Quantification of recurrence risk based on number of adverse prognostic factors in women with stage I uterine endometrioid carcinoma

Objective: The goal was to develop an updated model to predict the risk of recurrence, based on the number of adverse pathologic features in women with International Federation of Gynecology and Obstetrics stage I uterine endometrioid carcinoma, who did not undergo any adjuvant treatment. Material and Methods: Women at a single center who underwent surgical staging without adjuvant therapy between January 1990 and December 2019 were included. Cox proportional hazards model was used to identify independent predictors of relapse free survival (RFS). Prognostic groups were then created based on the number of independent predictors of recurrence that were identified (0, 1, or 2-3 risk factors). Overall survival (OS) and disease specific survival (DSS) were also calculated for each group. Results: In total 1133 women were eligible for inclusion. Median follow-up was 84 months. Independent prognostic factors of recurrence included: age ≥60; grade 2 or 3 differentiation; and presence of lymphovascular space invasion (LVSI). Due to the small number of patients with either 2 or 3 risk factors, these groups were combined into one (group 2/3). Isolated vaginal cuff recurrence was the most common site of recurrence in all study groups (2%, 7%, and 17% for groups 0, 1, and 2/3, respectively). Five-year RFS rates were 96%, 85%, and 57% for groups 0, 1, and 2/3 (p<0.01), respectively. Five-year DSS rates were 99%, 96%, and 85% and 5-year OS rates were 94%, 85%, and 62% (p<0.01), respectively. Conclusion: We identified older age, high grade, and presence of LVSI as independent predictors of recurrence for women with stage I uterine endometrioid carcinoma. Using these prognostic factors, recurrence risk can be quantified for individual patients, and these factors can be used in deciding the appropriate adjuvant management course.

Amycolatopsis umgeniensis sp. nov., isolated from soil from the banks of the Umgeni River in South Africa.

A novel member of the genus Amycolatopsis was isolated from soil collected from the banks of the Umgeni River, KwaZulu Natal province, South Africa. The strain, designated UM16(T), grouped with the type strains of Amycolatopsis alba, Amycolatopsis coloradensis and Amycolatopsis thailandensis by 16S rRNA gene based phylogeny. Genetic distance values, based on the gyrB and recN genes, between strain UM16(T) and its closest relatives were all above the threshold values of 0.02 and 0.04, respectively, that have been proposed to distinguish Amycolatopsis type strains. DNA-DNA hybridisation experiments confirmed that strain UM16(T) represents a unique genomic species, sharing 18.4 ± 5.1, 16.2 ± 1.8 and 45.8 ± 8.9 % DNA relatedness to the type strains of A. alba, A. coloradensis and A. thailandensis, respectively. The physiological, phylogenetic and DNA-relatedness data support the description of strain UM16(T) as the type strain of a novel species, for which the name Amycolatopsis umgeniensis sp. nov. is proposed (= DSM 45272(T) = NRRL B-24724(T)).

Evaluation of the use of recN sequence analysis in the phylogeny of the genus Amycolatopsis.

Partial recN gene sequences (>1 kb) were obtained from 35 type strains of the genus Amycolatopsis. Phylogenetic trees were constructed to determine the effectiveness of using this gene to predict taxonomic relationships within the genus. The use of recN sequence analysis as an alternative to DNA-DNA hybridization (DDH) for distinguishing closely related species was also assessed. The recN based phylogeny mostly confirmed the conventional 16S rRNA and gyrB gene-based phylogenies and thus provides further support for these phylogenetic groupings. As is the case for the gyrB gene, pairwise recN sequence similarities cannot be used to predict the DNA relatedness between type strains but the recN genetic distance can be used as a means to assess quickly whether an isolate is likely to represent a new species in the genus Amycolatopsis. A recN genetic distance of >0.04 between two Amycolatopsis strains is proposed to provide a good indication that they belong to different species (and that polyphasic taxonomic characterization of the unknown strain is worth undertaking).

Nocardia rhamnosiphila sp. nov., isolated from soil.

In this study two actinomycete strains were isolated in Cape Town (South Africa), one from a compost heap (strain 202GMO(T)) and the other from within the fynbos-rich area surrounded by the horseracing track at Kenilworth Racecourse (strain C2). Based on 16S rRNA gene sequence BLAST analysis, the strains were identified as members of the genus Nocardia. Phylogenetic analysis showed that the strains clustered together and are most closely related to Nocardia flavorosea NRRL B-16176(T), Nocardia testacea JCM 12235(T), Nocardia sienata IFM 10088(T) and Nocardia carnea DSM 43397(T). This association was also supported by gyrB based phylogenetic analysis. The results of DNA-DNA hybridization and physiological tests allowed genotypic and phenotypic differentiation of both strains 202GMO(T) and C2 from related species. However, their high DNA relatedness showed that they belong to the same species. Strain 202GMO(T) was selected as the type strain to represent this novel species, for which the name Nocardia rhamnosiphila is proposed (=DSM 45147(T)=NRRL B-24637(T)).

Granule formation mechanisms within an aerobic wastewater system for phosphorus removal.

Granular sludge is a novel alternative for the treatment of wastewater and offers numerous operational and economic advantages over conventional floccular-sludge systems. The majority of research on granular sludge has focused on optimization of engineering aspects relating to reactor operation with little emphasis on the fundamental microbiology. In this study, we hypothesize two novel mechanisms for granule formation as observed in three laboratory scale sequencing batch reactors operating for biological phosphorus removal and treating two different types of wastewater. During the initial stages of granulation, two distinct granule types (white and yellow) were distinguished within the mixed microbial population. White granules appeared as compact, smooth, dense aggregates dominated by 97.5% "Candidatus Accumulibacter phosphatis," and yellow granules appeared as loose, rough, irregular aggregates with a mixed microbial population of 12.3% "Candidatus Accumulibacter phosphatis" and 57.9% "Candidatus Competibacter phosphatis," among other bacteria. Microscopy showed white granules as homogeneous microbial aggregates and yellow granules as segregated, microcolony-like aggregates, with phylogenetic analysis suggesting that the granule types are likely not a result of strain-associated differences. The microbial community composition and arrangement suggest different formation mechanisms occur for each granule type. White granules are hypothesized to form by outgrowth from a single microcolony into a granule dominated by one bacterial type, while yellow granules are hypothesized to form via multiple microcolony aggregation into a microcolony-segregated granule with a mixed microbial population. Further understanding and application of these mechanisms and the associated microbial ecology may provide conceptual information benefiting start-up procedures for full-scale granular-sludge reactors.

Phylogenetic analysis of actinobacterial populations associated with Antarctic Dry Valley mineral soils.

Despite the apparent severity of the environmental conditions in the McMurdo Dry Valleys, Eastern Antarctica, recent phylogenetic studies conducted on mineral soil samples have revealed the presence of a wide diversity of microorganisms, with actinobacteria representing one of the largest phylotypic groups. Previous metagenomic studies have shown that the majority of Antarctic actinobacterial populations are classified as 'uncultured'. In this study, we assessed the diversity of actinobacteria in Antarctic cold desert soils by complementing traditional culture-based techniques with a metagenomic study. Phylogenetic analysis of clones generated with actinobacterium- and streptomycete-specific PCR primers revealed that the majority of the phylotypes were most closely related to uncultured Pseudonocardia and Nocardioides species. Phylotypes most closely related to a number of rarer actinobacteria genera, including Geodermatophilus, Modestobacter and Sporichthya, were also identified. While complementary culture-dependent studies isolated a number of Nocardia and Pseudonocardia species, the majority of the cultured isolates (> 80%) were Streptomyces species--although phylotypes affiliated to the genus Streptomyces were detected at a low frequency in the metagenomic study. This study confirms that Antarctic Dry Valley desert soil harbours highly diverse actinobacterial communities and suggests that many of the phylotypes identified may represent novel, uncultured species.

Actinomadura napierensis sp. nov., isolated from soil in South Africa.

An actinomycete, strain B60(T), was isolated from a soil sample in Napier, Western Cape province of South Africa. Based on 16S rRNA gene sequence analysis and chemotaxonomy, strain B60(T) was identified as a member of the genus Actinomadura. Strain B60(T) produced an antibiotic with activity against Escherichia coli, Enterococcus faecium and Mycobacterium aurum, but not against Mycobacterium tuberculosis. Significant differences in morphological and physiological characteristics indicate that strain B60(T) represents a novel species of the genus Actinomadura. The name Actinomadura napierensis sp. nov. is proposed. The type strain is B60(T) (=DSM 44846(T)=NRRL B-24319(T)).

Rapid identification of filamentous actinomycetes to the genus level using genus-specific 16S rRNA gene restriction fragment patterns.

A rapid method for identifying filamentous actinomycete genera was developed based on 16S rRNA gene restriction fragment patterns. The patterns were generated by using specific restriction endonucleases to perform in silico digestions on the 16S rRNA gene sequences of all validly published filamentous actinomycete species. The method was applied to identifying actinomycete isolates from soil. Amplified 16S rDNA of soil actinomycetes was restricted with selected endonucleases and electrophoresed on agarose gels. The restriction fragment patterns of the unknown isolates were easily compared to the established patterns. Significantly, the genus Streptomyces could be differentiated from all other actinomycete genera by using only four restriction endonucleases, Sau3AI, AsnI, KpnI and SphI. This could be achieved in a time period of as little as a week, following PCR-template DNA isolation by a simple method. The identification method allowed unknown, non-Streptomyces soil isolates to be identified to a genus or small subgroup of genera. The genera in these subgroups could, in some cases, be distinguished by virtue of colony-morphology differences.