primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other.

In both molecular epidemiology and microbial ecology, it is useful to be able to categorize specific strains of microorganisms in either an ingroup or an outgroup in a given population, e.g. to distinguish a pathogenic strain of interest from its non-virulent relatives.

PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training.

As public health laboratories expand their genomic sequencing and bioinformatics capacity for the surveillance of different pathogens, labs must carry out robust validation, training, and optimization of wet- and dry-lab procedures. Achieving these goals for algorithms, pipelines and instruments often requires that lower quality datasets be made available for analysis and comparison alongside those of higher quality. This range of data quality in reference sets can complicate the sharing of sub-optimal datasets that are vital for the community and for the reproducibility of assays.

Rapid identification of enteric bacteria from whole genome sequences using average nucleotide identity metrics.

Identification of enteric bacteria species by whole genome sequence (WGS) analysis requires a rapid and an easily standardized approach. We leveraged the principles of average nucleotide identity using MUMmer (ANIm) software, which calculates the percent bases aligned between two bacterial genomes and their corresponding ANI values, to set threshold values for determining species consistent with the conventional identification methods of known species. The performance of species identification was evaluated using two datasets: the Reference Genome Dataset v2 (RGDv2), consisting of 43 enteric genome assemblies representing 32 species, and the Test Genome Dataset (TGDv1), comprising 454 genome assemblies which is designed to represent all species needed to query for identification, as well as rare and closely related species.

Magnetic resonance imaging quality in the context of a knee-spanning external fixator placed inside the MR bore: a literature review.

After emergent assessment of potentially limb-threatening injuries in knee dislocation or multi-ligament knee injury patients, magnetic resonance imaging is necessary to visualize ligamentous structures and plan for soft tissue repair. However, the application of a knee-spanning external fixator may introduce artifact and reduce overall image quality, which can limit the evaluation of soft tissue injury. As a result, the utility of MRI in the context of a knee-spanning external fixator has been called into question.

Predicting Food Sources of Based on Genomic Profiling Using Random Forest Model.

can cause severe foodborne illness, including miscarriage during pregnancy or death in newborn infants. When outbreaks of illness occur, it may be possible to determine the food source of the outbreak. However, most reported illnesses do not occur as part of a recognized outbreak and most of the time the food source of sporadic illness in people cannot be determined.

Perspectives and institutional policies on patient safety and image quality regarding the use of knee-spanning external fixators in MRI: A survey study of the Society of Skeletal Radiology.

Objective: Concerns regarding patient safety and image quality have made the use of knee-spanning external fixators in MRI a challenging clinical scenario. The purpose of our study was to poll practicing musculoskeletal radiologists on their personal experiences regarding the use of knee-spanning external fixators in MRI in an effort to consolidate practice trends for the radiologists' benefit.

Methods: A 27-item survey was created to address the institutional use, safety, adverse events, quality, and perspectives of the radiologist related to MRI of an externally fixated knee.

Reoccurring Escherichia coli O157:H7 Strain Linked to Leafy Greens-Associated Outbreaks, 2016-2019.

Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens-associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period.

Patient Safety in MRI with the Use of a Joint-Spanning External Fixator for Knee Dislocation: A Critical Analysis Review.

» Universal safety guidelines for the use of a knee-spanning external fixator in magnetic resonance imaging (MRI) are unlikely to be established considering the high variability in device construct configurations.» Per the US Food and Drug Administration, manufacturers are to provide parameters for safe MRI scanning for "MR Conditional" devices; however, such labeling may be limited in detail. Physicians should reference manufacturer labels as a starting point while making an educated clinical decision.

Characterization of a Nonagglutinating Toxigenic Vibrio cholerae Isolate.

Toxigenic Vibrio cholerae serogroup O1 is the etiologic agent of the disease cholera, and strains of this serogroup are responsible for pandemics. A few other serogroups have been found to carry cholera toxin genes-most notably, O139, O75, and O141-and public health surveillance in the United States is focused on these four serogroups. A toxigenic isolate was recovered from a case of vibriosis from Texas in 2008.

Examining the Distribution of Bone Bruise Patterns in Contact and Noncontact Acute Anterior Cruciate Ligament Injuries.

Background: Bone bruises are commonly seen on magnetic resonance imaging (MRI) in acute anterior cruciate ligament (ACL) injuries and can provide insight into the underlying mechanism of injury. There are limited reports that have compared the bone bruise patterns between contact and noncontact mechanisms of ACL injury.

Purpose: To examine and compare the number and location of bone bruises in contact and noncontact ACL injuries.

Cronobacter sakazakii Infections in Two Infants Linked to Powdered Infant Formula and Breast Pump Equipment - United States, 2021 and 2022.

Cronobacter sakazakii, a species of gram-negative bacteria belonging to the Enterobacteriaceae family, is known to cause severe and often fatal meningitis and sepsis in young infants. C. sakazakii is ubiquitous in the environment, and most reported infant cases have been attributed to contaminated powdered infant formula (powdered formula) or breast milk that was expressed using contaminated breast pump equipment (1-3).

Spontaneous Healing of a Posteriorly Displaced Lateral Meniscus Bucket-Handle Tear in a Multiligament Knee Injury: A Case Report.

Case: Bucket-handle meniscus tears (BHMTs) typically involve the medial meniscus and often occur with concomitant rupture of the anterior cruciate ligament. We report an unusual case of a polytrauma patient who sustained a bicruciate multiligament knee injury (MLKI) with a posteriorly displaced lateral BHMT that spontaneously healed after reduction of the fragment. At the 2-year follow-up, the lateral meniscus was clinically stable without pain.

Examining Preoperative MRI for Medial Meniscal Ramp Lesions in Patients Surgically Treated for Acute Grade 3 Combined Posterolateral Corner Knee Injury.

Background: While medial meniscocapsular tears (ramp lesions) are commonly associated with isolated anterior cruciate ligament injuries, there are limited descriptions of these meniscal injuries in multiligament knee injuries (MLKIs).

Purpose: To (1) retrospectively evaluate preoperative magnetic resonance imaging (MRI) scans for the presence of ramp lesions in patients surgically treated for acute grade 3 combined posterolateral corner (PLC) knee injuries and (2) determine if a preoperative posteromedial tibial plateau (PMTP) bone bruise is associated with the presence of preoperative ramp lesions on MRI in these same patients.

Study Design: Cross-sectional study; Level of evidence, 3.

Over One-Third of Patients With Multiligament Knee Injuries and an Intact Anterior Cruciate Ligament Demonstrate Medial Meniscal Ramp Lesions on Magnetic Resonance Imaging.

Purpose: To determine the incidence of ramp lesions and posteromedial tibial plateau (PMTP) bone bruising on magnetic resonance imaging (MRI) in patients with multiligament knee injuries (MLKIs) and an intact anterior cruciate ligament (ACL).

Methods: A retrospective review of consecutive patients surgically treated for MLKIs at 2 level I trauma centers between January 2001 and March 2021 was performed. Only MLKIs with an intact ACL that received MRI scans within 90 days of the injury were included.

Genome Sequences of Hemolytic and Nonhemolytic Listeria innocua Strains from Human, Food, and Environmental Sources.

This report describes genome sequences for nine Listeria innocua strains that varied in hemolytic phenotypes on sheep blood agar. All strains were sequenced using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) chemistry; overall, the average read length of these sequences was 2,869,880 bp, with an average GC content of 37%.

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis.

Molecular characterization of circulating Salmonella Typhi strains in an urban informal settlement in Kenya.

A high burden of Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) bacteremia has been reported from urban informal settlements in sub-Saharan Africa, yet little is known about the introduction of these strains to the region. Understanding regional differences in the predominant strains of S.

Posteromedial tibial plateau bone bruises are associated with medial meniscal ramp lesions in patients with concomitant anterior cruciate ligament ruptures: a systematic review & meta-analysis.

Objective: To determine if posteromedial tibial plateau (PMTP) bone bruising on pre-operative MRI is significantly associated with a ramp lesion identified during arthroscopy in patients with concomitant ACL ruptures.

Methods: PubMed, CINAHL, Scopus, Web of Sciences, EMBASE, and Cochrane Library were searched systematically for studies that investigated the association between PMTP bone bruises on preoperative MRI and ramp lesions confirmed during arthroscopy. Eight studies met inclusion criteria.

Arthroscopic Synovectomy for Tenosynovial Giant Cell Tumor/Pigmented Villonodular Synovitis in the Posterior Knee Using the Posterior Trans-Septal Portal Technique.

Unlabelled: Tenosynovial giant cell tumor (T-GCT) and pigmented villonodular synovitis (PVNS) are interchangeable terms for an uncommon benign proliferation of synovial tissue. Although neoplastic and inflammatory origins have been hypothesized, the etiology of this condition is unknown. There is controversy regarding surgical treatment, as the open and arthroscopic approaches to synovectomy have shown comparable reported outcomes in the literature.

A Novel MRI Mapping Technique for Evaluating Bone Bruising Patterns Associated With Noncontact ACL Ruptures.

Background: Bone bruise patterns in the knee can aid in understanding the mechanism of injury in anterior cruciate ligament (ACL) ruptures. There is no universally accepted magnetic resonance imaging (MRI) mapping technique to describe the specific locations of bone bruises.

Hypothesis: The authors hypothesized that (1) our novel mapping technique would show high interrater and intrarater reliability for the location of bone bruises in noncontact ACL-injured knees and (2) the bone bruise patterns reported from this technique would support the most common mechanisms of noncontact ACL injury, including valgus stress, anterior tibial translation, and internal tibial rotation.

Examining the Bone Bruise Patterns in Multiligament Knee Injuries With Peroneal Nerve Injury.

Background: Tibiofemoral bone bruise patterns seen on magnetic resonance imaging (MRI) are associated with ligamentous injuries in the acutely injured knee. Bone bruise patterns in multiligament knee injuries (MLKIs) and particularly their association with common peroneal nerve (CPN) injuries are not well described.

Purpose: To analyze the tibiofemoral bone bruise patterns in MLKIs with and without peroneal nerve injury.

SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data.

Laboratories that run Whole Genome Sequencing (WGS) produce a tremendous amount of data, up to 10 gigabytes for some common instruments. There is a need to standardize the quality assurance and quality control process (QA/QC). Therefore we have created SneakerNet to automate the QA/QC for WGS.