 nucleotide identity. In this case, I propose that a virus would be considered a novel type if it shares less than 90% identity with its closest neighbors in the E1, E2, L1 phylogenetic tree.

Animals↗
PubMed1978

The taxonomy of binding sites in proteins.

Conservation of polypeptide fold and mode of ligand binding is frequently found within proteins of related function. Examples illustrating this phenomenon are taken from NAD linked enzymes, nucleotide binding proteins, polysaccharide binding proteins, heme binding proteins and enzymes with essential Fe--S complexes or zinc atoms.

Amino Acid Sequence↗
PubMed1978

Taxonomy of Leucochloridium sp. (Digenea) infecting Succinea pfeifferi Rossmässler, 1835.

The anatomical and morphological variability of sporocysts and metacercariae of Leucochloridium sp. recovered from natural infected Succinea pfeifferi Rossmässler collected in the Agdenes area. Norway (63 degrees 35'N, 9 degrees 45'E), was studied by light microscopy. The results are compared with five species from the Nearctic and Palearctic with known adult stage (L. variae McIntosh, 1932; L. fuscostriatum Robinson, 1947; L. perturbatum Pojmanska, 1969; L. subtilis Pojmanska, 1969; L. fuscum Rietschel, 1970) and nine species with unknown adult stage. In the larval stages no morphological taxonomical characters were found to separate Leucochloridium sp. as a species distinct from the five (and nine) species. The variability and validity of the characters used is discussed.

Animals↗
PubMed1978

Taxonomy of coagulase-negative staphylococci: a comparison of two widely used classification schemes.

In a comparative study 351 strains of Micrococcus subgroups 1-3 (Baird-Parker, 1963, 1965, 1974) were classified according to the Kloos and Schleifer scheme (1975b). The results showed that Micrococcus subgroups 1, 2 and 3 are heterogeneous groups in the Kloos and Schleifer scheme. Strains belonging to Micrococcus subgroups 1 and 2 were mostly classified by the Kloos and Schleifer criteria as Staphylococcus hominis, Micrococcus subgroup 3 strains from the skin as S. cohnii, while Micrococcus subgroup 3 strains from urinary infections were classified mainly as S. saprophyticus. The correlation of novobiocin resistant S. saprophyticus biotype III (Baird-Parker, 1974) with S. saprophyticus (Kloos and Schleifer, 1975a, 1975b) when isolated from urine, was 80%. Although the Kloos and Schleifer scheme provides more information about biochemical characters, doubts are expressed about the validity of some of the species so delineated.

Bacteriological Techniques↗
PubMed1979

Carbohydrate composition and taxonomy of Geotrichum, Trichosporon and allied genera.

The yeast-like genera Geotrichum and Trichosporon are heterogeneous and are related with anamorphs of both ascomycetous and basidiomycetous fungi. A rearrangement can be obtained using carbohydrate composition of intact cells, studied with the aid of gas-liquid chromatography. The genus Geotrichum is restricted to ascomycetous species with a dominance of galactomannans, whereas Trichosporon is reserved for basidiomycete-like, xylose-containing species. Consequently, some new combinations are introduced in both genera. Representatives of related genera are included for comparison: e.g. Dipodascus, Hyphophichia, Cryptococcus and Filobasidium.

Carbohydrates↗
PubMed1978

Physiological and biochemical contributions to the taxonomy of the genus Chlorella. XI. DNA hybridization.

1. DNA homology was studied in 12 Chlorella species. The DNA of 88 strains was hybridized with 3H-labelled DNA from C. fusca var. vacuolata 211-8 b and from C. vulgaris 211-8m. The results indicate that the genus Chlorella is a heterogenous taxon which consists of several groups of species. 2. The "C. fusca group" comprises C. fusca var. vacuolata, C. fusca var. rubescens, and C. zofingiensis. Within this group, C. zofingiensis appears to be more closely related to C. fusca var. vacuolata than is C. fusca var. rubescens. C. fusca var. fusca does not belong to this group of taxa. 3. The "C. vulgaris group" consists of C. vulgaris, C. sorokiniana, and C. saccharophila. There are several strains which seem to assume a position intermediate between C. vulgaris and C. saccharophila. C. protothecoides is not related to this group of species. 4. Several groups of strains of C. sorokiniana with different base compositions (guanine + cytosine content) of their DNA appear to belong to the same taxon. 5. In addition to C. fusca var. fusca and C. protothecoides, also C. luteoviridis, C. minutissima, C. kessleri, and C. homosphaera seem to have so little relationship with the other species that their assignment to the genus Chlorella appears questionable.

Chlorella↗