High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies

Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, spike (S). Here, we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using coronavirus disease 2019 (COVID-19) convalescent plasma. Antibody binding was common in two regions, the fusion peptide and the linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.

Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies

A prerequisite for the design of an HIV vaccine that elicits protective antibodies is understanding the developmental pathways that result in desirable antibody features. The development of antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) is particularly relevant because such antibodies have been associated with HIV protection in humans. We reconstructed the developmental pathways of six human HIV-specific ADCC antibodies using longitudinal antibody sequencing data. Most of the inferred naive antibodies did not mediate detectable ADCC. Gain of antigen binding and ADCC function typically required mutations in complementarity determining regions of one or both chains. Enhancement of ADCC potency often required additional mutations in framework regions. Antigen binding affinity and ADCC activity were correlated, but affinity alone was not sufficient to predict ADCC potency. Thus, elicitation of broadly active ADCC antibodies may require mutations that enable high-affinity antigen recognition along with mutations that optimize factors contributing to functional ADCC activity.

Anatomic Total Shoulder Arthroplasty with All-Polyethylene Glenoid Component for Primary Osteoarthritis with Glenoid Deficiencies

This study evaluated the ability of shoulder arthroplasty using a standard glenoid component to improve patient self-assessed comfort and function and to correct preoperative humeral-head decentering on the face of the glenoid in patients with primary glenohumeral arthritis and type-B2 or B3 glenoids.

High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies

Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, Spike (S). Here we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using COVID-19 convalescent plasma. Antibody binding was common in two regions: the fusion peptide and linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.

Using B cell receptor lineage structures to predict affinity

We are frequently faced with a large collection of antibodies, and want to select those with highest affinity for their cognate antigen. When developing a first-line therapeutic for a novel pathogen, for instance, we might look for such antibodies in patients that have recovered. There exist effective experimental methods of accomplishing this, such as cell sorting and baiting; however they are time consuming and expensive. Next generation sequencing of B cell receptor (BCR) repertoires offers an additional source of sequences that could be tapped if we had a reliable method of selecting those coding for the best antibodies. In this paper we introduce a method that uses evolutionary information from the family of related sequences that share a naive ancestor to predict the affinity of each resulting antibody for its antigen. When combined with information on the identity of the antigen, this method should provide a source of effective new antibodies. We also introduce a method for a related task: given an antibody of interest and its inferred ancestral lineage, which branches in the tree are likely to harbor key affinity-increasing mutations? We evaluate the performance of these methods on a wide variety of simulated samples, as well as two real data samples. These methods are implemented as part of continuing development of the partis BCR inference package, available at https://github.com/psathyrella/partis. Comments Please post comments or questions on this paper as new issues at https://git.io/Jvxkn.

Impact of previous non-arthroplasty surgery on clinical outcomes after primary anatomic shoulder arthroplasty

BACKGROUND

The objectives of this study were to address the following questions regarding previous non-arthroplasty surgery prior to primary anatomic shoulder arthroplasty (either total shoulder arthroplasty [TSA] or ream-and-run arthroplasty): (1) To what degree is primary anatomic shoulder arthroplasty after prior non-arthroplasty surgery associated with inferior clinical outcomes and higher revision rates compared with arthroplasty without previous surgery? (2) Does type, approach, or timing of previous surgery affect outcomes after anatomic arthroplasty?

METHODS

A retrospective review of a primary shoulder arthroplasty database was performed and identified 640 patients undergoing anatomic shoulder arthroplasty (345 TSAs and 295 ream-and-run arthroplasties). Of these patients, 183 (29%) underwent previous non-arthroplasty surgery. Baseline and demographic information, 2-year postoperative outcome scores, and revision surgical procedures with associated culture results were collected.

RESULTS

In patients undergoing TSA, previous non-arthroplasty surgery was associated with a significantly lower 2-year Simple Shoulder Test (SST) score (P = .010), percentage maximum possible improvement (MPI) (P = .024), and Single Assessment Numeric Evaluation (SANE) score (P < .001) and a higher rate of reoperation (P < .001). In patients undergoing ream-and-run arthroplasty, previous non-arthroplasty surgery was associated with a nonsignificantly lower 2-year SST score, percentage MPI, and SANE score and higher reoperation rate. Prior fracture surgery carried a higher risk of reoperation than other types of surgery including rotator cuff repair and instability surgery. Among TSA and ream-and-run arthroplasty cases with prior non-arthroplasty surgery, prior open surgery and the time interval from most recent surgery were associated with nonsignificant differences in the 2-year SST score, percentage MPI, SANE score, and revision risk.

CONCLUSION

Previous surgery is associated with inferior clinical outcomes and higher revision rates in patients undergoing index TSA but not in those undergoing the ream-and-run procedure. Patients with previous fracture surgery carry the highest risk of reoperation.

Cutibacterium subtype distribution on the skin of primary and revision shoulder arthroplasty patients

BACKGROUND

The skin of healthy shoulders is known to harbor multiple different subtypes of Cutibacterium (formerly Propionibacterium) acnes at the same time. C acnes can often be isolated from deep tissue and explant samples obtained during revision of a failed shoulder arthroplasty, presumably because the shoulder was inoculated with organisms from the patient's skin at the time of the index arthroplasty. It is possible that specific subtypes or distributions of subtypes may be associated with an increased pathogenic potential and that the skin of patients undergoing revision arthroplasty contains different distributions of the subtypes than in patients undergoing primary arthroplasty. We analyzed the subtype distribution of Cutibacterium from the skin of shoulders undergoing revision arthroplasty vs. primary arthroplasty.

METHODS

Preoperative skin swabs were collected from 25 patients who underwent primary shoulder arthroplasty and 27 patients who underwent revision shoulder arthroplasty. The results of semiquantitative cultures of the skin and deep tissues were reported as specimen Cutibacterium values, and scores from all deep tissue samples were added to report the total shoulder Cutibacterium score. Single-locus sequence typing (SLST) of C acnes from the skin swabs was used to determine the subtype distribution for each patient. The percentage of each subtype for each patient was averaged in patients undergoing revision arthroplasty and then compared with that in patients undergoing primary arthroplasty.

RESULTS

The C acnes subtype distribution on the skin of revision arthroplasty patients was different from that of primary shoulder arthroplasty patients, with a significantly higher percentage of SLST subtype A (36.9% vs. 16.0%, P = .0018). The distribution of SLST subtypes was similar between revision arthroplasty patients with strongly positive culture findings vs. those with weakly positive or negative culture findings.

CONCLUSIONS

Significant differences in the skin Cutibacterium subtype distributions were found between shoulders undergoing revision shoulder arthroplasty and those undergoing primary shoulder arthroplasty. Future studies are needed to determine whether certain Cutibacterium subtype distributions are associated with an increased risk of arthroplasty revision.

Preoperative Skin Cultures Predict Periprosthetic Infections in Revised Shoulder Arthroplasties: A Preliminary Report

Current approaches do not provide a practical method for the accurate prediction of a Cutibacterium periprosthetic joint infection (PJI) in failed arthroplasties. Thus, surgeons revising failed arthroplasties must decide whether to exchange the implants and to institute antibiotic treatment without knowing the results of cultures of deep specimens obtained at the revision procedure. This study tests the hypothesis that the results of preoperative culture specimens of the skin surface obtained in the clinic can predict the presence of culture-positive Cutibacterium PJIs.

METHODS

Revision shoulder arthroplasties performed between October 3, 2017, and February 4, 2020, that had both preoperative clinic culture specimens and surgical culture specimens were included in this analysis. Culture results were assigned a value from 0 to 4. The percentage of the total skin bacterial load contributed by Cutibacterium (Cutibacterium percentage) was determined. To reduce concern about contamination, a robust criterion for culture-positive Cutibacterium PJI was applied: ≥2 surgical specimens with a Cutibacterium value of ≥1. The predictive values for a culture-positive Cutibacterium PJI were determined for a clinic skin culture Cutibacterium value of >1 and a clinic skin percentage of Cutibacterium of ≥75%.

RESULTS

Eighteen cases met the inclusion criteria; of these, 7 (6 male patients) met our criterion for a culture-positive Cutibacterium PJI. For all patients, a preoperative clinic skin Cutibacterium value of >1 predicted the presence of a culture-positive Cutibacterium PJI with an accuracy of 89%, and a clinic skin Cutibacterium percentage of ≥75% predicted the presence of a culture-positive Cutibacterium PJI with an accuracy of 94%. For male patients, a preoperative clinic skin Cutibacterium value of >1 predicted the presence of a culture-positive Cutibacterium PJI with an accuracy of 91%, and a clinic skin Cutibacterium percentage of ≥75% predicted the presence of a culture-positive Cutibacterium PJI with an accuracy of 100%.

CONCLUSIONS

A simple culture specimen of the unprepared skin surface obtained in a clinic prior to revision shoulder arthroplasty may provide valuable assistance to surgeons planning a revision arthroplasty.

LEVEL OF EVIDENCE

Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.

Efficacy of Home Prophylactic Benzoyl Peroxide and Chlorhexidine in Shoulder Surgery: A Systematic Review and Meta-Analysis

Two predominant prophylactic home skin-disinfection regimens exist in shoulder surgery, benzoyl peroxide and chlorhexidine. Of these 2 regimens, benzoyl peroxide gel is more effective than chlorhexidine in reducing the rate of positive Cutibacterium cultures on the skin surface. At present, there are no studies that assess the impact of these home prophylactic measures on clinical infection rates.

Lack of Evidence for a Substantial Rate of Templated Mutagenesis in B Cell Diversification

BCR sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is a major contributor to somatic hypermutation and therefore Ig diversification in mice and humans. In this proposed process, mutations in the Ig locus are introduced by copying short segments from other Ig genes. If true, this would overturn decades of research on B cell diversification and would require a complete rewrite of computational methods to analyze B cell data for these species. In this paper, we re-evaluate the templated mutagenesis hypothesis. By applying the original inferential method using potential donor templates absent from B cell genomes, we obtain estimates of the methods' false positive rates. We find false positive rates of templated mutagenesis in murine and human Ig loci that are similar to or even higher than the original rate inferences, and by considering the bases used in substitution, we find evidence that if templated mutagenesis occurs, it is at a low rate. We also show that the statistically significant results in the original paper can easily result from a slight misspecification of the null model.

Cutaneous microbiology of patients having primary shoulder arthroplasty

BACKGROUND

Shoulder periprosthetic infections are predominantly caused by bacteria residing in the skin of healthy individuals. Knowledge of the factors associated with the loads of the different cutaneous bacteria in individuals having shoulder arthroplasty may help identify patients at higher risk of periprosthetic infection and help guide preventive measures. For this reason, we tested the hypothesis that easy-to-obtain preoperative characteristics were significantly associated with the cutaneous microbiology and the loads of specific bacteria in shoulders having joint replacement.

METHODS

This study identified the microbiology of the unprepared epidermal skin surface and of the dermal edge freshly incised at surgery in 332 patients having primary shoulder arthroplasty. The load of bacteria in each sample was characterized as a value based on the laboratory report: 0 for "no growth"; 0.1 for "one colony only" or for "broth only"; and 1, 2, 3, and 4 for 1+, 2+, 3+, and 4+ growth, respectively. The relationships between preoperative patient characteristics and these semiquantitative results of the cutaneous cultures were analyzed.

RESULTS

Cultures of the unprepared epidermal skin surface showed positive results for a wide variety of organisms, including Cutibacterium in 72%, coagulase-negative Staphylococcus in 61%, and a spectrum of other organisms in 32%. By contrast, cultures of the freshly incised dermal edge showed a great preponderance of Cutibacterium (34%) in comparison to low levels of coagulase-negative Staphylococcus (8%) and other organisms (2%). An increased dermal load of Cutibacterium was significantly associated with male sex, younger patient age, American Society of Anesthesiologists class 1, use of testosterone supplements, prior shoulder surgery, and higher Cutibacterium loads on the unprepared skin surface.

CONCLUSIONS

Although the microbiology of the unprepared skin surface is diverse, the same is not true for the freshly incised dermis, where Cutibacterium is the predominant organism. Readily available preoperative patient characteristics are significantly associated with the load of Cutibacterium in the incised dermis. Preoperative cultures of the unprepared skin surface appear to be a new method for predicting the type and load of bacteria found in the freshly incised dermis at the time of surgery. Additional studies are needed to determine whether preoperative cultures of the unprepared epidermal skin surface can provide a method for identifying patients at increased risk of shoulder periprosthetic infections.

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling.

Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO

Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special features, including sampled ancestors in which we sequence a genotype along with its direct descendants, and polytomies in which multiple descendants arise simultaneously. These features are apparent after identifying zero-length branches in the tree. However, current maximum-likelihood based approaches are not capable of revealing such zero-length branches. In this paper, we find these zero-length branches by introducing adaptive-LASSO-type regularization estimators for the branch lengths of phylogenetic trees, deriving their properties, and showing regularization to be a practically useful approach for phylogenetics.

The Use and Adverse Effects of Oral and Intravenous Antibiotic Administration for Suspected Infection After Revision Shoulder Arthroplasty

BACKGROUND

When performing revision shoulder arthroplasty, surgeons do not have access to the results of intraoperative culture specimens and will administer empiric antibiotics to cover for the possibility of deep infection until the culture results are finalized. The purpose of this study was to report the factors associated with the initiation, modification, and adverse events of 2 different postoperative antibiotic protocols in a series of revision shoulder arthroplasties.

METHODS

In this study, 175 patients undergoing revision shoulder arthroplasty were treated with either a protocol of intravenous (IV) antibiotics if there was a high index of suspicion for infection or a protocol of oral antibiotics if the index of suspicion was low. Antibiotics were withdrawn if cultures were negative and were modified as indicated if the cultures were positive. Antibiotic course, modification, and adverse effects to antibiotic administration were documented.

RESULTS

On univariate analysis, factors significantly associated with the initiation of IV antibiotics were male sex (p < 0.001), history of infection (p < 0.001), intraoperative humeral loosening (p = 0.003), and membrane formation (p < 0.001). On multivariate analysis, male sex (p = 0.003), history of infection (p = 0.003), and membrane formation (p < 0.001) were found to be independent predictors of the initiation of IV antibiotics. On the basis of preoperative and intraoperative characteristics, surgeons anticipated the culture results in 75% of cases, and modification of antibiotic therapy was required in 25%. The modification from oral to IV antibiotics due to positive culture results was made significantly more often in male patients (p < 0.001). Adverse effects of antibiotic administration occurred in 19% of patients. The rates of complications were significantly lower in the patients treated with oral antibiotics and a shorter course of antibiotics (p < 0.001).

CONCLUSIONS

Complications associated with antibiotic administration after revision shoulder arthroplasty are not infrequent and are more common in patients whose initial protocol is IV antibiotics. Further study is needed to balance the effectiveness and risks of post-revision antibiotic treatment given the frequency of antibiotic-related complications.

LEVEL OF EVIDENCE

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.

OGRDB: a reference database of inferred immune receptor genes

High-throughput sequencing of the adaptive immune receptor repertoire (AIRR-seq) is providing unprecedented insights into the immune response to disease and into the development of immune disorders. The accurate interpretation of AIRR-seq data depends on the existence of comprehensive germline gene reference sets. Current sets are known to be incomplete and unrepresentative of the degree of polymorphism and diversity in human and animal populations. A key issue is the complexity of the genomic regions in which they lie, which, because of the presence of multiple repeats, insertions and deletions, have not proved tractable with short-read whole genome sequencing. Recently, tools and methods for inferring such gene sequences from AIRR-seq datasets have become available, and a community approach has been developed for the expert review and publication of such inferences. Here, we present OGRDB, the Open Germline Receptor Database (https://ogrdb.airr-community.org), a public resource for the submission, review and publication of previously unknown receptor germline sequences together with supporting evidence.

19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology

The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for the posterior density, obtained by integrating the product of the likelihood and the prior with respect to model parameters. Thus, the computational burden of computing the marginal likelihood scales with the dimension of the parameter space. In phylogenetics, where we work with tree topologies that are high-dimensional models, standard approaches to computing marginal likelihoods are very slow. Here, we study methods to quickly compute the marginal likelihood of a single fixed tree topology. We benchmark the speed and accuracy of 19 different methods to compute the marginal likelihood of phylogenetic topologies on a suite of real data sets under the JC69 model. These methods include several new ones that we develop explicitly to solve this problem, as well as existing algorithms that we apply to phylogenetic models for the first time. Altogether, our results show that the accuracy of these methods varies widely, and that accuracy does not necessarily correlate with computational burden. Our newly developed methods are orders of magnitude faster than standard approaches, and in some cases, their accuracy rivals the best established estimators.

Diversity and Function of Maternal HIV-1-Specific Antibodies at the Time of Vertical Transmission

Infants of HIV-positive mothers can acquire HIV infection by various routes, but even in the absence of antiviral treatment, the majority of these infants do not become infected. There is evidence that maternal antibodies provide some protection from infection, but gestational maternal antibodies have not yet been characterized in detail. One of the most studied vertically infected infants is BG505, as the virus from this infant yielded an Envelope protein that was successfully developed as a stable trimer. Here, we isolated and characterized 39 HIV-specific neutralizing monoclonal antibodies (nAbs) from MG505, the mother of BG505, at a time point just prior to vertical transmission. These nAbs belonged to 21 clonal families and employed a variety of VH genes. Many were specific for the HIV-1 Env V3 loop, and this V3 specificity correlated with measurable antibody-dependent cellular cytotoxicity (ADCC) activity. The isolated nAbs did not recapitulate the full breadth of heterologous or autologous virus neutralization by contemporaneous plasma. Notably, we found that the V3-targeting nAb families neutralized one particular maternal Env variant, even though all tested variants had low V3 sequence diversity and were measurably bound by these nAbs. None of the nAbs neutralized BG505 transmitted virus. Furthermore, the MG505 nAb families were found at relatively low frequencies within the maternal B cell repertoire; all were less than 0.25% of total IgG sequences. Our findings illustrate an example of the diversity of HIV-1 nAbs within one mother, cumulatively resulting in a collection of antibody specificities that can contribute to the transmission bottleneck.IMPORTANCE Mother-to-child-transmission of HIV-1 offers a unique setting in which maternal antibodies both within the mother and passively transferred to the infant are present at the time of viral exposure. Untreated HIV-exposed human infants are infected at a rate of 30 to 40%, meaning that some infants do not get infected despite continued exposure to virus. Since the potential of HIV-specific immune responses to provide protection against HIV is a central goal of HIV vaccine design, understanding the nature of maternal antibodies may provide insights into immune mechanisms of protection. In this study, we isolated and characterized HIV-specific antibodies from the mother of an infant whose transmitted virus has been well studied.

Industry payments to authors of Journal of Shoulder and Elbow Surgery shoulder arthroplasty manuscripts are accurately disclosed by most authors and are not significantly associated with better reported treatment outcomes

BACKGROUND

Author transparency in disclosing potential conflicts of interest when reporting outcomes for shoulder arthroplasty implants is important. Using the Centers for Medicare & Medicaid Services Open Payments Program (OPP) database, we analyzed articles in the Journal of Shoulder and Elbow Surgery to evaluate (1) discrepancies between the stated conflicts of interest and associated payments recorded in the database, (2) the magnitude and types of payments received, and (3) possible relationships between industry financial support and positive study outcomes.

METHODS

Articles reporting clinical outcomes of shoulder arthroplasty from 2016 and 2017 were reviewed. Articles identifying a specific shoulder arthroplasty implant and having at least 1 author based in the United States were included. Payment types, amounts, and sources were extracted from disclosure statements in the manuscript and considered relevant if they were received from the implant manufacturer. Published disclosure statements were compared against the OPP database. Study outcomes demonstrating a clinical benefit were considered "positive." Payments to authors reporting positive outcomes were compared with those reporting nonpositive outcomes.

RESULTS

Implant manufacturers provided $16,051,261 to authors of shoulder arthroplasty publications over a 2-year period. Approximately half of senior authors (46%) received royalty payments, more than 90% of which ($14,910,873; 93%) were reported in disclosure statements. Although authors of articles with positive outcomes received greater payments than those reporting nonpositive outcomes, these differences were not statistically significant.

CONCLUSION

The majority of author disclosure statements accurately reflected the OPP data. Payments were not significantly associated with positive outcomes reported for the specific implant.

Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies

Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In this article, we present an efficient parallelized method to map out the high likelihood set of phylogenetic tree topologies via systematic search, which we show to be a good approximation of the high posterior set of tree topologies on the data sets analyzed. Here, "likelihood" of a topology refers to the tree likelihood for the corresponding tree with optimized branch lengths. We call this method "phylogenetic topographer" (PT). The PT strategy is very simple: starting in a number of local topology maxima (obtained by hill-climbing from random starting points), explore out using local topology rearrangements, only continuing through topologies that are better than some likelihood threshold below the best observed topology. We show that the normalized topology likelihoods are a useful proxy for the Bayesian posterior probability of those topologies. By using a nonblocking hash table keyed on unique representations of tree topologies, we avoid visiting topologies more than once across all concurrent threads exploring tree space. We demonstrate that PT can be used directly to approximate a Bayesian consensus tree topology. When combined with an accurate means of evaluating per-topology marginal likelihoods, PT gives an alternative procedure for obtaining Bayesian posterior distributions on phylogenetic tree topologies.

While home chlorhexidine washes prior to shoulder surgery lower skin loads of most bacteria, they are not effective against Cutibacterium (Propionibacterium)

PURPOSE

Chlorhexidine showers prior to shoulder arthroplasty are commonly recommended by surgeons to lower the risk of periprosthetic infection; however, the effectiveness of these washes in eliminating bacteria from the skin of the shoulder has not been thoroughly evaluated. The objective of this study was to determine the degree to which pre-operative chlorhexidine washes effectively eliminate bacteria from the epidermal skin surface and from the dermis freshly incised during shoulder arthroplasty.

METHODS

Around 66 patients undergoing primary shoulder arthroplasty were instructed to shower with chlorhexidine before surgery. Each patient had three skin swabs: (1) the epidermis at a pre-operative clinic appointment, (2) the epidermis at surgery after home chlorhexidine showers but prior to skin preparation, and (3) the dermis after incision of the prepared skin. The bacterial loads of Cutibacterium and other bacterial types from each swab were compared to determine whether the showers were effective in altering the bacterial loads.

RESULTS

Chlorhexidine washes were effective in reducing the skin load of other bacterial species (p < 0.005), but they did not decrease the skin load of Cutibacterium (p = 0.585).

CONCLUSIONS

Pre-operative skin showers with chlorhexidine were not effective in reducing the load of Cutibacterium on the skin of patients having shoulder arthroplasty. Since Cutibacterium is responsible for the highest percentage of shoulder periprosthetic infections, research is needed to identify more effective means of removing these bacteria from the surgical field.

On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model

Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to converge to the true value in the independent-sample case, we cannot appeal to this result because trait values of different species are correlated due to shared evolutionary history. In this paper, we consider a 2-state symmetric model for a single binary trait and investigate the theoretical properties of the MLE for the transition rate in the large-tree limit. Here, the large-tree limit is a theoretical scenario where the number of taxa increases to infinity and we can observe the trait values for all species. Specifically, we prove that the MLE converges to the true value under some regularity conditions. These conditions ensure that the tree shape is not too irregular, and holds for many practical scenarios such as trees with bounded edges, trees generated from the Yule (pure birth) process, and trees generated from the coalescent point process. Our result also provides an upper bound for the distance between the MLE and the true value.

sumrep: A Summary Statistic Framework for Immune Receptor Repertoire Comparison and Model Validation

The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. The DNA sequences coding for these receptors arise by a complex recombination process followed by a series of productivity-based filters, as well as affinity maturation for B cells, giving considerable diversity to the circulating pool of receptor sequences. Although these datasets hold considerable promise for medical and public health applications, the complex structure of the resulting adaptive immune receptor repertoire sequencing (AIRR-seq) datasets makes analysis difficult. In this paper we introduce sumrep, an R package that efficiently performs a wide variety of repertoire summaries and comparisons, and show how sumrep can be used to perform model validation. We find that summaries vary in their ability to differentiate between datasets, although many are able to distinguish between covariates such as donor, timepoint, and cell type for BCR and TCR repertoires. We show that deletion and insertion lengths resulting from V(D)J recombination tend to be more discriminative characterizations of a repertoire than summaries that describe the amino acid composition of the CDR3 region. We also find that state-of-the-art generative models excel at recapitulating gene usage and recombination statistics in a given experimental repertoire, but struggle to capture many physiochemical properties of real repertoires.

Radiographic outcomes of impaction-grafted standard-length humeral components in total shoulder and ream-and-run arthroplasty: is stress shielding an issue?

BACKGROUND

The purpose of this study was to evaluate humeral stress shielding in shoulder arthroplasties performed with a smooth, standard-length humeral stem fixed with impaction autografting.

METHODS

Two-year outcomes were evaluated for 48 ream-and-run arthroplasties and 78 total shoulder arthroplasties (TSAs) performed at a single institution. Postoperative radiographs were analyzed for adaptive changes, calcar osteolysis, and component shift or subsidence. Radiographic outcomes were analyzed for associations with patient demographic characteristics, humeral stem filling ratios, and glenoid loosening; clinical outcomes were assessed using the Simple Shoulder Test.

RESULTS

At 2 years after surgery, the ream-and-run procedures showed partial calcar osteolysis in 9 cases (19%). The TSAs showed partial calcar osteolysis in 19 cases (24%) and complete calcar osteolysis in 2 (3%). Humeral component subsidence or component shift was observed in 3 ream-and-run procedures (6%) and in 8 TSAs (10%). These radiographic findings were not significantly associated with patient demographic characteristics, canal-filling ratios, or clinical outcomes.

CONCLUSION

When inserted with impaction autografting, a smooth, standard-length humeral stem offers a secure bone-preserving approach for humeral component fixation in shoulder arthroplasty. These results with a conventional prosthesis can serve as a basis for comparison for new component designs and fixation methods.