Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance.

BACKGROUND: Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. METHODS: To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years. RESULTS: Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. CONCLUSIONS: Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.

Capacity for Hand-as-a-Holder Function of the Spastic Combination Hand: A Proof-of-Concept Study.

ABSTRACT: We call a hemiparetic hand with paralyzed finger extensors and volitional but spastic flexors a "spastic combination hand." Anecdotally, patients report hand-as-a-holder function with objects like pill bottles, motivating us to formally study spastic combination hand holding capacity using cylinders with different diameters. Nine participants with spastic hemiparesis and spastic combination hand more than 24 mos performed a standardized motor task with 10 cylinder diameters ranging between 1.3 and 9.5 cm and weighing 0.8 and 8.4 oz. Using the unaffected hand, participants attempted to insert a given cylinder into their spastic combination hand, holding it independently for 5 secs. Successful holds were counted during two sessions before and one session after botulinum toxin intervention of Ashworth 3 hand muscles. Findings revealed that a median capacity of six different cylinder diameters was successfully inserted into spastic combination hand at least once before block and a median capacity of 10 cylinders was inserted after block. A mixed-effect statistical model using fixed effects of cylinder diameter and session revealed that total number of successful holds was 43% higher after botulinum. We conclude that this proof-of-concept study does support the idea that spastic combination hand has holding capacity for cylindrical objects of specified diameter and weight and that botulinum neurotoxin offers potential for enlarging spastic combination hand capacity.

Recommendations for Reporting on Rehabilitation Interventions.

ABSTRACT: Clear reporting on rehabilitation treatments is critical for interpreting and replicating study results and for translating treatment research into clinical practice. This article reports the recommendations of a working group on improved reporting on rehabilitation treatments. These recommendations are intended to be combined with the efforts of other working groups, through a consensus process, to arrive at a reporting guideline for randomized controlled trials in physical medicine and rehabilitation (Randomized Controlled Trials Rehabilitation Checklist). The work group conducted a scoping review of 156 diverse guidelines for randomized controlled trial reporting, to identify themes that might be usefully applied to the field of rehabilitation. Themes were developed by identifying content that might improve or enhance existing items from the Template for Intervention Description and Replication. Guidelines addressing broad research domains tended to define reporting items generally, from the investigator's perspective of relevance, whereas those addressing more circumscribed domains provided more specific and operationalized items. Rehabilitation is a diverse field, but a clear description of the treatment's separable components, along with distinct treatment theories for each, can improve reporting of relevant information. Over time, expert consensus groups should develop more specific guideline extensions for circumscribed research domains, around coalescing bodies of treatment theory.

Improving communication with patients in post-traumatic amnesia: development and impact of a clinical protocol.

OBJECTIVE: To assess the impact of staff training focused on improved treatment and communication with patients in post-traumatic amnesia (PTA) or other disorders of explicit (declarative) memory. A major aim was to minimize questions demanding recall from explicit memory, e.g., orientation quizzing, and personal/medical history questions, which may produce unreliable information and exacerbate patient frustration and anxiety. METHODS: Mixed-methods design. Inpatients with impairments of explicit memory were observed before (n = 4) and after (n = 4) training, with staff interactions recorded verbatim. Records were coded for types of questions and patient responses. Clinicians who worked before and after training were surveyed regarding perceived changes in practice, team functioning, and patient behavior. RESULTS: Explicit memory questions decreased significantly, as did irrelevant or "don't know" responses from patients, with large nonparametric effect sizes noted. The frequency of questions not relying on explicit memory remained stable. Most clinicians reported positive effects on their own and others' practice with memory impaired patients, and one-quarter noted less patient frustration or agitation. CONCLUSIONS: Although questioning patients is a natural part of medical care, targeted staff training can result in positive changes in communication practice and should be considered for facilities treating patients in PTA.

Rationale for a Neisseria gonorrhoeae Susceptible-only Interpretive Breakpoint for Azithromycin.

BACKGROUND: Azithromycin (AZI) is recommended with ceftriaxone (CRO) for treatment of uncomplicated gonococcal urethritis and cervicitis in the United States, and an AZI-susceptibility breakpoint is needed. Neither the Food and Drug Administration (FDA) nor the Clinical and Laboratory Standards Institute (CLSI) has set interpretive breakpoints for AZI susceptibility. As a result, AZI antimicrobial susceptibility testing (AST) cannot be interpreted using recognized standards. This has contributed to increasingly unavailable clinical laboratory AST, although gonorrhea is on the rise with >550 000 US gonorrhea cases reported to the Centers for Disease Control and Prevention in 2017, the highest number of cases since 1991. METHODS: This article summarizes the rationale data reviewed by the CLSI in June 2018. RESULTS: The CLSI decided to set a susceptible-only interpretive breakpoint at the minimum inhibitory concentration of ≤1 µg/mL. This is also the epidemiological cutoff value (ECV) (ie, the end of the wild-type susceptibility distribution). This breakpoint presumes that AZI (1-g single dose) is used in an approved regimen that includes an additional antimicrobial agent (ie, CRO 250 mg, intramuscular single dose). CONCLUSIONS: Having a breakpoint can improve patient care and surveillance and allow future development and FDA regulatory approval of modernized AST to guide treatment. The breakpoint coincides with a European Committee on AST decision to remove previously established, differing AZI breakpoints and use the ECV as guidance for testing. The CLSI breakpoint is now the recognized standard that defines AZI susceptibility for gonococcal infections.

Occupational Therapy Can Benefit From an Interprofessional Rehabilitation Treatment Specification System.

To advance evidence-based practice across rehabilitation professions, clinicians, and researchers could benefit from a structured way to clearly describe the treatment interventions used by their discipline. Development of the Rehabilitation Treatment Specification System is an interprofessional effort to use a theory-driven and systematic approach to define, specify, and quantify the complex nature of rehabilitation treatments. In this article, we introduce this novel approach and provide a case example that illustrates application to clinical practice. We invite occupational therapy practitioners to consider how clear specification of the content and process of their interventions could benefit practice, research, and education.

Microplate-based surface area assay for rapid phenotypic antibiotic susceptibility testing.

Rapid delivery of proper antibiotic therapies to infectious disease patients is essential for improving patient outcomes, decreasing hospital lengths-of-stay, and combating the antibiotic resistance epidemic. Antibiotic stewardship programs are designed to address these issues by coordinating hospital efforts to rapidly deliver the most effective antibiotics for each patient, which requires bacterial identification and antimicrobial susceptibility testing (AST). Despite the clinical need for fast susceptibility testing over a wide range of antibiotics, conventional phenotypic AST requires overnight incubations, and new rapid phenotypic AST platforms restrict the number of antibiotics tested for each patient. Here, we introduce a novel approach to AST based on signal amplification of bacterial surfaces that enables phenotypic AST within 5 hours for non-fastidious bacteria. By binding bacterial surfaces, this novel method allows more accurate measurements of bacterial replication in instances where organisms filament or swell in response to antibiotic exposure. Further, as an endpoint assay performed on standard microplates, this method should enable parallel testing of more antibiotics than is currently possible with available automated systems. This technology has the potential to revolutionize clinical practice by providing rapid and accurate phenotypic AST data for virtually all available antibiotics in a single test.

The Importance of Voluntary Behavior in Rehabilitation Treatment and Outcomes.

Most rehabilitation treatments are volitional in nature, meaning that they require the patient's active engagement and effort. Volitional treatments are particularly challenging to define in a standardized fashion, because the clinician is not in complete control of the patient's role in enacting these treatments. Current recommendations for describing treatments in research reports fail to distinguish between 2 fundamentally different aspects of treatment design: the selection of treatment ingredients to produce the desired functional change and the selection of ingredients that will ensure the patient's volitional performance. The Rehabilitation Treatment Specification System (RTSS) is a conceptual scheme for standardizing the way that rehabilitation treatments are defined by all disciplines across all areas of rehabilitation. The RTSS highlights the importance of volitional behavior in many treatment areas and provides specific guidance for how volitional treatments should be specified. In doing so, it suggests important crosscutting research questions about the nature of volitional behavior, factors that make it more or less likely to occur, and ingredients that are most effective in ensuring that patients perform desired treatment activities.

A Theory-Driven System for the Specification of Rehabilitation Treatments.

The field of rehabilitation remains captive to the black-box problem: our inability to characterize treatments in a systematic fashion across diagnoses, settings, and disciplines, so as to identify and disseminate the active ingredients of those treatments. In this article, we describe the Rehabilitation Treatment Specification System (RTSS), by which any treatment employed in rehabilitation may be characterized, and ultimately classified according to shared properties, via the 3 elements of treatment theory: targets, ingredients, and (hypothesized) mechanisms of action. We discuss important concepts in the RTSS such as the distinction between treatments and treatment components, which consist of 1 target and its associated ingredients; and the distinction between targets, which are the direct effects of treatment, and aims, which are downstream or distal effects. The RTSS includes 3 groups of mutually exclusive treatment components: Organ Functions, Skills and Habits, and Representations. The last of these comprises not only thoughts and feelings, but also internal representations underlying volitional action; the RTSS addresses the concept of volition (effort) as a critical element for many rehabilitation treatments. We have developed an algorithm for treatment specification which is illustrated and described in brief. The RTSS stands to benefit the field in numerous ways by supplying a coherent, theory-based framework encompassing all rehabilitation treatments. Using a common framework, researchers will be able to test systematically the effects of specific ingredients on specific targets; and their work will be more readily replicated and translated into clinical practice.

Advancing Rehabilitation Practice Through Improved Specification of Interventions.

Rehabilitation clinicians strive to provide cost-effective, patient-centered care that optimizes outcomes. A barrier to this ideal is the lack of a universal system for describing, or specifying, rehabilitation interventions. Current methods of description vary across disciplines and settings, creating barriers to collaboration, and tend to focus mostly on functional deficits and anticipated outcomes, obscuring connections between clinician behaviors and changes in functioning. The Rehabilitation Treatment Specification System (RTSS) is the result of more than a decade of effort by a multidisciplinary group of rehabilitation clinicians and researchers to develop a theory-based framework to specify rehabilitation interventions. The RTSS describes interventions for treatment components, which consist of a target (functional change brought about as a direct result of treatment), ingredients (actions taken by clinicians to change the target), and a hypothesized mechanism of action, as stated in a treatment theory. The RTSS makes explicit the connections between functional change and clinician behavior, and recognizes the role of patient effort in treatment implementation. In so doing, the RTSS supports clinicians' efforts to work with their patients to set achievable goals, select appropriate treatments, adjust treatment plans as needed, encourage patient participation in the treatment process, communicate with team members, and translate research findings to clinical care. The RTSS may help both expert and novice clinicians articulate their clinical reasoning processes in ways that benefit treatment planning and clinical education, and may improve the design of clinical documentation systems, leading to more effective justification and reimbursement for services. Interested clinicians are invited to apply the RTSS in their local settings.

Twenty-first Century Cures Act and Antimicrobial Susceptibility Testing: Clinical Implications in the Era of Multidrug Resistance.

Clinical laboratories act at the frontline of identification of infections caused by multidrug-resistant organisms, and yet the tools they apply are often woefully out of date. Incomplete adoption of current testing standards, updated breakpoints, and tests for new drugs across laboratories has been exacerbated by lack of coordination between standards development organizations (SDOs), pharmaceutical companies, susceptibility test manufacturers, and the US Food and Drug Administration. The 21st Century Cures Act includes provisions to enable alignment between these groups by (1) allowing recognition of breakpoints set by qualified SDOs; (2) publicly posting recognized breakpoints; and (3) reviewing breakpoints for necessary updates, every 6 months. Combined, these provisions will ensure more rapid recognition of current breakpoints, improving detection and management of resistant infections. Although several limitations remain, this will ultimately allow susceptibility test manufacturers to more readily update to current breakpoints.

Impact of 21st Century Cures Act on Breakpoints and Commercial Antimicrobial Susceptibility Test Systems: Progress and Pitfalls.

Antimicrobial resistance is the most pressing medical challenge of the past decade. At the front line are clinical laboratories, which are responsible for accurately reporting antimicrobial susceptibility test (AST) results to clinicians and public health authorities. The ability of the laboratory to detect resistance has been hampered by several factors. In 2016, the 21st Century Cures Act was signed into law, marking an important step toward resolving many regulatory dilemmas that hampered development and updates to commercial AST systems (cASTs). We describe the pathway and history of U.S. regulation of cASTs and outline both the rewards and unmet needs possible from the 21st Century Cures Act.

Modified Carbapenem Inactivation Method for Phenotypic Detection of Carbapenemase Production among Enterobacteriaceae.

The ability of clinical microbiology laboratories to reliably detect carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is an important element of the effort to prevent and contain the spread of these pathogens and an integral part of antimicrobial stewardship. All existing methods have limitations. A new, straightforward, inexpensive, and specific phenotypic method for the detection of carbapenemase production, the carbapenem inactivation method (CIM), was recently described. Here we describe a two-stage evaluation of a modified carbapenem inactivation method (mCIM), in which tryptic soy broth was substituted for water during the inactivation step and the length of this incubation was extended. A validation study was performed in a single clinical laboratory to determine the accuracy of the mCIM, followed by a nine-laboratory study to verify the reproducibility of these results and define the zone size cutoff that best discriminated between CP-CRE and members of the family Enterobacteriaceae that do not produce carbapenemases. Bacterial isolates previously characterized through whole-genome sequencing or targeted PCR as to the presence or absence of carbapenemase genes were tested for carbapenemase production using the mCIM; isolates with Ambler class A, B, and D carbapenemases, non-CP-CRE isolates, and carbapenem-susceptible isolates were included. The sensitivity of the mCIM observed in the validation study was 99% (95% confidence interval [95% CI], 93% to 100%), and the specificity was 100% (95% CI, 82% to 100%). In the second stage of the study, the range of sensitivities observed across nine laboratories was 93% to 100%, with a mean of 97%; the range of specificities was 97% to 100%, with a mean of 99%. The mCIM was easy to perform and interpret for Enterobacteriaceae, with results in less than 24 h and excellent reproducibility across laboratories.

Evaluation of Modified 2-Tiered Serodiagnostic Testing Algorithms for Early Lyme Disease.

Background: The conventional 2-tiered serologic testing protocol for Lyme disease (LD), an enzyme immunoassay (EIA) followed by immunoglobulin M and immunoglobulin G Western blots, performs well in late-stage LD but is insensitive in patients with erythema migrans (EM), the most common manifestation of the illness. Western blots are also complex, difficult to interpret, and relatively expensive. In an effort to improve test performance and simplify testing in early LD, we evaluated several modified 2-tiered testing (MTTT) protocols, which use 2 assays designed as first-tier tests sequentially, without the need of Western blots. Methods: The MTTT protocols included (1) a whole-cell sonicate (WCS) EIA followed by a C6 EIA; (2) a WCS EIA followed by a VlsE chemiluminescence immunoassay (CLIA); and (3) a variable major protein-like sequence, expressed (VlsE) CLIA followed by a C6 EIA. Sensitivity was determined using serum from 55 patients with erythema migrans; specificity was determined using serum from 50 patients with other illnesses and 1227 healthy subjects. Results: Sensitivity of the various MTTT protocols in patients with acute erythema migrans ranged from 36% (95% confidence interval [CI], 25%-50%) to 54% (95% CI, 42%-67%), compared with 25% (95% CI, 16%-38%) using the conventional protocol (P = .003-0.3). Among control subjects, the 3 MTTT protocols were similarly specific (99.3%-99.5%) compared with conventional 2-tiered testing (99.5% specificity; P = .6-1.0). Conclusions: Although there were minor differences in sensitivity and specificity among MTTT protocols, each provides comparable or greater sensitivity in acute EM, and similar specificity compared with conventional 2-tiered testing, obviating the need for Western blots.

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks.

Carbapenem-resistant Enterobacteriaceae (CRE) are among the most severe threats to the antibiotic era. Multiple different species can exhibit resistance due to many different mechanisms, and many different mobile elements are capable of transferring resistance between lineages. We prospectively sampled CRE from hospitalized patients from three Boston-area hospitals, together with a collection of CRE from a single California hospital, to define the frequency and characteristics of outbreaks and determine whether there is evidence for transfer of strains within and between hospitals and the frequency with which resistance is transferred between lineages or species. We found eight species exhibiting resistance, with the majority of our sample being the sequence type 258 (ST258) lineage of Klebsiella pneumoniae There was very little evidence of extensive hospital outbreaks, but a great deal of variation in resistance mechanisms and the genomic backgrounds carrying these mechanisms. Local transmission was evident in clear phylogeographic structure between the samples from the two coasts. The most common resistance mechanisms were KPC (K. pneumoniae carbapenemases) beta-lactamases encoded by blaKPC2, blaKPC3, and blaKPC4, which were transferred between strains and species by seven distinct subgroups of the Tn4401 element. We also found evidence for previously unrecognized resistance mechanisms that produced resistance when transformed into a susceptible genomic background. The extensive variation, together with evidence of transmission beyond limited clonal outbreaks, points to multiple unsampled transmission chains throughout the continuum of care, including asymptomatic carriage and transmission of CRE. This finding suggests that to control this threat, we need an aggressive approach to surveillance and isolation.

Asymmetric Response of Costa Rican White-Breasted Wood-Wrens (Henicorhina leucosticta) to Vocalizations from Allopatric Populations.

Divergence in song between allopatric populations can contribute to premating reproductive isolation in territorial birds. Song divergence is typically measured by quantifying divergence in vocal traits using audio recordings, but field playback experiments provide a more direct way to behaviorally measure song divergence between allopatric populations. The White-breasted Wood-Wren (Henicorhina leucosticta; hereafter "WBWW") is an abundant Neotropical species with four mitochondrial clades (in Central America, the Darién, the Chocó and the Amazon) that are deeply divergent (~5-16% sequence divergence). We assessed the possibility that the WBWW as currently defined may represent multiple biological species by conducting both statistical analysis of vocal characters and field playback experiments within three clades (Central America, Chocó and Amazon). Our analysis of vocal traits revealed that Central American songs overlapped in acoustic space with Chocó songs, indicating vocal similarity between these two populations, but that Central American songs were largely divergent from Amazonian songs. Playback experiments in the Caribbean lowlands of Costa Rica revealed that Central American WBWWs typically responded aggressively to songs from the Chocó population but did not respond to playback of songs from the Amazonian population, echoing the results of the vocal trait analysis. This marked difference in behavioral response demonstrates that the songs of Central American and Amazonian WBWWs (but not Central American and Chocó WBWWs) have diverged sufficiently that Central American WBWWs no longer recognize song from Amazonian WBWWs as a signal to elicit territorial defense. This suggests that significant premating reproductive isolation has evolved between these two populations, at least from the perspective of the Central American population, and is consistent with the possibility that Central American and Amazonian populations represent distinct biological species. We conclude by advocating for the further use of field playback experiments to assess premating reproductive isolation (and species limits) between allopatric songbird populations, a situation where behavioral systematics can answer questions that phylogenetic systematics cannot.

Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of Vibrio cholerae.

We evaluated the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MS) for the identification of Vibrio cholerae. MS identified all 42 isolates of V. cholerae O1 and O139 and 7 of 9 non-O1/O139 isolates. MS correctly discriminated between all Aeromonas and V. cholerae isolates. Overall, MS performed as well as or better than biochemical methods.

The practice of clinical pathology: a quantitative description of laboratory director activities at a large academic medical center.

OBJECTIVES: The scope of activities performed by clinical laboratory directors is sometimes unfamiliar to other physicians or hospital administrators. Consequently, hospital leadership may undervalue the role and assume that many director level activities could be delegated to a professional manager. In this study, we sought to define the activities of academic laboratory directors, and to determine which activities require doctorate level medical or scientific expertise. METHODS: We performed an audit of laboratory director activities at a large academic medical center by reviewing electronic calendars and other available records from the preceding 12 consecutive months. For episodic activities, the directors estimated the average number of hours devoted over the 1-year period. RESULTS: On average, directors worked 54.9 hours per week and performed at least some service work 47.7 weeks per year. Administrative duties accounted for the greatest proportion of effort (47.1%), followed by clinical activities (33.1%) and academic activities (19.8%). Among administrative duties, those that required doctorate level medical or scientific expertise comprised 60.3% of the total administrative effort, whereas the remaining 39.7% (18.7% of total activity) could be performed by a professional manager.. CONCLUSIONS: Although the activities of clinical laboratory directors have been described elsewhere, this is the first study detailing the effort allocated to these various activities in quantitative terms. The study demonstrated that less than 20% of an academic laboratory director's effort involves administrative activities that could potentially be performed by a professional manager lacking doctorate level medical or scientific expertise.

Cefepime vs other antibacterial agents for the treatment of Enterobacter species bacteremia.

BACKGROUND: Carbapenems are recommended for treatment of Enterobacter infections with AmpC phenotypes. Although isolates are typically susceptible to cefepime in vitro, there are few data supporting its clinical efficacy. METHODS: We reviewed all cases of Enterobacter species bacteremia at 2 academic hospitals from 2005 to 2011. Outcomes of interest were (1) persistent bacteremia ≥1 calendar day and (2) in-hospital mortality. We fit logistic regression models, adjusting for clinical risk factors and Pitt bacteremia score and performed propensity score analyses to compare the efficacy of cefepime and carbapenems. RESULTS: Three hundred sixty-eight patients experienced Enterobacter species bacteremia and received at least 1 antimicrobial agent, of whom 52 (14%) died during hospitalization. Median age was 59 years; 19% were neutropenic, and 22% were in an intensive care unit on the day of bacteremia. Twenty-nine (11%) patients had persistent bacteremia for ≥1 day after antibacterial initiation. None of the 36 patients who received single-agent cefepime (0%) had persistent bacteremia, as opposed to 4 of 16 (25%) of those who received single-agent carbapenem (P < .01). In multivariable models, there was no association between carbapenem use and persistent bacteremia (adjusted odds ratio [aOR], 1.52; 95% CI, .58-3.98; P = .39), and a nonsignificant lower odds ratio with cefepime use (aOR, 0.52; 95% CI, .19-1.40; P = .19). In-hospital mortality was similar for use of cefepime and carbapenems in adjusted regression models and propensity-score matched analyses. CONCLUSIONS: Cefepime has a similar efficacy as carbapenems for the treatment of Enterobacter species bacteremia. Its use should be further explored as a carbapenem-sparing agent in this clinical scenario.