bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of co-existence of PMQR genes and QRDR mutations on fluoroquinolones resistance in Enterobacteriaceae strains isolated from community and hospital acquired UTIs
Authors: Kotb Dalia Nabil , Mahdy Wafaa Khairy , Mahmoud Mahmoud Shokry , Khairy Rasha M. M. 
Published: November 2019

Abstract
Background
Fluoroquinolones are commonly recommended as treatment for urinary tract infections (UTIs). The development of resistance to these agents, particularly in gram-negative microorganisms complicates treatment of infections caused by these organisms. This study aimed to investigate antimicrobial resistance of different Enterobacteriaceae species isolated from hospital- acquired and community-acquired UTIs against fluoroquinolones and correlate its levels with the existing genetic mechanisms of resistance.

Methods
A total of 440 Enterobacteriaceae isolates recovered from UTIs were tested for antimicrobial susceptibility. Plasmid-mediated quinolone resistance (PMQR) genes and mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC genes were examined in quinolone-resistant strains.

Results
About (32.5%) of isolates were resistant to quinolones and (20.5%) were resistant to fluoroquinolones. All isolates with high and intermediate resistance phenotypes harbored one or more PMQR genes. QnrB was the most frequent gene (62.9%) of resistant isolates. Co-carriage of 2 PMQR genes was detected in isolates (46.9%) with high resistance to ciprofloxacin (CIP) (MICs > 128 μg/mL), while co-carriage of 3 PMQR genes was detected in (6.3%) of resistant isolates (MICs > 512 μg/mL). Carriage of one gene only was detected in intermediate resistance isolates (MICs of CIP = 1.5–2 μg/mL). Neither qnrA nor qnrC genes were detected. The mutation at code 83 of gyrA was the most frequent followed by Ser80-Ile in parC gene, while Asp-87 Asn mutation of gyrA gene was the least, where it was detected only in high resistant E. coli isolates (MIC ≥128 μg/mL). A double mutation in gyrA (Lys154Arg and Ser171Ala) was observed in high FQs resistant isolates (MIC of CIP < 128 μg/mL).

Conclusion
FQs resistance is caused by interact between PMQR genes and mutations in both gyrA and parC genes while a mutation in one gene only can explain quinolone resistance. Accumulation of PMQR genes and QRDR mutations confers high resistance to FQs.
Co-circulation of the two influenza B lineages during 13 consecutive influenza surveillance seasons in Italy, 2004–2017
Authors:   the Italian Influenza Laboratory Network, Puzelli Simona , Di Martino Angela , Facchini Marzia , Fabiani Concetta , Calzoletti Laura , Di Mario Giuseppina , Palmieri Annapina , Affanni Paola , Camilloni Barbara , Chironna Maria , D’Agaro Pierlanfranco , Giannecchini Simone , Pariani Elena , Serra Caterina , Rizzo Caterina , Bella Antonino , Donatelli Isabella , Castrucci Maria Rita 
Published: November 2019

AbstractBackgroundSince 1985, two antigenically distinct lineages of influenza B viruses (Victoria-like and Yamagata-like) have circulated globally. Trivalent seasonal influenza vaccines contain two circulating influenza A strains but a single B strain and thus provide limited immunity against circulating B strains of the lineage not included in the vaccine. In this study, we describe the characteristics of influenza B viruses that caused respiratory illness in the population in Italy over 13 consecutive seasons of virological surveillance, and the match between the predominant influenza B lineage and the vaccine B lineage, in each season.MethodsFrom 2004 to 2017, 26,886 laboratory-confirmed influenza cases were registered in Italy, of which 18.7% were type B. Among them, the lineage of 2465 strains (49%) was retrieved or characterized in this study by a real-time RT-PCR assay and/or sequencing of the hemagglutinin (HA) gene.ResultsCo-circulation of both B lineages was observed each season, although in different proportions every year. Overall, viruses of B/Victoria and B/Yamagata lineages caused 53.3 and 46.7% of influenza B infections, respectively. A higher proportion of infections with both lineages was detected in children, and there was a declining frequency of B/Victoria detections with age. A mismatch between the vaccine and the predominant influenza B lineage occurred in eight out of thirteen influenza seasons under study. Considering the seasons when B accounted for > 20% of all laboratory-confirmed influenza cases, a mismatch was observed in four out of six seasons. Phylogenetic analysis of the HA1 domain confirmed the co-circulation of both lineages and revealed a mixed circulation of distinct evolutionary viral variants, with different levels of match to the vaccine strains.ConclusionsThis study contributes to the understanding of the circulation of influenza B viruses in Italy. We found a continuous co-circulation of both B lineages in the period 2004–2017, and determined that children were particularly vulnerable to Victoria-lineage influenza B virus infections. An influenza B lineage mismatch with the trivalent vaccine occurred in about two-thirds of cases.
Rapid antimicrobial susceptibility testing on positive blood cultures through an innovative light scattering technology: performances and turnaround time evaluation
Authors: Boland Lidvine , Streel Corentin , De Wolf Hélène , Rodriguez Hector , Verroken Alexia 
Published: November 2019

Abstract
Background
A bacteremia diagnosis with speeded-up identification and antimicrobial susceptibility testing (AST) is mandatory to adjust empirical broad-spectrum antibiotherapy and avoid the emergence of multi-resistant bacteria. Alfred 60AST (Alifax, Polverara, PD, Italy) is an innovative automated system based on light scattering measurements allowing direct AST from positive blood cultures with rapid results. In this study we aimed to evaluate the system’s performances and turnaround time (TAT) compared to routine AST.

Methods
The study was conducted during 2 non-consecutive 3-month periods at the microbiology laboratory of the Cliniques universitaires Saint-Luc. All blood cultures detected positive in the 0 AM–10 AM time frame with a pure Gram-positive cocci or Gram-negative bacilli stain were included for Alfred 60AST testing. Two customized EUCAST antibiotic panels were set up composed of 1) a “Gram-negative” panel including cefuroxime, ceftazidime Enterobacteriaceae, piperacillin-tazobactam Enterobacteriaceae, ciprofloxacine, and ceftazidime Pseudomonas 2) a “Gram-positive” panel including cefoxitin Staphylococcus aureus, cefoxitin coagulase-negative (CNS) Staphylococci and ampicillin Enterococci. Categorical agreement (CA), very major errors (VME), major errors (ME), minor errors (mE) and TAT to Alfred 60AST results were calculated in comparison with AST results obtained from direct testing on positive blood cultures with the Phoenix system (Becton Dickinson, Franklin Lakes, NJ, USA).

Results
Five hundred seventy and one hundred nine antibiotics were evaluated on respectively 166 Gram-negative bacilli and 109 Gram-positive cocci included in the studied population. During the first study period regarding Gram-negative strains a CA of 89.5% was obtained with a high rate of VME (19 and 15.4% respectively) for cefuroxime and piperacillin-tazobactam Enterobacteriaceae. Considering this, Alifax reviewed these antibiotics’ formulations improving Gram-negative bacilli total CA to 92.2% with no VME during the second study period. For Gram-positive cocci, total CA was 88.1% with 2.3% VME, 13.8% ME (mainly cefoxitin CNS) and 12% mE rates both study periods combined. Median TAT to AST results was 5 h with Alfred versus 12 h34 with Phoenix.

Conclusion
The Alfred 60AST system shows correct yet improvable microbiological performances and a major TAT reduction compared to direct automated AST testing. Clinical studies measuring the impact of the approach on antibiotic management of patients with bacteremia are recommended.
Deep sequencing of hepatitis B surface antigen gene in the preserved umbilical cords in immunoprophylaxis failure against mother-to-child HBV transmission
Authors: Komatsu Haruki , Inui Ayano , Suzuki Yasuto , Sugiyama Masaya , Fujisawa Tomoo 
Published: November 2019

Abstract
Background
Vaccine escape mutants (VEMs) are one of the causes of breakthrough infections in the mother-to-child transmission of hepatitis B virus (HBV). We hypothesized that VEMs existing as minor populations in the maternal blood are associated with breakthrough infections in children. We sought to determine whether VEMs exist as minor populations in the preserved umbilical cords of children with breakthrough infections.

Case presentation
Two families (Family 1: three children, Family 2: two children) were enrolled. Despite immunoprophylaxis, a breakthrough infection occurred in two Family 1 children and two Family 2 children. Preserved umbilical cords, serum, and nails were used for the HBV DNA analysis. To detect VEMs, we performed direct and deep sequencing of hepatitis B surface antigen gene. The direct sequencing showed that there were no VEMs in the serum of the children or mother of Family 1 and family 2, but it identified a G145A mutant in the nails of the mother of Family 2. In Family 1, deep sequencing detected a T143S mutant as a minor population (1.7–2.0%) in the umbilical cords and serum of all three children and in the serum of the mother. A T126A mutant was also detected in the umbilical cord (9.2%) and serum (7.0%) of the first-born child of Family 1. In Family 2, the deep sequencing showed no VEMs in the umbilical cords, but it detected D144A (2.5%) and G145A (11.2%) mutants in the serum of the 2nd-born child.

Conclusions
VEMs were present as minor populations in the preserved umbilical cords of children with breakthrough infections. The VEMs did not become major populations after the breakthrough infections. The evolution of VEMs from a minor form to a major form might not be a prerequisite for breakthrough infections in mother-to-child transmission.
A comparative analysis of diffusion-weighted imaging and ultrasound in thyroid nodules
Authors: Kong Weidan , Yue Xiuhui , Ren Jiliang , Tao Xiaofeng 
Published: November 2019

Abstract
Background
Diffusion-weighted imaging (DWI) and ultrasound are commonly used methods to examine thyroid nodules, but their comparative value is rarely studied. We evaluated the utility of DWI and ultrasound in differentiating benign and malignant thyroid nodules.

Methods
A total of 100 patients with 137 nodules who underwent both DWI and ultrasound before operation were enrolled. The T1 and T2 signal intensity ratio (SIR) of each thyroid nodule was calculated by measuring the mean signal intensity divided by that of paraspinal muscle. The apparent diffusion coefficient (ADC) value and the SIR of benign and malignant thyroid nodules were analyzed by two-sample independent t tests. The sensitivity, specificity, and accuracy of DWI and ultrasound were compared with chi-square tests.

Results
There was no significant difference in the SIR between benign and malignant thyroid nodules. The ADC value was significantly different. At the threshold value was 1.12 × 10− 3 mm2/s, the maximum area under the curve was 0.944. The sensitivity, specificity, and accuracy were 84.9, 92.2, and 87.6% respectively. The corresponding values of ultrasound diagnosis were 90.1, 80.4, and 86.9%.

Conclusions
Ultrasound has high sensitivity in differentiating benign and malignant thyroid nodules, and the ADC value has high specificity, but there is no statistical difference in sensitivity or specificity between the two modalities. DWI and ultrasound each have their own advantages in differentiating benign and malignant thyroid nodules.
A case report of IgG4-related disease: an insidious path to the diagnosis through kidney, heart and brain
Authors: Comai Giorgia , Cuna Vania , Fabbrizio Benedetta , Sabattini Elena , Leone Ornella , Tondolo Francesco , Angeletti Andrea , Cappuccilli Maria , Liguori Rocco , La Manna Gaetano 
Published: November 2019

AbstractBackgroundIgG4-related disease, described around the years 2000 as a form of autoimmune pancreatitis, is now increasingly accepted as a systemic syndrome. The diagnosis is based on both comprehensive and organ-specific criteria. For the kidney, Mayo clinic classification and the guidelines of the Japanese Nephrology Society are used. Ultimately, together with parameters that characterize every organ or apparatus involved, the key element is the confirmation of growing levels of IgG4 in blood or in tissues.Case presentationWe describe a male patient with chronic renal failure associated to hypertension without proteinuria. IgG4-related disease was diagnosed through renal biopsy. After an initial positive response to steroids, he presented tinnitus, and histological assessment showed cerebral and subsequently cardiac damage, both IgG4-related. This case appears unique for the type of histologically documented cardiac and neurological parenchymal involvement, and at the same time, exemplifies the subtle and pernicious course of the disease. Frequently, blurred and non-specific signs prevail. Here, kidney damage was associated with minimal urinary findings, slowly progressive renal dysfunction and other factors that can be equivocated in the differential diagnosis. Neurological involvement was represented by tinnitus alone, while cardiac alterations were completely asymptomatic.ConclusionsThis report is representative of the neurological and cardiac changes described in the literature for IgG4-related disease, which may be correlated or not with the renal form and highlights the need, in some cases, of targeted therapeutic approaches. In addition to glucocorticoids, as in this case, rituximab may be necessary.
Risk factors for foot ulceration in adults with end-stage renal disease on dialysis: a prospective observational cohort study
Authors: Kaminski Michelle R. , Lambert Katrina A. , Raspovic Anita , McMahon Lawrence P. , Erbas Bircan , Mount Peter F. , Kerr Peter G. , Landorf Karl B. 
Published: November 2019

Abstract
Background
Dialysis patients experience high rates of foot ulceration. Although risk factors for ulceration have been extensively studied in patients with diabetes, there is limited high-quality, longitudinal evidence in the dialysis population. Therefore, this study investigated risk factors for foot ulceration in a stable dialysis cohort.

Methods
We prospectively collected clinical, demographic, health status, and foot examination information on 450 adults with end-stage renal disease from satellite and home-therapy dialysis units in Melbourne, Australia over 12 months. The primary outcome was foot ulceration. Cox proportional hazard modelling and multinomial regression were used to investigate risk factors.

Results
Among 450 dialysis patients (mean age, 67.5 years; 64.7% male; 94% hemodialysis; 50.2% diabetes), new cases of foot ulceration were identified in 81 (18%) participants. Overall, risk factors for foot ulceration were neuropathy (HR 3.02; 95% CI 1.48 to 6.15) and previous ulceration (HR 2.86; CI 1.53 to 5.34). In those without history of ulceration, nail pathology (RR 3.85; CI 1.08 to 13.75) and neuropathy (RR 2.66; CI 1.04 to 6.82) were risk factors. In those with history of ulceration, neuropathy (RR 11.23; CI 3.16 to 39.87), peripheral arterial disease (RR 7.15; CI 2.24 to 22.82) and cerebrovascular disease (RR 2.08; CI 1.04 to 4.16) were risk factors. There were 12 (2.7%) new amputations, 96 (21.3%) infections, 24 (5.3%) revascularizations, 42 (9.3%) foot-related hospitalizations, and 52 (11.6%) deaths.

Conclusions
Neuropathy and previous ulceration are major risk factors for foot ulceration in dialysis patients. Risk factors differ between those with and without prior ulceration. The risk factors identified will help to reduce the incidence of ulceration and its associated complications.
Depressive symptoms and dietary non-adherence among end stage renal disease patients undergoing hemodialysis therapy: systematic review
Authors: Gebrie Mignote Hailu , Ford Jodi 
Published: November 2019

AbstractBackgroundResearch suggests that patients with end stage renal disease undergoing hemodialysis have a higher rate of depression and dietary non adherence leading to hospitalization and mortality. The purpose of this review was to synthesize the quantitative evidence on the relationship between depressive symptoms and dietary non adherence among end stage renal disease (ESRD) patients receiving hemodialysis.MethodsA systematic review was undertaken. Three electronic databases were searched including PubMed, CINHAL and Web of Science. Only quantitative studies published between 2001 and 2016 were included in the review.ResultA total of 141 publications were reviewed during the search process and 28 articles that fulfilled the inclusion criteria were included in the review. Eleven studies (39.3%) reported on the prevalence of depressive symptoms or depression and its effect on patient outcomes. Ten studies (35.7%) focused on dietary adherence/non adherence in patients with ESRD and the remaining seven (25%) articles were descriptive studies on the relationship between depressive symptoms and dietary non adherence in patients with ESRD receiving hemodialysis. The prevalence of depressive symptoms and dietary non adherence ranged as 6–83.49% and from 41.1–98.3% respectively. Decreased quality of life & increased morbidity and mortality were positively associated with depressive symptoms. Other factors including urea, hemoglobin, creatinine and serum albumin had also association with depressive symptoms. Regarding dietary non adherence, age, social support, educational status, behavioral control and positive attitudes are important factors in ESRD patients receiving hemodialysis. Having depressive symptoms is more likely to increase dietary non adherence.ConclusionDepressive symptoms and dietary non adherence were highly prevalent in patients with end stage renal disease receiving hemodialysis therapy. Nearly all of the articles that examined the relationship between depressive symptoms and dietary non adherence found a significant association. Future research using experimental or longitudinal design and gold standard measures with established cut-points is needed to further explain the relationship.
Association between ovarian reserve and preeclampsia: a cohort study
Authors: Erfani Hadi , Rahmati Maryam , Mansournia Mohammad Ali , Azizi Fereidoun , Montazeri Seyed Ali , Shamshirsaz Alireza A. , Ramezani Tehrani Fahimeh 
Published: November 2019

Abstract
Background
The risk of cardiovascular disease in women increases after menopause. It has been shown that women with lower pre-menopausal ovarian reserve may experience increased cardiovascular risk. We sought to determine whether there is any association between ovarian reserve, as assessed by Anti-Mullerian hormone (AMH), and preeclampsia (PE).

Methods
Subjects of this study were selected from among participants of the Tehran Lipid and Glucose Study (TLGS), a population-based cohort with a 15-year follow-up (1998–2014). Out of 2412 women aged 20–50 years, there were 781 women who met eligibility criteria, including having comprehensive data on their reproductive assessment and ovarian reserve status, identified based on age-specific AMH levels according to the exponential–normal three-parameter model that was measured before pregnancy.
There were 80 and 701 participants in the preeclampsia and non-PE groups, respectively. The association between dichotomous outcome variable PE and age-specific AMH quartiles was evaluated using pooled logistic regression.

Results
PE was observed in 23 (11.1%), 12 (6.4%), 26 (13.3%) and 19 (10%) women in the 1st, 2nd, 3rd and 4th quartiles of pre-pregnancy age-specific AMH, respectively (P = 0.16). Median and inter-quartile range of serum AMH levels was 1.05 (0.36–2.2) mg/L in women who experienced PE compared with 0.85 (0.28–2.1) mg/L in women with normotensive pregnancies (P = 0.53). Based on the pooled logistic regression analysis, the effect of age-specific AMH quartiles on PE progression (adjusted for age, BMI, smoking status, and family history of hypertension) were not significant (OR1st vs 4th: 1.5, P-value: 0.1, CI: (0.9, 2.4)).

Conclusions
Age-specific AMH may not be a suitable marker for prediction of PE. Further longitudinal studies, considering pre-conception measurement of AMH, are recommended for better interpretation of the association between ovarian reserve status and PE.
Exploring survivor perceptions of pre-eclampsia and eclampsia in Nigeria through the health belief model
Authors: Sripad Pooja , Kirk Karen , Adoyi Gloria , Dempsey Amy , Ishaku Salisu , Warren Charlotte E. 
Published: November 2019

AbstractBackgroundIn Nigeria, hypertensive disorders have become the leading cause of facility-based maternal mortality. Many factors influence pregnant women’s health-seeking behaviors and perceptions around the importance of antenatal care. This qualitative study describes the care-seeking pathways of Nigerian women who suffer from pre-eclampsia and eclampsia. It identifies the influences – barriers and enablers – that affect their decision making, and proposes solutions articulated by women themselves to overcome the obstacles they face. Informing this study is the health belief model, a cognitive value-expectancy theory that provides a framework for exploring perceptions and understanding women’s narratives around pre-eclampsia and eclampsia-related care seeking.MethodsThis study adopted a qualitative design that enables fully capturing the narratives of women who experienced pre-eclampsia and eclampsia during their pregnancy. In-depth interviews were conducted with 42 women aged 17–48 years over five months in 2015 from Bauchi, Cross River, Ebonyi, Katsina, Kogi, Ondo and Sokoto states to ensure representation from each geo-political zone in Nigeria. These qualitative data were analyzed through coding and memo-writing, using NVivo 11 software.ResultsWe found that many of the beliefs, attitudes, knowledge and behaviors of women are consistent across the country, with some variation between the north and south. In Nigeria, women’s perceived susceptibility and threat of health complications during pregnancy and childbirth, including pre-eclampsia and eclampsia, influence care-seeking behaviors. Moderating influences include acquisition of knowledge of causes and signs of pre-eclampsia, the quality of patient-provider antenatal care interactions, and supportive discussions and care seeking-enabling decisions with families and communities. These cues to action mitigate perceived mobility, financial, mistrust, and contextual barriers to seeking timely care and promote the benefits of maternal and newborn survival and greater confidence in and access to the health system.ConclusionsThe health belief model reveals intersectional effects of childbearing norms, socio-cultural beliefs and trust in the health system and elucidates opportunities to intervene and improve access to quality and respectful care throughout a woman’s pregnancy and childbirth. Across Nigerian settings, it is critical to enhance context-adapted community awareness programs and interventions to promote birth preparedness and social support.