SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19.

BACKGROUND: The determinants of coronavirus disease 2019 (COVID-19) disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterized relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNAemia and disease severity, clinical deterioration, and specific EPCs. METHODS: We used quantitative and digital polymerase chain reaction (qPCR and dPCR) to quantify SARS-CoV-2 RNA from plasma in 191 patients presenting to the emergency department with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterized the role of RNAemia in predicting clinical severity and EPCs using elastic net regression. RESULTS: Of SARS-CoV-2-positive patients, 23.0% (44 of 191) had viral RNA detected in plasma by dPCR, compared with 1.4% (2 of 147) by qPCR. Most patients with serial measurements had undetectable RNAemia within 10 days of symptom onset, reached maximum clinical severity within 16 days, and symptom resolution within 33 days. Initially RNAemic patients were more likely to manifest severe disease (odds ratio, 6.72 [95% confidence interval, 2.45-19.79]), worsening of disease severity (2.43 [1.07-5.38]), and EPCs (2.81 [1.26-6.36]). RNA loads were correlated with maximum severity (r = 0.47 [95% confidence interval, .20-.67]). CONCLUSIONS: dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Because many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.

Caffeine-induced neurotoxicity mediated by Nrf2 pathway in PC12 cells and zebrafish larvae.

Caffeine is one of the most widely used psychostimulants in the world and possesses central excitative, anti-depressive, and neuroprotective properties. However, excessive ingestion or abuse of caffeine can lead to intoxication. Many toxic effects are attributed to oxidative damage, and nuclear factor erythroid 2-related factor 2 (Nrf2) is a critical intracellular regulator of the oxidative stress response. Here, we investigated the neurotoxicity of caffeine in rat pheochromocytoma PC12 cells and zebrafish larvae. It was found that caffeine inhibited the viability of PC12 cells in a dose- and time-dependent manner. Furthermore, it induced PC12 cell apoptosis and elevated reactive oxygen species (ROS) production. Quantitative polymerase chain reaction (qPCR) and western blotting revealed that caffeine also inhibited the expression levels of Nrf2 mRNA and protein and its target genes (e.g., NADPH quinone oxidoreductase 1 [NQO1]). Furthermore, Nrf2 silencing attenuated the toxic effects of caffeine. In addition, zebrafish larvae were treated with different doses of caffeine. Behavioral experiments showed that a low dose of caffeine (0.05 to 0.3 mM) increased the average distance of movement and promoted excitation. Survivorship curves showed that caffeine (0.2 to 1.5 mM) caused lethality. Finally, qPCR revealed that a higher dose of caffeine inhibited mRNA levels in the Nrf2 pathway. Based on these results, this study identified for the first time that overuse of caffeine can induce neurotoxicity by inhibiting the Nrf2 pathway. These results will provide a new perspective for studies on caffeine toxicity.

Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation.

Before the anthrax letter attacks of 2001, the developing field of microbial forensics relied on microbial genotyping schemes based on a small portion of a genome sequence. Amerithrax, the investigation into the anthrax letter attacks, applied high-resolution whole-genome sequencing and comparative genomics to identify key genetic features of the letters' Bacillus anthracis Ames strain. During systematic microbiological analysis of the spore material from the letters, we identified a number of morphological variants based on phenotypic characteristics and the ability to sporulate. The genomes of these morphological variants were sequenced and compared with that of the B. anthracis Ames ancestor, the progenitor of all B. anthracis Ames strains. Through comparative genomics, we identified four distinct loci with verifiable genetic mutations. Three of the four mutations could be directly linked to sporulation pathways in B. anthracis and more specifically to the regulation of the phosphorylation state of Spo0F, a key regulatory protein in the initiation of the sporulation cascade, thus linking phenotype to genotype. None of these variant genotypes were identified in single-colony environmental B. anthracis Ames isolates associated with the investigation. These genotypes were identified only in B. anthracis morphotypes isolated from the letters, indicating that the variants were not prevalent in the environment, not even the environments associated with the investigation. This study demonstrates the forensic value of systematic microbiological analysis combined with whole-genome sequencing and comparative genomics.

Association between incubator standards and newborn nosocomial infection with machine-learning prediction.

Background: Newborns have a high incidence of nosocomial infection (NI). We conducted a logistic regression to analyze different incubator standards and other risk factors for newborn NI, which could better help clinical choice of incubator standard. Methods: Newborns with complete necessary clinical data were included. We collected the demographic and incubator data of 76 patients (40 uninfected and 36 infected) at the Heping Hospital Affiliated to Changzhi Medical College. An analysis of variance, Pearson correlation matrix analysis, and logistic regression analysis were conducted to explore the different incubator standards and other risk factors for neonatal hospital infections. In addition, 4 machine-learning algorithms were used to predict neonatal hospital infections. Results: We found differences in the gestational age, incubator type, paternal age, and maternal age between the 2 groups. The correlation analysis only revealed a correlation between paternal age and maternal age. The logistic regression showed that gestational age [odds ratio (OR)= 0.77574, 95% confidence interval (CI): 0.583513-0.996354] and the new standard incubator (OR =0.011639, 95% CI: 0.000958-0.067897) may be protective factors for infant infection during hospitalization. Among the extreme gradient boosting (XGBoost), random forest (RF), support vector machine (SVM), and decision tree (DT) algorithms, XGBoost had the best performance in terms of accuracy, sensitivity, specificity, and precision. Conclusions: We found early gestational age and incubator standards may be risk factors for the NIs of newborns, which might help clinicians to improve the health and safety standards for incubators. XGBoost can be used to predict newborn NIs.

[Differentiation of subtypes of renal cell carcinoma by double-phase helical computed tomography].

OBJECTIVE: To evaluate the imaging features of different subtypes of renal cell carcinoma (RCC) by double-phase helical computed tomography (CT) and to enhance its pre-operative diagnosis level. METHODS: A total of 460 RCC were reviewed retrospectively. Tumor size, enhancement degree, enhancement drop between corticomedullary (CMP), nephrographic (NP), enhancement pattern, and tumor density (homogeneity, degeneration or necrosis, calcification) were observed respectively. The clear cell, chromophobe and papillary types were analyzed for statistical analysis. RESULTS: They had difference in enhancement pattern and tumor density of clear cell, chromophobe (P < 0.05) and papillary types (P < 0.05). There were differences in enhancement degree, enhancement drop and combine degeneration or necrosis in all subtypes of RCC (P < 0.05). The clear cell type was of hypervascular tumor and showed a stronger enhancement (80.9%) than other types. The enhancement drop was also higher than other types and 57.9% of it was ≥ 30 HU. As for ≥ 30 HU, the clear cell type was diagnosed with a 57.9% sensitivity and a 91.9% specificity. Clear cell type tended to appear as peripheral and heterogeneous enhancement (66.3%, 94.6%); it was likely heterogeneous in density (91.6%) with frequent degeneration or necrosis (60.5%). The chromophobe type was of moderate vascular tumor and it exhibited middle-level enhancement (77.1%). The enhancement drop was low (< 30 HU, 80.0%). As for 0-30 HU, the chromophobe type was diagnosed with an 80.0% sensitivity and a 66.1% specificity. Its pattern ended to appear as homogeneous enhancement (65.7%); Homogeneous density, degeneration and necrosis were characteristic signs of chromophobe type. The papillary type was of hypovascular tumor and it exhibited slight or no enhancement (70.4%). The enhancement drop was low (< 30 HU, 92.6%) and the gradual enhancement (63.0%) was characteristic of this type. As for 0 Hu, the papillary type was diagnosed with a 63.0% sensitivity and a 91.8% specificity. It tended to appear as homogeneous density (63.0%). The unclassified type tended to appear as peripheral (9/12 cases) and stronger enhancement (7/12 cases) and heterogeneous density with degeneration or necrosis (9/12 cases). The multilocular cystic RCC appeared as complex cyst. And cystic wall enhancement was an important diagnostic point of cystic RCC. CONCLUSION: Double-phase helical CT plays an important role in the pre-operative differentiation of subtypes of RCC. Each type of RCC has its own features. A clinician may reach a correct pre-operative diagnosis.

Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument.

Digital PCR (dPCR) technology has been proven to be highly sensitive and accurate in detecting copy number variations (CNV). However, a higher-order multiplexing dPCR assay for measuring SMN1 and SMN2 copy numbers in spinal muscular atrophy (SMA) samples has not been reported. Described here is a rapid multiplex SMA dPCR genotyping assay run on a fully integrated dPCR instrument with five optical channels. The hydrolysis probe-based multiplex dPCR assay quantifies SMN1, SMN2, and the total SMN (SMN1 + SMN2) while using RPPH1 gene as an internal reference control. The quadruplex assay was evaluated with characterized control DNA samples and validated with 15 blinded clinical samples from a previously published study. SMN1 and SMN2 copy numbers were completely concordant with previous results for both the control and blinded samples. The dPCR-based SMA copy number determination was accomplished in 90 min with a walk-away workflow identical to real-time quantitative PCR (qPCR). In summary, presented here is a simple higher-order multiplexing solution on a novel digital PCR platform to meet the growing demand for SMA genotyping and prognostics.

SARS-CoV-2 RNAaemia predicts clinical deterioration and extrapulmonary complications from COVID-19.

Background: The determinants of COVID-19 disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterise the relationships between SARS-CoV-2 RNAaemia and disease severity, clinical deterioration, and specific EPCs. Methods: We used quantitative (qPCR) and digital (dPCR) PCR to quantify SARS-CoV-2 RNA from nasopharyngeal swabs and plasma in 191 patients presenting to the Emergency Department (ED) with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterised the role of RNAaemia in predicting clinical severity and EPCs using elastic net regression. Findings: 23·0% (44/191) of SARS-CoV-2 positive patients had viral RNA detected in plasma by dPCR, compared to 1·4% (2/147) by qPCR. Most patients with serial measurements had undetectable RNAaemia 10 days after onset of symptoms, but took 16 days to reach maximum severity, and 33 days for symptoms to resolve. Initially RNAaemic patients were more likely to manifest severe disease (OR 6·72 [95% CI, 2·45 - 19·79]), worsening of disease severity (OR 2·43 [95% CI, 1·07 - 5·38]), and EPCs (OR 2·81 [95% CI, 1·26 - 6·36]). RNA load correlated with maximum severity (r = 0·47 [95% CI, 0·20 - 0·67]). Interpretation: dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAaemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Since many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAaemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.

The complete genome sequence of Bacillus anthracis Ames "Ancestor".

The pathogenic bacterium Bacillus anthracis has become the subject of intense study as a result of its use in a bioterrorism attack in the United States in September and October 2001. Previous studies suggested that B. anthracis Ames Ancestor, the original Ames fully virulent plasmid-containing isolate, was the ideal reference. This study describes the complete genome sequence of that original isolate, derived from a sample kept in cold storage since 1981.

Precision cancer monitoring using a novel, fully integrated, microfluidic array partitioning digital PCR platform.

A novel digital PCR (dPCR) platform combining off-the-shelf reagents, a micro-molded plastic microfluidic consumable with a fully integrated single dPCR instrument was developed to address the needs for routine clinical diagnostics. This new platform offers a simplified workflow that enables: rapid time-to-answer; low potential for cross contamination; minimal sample waste; all within a single integrated instrument. Here we showcase the capability of this fully integrated platform to detect and quantify non-small cell lung carcinoma (NSCLC) rare genetic mutants (EGFR T790M) with precision cell-free DNA (cfDNA) standards. Next, we validated the platform with an established chronic myeloid leukemia (CML) fusion gene (BCR-ABL1) assay down to 0.01% mutant allele frequency to highlight the platform's utility for precision cancer monitoring. Thirdly, using a juvenile myelomonocytic leukemia (JMML) patient-specific assay we demonstrate the ability to precisely track an individual cancer patient's response to therapy and show the patient's achievement of complete molecular remission. These three applications highlight the flexibility and utility of this novel fully integrated dPCR platform that has the potential to transform personalized medicine for cancer recurrence monitoring.

Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).

Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath), obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath) deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for genetic components that may have biotechnological potential.

The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1.

We sequenced the complete genome of Bacillus cereus ATCC 10987, a non-lethal dairy isolate in the same genetic subgroup as Bacillus anthracis. Comparison of the chromosomes demonstrated that B.cereus ATCC 10987 was more similar to B.anthracis Ames than B.cereus ATCC 14579, while containing a number of unique metabolic capabilities such as urease and xylose utilization and lacking the ability to utilize nitrate and nitrite. Additionally, genetic mechanisms for variation of capsule carbohydrate and flagella surface structures were identified. Bacillus cereus ATCC 10987 contains a single large plasmid (pBc10987), of approximately 208 kb, that is similar in gene content and organization to B.anthracis pXO1 but is lacking the pathogenicity-associated island containing the anthrax lethal and edema toxin complex genes. The chromosomal similarity of B.cereus ATCC 10987 to B.anthracis Ames, as well as the fact that it contains a large pXO1-like plasmid, may make it a possible model for studying B.anthracis plasmid biology and regulatory cross-talk.

[Value of CT scanning in the diagnosis of early cervical carcinoma].

OBJECTIVE: To investigate the value of CT scanning in preoperative diagnosis of early cervical carcinoma. METHODS: Abdominal and pelvic CT scans (MPR pictures for 50 patients) in 102 cervical carcinoma patients proven by biopsy pathology were retrospectively analyzed and compared with surgical pathologic findings. The pathological stages included > or = Ia in 39 patients, Ib 1 in 35, Ib 2 in 21, IIa in 6, IIb in 1. The tumor detection ability, thickness of cervical tumor invasion, T stage and lymph node stage showed by CT scan were evaluated. RESULTS: CT was not able to detect < or = Ia cervical carcinoma, however, CT was able to detect tumors in 71.4% of > or = Ib 1 stage (45/63) and 71.4% > or = Ib 2 (20/28), it also showed the depth of tumor invasion in 39.7% > or = Ib 1 (25/63). The overall accuracy of CT staging for tumor was 69.6% and the rate of metastatic lymph node detection 63.6% (7/11). With additional MPR pictures of spiral CT, the detection ability, vaginal involvement and objective shape of cervical tumor was improved. The cervical carcinoma in CT scan was found to be as homogeneous in 54.9% of patients (56/102), hypodense or heterogeneous in 42.2% (43/102), lower density nodual in 41.9% (18/43); occasionally as heterogeneous or hyperdensity noduals or irregular border of the cervix. The features of metastatic lymph nodes in CT scan were rounded or spheroid shape of soft tissue noduals with heterogeneous density caused by central necrosis and rim enhancement. CONCLUSION: CT scanning may be valuable in detection of > or = Ib 1 rather than < Ib 1 stage early cervical carcinoma. The additional MPR pictures of spiral CT is not only helpful in detecting tumor but also in determining the extension of cervical carcinoma.

Automated Classification and Cluster Visualization of Genotypes Derived from High Resolution Melt Curves.

INTRODUCTION: High Resolution Melting (HRM) following PCR has been used to identify DNA genotypes. Fluorescent dyes bounded to double strand DNA lose their fluorescence with increasing temperature, yielding different signatures for different genotypes. Recent software tools have been made available to aid in the distinction of different genotypes, but they are not fully automated, used only for research purposes, or require some level of interaction or confirmation from an analyst. MATERIALS AND METHODS: We describe a fully automated machine learning software algorithm that classifies unknown genotypes. Dynamic melt curves are transformed to multidimensional clusters of points whereby a training set is used to establish the distribution of genotype clusters. Subsequently, probabilistic and statistical methods were used to classify the genotypes of unknown DNA samples on 4 different assays (40 VKORC1, CYP2C9*2, CYP2C9*3 samples in triplicate, and 49 MTHFR c.665C>T samples in triplicate) run on the Roche LC480. Melt curves of each of the triplicates were genotyped separately. RESULTS: Automated genotyping called 100% of VKORC1, CYP2C9*3 and MTHFR c.665C>T samples correctly. 97.5% of CYP2C9*2 melt curves were genotyped correctly with the remaining 2.5% given a no call due to the inability to decipher 3 melt curves in close proximity as either homozygous mutant or wild-type with greater than 99.5% posterior probability. CONCLUSIONS: We demonstrate the ability to fully automate DNA genotyping from HRM curves systematically and accurately without requiring any user interpretation or interaction with the data. Visualization of genotype clusters and quantification of the expected misclassification rate is also available to provide feedback to assay scientists and engineers as changes are made to the assay or instrument.

The biomarkers changes in serum and the correlation with quantitative MRI markers by histopathologic evaluation of the cartilage in surgically-induced osteoarthritis rabbit model.

PURPOSE: To investigate the biomarkers change in serum and the correlation with quantitative MRI markers by histopathologic evaluation of the cartilage in surgically-induced osteoarthritis(OA) rabbit model. MATERIALS AND METHODS: Thirty-six mature New Zealand rabbits were used. Eighteen rabbits were divided into six groups randomly and equally and subjected to surgery using the improved Hulth method. The other eighteen rabbits were also allocated into six groups randomly and equally which served as the control. At multiple time points after surgery, the BMP-2, CTX-II and COMP levels in the serum were analyzed by ELISA, and quantitative MRI was performed. Histopathology was examined with HE, and Mankin scores were assessed. The changes in the biochemical biomarkers and imaging markers in the OA groups were compared with those in the control groups using paired-samples T tests. The correlation of quantitative MRI markers with biomarkers and Mankin scores were analyzed. The analysis of Mankin scores was conducted with non-parametric wilcoxon signed rank tests. RESULTS: The BMP-2 levels were increased at various times after surgery, and significant differences were observed between the OA and control groups(all the P values <0.001). CTX-II levels were significantly elevated at several intervals after surgery, including W2, W8, W12, W16 and W20(P=0.019, 0.004, 0.007, <0.001 and 0.016 respectively), but not at W4(P=0.764). Significant differences in the COMP levels from W2 to W20 were observed between the OA and the control groups(P<0.001, <0.001, <0.001, <0.001,=0.002 and =0.004 respectively). The T2 values increased at W8 post-surgery and were significantly different between the OA and control groups(P=0.001, <0.001, <0.001 and <0.001 respectively). T2* values increased from W2 to W20 and were significantly different between the control and OA groups(P=0.002, =0.001, <0.001, <0.001, =0.001 and <0.001 respectively). T2 values had significant correlation with BMP-2 and CTX-II(P<0.001 and =0.014), except COMP(P=0.305)., while the correlation of T2* values with BMP-2, CTX-II and COMP was significant(P=0.043, 0.005 and 0.025 respectively). In addition, a positive correlation of T2 values and Mankin scores was observed(P<0.001). CONCLUSION: With the relevance of the multiple time point analysis of the serum biomarkers and imaging markers compared with histological findings, BMP-2, CTX-II and COMP combined with T2 and T2* can be used to reflect and monitor OA progression potentially.

[Peritoneal tuberculosis mimicking advanced ovarian carcinoma: distinction based on CT findings].

OBJECTIVE: To evaluate the computed tomography (CT) findings of peritoneal tuberculosis mimicking advanced ovarian carcinoma for better understanding of the CT manifestations and accurate preoperative diagnosis. METHODS: CT findings of 18 cases with tuberculous peritonitis clinically simulating advanced ovarian cancer but pathologically proved otherwise were retrospectively reviewed. RESULTS: 1. Masses with solid and cystic structures were found in 6 cases and tumor-like flakes were found in 7 cases in the adnexal regions. The solid components and tumor-like flakes were moderately to markedly enhanced with dynamic CT scanning. 2. The peritoneum was smooth and slightly thickened in 10 cases; irregular thickening was seen in 4 cases, and patches of calcification in 3 cases. Thickened peritoneum with pronounced enhancement was noted in 7 cases. 3. Omentum with flake-like thickening was noted in 11 cases, coarse reticulate thickening in 2 cases and omental cakes in 2 cases. The margin of the thickened omentum with enhancement was ill-defined. 4. Nodular and stripe-like thickening of the mesentery was noted in 16 cases. 5. Ascites was present in all of the 18 cases, being encapsulated in 14 of them. 6. Lymphadenopathy was seen in 9 cases, all at located in the diaphragmatic levels. Enhancement of the lymph nodes was marked in 8 of the 8 patients examined. They appeared as ring-like (> 1 cm in diameter) or uniform (

Pre-Columbian origins for North American anthrax.

Disease introduction into the New World during colonial expansion is well documented and had a major impact on indigenous populations; however, few diseases have been associated with early human migrations into North America. During the late Pleistocene epoch, Asia and North America were joined by the Beringian Steppe ecosystem which allowed animals and humans to freely cross what would become a water barrier in the Holocene. Anthrax has clearly been shown to be dispersed by human commerce and trade in animal products contaminated with Bacillus anthracis spores. Humans appear to have brought B. anthracis to this area from Asia and then moved it further south as an ice-free corridor opened in central Canada approximately 13,000 ybp. In this study, we have defined the evolutionary history of Western North American (WNA) anthrax using 2,850 single nucleotide polymorphisms (SNPs) and 285 geographically diverse B. anthracis isolates. Phylogeography of the major WNA B. anthracis clone reveals ancestral populations in northern Canada with progressively derived populations to the south; the most recent ancestor of this clonal lineage is in Eurasia. Our phylogeographic patterns are consistent with B. anthracis arriving with humans via the Bering Land Bridge. This northern-origin hypothesis is highly consistent with our phylogeographic patterns and rates of SNP accumulation observed in current day B. anthracis isolates. Continent-wide dispersal of WNA B. anthracis likely required movement by later European colonizers, but the continent's first inhabitants may have seeded the initial North American populations.

Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1.

The plasmids of the members of the Bacillus cereus sensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example, Bacillus anthracis contains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid defines Bacillus thuringiensis isolates. In this study the plasmids from B. cereus isolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal isolates examined contained almost identical approximately 272-kb plasmids, named pPER272. The emetic toxin-producing isolate contained one approximately 270-kb plasmid, named pCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequence analyses of these B. cereus plasmids revealed a high degree of sequence similarity to the B. anthracis pXO1 plasmid, especially in a putative replication region. These plasmids form a newly defined group of pXO1-like plasmids. However, these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identified B. cereus plasmids. Screening of a population of B. cereus group isolates revealed that pXO1-like plasmids are more often found in association with clinical isolates. This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species.

Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry.

The genetic relatedness of the Bacillus anthracis typing phages Gamma and Cherry was determined by nucleotide sequencing and comparative analysis. The genomes of these two phages were identical except at three variable loci, which showed heterogeneity within individual lysates and among Cherry, Wbeta, Fah, and four Gamma bacteriophage sequences.

Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.

Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- and community-acquired infections. Staphylococcus epidermidis has emerged as a causative agent of infections often associated with implanted medical devices. We have sequenced the approximately 2.8-Mb genome of S. aureus COL, an early methicillin-resistant isolate, and the approximately 2.6-Mb genome of S. epidermidis RP62a, a methicillin-resistant biofilm isolate. Comparative analysis of these and other staphylococcal genomes was used to explore the evolution of virulence and resistance between these two species. The S. aureus and S. epidermidis genomes are syntenic throughout their lengths and share a core set of 1,681 open reading frames. Genome islands in nonsyntenic regions are the primary source of variations in pathogenicity and resistance. Gene transfer between staphylococci and low-GC-content gram-positive bacteria appears to have shaped their virulence and resistance profiles. Integrated plasmids in S. epidermidis carry genes encoding resistance to cadmium and species-specific LPXTG surface proteins. A novel genome island encodes multiple phenol-soluble modulins, a potential S. epidermidis virulence factor. S. epidermidis contains the cap operon, encoding the polyglutamate capsule, a major virulence factor in Bacillus anthracis. Additional phenotypic differences are likely the result of single nucleotide polymorphisms, which are most numerous in cell envelope proteins. Overall differences in pathogenicity can be attributed to genome islands in S. aureus which encode enterotoxins, exotoxins, leukocidins, and leukotoxins not found in S. epidermidis.

Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes.

We report the genome sequence of Theileria parva, an apicomplexan pathogen causing economic losses to smallholder farmers in Africa. The parasite chromosomes exhibit limited conservation of gene synteny with Plasmodium falciparum, and its plastid-like genome represents the first example where all apicoplast genes are encoded on one DNA strand. We tentatively identify proteins that facilitate parasite segregation during host cell cytokinesis and contribute to persistent infection of transformed host cells. Several biosynthetic pathways are incomplete or absent, suggesting substantial metabolic dependence on the host cell. One protein family that may generate parasite antigenic diversity is not telomere-associated.