ABSTRACT
Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the "life cycle" (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as "signatures" of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses.
Subject(s)
Bacteriophages , DNA Transposable Elements , Bacteria/genetics , Bacteriophages/genetics , Computational Biology/methods , Plasmids/geneticsABSTRACT
BACKGROUND: The COVID-19 outbreak was declared a pandemic in March 2020, forcing the United Kingdom into a national lockdown. The aim was to evaluate the effect of this lockdown on hand injuries referred through the trauma and orthopedics virtual fracture clinic (VFC) service and their subsequent management given limited resources. This study also aimed to identify complications and evaluate functional outcomes. METHODS: Patients referred through VFC at Queen Alexandra Hospital during April and May 2020 with hand injuries were analyzed. Isolated injuries to the carpus and wrist were excluded. Controls were compared over identical time spans prior to lockdown and after the restrictions were eased. Functional outcomes were measured using the Quick Disabilities of the Arm, Shoulder, and Hand (QuickDASH) score, at 12 months after injury. RESULTS: There was a 68% reduction in referrals of hand injuries during lockdown. Lower numbers of sporting injuries were seen, in contrast to an increased rate of falls, crush injuries, and recreational cycling. Despite a higher number of patients being discharged from VFC during lockdown, there were no increased rates of complications from conservatively managed hand fractures. Eighty percent reported low QuickDASH scores with a median of 2.3. Satisfaction was high, with 73% either satisfied or very satisfied with their treatment and outcome. CONCLUSION: This study demonstrates that there remains a burden of hand trauma during lockdowns, and therefore, service provision for future lockdowns should consider this. Most patients can be managed conservatively, and a high proportion can be discharged from VFC with low complication rates and high satisfaction.
ABSTRACT
PURPOSE: To review the relative accuracy of preoperative magnetic resonance imaging (MRI) and fluoroscopically guided examination-under-sedation (EUS) findings and to explore the validity of the anterior acetabular sector angle (AASA) as a radiologic MRI-based marker of anterior acetabular coverage in pincer-type impingement. METHODS: A cohort of 150 consecutive patients undergoing primary hip arthroscopy for femoroacetabular impingement (FAI) in 2018 to 2019 was reviewed. The inclusion criteria were pure FAI unilateral symptomatic pathology and the availability of complete data sets (MRI, EUS, and intraoperative records). Preoperative MRI and EUS findings were compared with gold-standard intraoperative arthroscopic findings, specifically evaluating the alpha angle in the presence of cam lesions, AASA in the presence of pincer lesions, as well as soft-tissue lesions. An alpha angle greater than 50° and an AASA greater than 65° were deemed pathologic. RESULTS: The patient cohort included 78 women and 72 men with an average age of 38 years (range, 18-53 years). Intraoperatively, pincer lesions were present in 20% of patients; cam lesions, 26%; and mixed impingement, 54%. MRI versus EUS correctly identified pincer lesions in 36% versus 89% of cases and identified cam lesions in 44% versus 77% of cases. MRI findings characterizing labral tears and articular cartilage pathology were accurate in 80% and 10% of cases, respectively. Although there was no difference in the AASA between pure pincer- and mixed-type impingements (62° and 63°, respectively; P = .62), there was a statistically significant difference in reported AASA values between pure cam-type impingement and impingement involving the presence of pincer lesions (57° and 63°, respectively; P = .03). Furthermore, 31% of patients with intraoperatively identified pincer lesions had an AASA of 60° to 65°. CONCLUSIONS: Fluoroscopic EUS is accurate in characterizing FAI pathology. In addition, MRI is useful to diagnose or rule out non-FAI pathology, ascertain labral pathology, and outline hip alignment. These methods of preoperative planning are complementary. LEVEL OF EVIDENCE: Level IV, therapeutic case series.
ABSTRACT
Arterial complications following traumatic knee injury are relatively rare but mandate timely recognition and treatment to avoid significant comorbidity and medicolegal ramifications. In this report we describe a case of acute thrombotic occlusion of the popliteal artery occurring after knee dislocation, successfully repaired by intimal fixation and a limited venous patch reconstruction. We present a review of local practice in screening vascular injuries following knee dislocation, aligned with a review of the literature and considerations for practice.