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. Signal-to-noise ratio, contrast-to-noise ratio, and qualitative scales have been used to assess image quality of MRI in the context of a knee-spanning external fixator. Despite the potential for artifact, studies have demonstrated that useful diagnostic information may be obtained from MRI in the presence of an external fixator. This review examines the general principles of anatomical assessment, magnetic field strength, device composition and design, radiofrequency coil use, and MRI sequences and artifact reduction as they pertain to MRI in the presence of a knee-spanning external fixator.

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. The survey was distributed to 1739 members of the Society of Skeletal Radiology. RESULTS: A total of 72 members of the Society of Skeletal Radiology completed the survey. Most notably, 40 of 72 (55.56%) respondents are permitted to place a knee-spanning external fixator inside the MR bore at their institution, while19 of 72 (26.39%) respondents are not permitted to do so. Fourteen of 32 (43.75%) respondents have institutional guidelines for safely performing an MRI of an externally fixated knee. Twenty-five of 32 (78.13%) respondents are comfortable permitting an MRI of an externally fixated knee. CONCLUSION: We found a general lack of consensus regarding the decision to scan a patient with a knee-spanning external fixator in MRI. Many institutions lack safety guidelines, and providers rely upon a heterogeneous breadth of resources for safety information. A re-examination of the FDA device labeling nomenclature and expectations of the individual manufacturers may be needed to bridge this gap and help direct management decisions placed upon the provider.

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.

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). Previous investigations of cases and outbreaks have identified C. sakazakii in opened powdered formula, breast pump parts, environmental surfaces in the home, and, rarely, in unopened powdered formula and formula manufacturing facilities (2,4-6). This report describes two infants with C. sakazakii meningitis reported to CDC in September 2021 and February 2022. CDC used whole genome sequencing (WGS) analysis to link one case to contaminated opened powdered formula from the patient's home and the other to contaminated breast pump equipment. These cases highlight the importance of expanding awareness about C. sakazakii infections in infants, safe preparation and storage of powdered formula, proper cleaning and sanitizing of breast pump equipment, and using WGS as a tool for C. sakazakii investigations.

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. All MLKIs were diagnosed on MRI and confirmed with operative reports. Two musculoskeletal radiologists retrospectively rereviewed preoperative MRIs for evidence of medial meniscus ramp lesions (MMRLs) and PMTP bone bruises using previously established classification systems. Intraclass correlation coefficients were used to calculate the reliability between the radiologists. The incidence of MMRLs and PMTP bone bruises was quantified using descriptive statistics. RESULTS: A total of 221 MLKIs were identified, of which 32 (14.5%) had an intact ACL (87.5% male; mean age of 29.9 ± 8.6 years) and were included. The most common MLKI pattern was combined injury to the posterior cruciate ligament and posterolateral corner (n = 27, 84.4%). PMTP bone bruises were observed in 12 of 32 (37.5%) patients. Similarly, MMRLs were diagnosed in 12 of 32 (37.5%) patients. A total of 8 of 12 (66.7%) patients with MMRLs demonstrated evidence PMTP bone bruising. CONCLUSIONS: Over one-third of MLKI patients with an intact ACL were diagnosed with MMRLs on MRI in this series. PMTP bone bruising was observed in 66.7% of patients with MMRLs, suggesting that increased vigilance for identifying MMRLs at the time of ligament reconstruction should be practiced in patients with this bone bruising pattern. LEVEL OF EVIDENCE: Level IV, retrospective case series.

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

Listeria monocytogenes can cause severe foodborne illness, including miscarriage during pregnancy or death in newborn infants. When outbreaks of L. monocytogenes illness occur, it may be possible to determine the food source of the outbreak. However, most reported L. monocytogenes illnesses do not occur as part of a recognized outbreak and most of the time the food source of sporadic L. monocytogenes illness in people cannot be determined. In the United States, L. monocytogenes isolates from patients, foods, and environments are routinely sequenced and analyzed by whole genome multilocus sequence typing (wgMLST) for outbreak detection by PulseNet, the national molecular surveillance system for foodborne illnesses. We investigated whether machine learning approaches applied to wgMLST allele call data could assist in attribution analysis of food source of L. monocytogenes isolates. We compiled isolates with a known source from five food categories (dairy, fruit, meat, seafood, and vegetable) using the metadata of L. monocytogenes isolates in PulseNet, deduplicated closely genetically related isolates, and developed random forest models to predict the food sources of isolates. Prediction accuracy of the final model varied across the food categories; it was highest for meat (65%), followed by fruit (45%), vegetable (45%), dairy (44%), and seafood (37%); overall accuracy was 49%, compared with the naive prediction accuracy of 28%. Our results show that random forest can be used to capture genetically complex features of high-resolution wgMLST for attribution of isolates to their sources.

Clinical and Laboratory Findings in Patients With Potential Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reinfection, May-July 2020.

BACKGROUND: We investigated patients with potential severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection in the United States during May-July 2020. METHODS: We conducted case finding for patients with potential SARS-CoV-2 reinfection through the Emerging Infections Network. Cases reported were screened for laboratory and clinical findings of potential reinfection followed by requests for medical records and laboratory specimens. Available medical records were abstracted to characterize patient demographics, comorbidities, clinical course, and laboratory test results. Submitted specimens underwent further testing, including reverse transcription polymerase chain reaction (RT-PCR), viral culture, whole genome sequencing, subgenomic RNA PCR, and testing for anti-SARS-CoV-2 total antibody. RESULTS: Among 73 potential reinfection patients with available records, 30 patients had recurrent coronavirus disease 2019 (COVID-19) symptoms explained by alternative diagnoses with concurrent SARS-CoV-2 positive RT-PCR, 24 patients remained asymptomatic after recovery but had recurrent or persistent RT-PCR, and 19 patients had recurrent COVID-19 symptoms with concurrent SARS-CoV-2 positive RT-PCR but no alternative diagnoses. These 19 patients had symptom recurrence a median of 57 days after initial symptom onset (interquartile range: 47-76). Six of these patients had paired specimens available for further testing, but none had laboratory findings confirming reinfections. Testing of an additional 3 patients with recurrent symptoms and alternative diagnoses also did not confirm reinfection. CONCLUSIONS: We did not confirm SARS-CoV-2 reinfection within 90 days of the initial infection based on the clinical and laboratory characteristics of cases in this investigation. Our findings support current Centers for Disease Control and Prevention (CDC) guidance around quarantine and testing for patients who have recovered from COVID-19.

Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations.

Single-nucleotide polymorphisms (SNPs) are widely used for whole-genome sequencing (WGS)-based subtyping of foodborne pathogens in outbreak and source tracking investigations. Mobile genetic elements (MGEs) are commonly present in bacterial genomes and may affect SNP subtyping results if their evolutionary history and dynamics differ from that of the bacterial chromosomes. Using Salmonella enterica as a model organism, we surveyed major categories of MGEs, including plasmids, phages, insertion sequences, integrons, and integrative and conjugative elements (ICEs), in 990 genomes representing 21 major serotypes of S. enterica We evaluated whether plasmids and chromosomal MGEs affect SNP subtyping with 9 outbreak clusters of different serotypes found in the United States in 2018. The median total length of chromosomal MGEs accounted for 2.5% of a typical S. enterica chromosome. Of the 990 analyzed S. enterica isolates, 68.9% contained at least one assembled plasmid sequence. The median total length of assembled plasmids in these isolates was 93,671 bp. Plasmids that carry high densities of SNPs were found to substantially affect both SNP phylogenies and SNP distances among closely related isolates if they were present in the reference genome for SNP subtyping. In comparison, chromosomal MGEs were found to have limited impact on SNP subtyping. We recommend the identification of plasmid sequences in the reference genome and the exclusion of plasmid-borne SNPs from SNP subtyping analysis.IMPORTANCE Despite increasingly routine use of WGS and SNP subtyping in outbreak and source tracking investigations, whether and how MGEs affect SNP subtyping has not been thoroughly investigated. Besides chromosomal MGEs, plasmids are frequently entangled in draft genome assemblies and yet to be assessed for their impact on SNP subtyping. This study provides evidence-based guidance on the treatment of MGEs in SNP analysis for Salmonella to infer phylogenetic relationship and SNP distance between isolates.

Molecular Characterization of Clostridium botulinum Harboring the bont/B7 Gene.

Clostridium botulinum produces botulinum neurotoxin (BoNT), which is the causative agent of botulism, a rare but serious disease that can result in death if not treated. Infant botulism occurs when C. botulinum colonizes the intestinal tract of infants and produces BoNT. It has been proposed that infants under the age of 1 year are uniquely susceptible to colonization by C. botulinum as their intestinal microbiota is not fully developed and provides little competition, allowing C. botulinum to thrive and produce BoNT in the gut. There are seven well-characterized serotypes (A-G) of BoNT identified by the ability of specific antitoxins to neutralize BoNTs. Molecular technology has allowed researchers to narrow these further into subtypes based on nucleic acid sequences of the botulinum toxin (bont) gene. One of the most recently recognized subtypes for bont/B is subtype bont/B7. We identified through whole genome sequencing five C. botulinum isolates harboring bont/B7 from CDC's strain collection, including patient isolates and an epidemiologically linked isolate from an opened infant formula container. In this study, we report the results of whole genome sequencing analysis of these C. botulinum subtype bont/B7 isolates. Average nucleotide identity and high quality single nucleotide polymorphism (hqSNP) analysis resulted in two major clades. The epidemiologically linked isolates differed from each other by 2-6 hqSNPs, and this clade separated from the other isolates by 95-119 hqSNPs, corroborating available epidemiological evidence.

Whole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, United States, 2013.

Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS 3 months later revealed that the equipment purchased by company B from company A yielded an environmental isolate highly similar to all outbreak isolates. The whole genome and core genome multilocus sequence typing and single nucleotide polymorphism (SNP) analyses results were compared to demonstrate the maximum discriminatory power obtained by using multiple analyses, which were needed to differentiate outbreak-associated isolates from a PFGE-indistinguishable isolate collected in a nonimplicated food source in 2012. This unrelated isolate differed from the outbreak isolates by only 7 to 14 SNPs, and as a result, the minimum spanning tree from the whole genome analyses and certain variant calling approach and phylogenetic algorithm for core genome-based analyses could not provide differentiation between unrelated isolates. Our data also suggest that SNP/allele counts should always be combined with WGS clustering analysis generated by phylogenetically meaningful algorithms on a sufficient number of isolates, and the SNP/allele threshold alone does not provide sufficient evidence to delineate an outbreak. The putative prophages were conserved across all the outbreak isolates. All outbreak isolates belonged to clonal complex 5 and serotype 1/2b and had an identical inlA sequence which did not have premature stop codons.IMPORTANCE In this outbreak, multiple analytical approaches were used for maximum discriminatory power. A PFGE-matched, epidemiologically unrelated isolate had high genetic similarity to the outbreak-associated isolates, with as few as 7 SNP differences. Therefore, the SNP/allele threshold should not be used as the only evidence to define the scope of an outbreak. It is critical that the SNP/allele counts be complemented by WGS clustering analysis generated by phylogenetically meaningful algorithms to distinguish outbreak-associated isolates from epidemiologically unrelated isolates. Careful selection of a variant calling approach and phylogenetic algorithm is critical for core-genome-based analyses. The whole-genome-based analyses were able to construct the highly resolved phylogeny needed to support the findings of the outbreak investigation. Ultimately, epidemiologic evidence and multiple WGS analyses should be combined to increase confidence levels during outbreak investigations.

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.

Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens.

Two Listeria monocytogenes Pseudo-outbreaks Caused by Contaminated Laboratory Culture Media.

Listeriosis is a serious foodborne infection that disproportionately affects elderly adults, pregnant women, newborns, and immunocompromised individuals. Diagnosis is made by culturing Listeria monocytogenes from sterile body fluids or from products of conception. This report describes the investigations of two listeriosis pseudo-outbreaks caused by contaminated laboratory media made from sheep blood.

Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing.

We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or "epidemic clones" that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.

Notes from the field: listeriosis associated with stone fruit--United States, 2014.

On July 19, 2014, a packing company in California (company A) voluntarily recalled certain lots of stone fruits, including whole peaches, nectarines, plums, and pluots, because of concern about contamination with Listeria monocytogenes based on internal company testing. On July 31, the recall was expanded to cover all fruit packed at their facility during June 1-July 17. After the initial recall, clinicians, state and local health departments, CDC, and the Food and Drug Administration (FDA) received many inquiries about listeriosis from concerned consumers, many of whom had received automated telephone calls informing them that they had purchased recalled fruit. During July 19-31, the CDC Listeria website received >500,000 page views, more than seven times the views received during the previous 52 weeks. However, no molecular information from L. monocytogenes isolates was available to assess whether human illnesses might be linked to these products.

Lateral dislocation and incarceration of the posterior tibial tendon through the distal tibiofibular syndesmosis.

A case of acute, traumatic, lateral dislocation of the posterior tibial tendon is presented as a unique pattern of posterior tibial tendon dislocation. Several attempts at both closed and open reduction were required to relocate the tendon and reduce the fracture-dislocation. This case is being presented to demonstrate the use of cross-sectional imaging to both recognize the initial bony injury and to identify tendon anatomy and pathology that may not be seen in the operating room with limited visualization.

Isolated avulsion fracture at the medial head of the gastrocnemius muscle.

An isolated avulsion fracture involving the femoral origin of the medial head of the gastrocnemius muscle without an associated muscular, meniscal, or ligamentous injury is extremely rare. We report a case of a 14-year-old male wrestler who presented with a radiographically occult avulsion fracture of the medial gastrocnemius tendon sustained during competition. To our knowledge, this is the first case to describe a mechanism of injury as well as to report a return to competition after non-operative management.

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. Sharing of useful, but sub-optimal datasets requires careful annotation and documentation of known issues to enable appropriate interpretation, avoid being mistaken for better quality information, and for these data (and their derivatives) to be easily identifiable in repositories. Unfortunately, there are currently no standardized attributes or mechanisms for tagging poor-quality datasets, or datasets generated for a specific purpose, to maximize their utility, searchability, accessibility and reuse. The Public Health Alliance for Genomic Epidemiology (PHA4GE) is an international community of scientists from public health, industry and academia focused on improving the reproducibility, interoperability, portability, and openness of public health bioinformatic software, skills, tools and data. To address the challenges of sharing lower quality datasets, PHA4GE has developed a set of standardized contextual data tags, namely fields and terms, that can be included in public repository submissions as a means of flagging pathogen sequence data with known quality issues, increasing their discoverability. The contextual data tags were developed through consultations with the community including input from the International Nucleotide Sequence Data Collaboration (INSDC), and have been standardized using ontologies - community-based resources for defining the tag properties and the relationships between them. The standardized tags are agnostic to the organism and the sequencing technique used and thus can be applied to data generated from any pathogen using an array of sequencing techniques. The tags can also be applied to synthetic (lab created) data. The list of standardized tags is maintained by PHA4GE and can be found at https://github.com/pha4ge/contextual_data_QC_tags. Definitions, ontology IDs, examples of use, as well as a JSON representation, are provided. The PHA4GE QC tags were tested, and are now implemented, by the FDA's GenomeTrakr laboratory network as part of its routine submission process for SARS-CoV-2 wastewater surveillance. We hope that these simple, standardized tags will help improve communication regarding quality control in public repositories, in addition to making datasets of variable quality more easily identifiable. Suggestions for additional tags can be submitted to PHA4GE via the New Term Request Form in the GitHub repository. By providing a mechanism for feedback and suggestions, we also expect that the tags will evolve with the needs of the community.

Novel epidemic clones of Listeria monocytogenes, United States, 2011.

We identified a novel serotype 1/2a outbreak strain and 2 novel epidemic clones of Listeria monocytogenes while investigating a foodborne outbreak of listeriosis associated with consumption of cantaloupe during 2011 in the United States. Comparative analyses of strains worldwide are essential to identification of novel outbreak strains and epidemic clones.

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

¼ 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.¼ 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.¼ Scanning of a knee-spanning external fixator inside the MR bore has been safely demonstrated in previous studies, although with small sample sizes.¼ When considering MRI in a patient treated with a knee-spanning external fixator, physicians should use all available resources and coordinate with their medical team to make a clinically reasonable decision contrasting patient benefit vs. potential harm.