High-Statistics Measurement of Neutrino Quasielasticlike Scattering at 6 GeV on a Hydrocarbon Target.

We measure neutrino charged-current quasielasticlike scattering on hydrocarbon at high statistics using the wideband Neutrinos at the Main Injector beam with neutrino energy peaked at 6 GeV. The double-differential cross section is reported in terms of muon longitudinal (p_{∥}) and transverse (p_{⊥}) momentum. Cross section contours versus lepton momentum components are approximately described by a conventional generator-based simulation, however, discrepancies are observed for transverse momenta above 0.5 GeV/c for longitudinal momentum ranges 3-5 and 9-20 GeV/c. The single differential cross section versus momentum transfer squared (dσ/dQ_{QE}^{2}) is measured over a four-decade range of Q^{2} that extends to 10 GeV^{2}. The cross section turnover and falloff in the Q^{2} range 0.3-10 GeV^{2} is not fully reproduced by generator predictions that rely on dipole form factors. Our measurement probes the axial-vector content of the hadronic current and complements the electromagnetic form factor data obtained using electron-nucleon elastic scattering. These results help oscillation experiments because they probe the importance of various correlations and final-state interaction effects within the nucleus, which have different effects on the visible energy in detectors.

Hip survival after plain core decompression alone versus bone morphogenetic protein and/or bone marrow reinjection with core decompression for avascular osteonecrosis of the femoral head: a retrospective case control study in ninety two patients.

INTRODUCTION: Injecting bone marrow or bone morphogenetic protein 7 (BMP) during core decompression for avascular osteonecrosis (AVN) may improve survival. We hypothesized that adding a complementary technique (injection of BMP and/or non-concentrated bone marrow) to core decompression would reduce the number of patients requiring a subsequent total hip arthroplasty (THA). METHODS: We retrospectively reviewed 92 cases from 2003 to 2018 with a minimum of 2 years of follow-up and an average follow-up of 64 months (24-204). Twenty-four patients had a core decompression (CD) (26.1% (24/92)), 25 had a CD associated with reinjection of bone marrow and BMP (rhBMP7) (27.2% (25/92)), and 43 patients had a CD with bone marrow reinjection (46.7% (43/92)). RESULTS: Hip survival after CD was 66.3% (61/92) at two years and 59.8% (55/92) at 10 years. CD with bone marrow and BMP reinjection had a better hip survival at ten years (HR: 0.492 (CI95%: 0.254-0.952) p = 0.035). A volume of necrosis greater than 30% (HR = 12.97 (CI95 [3.88-43.3] (p < 0.001))) and a Kerboul angle greater than 60° (HR: 12.5 (CI95 [2.84-54.6] (p < 0.001))) were risk factors for a subsequent THA. CONCLUSIONS: CD is an interesting non-invasive technique to preserve the native hip after AVN of the femoral head. Reinjection of bone marrow and/or BMP improved CD hip survival.

[Tourette syndrome: Research challenges to improve clinical practice]. / Syndrome de Gilles de la Tourette : défis de la recherche pour améliorer la pratique clinique.

Tourette syndrome is a neurodevelopmental disorder which is characterized by the presence of motor and phonic tics. These tics are generally more prevalent in childhood. Tics typically reach their maximum severity before puberty, around age 10 to 12. In most patients, tic severity usually decreases during late adolescence and adulthood. However, this is not true for all individuals. To date, the developmental trajectory leading to the persistence of tics into adulthood is still poorly understood. There are very few markers that can predict the evolution of tic symptoms from childhood to adulthood. Yet, while we cannot cure Tourette syndrome, it is possible to reduce tic severity with various treatments. The most common treatments are pharmacotherapy and behavioral and cognitive-behavioral therapy. However, there appears to be a limit to the proportion of tics that can be treated, since most treatments offer an average reduction in tics of no more than 50%. Thus, at first, this article reviews recent advances in treatment and symptom progression. Next, we propose some lines of research to improve the management and treatment of people with Tourette syndrome.

Impact of genetic polymorphisms determining leukocyte/neutrophil count on chemotherapy toxicity.

Neutropenia and infection are major dose-limiting side effects of chemotherapy. The risk of initial infection and subsequent complications are directly related to the depth and duration of neutropenia. Recent genome-wide association studies identified variants in DARC and CXCL2 genes, and in ORMDL3-GSDMA-CSF3 locus on chromosome 17q21 that influence white blood cell and neutrophil counts in healthy individuals. To investigate whether polymorphisms in these loci in conjunction with chemotherapy may modulate risk of treatment complications, we analyzed 21 SNPs across these genes for an association with chemotherapy-related neutropenia and infection in 286 Caucasian children with acute lymphoblastic leukemia. After correction for multiple testing, DARC polymorphism rs3027012 in 5'-UTR was associated with higher risk of low absolute phagocyte count (APC<500 and <1000 cells per microliter, P=0.001 and P<0.0005, respectively) and hospitalization due to febrile neutropenia (P=0.002). Protective effect was instead seen for DARC rs12075 A to G substitution (P=0.004). The SNP rs3859192 in the GSDMA were associated with hospitalization due to infection (P=0.004); infection was also modulated in the additive manner by the CXCL2 rs16850408 (P=0.002). This study shows for the first time that the variations in DARC, GSDMA and CXCL2 genes may play a role in the onset of chemotherapy complications.

Impact of baseline clinical and laboratory features on the risk of thrombosis in children with acute lymphoblastic leukemia: A prospective evaluation.

BACKGROUND: Children with acute lymphoblastic leukemia (ALL) have increased risk of thromboembolism (TE). However, the predictors of ALL-associated TE are as yet uncertain. OBJECTIVE: This exploratory, prospective cohort study evaluated the effects of clinical (age, gender, ALL risk group) and laboratory variables (hematological parameters, ABO blood group, inherited and acquired prothrombotic defects [PDs]) at diagnosis on the development of symptomatic TE (sTE) in children (aged 1 to ≤18) treated on the Dana-Farber Cancer Institute ALL 05-001 study. PROCEDURES: Samples collected prior to the start of ALL therapy were evaluated for genetic and acquired PDs (proteins C and S, antithrombin, procoagulant factors VIII (FVIII:C), IX, XI and von Willebrand factor antigen levels, gene polymorphisms of factor V G1691A, prothrombin gene G20210A and methylene tetrahydrofolate reductase C677T, anticardiolipin antibodies, fasting lipoprotein(a), and homocysteine). RESULTS: Of 131 enrolled patients (mean age [range] 6.4 [1-17] years) 70 were male patients and 20 patients (15%) developed sTE. Acquired or inherited PD had no impact on the risk of sTE. Multivariable analyses identified older age (odds ratio [OR] 1.13; 95% confidence interval [CI]: 1.01, 1.26) and non-O blood group (OR 3.64, 95% CI: 1.06, 12.51) as independent predictors for development of sTE. Patients with circulating blasts had higher odds of developing sTE (OR 6.66; 95% CI: 0.82, 53.85). CONCLUSION: Older age, non-O blood group, and presence of circulating blasts, but not PDs, predicted the risk of sTE during ALL therapy. We recommend evaluation of these novel risk factors in the development of ALL-associated TE. If confirmed, these easily accessible variables at diagnosis can help develop a risk-prediction model for ALL-associated TE.

Effectiveness of antibacterial prophylaxis during induction chemotherapy in children with acute lymphoblastic leukemia.

BACKGROUND: Pediatric patients receiving induction chemotherapy for newly diagnosed acute lymphoblastic leukemia (ALL) are at high risk of developing life-threatening infections. We investigated whether uniform antibacterial guidelines, including mandatory antibacterial prophylaxis in afebrile patients during induction, decreases the incidence of microbiologically documented bacteremia. METHODS: Between 2012 and 2015, 230 patients with newly diagnosed ALL (aged 1-21) were enrolled on Dana-Farber Cancer Institute ALL Consortium Protocol 11-001 (DFCI 11-001). Induction therapy, regardless of risk group, included vincristine, prednisone, doxorubicin, methotrexate, and PEG-asparaginase. Afebrile patients received fluoroquinolone prophylaxis at the initiation of induction and those presenting with fever received broad-spectrum antibiotics; antibiotics were continued until blood count recovery. Rates of documented bacteremias and fungal infections on DFCI 11-001 were compared to those on the predecessor protocol (DFCI 05-001), which included the same induction phase without antibiotic prophylaxis guidelines. RESULTS: Sixty-six (28.7%) patients received fluoroquinolone prophylaxis, the remaining patients received broad-spectrum antibiotics. Twenty-four (36.4%) patients on prophylaxis developed fever and seven (10.6%) developed bacteremia. The overall rate of infection during induction on DFCI 11-001 was lower than on DFCl 05-001 (14.3% vs. 26.3%, P < 0.0001) due to a decreased rate of bacteremia (10.9% vs. 24.4%, P < 0.0001). The rate of fungal infections (4.8% vs. 3.6%) and induction death (0.9% vs. 2%) was not significantly different. CONCLUSION: For children with newly diagnosed ALL, uniform antibiotic administration until blood count recovery, including fluoroquinolone prophylaxis for afebrile patients, reduced the incidence of bacteremia during the induction phase. Larger, randomized studies should be performed to confirm these findings.

The IVAIRE project--a randomized controlled study of the impact of ventilation on indoor air quality and the respiratory symptoms of asthmatic children in single family homes.

UNLABELLED: A randomized controlled trial was carried out to measure the impact of an intervention on ventilation, indoor air contaminants, and asthma symptoms of children. Eighty-three asthmatic children living in low-ventilated homes were followed over 2 years. Several environmental parameters were measured during the summer, fall, and winter. The children were randomized after Year 1 (43 Intervention; 40 Control). The intervention included the installation of either a Heat Recovery Ventilator (HRV) or Energy Recovery Ventilator (ERV). During the fall and winter seasons, there was a significant increase in the mean ventilation rate in the homes of the intervention group. A statistically significant reduction in mean formaldehyde, airborne mold spores, toluene, styrene, limonene, and α-pinene concentrations was observed in the intervention group. There was no significant group difference in change in the number of days with symptoms per 14 days. However, there was a significant decrease in the proportion of children who experienced any wheezing (≥1 episode) and those with ≥4 episodes in the 12-month period in the intervention group. This study indicates that improved ventilation reduces air contaminants and may prevent wheezing. Due to lack of power, a bigger study is needed. PRACTICAL IMPLICATIONS: Positive findings from this study include the fact that, upon recruitment, most of the single family homes with asthmatic children were already equipped with a mechanical ventilation system and had relatively good indoor air quality. However, the 8-h indoor guideline for formaldehyde (50 µg/m3) was frequently exceeded and the ventilation rates were low in most of the homes, even those with a ventilation system. Both ERVs and HRVs were equally effective at increasing air exchange rates above 0.30 ACH and at preventing formaldehyde concentrations from exceeding the 50 µg/m3 guideline during the fall and winter seasons. Furthermore, the ERVs were effective at preventing excessively low relative humidities in the homes. Based on observed difference of risk, intervention to increase ventilation in five sample homes and children would prevent 1 home to exceed the indoor air long-term formaldehyde guideline and prevent 1 asthmatic child experiencing at least one episode of wheezing over a year.

Evaluation of a new panel of six mononucleotide repeat markers for the detection of DNA mismatch repair-deficient tumours.

BACKGROUND: Microsatellite instability (MSI) is a molecular phenotype due to defective DNA mismatch repair (MMR) system. It is used to predict outcome of colorectal tumours and to screen tumours for Lynch syndrome (LS). A pentaplex panel composed of five mononucleotide markers has been largely recommended for determination of the MSI status. However, its sensitivity may be taken in default in occasional situations. The aim of the study was to optimise this panel for the detection of MSI. METHODS: We developed an assay allowing co-amplification of six mononucleotide repeat markers (BAT25, BAT26, BAT40, NR21, NR22, NR27) and one polymorphic dinucleotide marker (D3S1260) in a single reaction. Performances of the new panel were evaluated on a cohort of patients suspected of LS. RESULTS: We demonstrate that our assay is technically as easy to use as the pentaplex assay. The hexaplex panel shows similar performances for the identification of colorectal and non-MSH6-deficient tumours. On the other hand, the hexaplex panel has higher sensitivity for the identification of MSH6-deficient tumours (94.7% vs 84.2%) and MMR-deficient tumours other than colorectal cancer (92.9% vs 85.7%). CONCLUSION: The hexaplex panel could thus be an attractive alternative to the pentaplex panel for the identification of patients with LS.

The Pathogen-annotated Tracking Resource Network (PATRN) system: a web-based resource to aid food safety, regulatory science, and investigations of foodborne pathogens and disease.

Investigation of foodborne diseases requires the capture and analysis of time-sensitive information on microbial pathogens that is derived from multiple analytical methods and sources. The web-based Pathogen-annotated Tracking Resource Network (PATRN) system (www.patrn.net) was developed to address the data aggregation, analysis, and communication needs important to the global food safety community for the investigation of foodborne disease. PATRN incorporates a standard vocabulary for describing isolate metadata and provides a representational schema for a prototypic data exchange standard using a novel data loading wizard for aggregation of assay and attribution information. PATRN currently houses expert-curated, high-quality "foundational datasets" consisting of published experimental results from conventional assays and next generation analysis platforms for isolates of Escherichia coli, Listeria monocytogenes, and Salmonella, Shigella, Vibrio and Cronobacter species. A suite of computational tools for data mining, clustering, and graphical representation is available. Within PATRN, the public curated data repository is complemented by a secure private workspace for user-driven analyses, and for sharing data among collaborators. To demonstrate the data curation, loading wizard features, and analytical capabilities of PATRN, three use-case scenarios are presented. Use-case scenario one is a comparison of the distribution and prevalence of plasmid-encoded virulence factor genes among 249 Cronobacter strains with similar attributes to that of nine Cronobacter isolates from recent cases obtained between March and October, 2010-2011. To highlight PATRN's data management and trend finding tools, analysis of datasets, stored in PATRN as part of an ongoing surveillance project to identify the predominant molecular serogroups among Cronobacter sakazakii isolates observed in the USA is shown. Use-case scenario two demonstrates the secure workspace available for private users to upload and analyze sensitive data, and for collating cross-platform datasets to identify and validate congruent datapoints. SNP datasets from WGS assemblies and pan-genome microarrays are analyzed in a combinatorial fashion to determine relatedness of 33 Salmonella enterica strains to six strains collected as part of an outbreak investigation. Use-case scenario three utilizes published surveillance results that describe the incidence and sources of O157:H7 E. coli isolates associated with a produce pre-harvest surveillance study that occurred during 2002-2006. In summary, PATRN is a web-based integrated platform containing tools for the management, analysis and visualization of data about foodborne pathogens.

Determinants of masked hypertension in hypertensive patients treated in a primary care setting.

BACKGROUND: Recent data suggest that masked hypertension (MH) carries a cardiovascular risk similar to that of uncontrolled hypertension. AIMS: The objective of this study was to determine the prevalence and determinants of MH in patients treated for hypertension in a Canadian primary care setting. METHODS: Office blood pressure (OBP) was measured at baseline and after 3 months of valsartan-based therapy in 5636 hypertensive patients who had recorded their home blood pressure monitoring (HBPM) for seven consecutive days at month 3 using an Omron HEM-711 apparatus. MH was defined in nondiabetic patients as an OBP <140/90 mmHg and an HBPM ≥135/85 mmHg, and in those with diabetes as an OBP <130/80 mmHg and an HBPM ≥125/75 mmHg. RESULTS: Of the 5636 patients, 1025 had diabetes. OBP was controlled at 3 months in 268 (26.1%) of them, but 167 (62.3%) had MH. OBP was controlled in 2728 (59.1%) of the 4611 patients without diabetes, and 935 (34.3%) of them had MH. Overall, 1102 patients had MH, representing 36.8% of patients with controlled OBP and 19.6% of the entire hypertensive study population. Stepwise multiple logistic regression analysis in nondiabetic patients with controlled OBP at 3 months revealed that older age, male sex, higher body mass index and higher office systolic blood pressure were determinants of MH. CONCLUSION: Our results indicate that one of five hypertensive patients and more than one of three with controlled OBP will have MH. MH is associated with other cardiovascular risk factors, such as diabetes, and in nondiabetics, with male sex, older age and obesity.

Speech restoration with tracheoesophageal prosthesis after total laryngectomy: An observational study of vocal results, complications and quality of life.

OBJECTIVES: To study voice prosthesis survival, complications, efficacy and impact on quality of life. METHODS: A single-center observational study was performed in patients treated for squamous cell carcinoma of the larynx or hypopharynx by total (pharyngo)-laryngectomy between 2010 and 2015. Study data comprised: maximum phonation time (sec), number of and reasons for prosthesis exchanges (leakage through or around the prosthesis, expulsion or inclusion of the prosthesis), plus 2 quality of life questionnaires (QLQ-C30, QLQ-H&N35) and the Voice Handicap Inventory (VHI 30). RESULTS: Forty-nine patients were included. The most common causes of prosthesis exchange were leakage through (73.2%) or around the prosthesis (18.5%). The median time between exchanges was 4 months. Global quality of life status on the QLQ-C30 was 63.5. Mean maximum phonation time was 7.4sec. Mean VHI was 46/120; 10 patients had a mild voice handicap, 12 moderate and 10 severe. No relation emerged between the number of prosthesis exchanges per year and quality of life. Voice handicap significantly decreased quality of life, with QLQ-C30 72.3 for the 22 patients with mild to moderate voice handicap and 44.2 for the 10 patients with severe voice handicap (P=0.001). CONCLUSION: Voice restoration by tracheoesophageal prosthesis after total (pharyngo)-laryngectomy is a reliable technique that decreases voice handicap and, despite potentially serious complications, has little negative impact on quality of life.

Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.

Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between S. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks.

"Shame on you": The impact of shame in body-focused repetitive behaviors and binge eating.

Body-focused repetitive behaviors (BFRBs), such as hair-pulling, skin-picking, and nail-biting, have been associated with difficulties in emotion regulation. Studies have suggested that aversive emotions are important triggers for impulsive behaviors such as BFRBs and binge eating. In particular, shame has been hypothesized to be a key emotion before and after these behaviors, but no experimental studies yet have investigated its impact on BFRBs. We aimed to evaluate the role of shame in BFRB and binge eating episodes and the presence of shame following these behaviors. Eighteen women with BFRBs, 18 with binge eating, and 18 community controls participated in the study. Results showed that an experimental shame condition triggered more shame in the binge eating and BFRB groups than in the control group. In addition, the shame induced condition increased the urge to engage in BFRBs, but not in binge eating. Results showed that participants from the BFRB and the binge eating groups reported more shame after engaging in their pathological behaviors compared to following the neutral condition. Future studies should replicate these findings with larger samples and different shame-inducing conditions.

Direct evidence that natural killer cells in nonimmune spleen cell populations prevent tumor growth in vivo.

Relatively large numbers of nonimmune spleen cells do not protect against the local growth of two lymphomas. However, this heterogeneous population of splenic lymphocytes contains a subset of cells that efficiently protects against in vivo tumor growth. This cell population (cell-surface phenotype Thyl.2(-)Ig(-)Ly5.1(+)) represents less than 5 percent of the spleen cell population and is responsible for in vitro NK-mediated lysis. Although these studies clearly and directly demonstrate that Ly5(+) NK cells selected from a heterogeneous lymphoid population from nonimmune mice can protect syngeneic mice against local in vivo growth of two different types of tumor cells (in contrast to other lymphocyte sets within the spleen), they do not directly bear upon the role of NK cells in immunosurveillance. They do indicate that highly enriched Ig(-)Thyl(-)Ly5(+) cells, which account for virtually all in vitro NK activity, can retard tumor growth in vivo. It is difficult to ascribe all anti-tumor surveillance activity to NK cells, because they probably do not recirculate freely throughout the various organ systems of the body. Perhaps NK ceils may play a role in prevention of neoplastic growth within discrete anatomic compartments where there is rapid differentiation of stem cells to mature progeny (e.g., bone marrow, spleen, and portions of the gastrointestinal tract)and may normally act to regulate the growth and differentiation of non-neoplastic stem cells. Long-term observation of chimeric mice repopulated with bone marrow from congenic or mutant donors expressing very low or very high NK activity may help to answer these questions.

The very low penetrance of cystic fibrosis for the R117H mutation: a reappraisal for genetic counselling and newborn screening.

BACKGROUND: Cystic fibrosis (CF) is caused by compound heterozygosity or homozygosity of CF transmembrane conductance regulator gene (CFTR) mutations. Phenotypic variability associated with certain mutations makes genetic counselling difficult, notably for R117H, whose disease phenotype varies from asymptomatic to classical CF. The high frequency of R117H observed in CF newborn screening has also introduced diagnostic dilemmas. The aim of this study was to evaluate the disease penetrance for R117H in order to improve clinical practice. METHODS: The phenotypes in all individuals identified in France as compound heterozygous for R117H and F508del, the most frequent CF mutation, were described. The allelic prevalences of R117H (p(R117H)), on either intron 8 T5 or T7 background, and F508del (p(F508del)) were determined in the French population, to permit an evaluation of the penetrance of CF for the [R117H]+[F508del] genotype. RESULTS: Clinical details were documented for 184 [R117H]+[F508del] individuals, including 72 newborns. The disease phenotype was predominantly mild; one child had classical CF, and three adults' severe pulmonary symptoms. In 5245 healthy adults, p(F508del) was 1.06%, p(R117H;T7) 0.27% and p(R117H;T5)<0.01%. The theoretical number of [R117H;T7]+[F508del] individuals in the French population was estimated at 3650, whereas only 112 were known with CF related symptoms (3.1%). The penetrance of classical CF for [R117H;T7]+[F508del] was estimated at 0.03% and that of severe CF in adulthood at 0.06%. CONCLUSIONS: These results suggest that R117H should be withdrawn from CF mutation panels used for screening programmes. The real impact of so-called disease mutations should be assessed before including them in newborn or preconceptional carrier screening programmes.

Histoire Du Traitement Des Brûlures En France. La Place De L'Hôpital Léon Bérard (Hyères) : Rééducation, Société Savante, Association De Patients.

In the 50s and 60s, before burn centres appeared, burn patients were primarily treated in surgical departments. They were then referred to sanatorium-type institutions, moving towards functional rehabilitation but without a really structured service. In the early 70s, Jean-Pierre Jouglard, Marseille Surgeon, Head of the Burn Treatment Center of the University Hospital of Marseille, collaborated with Dr. Madeleine Malavaud, in an RRF establishment, the Léon Bérard Hospital in Hyères (Var), to create, in 1974, the first French service dedicated to the rehabilitation of burn patients. The Léon Bérard hospital's burn rehabilitation service, which is still active today, helped spread new techniques from the United States of America to France in the 80s, by training young doctors to become rehabilitators. In 1979, it contributed to the creation of the French Society for the Study and Treatment of Burns, enabling patients to compare their experience by promoting the creation of the Association des Brûlés de France in 1983. The Léon Bérard hospital's burn rehabilitation service therefore occupies a prominent place in the history of burn rehabilitation in France.

Comparative genomics of the IncA/C multidrug resistance plasmid family.

Multidrug resistance (MDR) plasmids belonging to the IncA/C plasmid family are widely distributed among Salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant Yersinia pestis isolate (IP275) from Madagascar. Here, we present the complete plasmid sequences of the IncA/C reference plasmid pRA1 (143,963 bp), isolated in 1971 from the fish pathogen Aeromonas hydrophila, and of the cryptic IncA/C plasmid pRAx (49,763 bp), isolated from Escherichia coli transconjugant D7-3, which was obtained through pRA1 transfer in 1980. Using comparative sequence analysis of pRA1 and pRAx with recent members of the IncA/C plasmid family, we show that both plasmids provide novel insights into the evolution of the IncA/C MDR plasmid family and the minimal machinery necessary for stable IncA/C plasmid maintenance. Our results indicate that recent members of the IncA/C plasmid family evolved from a common ancestor, similar in composition to pRA1, through stepwise integration of horizontally acquired resistance gene arrays into a conserved plasmid backbone. Phylogenetic comparisons predict type IV secretion-like conjugative transfer operons encoded on the shared plasmid backbones to be closely related to a group of integrating conjugative elements, which use conjugative transfer for horizontal propagation but stably integrate into the host chromosome during vegetative growth. A hipAB toxin-antitoxin gene cluster found on pRA1, which in Escherichia coli is involved in the formation of persister cell subpopulations, suggests persistence as an early broad-spectrum antimicrobial resistance mechanism in the evolution of IncA/C resistance plasmids.

Antimicrobial resistance-conferring plasmids with similarity to virulence plasmids from avian pathogenic Escherichia coli strains in Salmonella enterica serovar Kentucky isolates from poultry.

Salmonella enterica, a leading cause of food-borne gastroenteritis worldwide, may be found in any raw food of animal, vegetable, or fruit origin. Salmonella serovars differ in distribution, virulence, and host specificity. Salmonella enterica serovar Kentucky, though often found in the food supply, is less commonly isolated from ill humans. The multidrug-resistant isolate S. Kentucky CVM29188, isolated from a chicken breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp, and 46,121 bp), two of which carry resistance determinants (pCVM29188_146 [strAB and tetRA] and pCVM29188_101 [bla(CMY-2) and sugE]). Both resistance plasmids were transferable by conjugation, alone or in combination, to S. Kentucky, Salmonella enterica serovar Newport, and Escherichia coli recipients. pCVM29188_146 shares a highly conserved plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence plasmids from avian pathogenic Escherichia coli strains (pAPEC-O1-ColBM and pAPEC-O2-ColV). Shared avian pathogenic E. coli (APEC) virulence factors include iutA iucABCD, sitABCD, etsABC, iss, and iroBCDEN. PCR analyses of recent (1997 to 2005) S. Kentucky isolates from food animal, retail meat, and human sources revealed that 172 (60%) contained similar APEC-like plasmid backbones. Notably, though rare in human- and cattle-derived isolates, this plasmid backbone was found at a high frequency (50 to 100%) among S. Kentucky isolates from chickens within the same time span. Ninety-four percent of the APEC-positive isolates showed resistance to tetracycline and streptomycin. Together, our findings of a resistance-conferring APEC virulence plasmid in a poultry-derived S. Kentucky isolate and of similar resistance/virulence plasmids in most recent S. Kentucky isolates from chickens and, to lesser degree, from humans and cattle highlight the need for additional research in order to examine the prevalence and spread of combined virulence and resistance plasmids in bacteria in agricultural, environmental, and clinical settings.

High mutation frequencies among Escherichia coli and Salmonella pathogens.

Here it is reported that the incidence of mutators among isolates of pathogenic Escherichia coli and Salmonella enterica is high (over 1 percent). These findings counter the theory, founded on studies with laboratory-attenuated strains, that suggests mutators are rare among bacterial populations. Defects in methyl-directed mismatch repair underlie all mutator phenotypes described here. Of nine independently derived hypermutable strains, seven contained a defective mutS allele. Because these mutant alleles increase the mutation rate and enhance recombination among diverse species, these studies may help explain both the rapid emergence of antibiotic resistance and the penetrance of virulence genes within the prokaryotic community.

Altered utilization of N-acetyl-D-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak.

In silico analyses of previously sequenced strains of Escherichia coli O157:H7, EDL933 and Sakai, localized the gene cluster for the utilization of N-acetyl-D-galactosamine (Aga) and D-galactosamine (Gam). This gene cluster encodes the Aga phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) and other catabolic enzymes responsible for transport and catabolism of Aga. As the complete coding sequences for enzyme IIA (EIIA)(Aga/Gam), EIIB(Aga), EIIC(Aga), and EIID(Aga) of the Aga PTS are present, E. coli O157:H7 strains normally are able to utilize Aga as a sole carbon source. The Gam PTS complex, in contrast, lacks EIIC(Gam), and consequently, E. coli O157:H7 strains cannot utilize Gam. Phenotypic analyses of 120 independent isolates of E. coli O157:H7 from our culture collection revealed that the overwhelming majority (118/120) displayed the expected Aga+ Gam- phenotype. Yet, when 194 individual isolates, derived from a 2006 spinach-associated E. coli O157:H7 outbreak, were analyzed, all (194/194) displayed an Aga- Gam- phenotype. Comparison of aga/gam sequences from two spinach isolates with those of EDL933 and Sakai revealed a single nucleotide change (G:C-->A:T) in the agaF gene in the spinach-associated isolates. The base substitution in agaF, which encodes EIIA(Aga/Gam) of the PTS, changes a conserved glycine residue to serine (Gly91Ser). Pyrosequencing of this region showed that all spinach-associated E. coli O157:H7 isolates harbored this same G:C-->A:T substitution. Notably, when agaF+ was cloned into an expression vector and transformed into six spinach isolates, all (6/6) were able to grow on Aga, thus demonstrating that the Gly91Ser substitution underlies the Aga- phenotype in these isolates.