Complete Bacteriophage Transfer in a Bacterial Endosymbiont (Wolbachia) Determined by Targeted Genome Capture

Bacteriophage flux can cause the majority of genetic diversity in free-living bacteria. This tenet of bacterial genome evolution generally does not extend to obligate intracellular bacteria owing to their reduced contact with other microbes and a predominance of gene deletion over gene transfer. However, recent studies suggest intracellular coinfections in the same host can facilitate exchange of mobile elements between obligate intracellular bacteria—a means by which these bacteria can partially mitigate the reductive forces of the intracellular lifestyle. To test whether bacteriophages transfer as single genes or larger regions between coinfections, we sequenced the genome of the obligate intracellular Wolbachia strain wVitB from the parasitic wasp Nasonia vitripennis and compared it against the prophage sequences of the divergent wVitA coinfection. We applied, for the first time, a targeted sequence capture array to specifically trap the symbiont's DNA from a heterogeneous mixture of eukaryotic, bacterial, and viral DNA. The tiled array successfully captured the genome with 98.3% efficiency. Examination of the genome sequence revealed the largest transfer of bacteriophage and flanking genes (52.2 kb) to date between two obligate intracellular coinfections. The mobile element transfer occurred in the recent evolutionary past based on the 99.9% average nucleotide identity of the phage sequences between the two strains. In addition to discovering an evolutionary recent and large-scale horizontal phage transfer between coinfecting obligate intracellular bacteria, we demonstrate that “targeted genome capture” can enrich target DNA to alleviate the problem of isolating symbiotic microbes that are difficult to culture or purify from the conglomerate of organisms inside eukaryotes

Evolutionary Genomics of a Temperate Bacteriophage in an Obligate Intracellular Bacteria (Wolbachia)

Genome evolution of bacteria is usually influenced by ecology, such that bacteria with a free-living stage have large genomes and high rates of horizontal gene transfer, while obligate intracellular bacteria have small genomes with typically low amounts of gene exchange. However, recent studies indicate that obligate intracellular species that host-switch frequently harbor agents of horizontal transfer such as mobile elements. For example, the temperate double-stranded DNA bacteriophage WO in Wolbachia persistently transfers between bacterial coinfections in the same host. Here we show that despite the phage's rampant mobility between coinfections, the prophage's genome displays features of constraint related to its intracellular niche. First, there is always at least one intact prophage WO and usually several degenerate, independently-acquired WO prophages in each Wolbachia genome. Second, while the prophage genomes are modular in composition with genes of similar function grouping together, the modules are generally not interchangeable with other unrelated phages and thus do not evolve by the Modular Theory. Third, there is an unusual core genome that strictly consists of head and baseplate genes; other gene modules are frequently deleted. Fourth, the prophage recombinases are diverse and there is no conserved integration sequence. Finally, the molecular evolutionary forces acting on prophage WO are point mutation, intragenic recombination, deletion, and purifying selection. Taken together, these analyses indicate that while lateral transfer of phage WO is pervasive between Wolbachia with occasional new gene uptake, constraints of the intracellular niche obstruct extensive mixture between WO and the global phage population. Although the Modular Theory has long been considered the paradigm of temperate bacteriophage evolution in free-living bacteria, it appears irrelevant in phages of obligate intracellular bacteria

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Functional characterization of two putative mobile elements of the 'Mycoplasma mycoides cluster'

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Title from PDF of title page (University of Missouri--Columbia, viewed on November 19, 2010).Vita.Thesis advisor: Michael J. Calcutt."December 2008"Ph. D. University of Missouri-Columbia 2008.[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT REQUEST OF AUTHOR.] Horizontal gene transfer has played a major role in bacterial evolution, including in the genus Mycoplasma, which is comprised of some of the simplest and smallest free-living organisms. This dissertation focuses on the functional characteristics of two recently characterized putative mobile elements of the ruminant-infecting Mycoplasma mycoides cluster: a 3.4-kb cryptic plasmid, pMyBK1, of Mycoplasma yeatsii, and an approximately 24-kb member of the mycoplasmal family of Integrative, Conjugative Elements (ICE), ICEC, of Mycoplasma capricolum subsp. capricolum strain Kid. Vectors were constructed using pMyBK1 as a backbone and replication of vector derivatives in M. yeatsii identified the ORF required for survival of the plasmid. Showing the utility of the vector system, heterologous proteins were expressed in M. yeatsii from pMyBK1 derivatives. To determine which ORF of ICEC acts as an integrase, mini-ICEC derivatives were constructed. The right-hand terminal ORF, MCAP_0571, was shown to be the ORF required to integrate the mini-element into Mycoplasma capricolum subsp. capricolum strain GM262G.Includes bibliographical reference

Psychometric properties of the Trauma Checklist 2.0 and its predictive utility of felony re-offending among high-risk juvenile offenders

Abstract Background Incarcerated youth are characterized by particularly high rates of childhood trauma, a significant risk factor for outcomes including risky behaviors and recidivism. Trauma-based interventions can ameliorate the negative effects of childhood trauma; however, a critical part of success is careful trauma screening. Due to the limitations associated with commonly used self-report trauma assessments, our team developed the Trauma Checklist (TCL), a trained-rater assessment of childhood trauma specifically created for use with forensic populations. The TCL is designed to provide a more comprehensive assessment of trauma, incorporating categories that are of specific relevance for incarcerated individuals (e.g., traumatic loss). Here, we discuss the continued development made to our original trauma assessment and explore the psychometric properties of this expanded assessment (herein termed the TCL 2.0). Method We examined relationships between TCL 2.0 scores, measures of psychopathology, and psychopathic traits in a sample of incarcerated male juvenile offenders (n = 237). In addition, we examined whether TCL 2.0 scores were associated with time to felony re-offense via Cox proportional-hazard regression analyses. Results We examined dimensionality of the TCL 2.0 using a principal component analysis (PCA), the results of which were confirmed via exploratory structural equation modeling; the PCA yielded a two-component solution (i.e., PC1 and PC2). We observed that PC1 (Experienced Trauma) scores were positively correlated with mood disorder diagnoses. TCL 2.0 total scores were positively correlated with post-traumatic stress disorder symptomatology and psychopathic traits. Finally, higher PC2 (Community Trauma) scores were associated with faster time to felony re-offending. Conclusions These results suggest that the TCL 2.0 may be a beneficial screening tool to provide high-risk youth with appropriate trauma-informed treatment