Proteomic analyses of urinary exosomes identify novel potential biomarkers for early diagnosis of sickle cell nephropathy, a sex-based study

Sickle cell nephropathy (SCN) is a leading cause of morbidity and mortality in sickle cell disease (SCD). Early intervention is crucial for mitigating its effects. However, current diagnostic methods rely on generic tests and may not detect SCN until irreversible renal damage occurs. Therefore, specific biomarkers for early diagnosis of SCN are needed. Urinary exosomes, membrane-bound vesicles secreted by renal podocytes and epithelial cells, contain both common and cell type-specific membrane and cytosolic proteins, reflecting the physiologic and pathophysiologic states of the kidney. Using proteomics, we analyzed the proteomes of urinary exosomes from humanized SCD mice at 2 months (without albuminuria) and 4 months (with albuminuria) of age. Excretion of 164 proteins were significantly increased and 176 proteins was significantly decreased in the exosomes when mice developed albuminuria. Based on the relevance to SCD, chronic kidney disease and Western blot confirmation in mice, we analyzed protein abundance of heparanase, cathepsin C, α2-macroglobulin and sarcoplasmic endoplasmic Ca2+ ATPase-3 (SERCA3) in the urinary exosomes and urine of 18 SCD subjects without albuminuria and 12 subjects with albuminuria using Western blot analyses. Both male and female subjects increased or tended to increase the excretion of these proteins in their urinary exosomes upon developing albuminuria, but female subjects demonstrated stronger correlations between the excretion of these proteins and urine albumin creatinine ratio (UACR) compared to male subjects. In contrast, exosomal excretion of Tamm-Horsfall protein, β-actin and SHP-1 was independent of albuminuria. These findings provide a foundation for a time-course study to determine whether increases in the levels of these proteins precede the onset of albuminuria in patients, which will help determine the potential of these proteins as biomarkers for early detection of SCN.

Climate warming and increasing Vibrio vulnificus infections in North America

Vibrio vulnificus is an opportunistic bacterial pathogen, occurring in warm low-salinity waters. V. vulnificus wound infections due to seawater exposure are infrequent but mortality rates are high (~ 18%). Seawater bacterial concentrations are increasing but changing disease pattern assessments or climate change projections are rare. Here, using a 30-year database of V. vulnificus cases for the Eastern USA, changing disease distribution was assessed. An ecological niche model was developed, trained and validated to identify links to oceanographic and climate data. This model was used to predict future disease distribution using data simulated by seven Global Climate Models (GCMs) which belong to the newest Coupled Model Intercomparison Project (CMIP6). Risk was estimated by calculating the total population within 200 km of the disease distribution. Predictions were generated for different "pathways" of global socioeconomic development which incorporate projections of greenhouse gas emissions and demographic change. In Eastern USA between 1988 and 2018, V. vulnificus wound infections increased eightfold (10-80 cases p.a.) and the northern case limit shifted northwards 48 km p.a. By 2041-2060, V. vulnificus infections may expand their current range to encompass major population centres around New York (40.7°N). Combined with a growing and increasingly elderly population, annual case numbers may double. By 2081-2100 V. vulnificus infections may be present in every Eastern USA State under medium-to-high future emissions and warming. The projected expansion of V. vulnificus wound infections stresses the need for increased individual and public health awareness in these areas.

Prevalence and Characteristics of CKD in the US Military Health System: A Retrospective Cohort Study

Rationale & Objective

The US Military Health System (MHS) is a global health care network with a diverse population that is more representative of the US population than other study cohorts and with fewer disparities in health care access. We aimed to examine the prevalence of chronic kidney disease (CKD) in the MHS and within demographic subpopulations.

Study Design

Multiple cross-sectional analyses of demographic and claims-based data extracted from the MHS Data Repository, 1 for each fiscal year from 2006-2015.

Setting & Population

Multicenter health care network including active-duty military, retirees, and dependents. The average yearly sample size was 3,285,348 individuals.

Exposures

Age, sex, race, active-duty status, and active-duty rank (a surrogate for socioeconomic status).

Outcome

CKD, defined as the presence of matching International Classification of Diseases, Ninth Revision, codes on either 1 or more inpatient or 2 or more outpatient encounters.

Analytical Approach

t test for continuous variables and χ² test for categorical variables; multivariable logistic regression for odds ratios.

Results

For 2015, the mean (standard deviation) age was 38 (16). Crude CKD prevalence was 2.9%. Age-adjusted prevalence was 4.9% overall—1.9% active-duty and 5.4% non–active-duty individuals. ORs for CKD were calculated with multiple imputations to account for missing data on race. After adjustment, the ORs for CKD (all P < 0.001) were 1.63 (95% CI, 1.62-1.64) for an age greater than 40 years, 1.16 (95% CI, 1.15-1.17) for Black race, 1.15 (95% CI, 1.14-1.16) for senior enlisted rank, 0.94 (95% CI, 0.93-0.95) for women, and 0.50 (95% CI, 0.49-0.51) for active-duty status.

Limitations

Retrospective study based on International Classification of Diseases, Ninth Revision, coding.

Conclusions

Within the MHS, older age, Black race, and senior enlisted rank were associated with a higher risk of CKD, whereas female sex and active-duty status were associated with a lower risk.

VBNC, previously unrecognized in the life cycle of Porphyromonas gingivalis?

Bacteria are exposed to stresses during their growth and multiplication in their ecological systems to which they respond in multiple ways as expert survivalists. One such response mechanism is to convert to a viable but not culturable (VBNC) state. As the name indicates, bacteria in the VBNC state have lost their ability to grow on routine growth medium. A large number of bacteria including many pathogenic species have been reported to be able to enter a VBNC state. VBNC differs from culturable cells in various physiological properties which may result in changes in chemical resistance, adhesion, cellular morphology, metabolism, gene expression, membrane and cell wall composition and/or virulence. The ability of VBNC bacteria to return to the culturable state or resuscitate, when the stressor is removed poses a considerable threat to public health. There have been few publications that overtly describe the ability of oral pathogenic species to enter the VBNC state. However, the presence of VBNCs among oral pathogens such as Porphyromonas gingivalis in human chronic infections may be an important virulence factor and have severe implications for therapy. In this review, we intend to i) define and summarize the significance of the VBNC state in general and ii) discuss the VBNC state of oral bacteria with regard to P. gingivalis. Future studies focused on this phenomenon of intraoral VBNC would provide novel molecular insights on the virulence and persistence of oral pathogens during chronic infections and identify potential novel therapies.

Phylogeography of the marine pathogen, Vibrio vulnificus, revealed the ancestral scenarios of its evolution

Vibrio vulnificus is the leading cause of seafood‐associated deaths worldwide. Despite the growing knowledge about the population structure of V. vulnificus, the evolutionary history and the ancestral relationships of strains isolated from various regions around the world have not been determined. Using the largest collection of sequence and isolate data of V. vulnificus to date, we applied ancestral character reconstruction to study the phylogeography of V. vulnificus. Multilocus sequence typing data from 10 housekeeping genes were used for the inference of ancestral states and reconstruction of the evolutionary history. The findings showed that the common ancestor of all V. vulnificus populations originated from East Asia, and later evolved into two main clusters that spread with time and eventually evolved into distinct populations in different parts of the world. While we found no meaningful insights concerning the evolution of V. vulnificus populations in the Middle East; however, we were able to reconstruct the ancestral scenarios of its evolution in East Asia, North America, and Western Europe.

Molecular Diagnostics and In Utero Therapeutics for Orofacial Clefts

Orofacial clefts and their management impose a substantial burden on patients, on their families, and on the health system. Under the current standard of care, affected patients are subjected to a lifelong journey of corrective surgeries and multidisciplinary management to replace bone and soft tissues, as well as restore esthetics and physiologic functions while restoring self-esteem and psychological health. Hence, a better understanding of the dynamic interplay of molecular signaling pathways at critical phases of palate development is necessary to pioneer novel prenatal interventions. Such pathways include transforming growth factor-β (Tgfβ), sonic hedgehog (Shh), wingless-integrated site (Wnt)/β-catenin, bone morphogenetic protein (Bmp), and fibroblast growth factor (Fgf) and its associated receptors, among others. Here, we summarize commonly used surgical methods used to correct cleft defects postnatally. We also review the advances made in prenatal diagnostics of clefts through imaging and genomics and the various in utero surgical corrections that have been attempted thus far. An overview of how key mediators of signaling that drive palatogenesis are emphasized in the context of the framework and rationale for the development and testing of therapeutics in animal model systems and in humans is provided. The pros and cons of in utero therapies that can potentially restore molecular homeostasis needed for the proper growth and fusion of palatal shelves are presented. The theme advanced throughout this review is the need to develop preclinical molecular therapies that could ultimately be translated into human trials that can correct orofacial clefts at earlier stages of development.

Survey of non-tunneled temporary hemodialysis catheter clinical practice and training

BACKGROUND

Nephrologists are placing fewer non-tunneled temporary hemodialysis catheters. Requiring competence for nephrology fellow graduation is controversial.

METHODS

Anonymous, online survey of all graduates from a single, military nephrology training program (n = 81; 1985-2017) and all US Nephrology program directors (n = 150).

RESULTS

Graduate response and completion rates were 59% and 100%, respectively; 93% agreed they had been adequately trained; 58% (26/45) place non-tunneled temporary hemodialysis catheters, independent of academic practice or time in practice, but 12/26 did ⩽5/year and 23/26 referred some or all. The most common reason for continuing non-tunneled temporary hemodialysis catheter placement was that it is an essential emergency procedure (92%). The single most significant barrier was time to do the procedure (49%). Program director response and completion rates were 50% and 79%, respectively. The single most important barrier to fellow competence was busyness of the service (36%), followed by disinterest (21%); 55% believed that non-tunneled temporary hemodialysis catheter insertion competence should be required, with 81% indicating it was an essential emergency procedure. The majority of graduates and program directors agreed that simulation training was valuable; 76% of programs employ simulation. Graduates who had simulation training and program directors with ⩽20 years of practice were significantly more likely to agree that simulation training was necessary.

CONCLUSION

Of the graduate respondents from a single training program, 58% continue to place non-tunneled temporary hemodialysis catheters; 55% of program directors believe non-tunneled temporary hemodialysis catheter procedural competence should be required. Graduates who had non-tunneled temporary hemodialysis catheter simulation training and younger program directors consider simulation training necessary. These findings should be considered in the discussion of non-tunneled temporary hemodialysis catheter curriculum requirements.

Survey of Kidney Biopsy Clinical Practice and Training in the United States

BACKGROUND AND OBJECTIVES

Practicing clinical nephrologists are performing fewer diagnostic kidney biopsies. Requiring biopsy procedural competence for graduating nephrology fellows is controversial.

DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS

An anonymous, on-line survey of all Walter Reed training program graduates (n=82; 1985-2017) and all United States nephrology program directors (n=149; August to October of 2017), regarding kidney biopsy practice and training, was undertaken.

RESULTS

Walter Reed graduates' response and completion rates were 71% and 98%, respectively. The majority felt adequately trained in native kidney biopsy (83%), transplant biopsy (82%), and tissue interpretation (78%), with no difference for ≤10 versus >10 practice years. Thirty-five percent continued to perform biopsies (13% did ≥10 native biopsies/year); 93% referred at least some biopsies. The most common barriers to performing biopsy were logistics (81%) and time (74%). Program director response and completion rates were 60% and 77%. Seventy-two percent cited ≥1 barrier to fellow competence. The most common barriers were logistics (45%), time (45%), and likelihood that biopsy would not be performed postgraduation (41%). Fifty-one percent indicated that fellows should not be required to demonstrate minimal procedural competence in biopsy, although 97% agreed that fellows should demonstrate competence in knowing/managing indications, contraindications, and complications. Program directors citing ≥1 barrier or whose fellows did <50 native biopsies/year in total were more likely to think that procedural competence should not be required versus those citing no barriers (P=0.02), or whose fellows performed ≥50 biopsies (P<0.01).

CONCLUSIONS

Almost two-thirds of graduate respondents from a single military training program no longer perform biopsy, and 51% of responding nephrology program directors indicated that biopsy procedural competence should not be required. These findings should inform discussion of kidney biopsy curriculum requirements.

Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy

Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). L1 comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. L2 is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is related to the aquaculture industry. L3 is also linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. Lastly, L4 and L5 include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. Based on these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name "piscis."

Different abundance and correlational patterns exist between total and presumed pathogenic Vibrio vulnificus and V. parahaemolyticus in shellfish and waters along the North Carolina coast

Monitoring of Vibrio vulnificus and V. parahaemolyticus abundance is pertinent due to the ability of these species to cause disease in humans through aquatic vectors. Previously, we performed a multiyear investigation tracking Vibrio spp. levels in five sites along the southeastern North Carolina coast. From February 2013 to October 2015, total V. vulnificus and V. parahaemolyticus abundance was measured in water, oysters and clams. In the current study, pathogenic subpopulations were identified in these isolates using molecular markers, revealing that 5.3% of V. vulnificus isolates possessed the virulence-correlated gene (vcgC), and 1.9% of V. parahaemolyticus isolates harbored one or both of the virulence-associated hemolysin genes (tdh and trh). Total V. parahaemolyticus abundance was not sufficient to predict the abundance of pathogenic subpopulations. Specifically, pathogenic V. parahaemolyticus isolates were more often isolated in cooler waters and were sometimes isolated when no other V. parahaemolyticus strains were detectable. Vibrio vulnificus clinical (C-) genotypes correlated with total V. vulnificus; however, salinity, water depth and total suspended solids influenced C- and E-genotypes differently. Lastly, we documented individual oysters harboring significantly higher V. vulnificus levels for which there was no ecological explanation, a phenomenon that deserves closer attention due to the potentially elevated health hazard associated with these 'hot' shellfish.

Interinstrumental transfer of a fast short-end injection capillary electrophoresis method: Application to the separation of niobium, tantalum, and their substituted ions

The interinstrumental transfer of a short-end CE method was studied. A model separation of the hexameric forms of niobium, tantalum, and their substituted ions (Nb_6-x Ta_x with 0 ≤ x ≤ 6) was selected as test case. The method was first optimized on a Beckman instrument and in a second step transferred to an Agilent instrument. The transfer needed updated guidelines that tackled differences in effective capillary length, 8.5 (Agilent) versus 10 cm (Beckman), because of instrumental different capillary cartridges. Differences in effective length lead to migration time and separation efficiency inequalities, illustrated by a decrease in resolution between the substituted ions. The difference in effective length was overcome by adapting the lift offset parameter of the Agilent instrument. The lift offset default setting is 4 mm and by increasing this parameter both the inlet and outlet lifts are lowered and thus the detection window can be displaced and consequently the effective length was increased. The decrease in effective length difference and the effect on the separation efficiency was investigated and led finally to a restored separation of the substituted ions. The adaptation of the lift offset parameter during short-end injection methods was added to earlier developed guidelines to facilitate interinstrumental method transfer of CE methods.

Impact of hypoxia on gene expression patterns by the human pathogen, Vibrio vulnificus, and bacterial community composition in a North Carolina estuary

Estuarine environments are continuously being shaped by both natural and anthropogenic sources which directly/indirectly influence the organisms that inhabit these important niches on both individual and community levels. Human infections caused by pathogenic Vibrio species are continuing to rise, and factors associated with global climate change have been suggested to be impacting their abundance and geographical range. Along with temperature, hypoxia has also increased dramatically in the last 40 years, which has led to persistent dead zones worldwide in areas where these infections are increasing. Thus, utilizing membrane diffusion chambers, we investigated the impact of in situ hypoxia on the gene expression of one such bacterium, Vibrio vulnificus, which is an inhabitant of these vulnerable areas worldwide. By coupling these data with multiple abiotic factors, we were able to demonstrate that genes involved in numerous functions, including those involved in virulence, environmental persistence, and stressosome production, were negatively correlated with dissolved oxygen. Furthermore, comparing 16S ribosomal RNA, we found similar overall community compositions during both hypoxia and normoxia. However, unweighted beta diversity analyses revealed that although certain classes of bacteria dominate in both low- and high-oxygen environments, there is the potential for quantitative shifts in lower abundant species, which may be important for effective risk assessment in areas that are becoming increasingly more hypoxic. This study emphasizes the importance of investigating hypoxia as a trigger for gene expression changes by marine Vibrio species and highlights the need for more in depth community analyses during estuarine hypoxia.

Combating Grade Inflation in Nephrology Clinical Rotation Evaluations Using Faculty Education and a 5-Point Centered Rating Scale

Background From 2010 to 2011, more than 70% of the clinical rotation competency evaluations for nephrology fellows in our program were rated "superior" using a 9-point Likert scale, suggesting some degree of "grade inflation." Objective We sought to assess the efficacy of a 5-point centered rotation evaluation in reducing grade inflation. Methods This retrospective cohort study of the impact of faculty education and a 5-point rotation evaluation on grade inflation was measured by superior item rating frequency and proportion of evaluations without superior ratings. The 5-point evaluation centered performance at the level expected for stage of training. Faculty education began in 2011-2012. The 5-point centered evaluation was introduced in 2012-2013 and used exclusively thereafter. A total of 68 evaluations, using the 9-point Likert scale, and 63 evaluations, using the 5-point centered scale, were performed after first-year fellow clinical rotations. Nine to 12 faculty members participated yearly. Results Faculty education alone was associated with fewer superior ratings from 2010-2011 to 2011-2012 (70.5% versus 48.3%, P = .001), declining further with 5-point centered scale introduction (2012-2013; 48.3% versus 35.6%; P = .012). Superior ratings declined with 5-point centered versus 9-point Likert scales (37.3% versus 59.3%, P = .001), specifically for medical knowledge, patient care, practice-based learning and improvement, and professionalism. On logistic regression, evaluations without superior scores were more likely for 5-point centered versus 9-point Likert scales (adjusted odds ratio [aOR] = 8.26; 95% CI 1.53-44.64; P = .014) and associated with faculty identifier (aOR= 1.18; 95% CI 1.03-1.35; P = .013), but not fellow identifier or training year quarter.

CONCLUSIONS

Grade inflation was reduced with faculty education and the 5-point centered evaluation scale.

Clinical and environmental genotypes of Vibrio vulnificus display distinct, quorum-sensing-mediated, chitin detachment dynamics

The ability for bacteria to attach to and detach from various substrata is important for colonization, survival and transitioning to new environments. An opportunistic human pathogen, Vibrio vulnificus, can cause potentially fatal septicemia after ingestion of undercooked seafood. Based on genetic polymorphisms, strains of this species are subtyped into clinical (C) and environmental (E) genotypes. Vibrio vulnificus readily associates with chitin, thus we investigated chitin detachment dynamics in these disparate genotypes. We found that C-genotypes detach significantly more than E-genotypes after 24 hours in aerobic as well as anaerobic conditions. Furthermore, expression of genes involved in type IV pilin production was significantly downregulated in C-genotypes compared to E-genotypes, suggesting an importance in detachment. Interestingly, gbpA, a gene that has been shown to be important in host colonization in V. cholerae, was upregulated in the C-genotypes during detachment. Additionally, we found that C-genotypes detached to a greater extent, and produced more quorum-sensing (QS) autoinducer-2 molecules relative to E-genotypes, which suggests a role for QS in detachment. These findings suggest that for V. vulnificus, QS-mediated detachment may be a potential mechanism for transitioning into a human host for C-genotypes, while facilitating E-genotype maintenance in the estuarine environment.

Derivation of candidates for the combat casualty critical care (C4) database

OBJECTIVE

To describe the development of the Combat Casualty Critical Care Database, a comprehensive database of critically injured combat casualties to identify potentially modifiable risk factors for morbidity and mortality in this population.

METHODS

The Department of Defense's Joint Theater Trauma Registry was queried for all combat casualties injured from February 1, 2002 through February 1, 2011. The search was limited to patients who required admission to the intensive care unit and survived to be evacuated to Landstuhl Regional Medical Center.

RESULTS

The query yielded 6,011 patients. The mean age was 25.7 ± 6.2 years. The majority of patients were male (98.3%), injured in Iraq (80%) and were members of the U. S. Army (72.6%). Most patients (58.0%) had an injury severity score in the lowest severity category (0-15). The mortality rate was 1.8%. The median day of death after injury (interquartile range) was 6 (3-14).

CONCLUSIONS

We identified a cohort of critically wounded combat casualties that encompasses the majority of such patients injured in the course of the wars in Iraq and Afghanistan. When this database is fully populated, rigorous epidemiologic analysis will seek to identify factors associated with morbidity and mortality to improve future care.

Implementation of nephrology subspecialty curricular milestones

Beginning in the 2014-2015 training year, the US Accreditation Council for Graduate Medical Education (ACGME) required that nephrology Clinical Competency Committees assess fellows' progress toward 23 subcompetency "context nonspecific" internal medicine subspecialty milestones. Fellows' advancement toward the "ready for unsupervised practice" target milestone now is tracked in each of the 6 competencies: Patient Care, Medical Knowledge, Professionalism, Interpersonal Communication Skills, Practice-Based Learning and Improvement, and Systems-Based Practice. Nephrology program directors and subspecialty societies must define nephrology-specific "curricular milestones," mapped to the nonspecific ACGME milestones. Although the ACGME goal is to produce data that can discriminate between successful and underperforming training programs, the approach is at risk to produce biased, inaccurate, and unhelpful information. We map the ACGME internal medicine subspecialty milestones to our previously published nephrology-specific milestone schema and describe entrustable professional activities and other objective assessment tools that inform milestone decisions. Mapping our schema onto the ACGME subspecialty milestone reporting form allows comparison with the ACGME subspecialty milestones and the curricular milestones developed by the American Society of Nephrology Program Directors. Clinical Competency Committees may easily adapt and directly translate milestone decisions reached using our schema onto the ACGME internal medicine subspecialty competency milestone-reporting format.

Impact of analytic provenance in genome analysis

Background

Many computational methods are available for assembly and annotation of newly sequenced microbial genomes. However, when new genomes are reported in the literature, there is frequently very little critical analysis of choices made during the sequence assembly and gene annotation stages. These choices have a direct impact on the biologically relevant products of a genomic analysis - for instance identification of common and differentiating regions among genomes in a comparison, or identification of enriched gene functional categories in a specific strain. Here, we examine the outcomes of different assembly and analysis steps in typical workflows in a comparison among strains of Vibrio vulnificus.

Results

Using six recently sequenced strains of V. vulnificus, we demonstrate the "alternate realities" of comparative genomics, and how they depend on the choice of a robust assembly method and accurate ab initio annotation. We apply several popular assemblers for paired-end Illumina data, and three well-regarded ab initio genefinders. We demonstrate significant differences in detected gene overlap among comparative genomics workflows that depend on these two steps. The divergence between workflows, even those using widely adopted methods, is obvious both at the single genome level and when a comparison is performed. In a typical example where multiple workflows are applied to the strain V. vulnificus CECT 4606, a workflow that uses the Velvet assembler and Glimmer gene finder identifies 3275 gene features, while a workflow that uses the Velvet assembler and the RAST annotation system identifies 5011 gene features. Only 3171 genes are identical between both workflows. When we examine 9 assembly/ annotation workflow scenarios as input to a three-way genome comparison, differentiating genes and even differentially represented functional categories change significantly from scenario to scenario.

Conclusions

Inconsistencies in genomic analysis can arise depending on the choices that are made during the assembly and annotation stages. These inconsistencies can have a significant impact on the interpretation of an individual genome's content. The impact is multiplied when comparison of content and function among multiple genomes is the goal. Tracking the analysis history of the data - its analytic provenance - is critical for reproducible analysis of genome data.

Bridging the gap between viable but non-culturable and antibiotic persistent bacteria

Microbial dormancy is a widespread phenomenon employed by bacteria to evade environmental threats including antibiotics. This intrinsic mechanism of antibiotic tolerance has drawn special attention to the role of dormancy in human disease, particularly in regards to recurrent infections. Two dormancy states, the viable but non-culturable state and bacterial persistence, both produce antibiotic-tolerant populations capable of withstanding prolonged lethal treatment. Currently described as two distinct forms of dormancy, they are rarely discussed in the same context. We argue here that these two dormant states are closely related phenomena which are part of a shared 'dormancy continuum'. This discussion is intended to stimulate discourse about these seemingly different but very similar dormant states.

Simple and robust monitoring of ethanol fermentations by capillary electrophoresis

Free-solution capillary electrophoresis (CE), or capillary zone electrophoresis, with direct UV detection was used for the first time for the determination of mono- and disaccharides, sugar alcohols, and ethanol in fermentation broths. Sample preparation proved to be minimal: no derivatization or specific sample purification was needed. The CE conditions can be adapted to the type of fermentation by simply altering the background electrolyte (BGE). KOH (130 mM) or NaOH (130 mM) as the BGE led to the fastest analysis time when monitoring simple fermentations. A mixture of 65 mM NaOH and 65 mM LiOH led to a 19% improvement in resolution for a complex mixture of carbohydrates. Quantification of a simple carbohydrate fermentation by CE showed values in close agreement with that of high-performance anion exchange chromatography and high-performance liquid chromatography (HPLC) on a cation exchange resin. For complex fermentations, quantification of carbohydrates by HPLC and CE led to similar results, whereas CE requires an injection volume of only 10-20 nL. Analysis of an ethanol fermentation of hydrolyzed plant fiber demonstrated the robustness of the separation and detection of carbohydrates, as well as ethanol. Ethanol determination is achieved by coupling the CE method to pressure mobilization, using the same instrument and the same sample.

Assessing achievement in nephrology training: using clinic chart audits to quantitatively screen competency

BACKGROUND

Entrustable professional activities (EPAs) are complex tasks representing vital physician functions in multiple competencies, used to demonstrate trainee development along milestones. Managing a nephrology outpatient clinic has been proposed as an EPA for nephrology fellowship training.

STUDY DESIGN

Retrospective cohort study of nephrology fellow outpatient clinic performance using a previously validated chart audit tool.

SETTING & PARTICIPANTS

Outpatient encounter chart audits for training years 2008-2009 through 2012-2013, corresponding to participation in the Nephrology In-Training Examination (ITE). A median of 7 auditors (attending nephrologists) audited a mean of 1,686±408 (SD) charts per year. 18 fellows were audited; 12, in both of their training years.

PREDICTORS

Proportion of chart audit and quality indicator deficiencies.

OUTCOMES

Longitudinal deficiency and ITE performance.

MEASUREMENTS & RESULTS

Among fellows audited in both their training years, chart audit deficiencies were fewer in the second versus the first year (5.4%±2.0% vs 17.3%±7.0%; P<0.001) and declined between the first and second halves of the first year (22.2%±6.4% vs 12.3%±9.5%; P=0.002). Most deficiencies were omission errors, regardless of training year. Quality indicator deficiencies for hypertension and chronic kidney disease-associated anemia recognition and management were fewer during the second year (P<0.001). Yearly audit deficiencies ≥5% were associated with an ITE score less than the 25th percentile for second-year fellows (P=0.03), with no significant association for first-year fellows. Auditor-reported deficiencies declined between the first and second halves of the year (17.0% vs 11.1%; P<0.001), with a stable positive/neutral comment rate (17.3% vs 17.8%; P=0.6), suggesting that the decline was not due to auditor fatigue.

LIMITATIONS

Retrospective design and small trainee numbers.

CONCLUSIONS

Managing a nephrology outpatient clinic is an EPA. The chart audit tool was used to assess longitudinal fellow performance in managing a nephrology outpatient clinic. Failure to progress may be quantitatively identified and remediated. The tool identifies deficiencies in all 6 competencies, not just medical knowledge, the primary focus of the ITE and the nephrology subspecialty board examination.

The importance of the viable but non-culturable state in human bacterial pathogens

Many bacterial species have been found to exist in a viable but non-culturable (VBNC) state since its discovery in 1982. VBNC cells are characterized by a loss of culturability on routine agar, which impairs their detection by conventional plate count techniques. This leads to an underestimation of total viable cells in environmental or clinical samples, and thus poses a risk to public health. In this review, we present recent findings on the VBNC state of human bacterial pathogens. The characteristics of VBNC cells, including the similarities and differences to viable, culturable cells and dead cells, and different detection methods are discussed. Exposure to various stresses can induce the VBNC state, and VBNC cells may be resuscitated back to culturable cells under suitable stimuli. The conditions that trigger the induction of the VBNC state and resuscitation from it are summarized and the mechanisms underlying these two processes are discussed. Last but not least, the significance of VBNC cells and their potential influence on human health are also reviewed.

Expanding the role of objectively structured clinical examinations in nephrology training

Objectively structured clinical examinations (OSCEs) are widely used in medical education, but we know of none described that are specifically for nephrology fellowship training. OSCEs use simulation to educate and evaluate. We describe a technically simple, multidisciplinary, low-cost OSCE developed by our program that contains both examination and training features and focuses on management and clinical knowledge of rare hemodialysis emergencies. The emergencies tested are venous air embolism, blood leak, dialysis membrane reaction, and hemolysis. Fifteen fellows have participated in the OSCE as examinees and/or preceptors since June 2010. All have passed the exercise. Thirteen responded to an anonymous survey in July 2013 that inquired about their confidence in managing each of the 4 tested emergencies pre- and post-OSCE. Fellows were significantly more confident in their ability to respond to the emergencies after the OSCE. Those who subsequently saw such an emergency reported that the OSCE experience was somewhat or very helpful in managing the event. The OSCE tested and trained fellows in the recognition and management of rare hemodialysis emergencies. OSCEs and simulation generally deserve greater use in nephrology subspecialty training; however, collaboration between training programs would be necessary to validate such exercises.

Cellular, physiological, and molecular adaptive responses of Erwinia amylovora to starvation

Erwinia amylovora causes fire blight, a destructive disease of rosaceous plants distributed worldwide. This bacterium is a nonobligate pathogen able to survive outside the host under starvation conditions, allowing its spread by various means such as rainwater. We studied E. amylovora responses to starvation using water microcosms to mimic natural oligotrophy. Initially, survivability under optimal (28 °C) and suboptimal (20 °C) growth temperatures was compared. Starvation induced a loss of culturability much more pronounced at 28 °C than at 20 °C. Natural water microcosms at 20 °C were then used to characterize cellular, physiological, and molecular starvation responses of E. amylovora. Challenged cells developed starvation-survival and viable but nonculturable responses, reduced their size, acquired rounded shapes and developed surface vesicles. Starved cells lost motility in a few days, but a fraction retained flagella. The expression of genes related to starvation, oxidative stress, motility, pathogenicity, and virulence was detected during the entire experimental period with different regulation patterns observed during the first 24 h. Further, starved cells remained as virulent as nonstressed cells. Overall, these results provide new knowledge on the biology of E. amylovora under conditions prevailing in nature, which could contribute to a better understanding of the life cycle of this pathogen.

Survival of Vibrio vulnificus genotypes in male and female serum, and production of siderophores in human serum and seawater

Vibrio vulnificus is an estuarine bacterium responsible for 95% of all seafood-related deaths in the United States. Several studies have demonstrated that V. vulnificus infections are enhanced when host iron availability is increased, such as occurs with chronic liver disease. Because of the gender difference seen in these infections, we examined whether there was a difference in the survival in both male and female serum by both the C (clinical) and E (environmental) genotypes of V. vulnificus. We further determined the significance of the catecholate and hydroxamate siderophores produced by this pathogen during both human infections and while in its natural estuarine environment. We found that only C-genotype strains were capable of growth in human serum, regardless of inoculum size, with growth in male and female serum being equal. We found the catecholate outer membrane receptor gene (vuuA) to be expressed significantly more than that for the hydroxamate siderophore (fhuA) when the cells were exposed to human serum, regardless of the genotype. When cells were exposed to natural seawater, fhuA showed increased expression over time, while vuuA showed decreased expression. Our data suggest that the catecholate siderophore is important during human infections, whereas the hydroxamate siderophore may be more important in the estuarine environment this pathogen inhabits.

Vibrio vulnificus: death on the half shell. A personal journey with the pathogen and its ecology

Vibrio vulnificus is an estuarine bacterium which occurs in high numbers in filter-feeding molluscan shellfish, such as oysters. In individuals with certain underlying diseases, ingestion of the bacterium, e.g., in raw or undercooked oysters, can lead to a rapid and extremely fatal infection. Indeed, this one bacterium is responsible for 95 % of all seafood-borne deaths. In addition, the bacterium is capable of entering a preexisting lesion or cut obtained during coastal recreational activities, resulting in potentially fatal wound infections. This brief review, which comprised a presentation made at the Gordon Research Conference on "Oceans and Human Health," reflects over 35 years of research on this bacterium in the author's laboratory. It describes some of the known virulence factors and why males account for ca 85 % of all V. vulnificus cases. It notes the two genotypes now known to exist and how this pathogen enters a dormant, "viable but nonculturable" state during the winter months. Finally, the review discusses how global warming may be causing worldwide increases in the frequency and geographical extent of Vibrio infections.

The interactions of Vibrio vulnificus and the oyster Crassostrea virginica

The human bacterial pathogen, Vibrio vulnificus, is found in brackish waters and is concentrated by filter-feeding molluscan shellfish, especially oysters, which inhabit those waters. Ingestion of raw or undercooked oysters containing virulent strains of V. vulnificus can result in rapid septicemia and death in 50 % of victims. This review summarizes the current knowledge of the environmental interactions between these two organisms, including the effects of salinity and temperature on colonization, uptake, and depuration rates of various phenotypes and genotypes of the bacterium, and host-microbe immunological interactions.

Simple and robust determination of monosaccharides in plant fibers in complex mixtures by capillary electrophoresis and high performance liquid chromatography

Carbohydrates partially liberated by acid hydrolysis of plant fiber can be separated by hydrophilic interaction liquid chromatography (HILIC), ligand-exchange liquid chromatography or other forms of LC with ion-exchange columns. However, the robust hydrogen-exchange columns show co-elution of galactose, xylose and mannose. Free solution capillary electrophoresis (CE) can be used without derivatization at pH 12.6 and was found to provide a higher resolution of galactose and xylose than common LC with no sample pre-treatment required, other than dilution, within 26min. CE was able to provide resolution higher than 0.79 for all separated carbohydrates, and the RSDs of determined concentrations lower than 10% for concentrations above 1.3gL(-1). A quantitative comparison between CE and HPLC revealed that up to 22% more carbohydrates are quantified with CE. Direct UV detection in CE of mono- and disaccharides is unexpectedly possible at 270nm. NMR analysis shows that alkaline degradation is too slow to explain this detection. This CE detection sensitivity is increased by the electric field and our CE and NMR analyses are consistent with a photo-oxidation process.

Resistance to environmental stresses by Vibrio vulnificus in the viable but nonculturable state

Vibrio vulnificus is responsible for 95% of all seafood-associated fatalities in the United States. When water temperatures drop below c. 13 °C, the cells enter into the viable but nonculturable (VBNC) state wherein they are unable to grow on routine media but retain viability and the ability to return to the culturable state. The aim of this study was to determine whether V. vulnificus cells in the VBNC state are protected against a variety of potentially lethal challenges (heat, oxidative, osmotic, pH, ethanol, antibiotic and heavy metal) and to examine genetic regulators that might underlie such protection. The data presented here indicate that VBNC cells of this pathogen are protected against a wide variety of stresses and retain the ability to return to the culturable state. Surprisingly, we found no significant difference in the expression of relA and spoT between VBNC and logarithmic cells, nor any significant difference in the expression of rpoS in the case of the clinical (C) genotype of this pathogen. However, expression of relA was significantly different in VBNC cells of the environmental (E) genotype compared with logarithmic cells. This might account for findings indicating an enhanced ability for E-genotype cells to withstand environmental changes better than C-genotype cells.

Apparent loss of Vibrio vulnificus from North Carolina oysters coincides with a drought-induced increase in salinity

Despite years of successful isolation of Vibrio vulnificus from estuarine waters, beginning in 2007, it was extremely difficult to culture V. vulnificus from either North Carolina estuarine water or oyster samples. After employing culture-based methods as well as PCR and quantitative PCR for the detection of V. vulnificus, always with negative results, we concluded that this pathogen had become nearly undetectable in the North Carolina estuarine ecosystem. We ensured that the techniques were sound by seeding North Carolina oysters with V. vulnificus and performing the same tests as those previously conducted on unadulterated oysters. V. vulnificus was readily detected in the seeded oysters using both classes of methods. Furthermore, oysters were obtained from the Gulf of Mexico, and V. vulnificus was easily isolated, confirming that the methodology was sound but that the oysters and waters of North Carolina were lacking the V. vulnificus population studied for decades. Strikingly, the apparent loss of detectable V. vulnificus coincided with the most severe drought in the history of North Carolina. The drought continued until the end of 2009, with an elevated water column salinity being observed throughout this period and with V. vulnificus being nearly nonexistent. When salinities returned to normal after the drought abated in 2010, we were again able to routinely isolate V. vulnificus from the water column, although we were still unable to culture it from oysters. We suggest that the oysters were colonized with a more salt-tolerant bacterium during the drought, which displaced V. vulnificus and may be preventing recolonization.

Pyrosequencing-based comparative genome analysis of Vibrio vulnificus environmental isolates

Between 1996 and 2006, the US Centers for Disease Control reported that the only category of food-borne infections increasing in frequency were those caused by members of the genus Vibrio. The Gram-negative bacterium Vibrio vulnificus is a ubiquitous inhabitant of estuarine waters, and is the number one cause of seafood-related deaths in the US. Many V. vulnificus isolates have been studied, and it has been shown that two genetically distinct subtypes, distinguished by 16S rDNA and other gene polymorphisms, are associated predominantly with either environmental or clinical isolation. While local genetic differences between the subtypes have been probed, only the genomes of clinical isolates have so far been completely sequenced. In order to better understand V. vulnificus as an agent of disease and to identify the molecular components of its virulence mechanisms, we have completed whole genome shotgun sequencing of three diverse environmental genotypes using a pyrosequencing approach. V. vulnificus strain JY1305 was sequenced to a depth of 33×, and strains E64MW and JY1701 were sequenced to lesser depth, covering approximately 99.9% of each genome. We have performed a comparative analysis of these sequences against the previously published sequences of three V. vulnificus clinical isolates. We find that the genome of V. vulnificus is dynamic, with 1.27% of genes in the C-genotype genomes not found in the E- genotype genomes. We identified key genes that differentiate between the genomes of the clinical and environmental genotypes. 167 genes were found to be specifically associated with environmental genotypes and 278 genes with clinical genotypes. Genes specific to the clinical strains include components of sialic acid catabolism, mannitol fermentation, and a component of a Type IV secretory pathway VirB4, as well as several other genes with potential significance for human virulence. Genes specific to environmental strains included several that may have implications for the balance between self-preservation under stress and nutritional competence.

Regional citrate anticoagulation for hemorrhage experiments in rats

INTRODUCTION

Hemorrhage alone without concomitant trauma often results in a hypercoagulable state that makes it difficult to prevent clotting within the blood withdrawal catheters. Although systemic administration of heparin can ameliorate this problem, heparin use has many additional actions that may confound interpretation of the hemorrhage experiments. The problem can be resolved by the use of a dual lumen catheter that anticoagulates only the blood within the withdrawal circuit. We describe the design of such a catheter and evaluate its function in studies of hemorrhagic shock in rats.

MATERIALS AND METHODS

Construction directions are provided for the dual lumen catheter along with a commercial source. The catheters were connected to computer controllable infusion syringes. Either citrate or heparin was used for regional extracorporeal anticoagulation. Rats were anesthetized and hemorrhaged to 40mmHg for more than 15min through the use of a computer program written in Labview. Ionized calcium measurements were obtained pre- and posthemorrhage.

RESULTS

The catheters remained patent throughout the experiments. There was no significant difference in the ionized calcium whether citrate or heparin was used for extracorporeal anticoagulation.

CONCLUSION

The dual lumen catheters are suitable for the study of hemorrhagic shock in rats without the need for systemic anticoagulation. The catheters can be used with computer-controlled hemorrhage procedures.

Interactive effects of cadmium and hypoxia on metabolic responses and bacterial loads of eastern oysters Crassostrea virginica Gmelin

Pollution by toxic metals including cadmium (Cd) and hypoxia are important stressors in estuaries and coastal waters which may interactively affect sessile benthic organisms, such as oysters. We studied metabolic responses to prolonged hypoxic acclimation (2 weeks at 5% O2) in control and Cd-exposed (30 d at 50 μg L(-1) Cd) oysters Crassostrea virginica, and analyzed the effects of these stressors on abundance of Vibrio spp. in oysters. Hypoxia-acclimated oysters retained normal standard metabolic rates (SMR) at 5% O2, in contrast to a decline of SMR observed during acute hypoxia. However, oysters spent more time actively ventilating in hypoxia than normoxia resulting in enhanced Cd uptake and 2.7-fold higher tissue Cd burdens in hypoxia. Cd exposure led to a significant decrease in tissue glycogen stores, increase in free glucose levels and elevated activity of glycolytic enzymes (hexokinase and aldolase) indicating a greater dependence on carbohydrate catabolism. A compensatory increase in activities of two key mitochondrial enzymes (citrate synthase and cytochrome c oxidase) was found during prolonged hypoxia in control oysters but suppressed in Cd-exposed ones. Cd exposure also resulted in a significant increase in abundance of Vibrio parahaemolyticus and Vibrio vulnificus levels during normoxia and hypoxia, respectively. Overall, Cd- and hypoxia-induced changes in metabolic profile, Cd accumulation and bacterial flora of oysters indicate that these stressors can synergistically impact energy homeostasis, performance and survival of oysters in polluted estuaries and have significant consequences for transfer of Cd and bacterial pathogens to the higher levels of the food chain.

Occurrence of Vibrio vulnificus in mussel farms from the Varano lagoon environment

AIMS

Monitoring the occurrence of the human pathogen Vibrio vulnificus in a mussel farm located in the lagoon of Varano (Italy).

METHODS AND RESULTS

A total of 72 samples of mussel, water and sediment, collected from two locations of Varano lagoon in the Gargano peninsula, during a 7-month survey, were analysed. Isolation and PCR characterization of six V. vulnificus environmental genotype strains revealed that this pathogen was isolated when with T was above 22 °C and salinity ranged between 22.7 and 26.4‰. No significant correlation of the occurrence of V. vulnificus with water pH or salinity was observed. Moreover, 8% of mussel samples were found to be contaminated by V. vulnificus. All of that positive mussel samples originated from the same sampling station.

CONCLUSION

It is suggested that warmer season are risky to eat raw or undercooked bivalve molluscs in the local area.

SIGNIFICANCE AND IMPACT OF THE STUDY

To increase knowledge about environmental conditions that may affect the occurrence of waterborne pathogen Vibrio vulnificus in seafood.