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We investigated genetic, epidemiologic, and environmental factors contributing to positive Staphylococcus epidermidis joint cultures.
Retrospective cohort study with whole-genome sequencing (WGS).
We identified S. epidermidis isolates from hip or knee cultures in patients with 1 or more prior corresponding intra-articular procedure at our hospital.
WGS and single-nucleotide polymorphism–based clonality analyses were performed, including species identification, in silico multilocus sequence typing (MLST), phylogenomic analysis, and genotypic assessment of the prevalence of specific antibiotic resistance and virulence genes. Epidemiologic review was performed to compare cluster and noncluster cases.
In total, 60 phenotypically distinct S. epidermidis isolates were identified. After removal of duplicates and impure samples, 48 isolates were used for the phylogenomic analysis, and 45 (93.7%) isolates were included in the clonality analysis. Notably, 5 S. epidermidis strains (10.4%) showed phenotypic susceptibility to oxacillin yet harbored mecA, and 3 (6.2%) strains showed phenotypic resistance despite not having mecA. Smr was found in all isolates, and mupA positivity was not observed. We also identified 6 clonal clusters from the clonality analysis, which accounted for 14 (31.1%) of the 45 S. epidermidis isolates. Our epidemiologic investigation revealed ties to common aspirations or operative procedures, although no specific common source was identified.
Most S. epidermidis isolates from clinical joint samples are diverse in origin, but we identified an important subset of 31.1% that belonged to subclinical healthcare–associated clusters. Clusters appeared to resolve spontaneously over time, suggesting the benefit of routine hospital infection control and disinfection practices.
Background: Prosthetic joint infections (PJIs) are costly and cause increased morbidity and mortality for patients. Staphylococcus epidermidis is a common cause of both early postoperative and late-presenting PJIs. Although S. epidermidis is a normal part of the human skin microflora, its ability to form biofilm on implanted medical devices make it an important causative pathogen of PJIs. We investigated genetic, epidemiologic, and environmental factors contributing to S. epidermidis PJIs by performing whole-genome sequencing and clinical epidemiologic investigation of isolates collected from infected patients between 2017 and 2020. Methods: Patients with S. epidermidis isolated from a prosthetic joint that was placed at our orthopedic specialty hospital were identified using the microbiology laboratory records and electronic medical records. Whole-genome sequencing and single-nucleotide polymorphism (SNP)–based clonality analyses were performed using the epiXact service at Day Zero Diagnostics. These analyses included species identification, in silico MLST typing, phylogenomic analysis, as well as genotypic assessment of the prevalence of specific antibiotic resistance genes, virulence genes, and other relevant genes. For clonal isolates, additional reviews of surgical history and clinical data were performed. Results: In total, 62 S. epidermidis joint isolates were identified from 46 patients. Among these isolates, 52 were of sufficient purity to be used for genomic analysis (Fig. 1). A number of genes appeared in every isolate including sepA, smr, cap, sesB, sesG, and embp. Also, 6 S. epidermidis samples had a discrepancy between phenotypic resistance to oxacillin and the presence of the mecA resistance gene. We also identified 6 distinct clusters of isolates, all of which had SNP distances <10 base pairs (Fig. 2). Each cluster consisted of 2–4 patients. Cluster isolates accounted for 29.8% of all S. epidermidis prosthetic joint isolates. Most clonal isolates occurred in patients who were heavily exposed to different healthcare settings. Further epidemiologic investigation showed that some of these clonal isolates had ties to aspirations or procedures, whereas no clear connection could be determined for others. Conclusions:S. epidermidis isolated from clinical prosthetic joint samples contains a high degree of genetic resistance, including a mismatch between presence of mecA and phenotypic oxacillin resistance and genetic propensity for chlorhexidine resistance. Mupirocin resistance was not observed. Of all isolates, 29.8% belonged to multiple clusters, confirming hospital spread of this commensal organism in some cases.
Oxygen isotope stage 3 (OIS3), an interstade between approximately 60,000 and 25,000 yr B.P., presents an ideal opportunity to compare high-resolution climate simulations with the geologic record. To facilitate this comparison, the results of a mesoscale climate model (RegCM2) embedded in the GENESIS GCM are utilized to drive a vegetation model (BIOME 3.5). The BIOME output is then compared with OIS3 compilations derived from pollen. The simulated biomes agree well with the pollen-based biomes in southern Europe; however, disagreements occur in the northern part of the domain. The most striking mismatch involves the distribution of tundra. The models fail to have tundra extend to its observed position as far south as 50°N in central Europe during OIS3. The model also fails to have permafrost extend southward to its observed position between 50°N and 55°N in western Europe during OIS3. A variety of sensitivity experiments are performed to investigate these mismatches. These experiments demonstrate the importance of annual and summer temperatures and the length of the winter season in creating improved matches between the model results and the inferred distributions of vegetation and permafrost in northern Europe.
European vegetation during representative “warm” and “cold” intervals of stage-3 was inferred from pollen analytical data. The inferred vegetation differs in character and spatial pattern from that of both fully glacial and fully interglacial conditions and exhibits contrasts between warm and cold intervals, consistent with other evidence for stage-3 palaeoenvironmental fluctuations. European vegetation thus appears to have been an integral component of millennial environmental fluctuations during stage-3; vegetation responded to this scale of environmental change and through feedback mechanisms may have had effects upon the environment. The pollen-inferred vegetation was compared with vegetation simulated using the BIOME 3.5 vegetation model for climatic conditions simulated using a regional climate model (RegCM2) nested within a coupled global climate and vegetation model (GENESIS-BIOME). Despite some discrepancies in detail, both approaches capture the principal features of the present vegetation of Europe. The simulated vegetation for stage-3 differs markedly from that inferred from pollen analytical data, implying substantial discrepancy between the simulated climate and that actually prevailing. Sensitivity analyses indicate that the simulated climate is too warm and probably has too short a winter season. These discrepancies may reflect incorrect specification of sea surface temperature or sea-ice conditions and may be exacerbated by vegetation–climate feedback in the coupled global model.
The degree of analogy between fossil and contemporary pollen spectra in Europe has been investigated using the chord-distance dissimilarity measure. No-analog pollen spectra represent vegetation without a modern analog and hence, by inference, represent macroclimatic conditions different from any occurring in the region today. Such spectra have minimum chord distances that exceed a threshold value assessed using contemporary samples from the same and different vegetation u units. Contoured maps of minimum chord distance portray the changing patterns of analogous and no-analog pollen spectra, and hence vegetation units, since 13,000 yr B.P. No-analog vegetation units have been extensive in some regions for much of the Holocene, persisting as recently as 1000 years ago in many areas. The chord-distance measure has also been used to explore the patterns, extent, and rates of change in European pollen spectra since 13,000 yr B.P. Pollen spectra changed rapidly during late-glacial and early Holocene times and during the last millennium. Paleoclimatic changes have brought about the major changes in the Holocene paleovegetation of Europe. Human impact upon European vegetation has obscured neither the contemporary relationship between pollen spectra and vegetation nor the climatically determined long-term changes of vegetation across the continent since 13,000 yr B.P.
Palynological and macrofossil evidence of the former presence and abundance of Salix spp. in the British Isles is discussed. The occurrence of Salix remains in archaeological excavations is reviewed. It is concluded that, whereas Salix spp. of shrub and dwarf-shrub habits were abundant during the glacial and late-glacial periods, tall-shrub and tree species have been of only local occurrence during the post-glacial. The wood of these species has been used opportunistically by humans since at least the Neolithic period.
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