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.

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.

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. The RGDv2 contains six Campylobacter spp., three Escherichia/Shigella spp., one Grimontia hollisae, six Listeria spp., one Photobacterium damselae, two Salmonella spp., and thirteen Vibrio spp., while the TGDv1 contains 454 enteric bacterial genomes representing 42 different species. The analysis showed that, when a standard minimum of 70% genome bases alignment existed, the ANI threshold values determined for these species were ≥95 for Escherichia/Shigella and Vibrio species, ≥93% for Salmonella species, and ≥92% for Campylobacter and Listeria species. Using these metrics, the RGDv2 accurately classified all validation strains in TGDv1 at the species level, which is consistent with the classification based on previous gold standard methods.

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.

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.

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.

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. This isolate did not agglutinate with any of the four different serogroups' antisera (O1, O139, O75, or O141) routinely used in phenotypic testing and did not display a rough phenotype. We investigated several hypotheses that might explain the recovery of this potential nonagglutinating (NAG) strain using whole-genome sequencing analysis and phylogenetic methods. The NAG strain formed a monophyletic cluster with O141 strains in a whole-genome phylogeny. Furthermore, a phylogeny of ctxAB and tcpA sequences revealed that the sequences from the NAG strain also formed a monophyletic cluster with toxigenic U.S. Gulf Coast (USGC) strains (O1, O75, and O141) that were recovered from vibriosis cases associated with exposures to Gulf Coast waters. A comparison of the NAG whole-genome sequence showed that the O-antigen-determining region of the NAG strain was closely related to those of O141 strains, and specific mutations were likely responsible for the inability to agglutinate. This work shows the utility of whole-genome sequence analysis tools for characterization of an atypical clinical isolate of V. cholerae originating from a USGC state. IMPORTANCE Clinical cases of vibriosis are on the rise due to climate events and ocean warming (1, 2), and increased surveillance of toxigenic Vibrio cholerae strains is now more crucial than ever. While traditional phenotyping using antisera against O1 and O139 is useful for monitoring currently circulating strains with pandemic or epidemic potential, reagents are limited for non-O1/non-O139 strains. With the increased use of next-generation sequencing technologies, analysis of less well-characterized strains and O-antigen regions is possible. The framework for advanced molecular analysis of O-antigen-determining regions presented herein will be useful in the absence of reagents for serotyping. Furthermore, molecular analyses based on whole-genome sequence data and using phylogenetic methods will help characterize both historical and novel strains of clinical importance. Closely monitoring emerging mutations and trends will improve our understanding of the epidemic potential of Vibrio cholerae to anticipate and rapidly respond to future public health emergencies.

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. STUDY DESIGN: Cross-sectional study; Level of evidence, 3. METHODS: Three hundred twenty patients who underwent ACL reconstruction surgery between 2015 and 2021 were identified. Inclusion criteria were clear documentation of the mechanism of injury and MRI within 30 days of the injury on a 3-T scanner. Patients with concomitant fractures, injuries to the posterolateral corner or posterior cruciate ligament, and/or previous ipsilateral knee injury were excluded. Patients were stratified into 2 cohorts based on a contact or noncontact mechanism. Preoperative MRI scans were retrospectively reviewed by 2 musculoskeletal radiologists for bone bruises. The number and location of the bone bruises were recorded in the coronal and sagittal planes using fat-suppressed T2-weighted images and a standardized mapping technique. Lateral and medial meniscal tears were recorded from the operative notes, while medial collateral ligament (MCL) injuries were graded on MRI. RESULTS: A total of 220 patients were included, with 142 (64.5%) noncontact injuries and 78 (35.5%) contact injuries. There was a significantly higher frequency of men in the contact cohort compared with the noncontact cohort (69.2% vs 54.2%, P = .030), while age and body mass index were comparable between the 2 cohorts. The bivariate analysis demonstrated a significantly higher rate of combined lateral tibiofemoral (lateral femoral condyle [LFC] + lateral tibial plateau [LTP]) bone bruises (82.1% vs 48.6%, P < .001) and a lower rate of combined medial tibiofemoral (medial femoral condyle [MFC] + medial tibial plateau [MTP]) bone bruises (39.7% vs 66.2%, P < .001) in knees with contact injuries. Similarly, noncontact injuries had a significantly higher rate of centrally located MFC bone bruises (80.3% vs 61.5%, P = .003) and posteriorly located MTP bruises (66.2% vs 52.6%, P = .047). When controlling for age and sex, the multivariate logistical regression model demonstrated that knees with contact injuries were more likely to have LTP bone bruises (OR, 4.721 [95% CI, 1.147-19.433], P = .032) and less likely to have combined medial tibiofemoral (MFC + MTP) bone bruises (OR, 0.331 [95% CI, 0.144-0.762], P = .009) compared with those with noncontact injuries. CONCLUSION: Significantly different bone bruise patterns were observed on MRI based on ACL injury mechanism, with contact and noncontact injuries demonstrating characteristic findings in the lateral tibiofemoral and medial tibiofemoral compartments, respectively.

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.

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. Methods: Data on consecutive patients at a level 1 trauma center with MLKIs between 2001 and 2021 were retrospectively reviewed. Only patients with acute grade 3 combined PLC injuries who received an MRI scan within 30 days of injury were assessed. Two musculoskeletal radiologists retrospectively reviewed each patient's preoperative MRI for evidence of ramp lesions and bone bruises. Intraclass correlation coefficients (ICCs) were used to calculate reliability among the reviewers. Multivariate analysis was used to evaluate the relationship between PMTP bruising and the presence of a ramp lesion on MRI. Results: A total of 68 patients (79.4% male; mean age, 33.8 ± 13.7 years) with an acute grade 3 combined PLC injury were included in the study. On MRI, the ICCs for detection of ramp lesions and PMTP bone bruising were 0.921 and 0.938, respectively. Medial meniscal ramp lesions were diagnosed in 18 of 68 (26.5%) patients. Eleven of 18 (61.1%) patients with ramp lesions also showed evidence of PMTP bruising, while 13 of 50 (26.0%) patients without ramp lesions had PMTP bruising (P = .008). When controlling for age and sex, PTMP bruising was significantly associated with the presence of a ramp lesion in combined PLC injuries (odds ratio, 4.62; P = .012). Conclusion: Preoperative medial meniscal ramp lesions were diagnosed on MRI in 26.5% of patients with acute grade 3 combined PLC injuries. PMTP bone bruising was significantly associated with the presence of a ramp lesion on MRI. These findings reinforce the need to assess for potential ramp lesions at the time of multiligament reconstruction.

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. The Methodological Index for Nonrandomized Studies (MINORS) checklist was used to assess quality. A meta-analysis was performed to analyze odds of a ramp lesion after PMTP bone bruising identified on magnetic resonance imaging (MRI). Publication bias was assessed by funnel plot and Egger's linear regression test. RESULTS: There are 2.05 greater odds of medial meniscal ramp lesions in patients with an ACL rupture when PMTP bone bruising is found on preoperative MRI (95% CI, 1.29-3.25; p = 0.002). Heterogeneity of the pooled studies may be substantial (I2 = 65%; p = 0.006). Funnel plot analysis and Egger's linear regression test (p > 0.5) determined no publication bias among the studies included in the meta-analysis. CONCLUSION: Patients with acute ACL injuries and PMTP bone bruising on MRI have 2.05 times greater odds of a concomitant medial meniscal ramp lesion than those without this bone bruise pattern.

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.

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. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods: We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results: The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion: The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines.

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. Typhi can provide insight into the genomic epidemiology. We genetically characterized 310 S. Typhi isolates from typhoid fever surveillance conducted over a 12-year period (2007-2019) in Kibera, an urban informal settlement in Nairobi, Kenya, to assess the circulating strains, their antimicrobial resistance attributes, and how they relate to global S. Typhi isolates. Whole genome multi-locus sequence typing (wgMLST) identified 4 clades, with up to 303 pairwise allelic differences. The identified genotypes correlated with wgMLST clades. The predominant clade contained 290 (93.5%) isolates with a median of 14 allele differences (range 0-52) and consisted entirely of genotypes 4.3.1.1 and 4.3.1.2. Resistance determinants were identified exclusively in the predominant clade. Determinants associated with resistance to aminoglycosides were observed in 245 isolates (79.0%), sulphonamide in 243 isolates (78.4%), trimethoprim in 247 isolates (79.7%), tetracycline in 224 isolates (72.3%), chloramphenicol in 247 isolates (79.6%), ß-lactams in 239 isolates (77.1%) and quinolones in 62 isolates (20.0%). Multidrug resistance (MDR) determinants (defined as determinants conferring resistance to ampicillin, chloramphenicol and cotrimoxazole) were found in 235 (75.8%) isolates. The prevalence of MDR associated genes was similar throughout the study period (2007-2012: 203, 76.3% vs 2013-2019: 32, 72.7%; Fisher's Exact Test: P = 0.5478, while the proportion of isolates harboring quinolone resistance determinants increased (2007-2012: 42, 15.8% and 2013-2019: 20, 45.5%; Fisher's Exact Test: P<0.0001) following a decline in S. Typhi in Kibera. Some isolates (49, 15.8%) harbored both MDR and quinolone resistance determinants. There were no determinants associated with resistance to cephalosporins or azithromycin detected among the isolates sequenced in this study. Plasmid markers were only identified in the main clade including IncHI1A and IncHI1B(R27) in 226 (72.9%) isolates, and IncQ1 in 238 (76.8%) isolates. Molecular clock analysis of global typhoid isolates and isolates from Kibera suggests that genotype 4.3.1 has been introduced multiple times in Kibera. Several genomes from Kibera formed a clade with genomes from Kenya, Malawi, South Africa, and Tanzania. The most recent common ancestor (MRCA) for these isolates was from around 1997. Another isolate from Kibera grouped with several isolates from Uganda, sharing a common ancestor from around 2009. In summary, S. Typhi in Kibera belong to four wgMLST clades one of which is frequently associated with MDR genes and this poses a challenge in treatment and control.

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

Tenosynovial giant cell tumor (T-GCT) and pigmented villonodular synovitis (PVNS) are interchangeable terms for an uncommon benign proliferation of synovial tissue1-6. 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 literature5-7. However, direct comparison of these 2 operative methods is problematic because of selective bias in the existing literature and the lack of any prospective, randomized controlled trials. In the posterior aspect of the knee, arthroscopic synovectomy is technically challenging because of anatomical blind spots when viewing this space from an anterior portal in a trans-notch fashion10-15. Additionally, incomplete arthroscopic synovectomies increase PVNS recurrence rates, making it imperative to remove the entire lesion8. The trans-septal portal (TSP) technique utilizes both posteromedial and posterolateral portals to create an intra-articular portal through the posterior septum that separates the 2 posterior compartments of the knee10-15. This portal allows working instruments to be passed back-and-forth across the posterior septum and increases the visualization of both the posterosuperior synovial lining of the condyles and the synovial reflection behind the posterior cruciate ligament, enabling a thorough assessment for arthroscopic PVNS resection10-16. In this video article, we describe a posterior arthroscopic synovectomy with use of a TSP for PVNS within the posterior compartment of the knee. Description: The patient is positioned such that the contralateral leg will not obstruct the ability to work in the posteromedial portal. Diagnostic arthroscopy is performed through standard anteromedial and anterolateral portals. Next, with visualization from the anterolateral portal and the knee in 90° of flexion, the posteromedial portal is created with use of a transilluminated spinal needle. The posterolateral portal is made in the same fashion as the posteromedial portal, with use of a trans-notch view from the anteromedial portal. With the arthroscope in the posteromedial portal, a blunt instrument or motorized shaver can be placed through the posterolateral portal to perforate the posterior septum and create the TSP. The mass can then be identified, biopsied, and removed with use of a motorized shaver or tissue grasper. Arthroscopic exploration through the TSP can then be done to confirm adequate excision. Alternatives: Alternatives include synovectomy either by arthrotomy, arthroscopy via a posteromedial or posterolateral portal with trans-notch views, or a combination of both. To limit the risk of recurrent diffuse PVNS, radiosynovectomy with yttrium-90 or phosphorus-32, either combined with surgery or alone, has been described2,17. External beam radiation has also been utilized, but radiation toxicity is seen as a major limitation17. Macrophage-colony stimulating factor (M-CSF) or CSF-1 inhibitors have recently been developed. In 2019, the FDA approved the use of CSF-1 inhibitors, and they are considered an acceptable treatment for patients who are not candidates for surgical resection17. Rationale: Advantages involve increased posterior anatomy visualization to ensure adequate synovectomy, more working capacity for instruments, and decreased disruption of anatomical planes and scar tissue formation around neurovascular structures compared with open dissection10-16. Expected Outcomes: Excellent clinical results (defined by return to full knee function) have been reported for the TSP technique for PVNS synovectomy. In a study of 10 cases of posterior-knee PVNS masses removed via arthroscopic synovectomy with use of a TSP, Shekhar et al. reported good functional outcomes and no operative complications2. Keyhani et al. reported a series of 21 patients who underwent the same procedure for diffuse PVNS with similar findings9. Patients can expect to retain close to full knee function following this procedure2,9. Baseline magnetic resonance imaging is recommended for all patients at 3 to 6 months after excision, as asymptomatic recurrence can occur, and patients should be followed for a minimum of 2 years post-excision2,3,7,9,18. Important Tips: Keeping the knee in 90° of flexion provides the furthest distance from the saphenous vein on the medial side, the peroneal nerve on the lateral side, and the popliteal artery near the posterior septum when making the posterior portals10-16.Transillumination of the posterior portals is recommended10-16.Perforation of the septum should be in the posterolateral to posteromedial direction, allowing surgeons to have a wider "safe zone" to decrease the chance of vascular injury to the popliteal artery14. Acronyms and Abbreviations: CSF = colony-stimulating factorMCL = medial collateral ligamentMRI = magnetic resonance imagingPL = posterolateralPM = posteromedialPA = popliteal arteryROM = range of motionTS = trans-septalIKDC = International Knee Documentation Committee.

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. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Included were 43 patients who underwent ACL reconstruction between 2018 and 2020, with MRI within 30 days of the injury on a 3.0-T scanner, documentation of a noncontact mechanism of injury, and no concomitant or previous knee injuries. Images were retrospectively reviewed by 2 radiologists blinded to all clinical data. The locations of bone bruises were mapped on fat-suppressed T2-weighted coronal and sagittal images using a novel technique that combined the International Cartilage Repair Society (ICRS) tibiofemoral articular cartilage surgical lesions diagram and the Whole-Organ Magnetic Resonance Imaging Scoring (WORMS) mapping system. Reliability between the reviewers was assessed using the intraclass correlation coefficient (ICC), where ICC >0.90 indicated excellent agreement. Results: The interrater and intrarater ICCs were 0.918 and 0.974, respectively, for femoral edema mapping and 0.979 and 0.978, respectively, for tibial edema mapping. Significantly more bone bruises were seen within the lateral femoral condyle compared with the medial femoral condyle (67% vs 33%; P < .0001), and more bruises were seen within the lateral tibial plateau compared with the medial tibial plateau (65% vs 35%; P < .0001). Femoral bruises were almost exclusively located in the anterior/central regions (98%) of the condyles as opposed to the posterior region (2%; P < .0001). Tibial bruises were localized to the posterior region (78%) of both plateaus as opposed to the anterior/central regions (22%; P < .0001). Conclusion: The combined mapping technique offered a standardized and reliable method for reporting bone bruises in noncontact ACL injuries. The contusion patterns identified using this technique were indicative of the most commonly reported mechanisms for noncontact ACL injuries.

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. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: We retrospectively identified 123 patients treated for an acute MLKI at a level 1 trauma center between January 2001 and March 2021. Patients were grouped into injury subtypes using the Schenck classification. Within this cohort, patients with clinically documented complete (motor and sensory loss) and/or partial CPN palsies on physical examination were identified. Imaging criteria required an MRI scan on a 1.5 or 3 Tesla scanner within 30 days of the initial MLKI. Images were retrospectively interpreted for bone bruising patterns by 2 board-certified musculoskeletal radiologists. The location of the bone bruises was mapped on fat-suppressed T2-weighted coronal and sagittal images. Bruise patterns were compared among patients with and without CPN injury. RESULTS: Of the 108 patients with a MLKI who met the a priori inclusion criteria, 26 (24.1%) were found to have a CPN injury (N = 20 complete; N = 6 partial) on physical examination. For CPN-injured patients, the most common mechanism of injury was high-energy trauma (N = 19 [73%]). The presence of a grade 3 posterolateral corner (PLC) injury (N = 25; odds ratio [OR], 23.81 [95% CI, 3.08-184.1]; P = .0024), anteromedial femoral condyle bone bruising (N = 24; OR, 21.9 [95% CI, 3.40-202.9]; P < .001), or a documented knee dislocation (N = 16; OR, 3.45 [95% CI, 1.38-8.62]; P = .007) was significantly associated with the presence of a CPN injury. Of the 26 patients with CPN injury, 24 (92.3%) had at least 1 anteromedial femoral condyle bone bruise. All 20 (100%) patients with complete CPN injury also had at least 1 anteromedial femoral condyle bone bruise on MRI. In our MLKI cohort, the presence of anteromedial femoral condyle bone bruising had a sensitivity of 92.3% and a specificity of 64.6% for the presence of CPN injury on physical examination. CONCLUSION: In our MLKI cohort, the presence of a grade 3 PLC injury had the greatest association with CPN injury. Additionally, anteromedial femoral condyle bone bruising on MRI was a highly sensitive finding that was significantly correlated with CPN injury on physical examination. The high prevalence of grade 3 PLC injuries and anteromedial tibiofemoral bone bruising suggests that these MLKIs with CPN injuries most commonly occurred from a hyperextension-varus mechanism caused by a high-energy blow to the anteromedial knee.