Molecular Identification of Staphylococcus aureus in Airway Samples from Children with Cystic Fibrosis

Background

Staphylococcus aureus is a common and significant pathogen in cystic fibrosis. We sought to determine if quantitative PCR (qPCR) and 16S rRNA gene sequencing could provide a rapid, culture-independent approach to the identification of S. aureus airway infections.

Methods

We examined the sensitivity and specificity of two qPCR assays, targeting the femA and 16S rRNA gene, using culture as the gold standard. In addition, 16S rRNA gene sequencing to identify S. aureus directly from airway samples was evaluated. DNA extraction was performed with and without prior enzymatic digestion.

Results

87 samples [42 oropharyngeal (OP) and 45 expectorated sputum (ES)] were analyzed. 59 samples (68%) cultured positive for S. aureus. Using standard extraction techniques, sequencing had the highest sensitivity for S. aureus detection (85%), followed by FemA qPCR (52%) and 16SrRNA qPCR (34%). For all assays, sensitivity was higher from ES samples compared to OP swabs. Specificity of the qPCR assays was 100%, but 21.4% for sequencing due to detection of S. aureus in low relative abundance from culture negative samples. Enzymatic digestion increased the sensitivity of qPCR assays, particularly for OP swabs.

Conclusion

Sequencing had a high sensitivity for S. aureus, but low specificity. While femA qPCR had higher sensitivity than 16S qPCR for detection of S. aureus, neither assay was as sensitive as sequencing. The significance of S. aureus detection with low relative abundance by sequencing in culture-negative specimens is not clear.     

Identification of Ganglioside GM3 Molecular Species in Human Serum Associated with Risk Factors of Metabolic Syndrome

Serum GM3 molecular species were quantified in 125 Japanese residents using tandem mass spectrometry multiple reaction monitoring. Individuals were categorized by the presence or absence of metabolic disease risk factors including visceral fat accumulation, hyperglycemia and dyslipidemia. A total of 23 GM3 molecular species were measured, of these, eight were found to be significantly elevated in individuals with visceral fat accumulation and metabolic disease, defined as the presence of hyperglycemia and dyslipidemia. All of the GM3 molecular species were composed of the sphingoid base sphingosine (d18:1 (Δ4)) and, interestingly, six of the eight elevated GM3 molecular species contained a hydroxylated ceramide moiety. The hydroxylated GM3 species were, in order of decreasing abundance, d18:1-h24:0 ≈ d18:1-h24:1 > d18:1-h22:0 » d18:1-h20:0 > d18:1-h21:0 > d18:1-h18:1. Univariate and multiple linear regression analyses were conducted using a number of clinical health variables associated with obesity, type 2 diabetes, metabolic disease, atherosclerosis and hypertension. GM3(d18:1-h24:1) was identified as the best candidate for metabolic screening, proving to be significantly correlated with intima-media thickness, used for the detection of atherosclerotic disease in humans, and a number of metabolic disease risk factors including autotaxin, LDL-c and homeostatic model assessment insulin resistance (HOMA-IR).     

Prevalence of Helicobacter pylori Infection and Identification of Risk Factors in Rural and Urban Beijing, China

Background:  The prevalence of Helicobacter pylori is higher in developing countries such as China. The aim of this study was to investigate the prevalence of H. pylori in one rural and one urban region of Beijing, China.
Materials and Methods:  Healthy individuals in rural Pinggu and urban Haidian voluntarily participated in this study. The diagnosis of H. pylori infection was reached using the ¹³C-urea breath test. Associations between H. pylori and sex, age, living area (i.e. rural vs urban), education level, smoking, and alcohol consumption were evaluated.
Results:  Of the 1232 included subjects, 54.7% of tested individuals residing in Pinggu and 41.3% in Haidian were positive for H. pylori . In urban region, more individuals were negative for H. pylori (429 of 731), whereas in the rural region, more individuals were positive for H. pylori ( p <  .05). Univariate analysis identified geographic area and lower education and annual income as significant factors associated with H. pylori . Men in rural areas were more likely than women in rural areas to be infected, and both men and women in the rural area were more likely to be positive for H. pylori than men and women in the urban area (all p  < .05).
Conclusions:  H. pylori infection is common in both rural and urban regions of Beijing. Residing in a rural area, having a lower family income, and lower education level are significant risk factors associated with infection.     

内蒙古地区白桦外生菌根形态类型及分子鉴定

以内蒙古不同地区白桦外生菌根为材料,采用形态解剖学方法和分子生物学手段对与白桦共生的外生菌根真菌多样性进行全面的调查,并经对所测序列与GenBank和Database比对。结果显示:在内蒙古地区与白桦共生的外生菌根真菌共13种,其中担子菌7种,子囊菌4种,分别来自于丝膜菌属、丝盖伞属、蜡壳耳属、毛革菌属、滑菇属和空团菌属、块菌属、地怀菌属。其中,菌根类型T₈和T₁₁未能提出其总DNA,根据其外生菌根形态类型并参照Agerer体视显微镜菌根图谱和Haug菌根图谱进行比较,分类鉴定为荷顿氏疣柄牛肝菌和白桦外生菌根真菌一种。结果表明,内蒙古地区白桦外生菌根真菌多样性相对较高,且与利用地上子实体鉴定的外生菌根真菌种类有一定的区别。     

Dried Blood Spot Sampling for Hepatitis B Virus Serology and Molecular Testing

Background & Aims

Dried blood spots (DBS) on filter paper have been successfully used to diagnose and monitor several infectious diseases. The aim was to investigate the performance of DBS in hepatitis B virus (HBV) diagnosis using commercial tests in comparison to standard methods.

Methods

Paired DBS and plasma samples were collected from 200 patients: 100 patients with HBsAg negative status and 100 patients with HBsAg positive status. In the latter patient, HBeAg reactivity was tested. Ten samples of anti-HBs were collected from people vaccinated against HBV. We also studied 50 patients with positive HBV DNA viral load in plasma and 10 HBV DNA negative patients. HBV genotypes and gene polymerase mutations were determined in 10 randomly selected HBV-infected patients. The DBS sample consisted of 50 µL of whole blood, i.e. a 12-mm paper card.

Results

The sensitivity thresholds of HBsAg and anti-HBs antibody were 0.30±0.08 IU/mL and 18.11±6.05 IU/mL, respectively, for DBS with 98% sensitivity and 100% specificity. Sensitivity was 98% and specificity 100% for the detection of HBV DNA on a blotter, considering an HBV DNA threshold of 914.1±157.8 IU/ml. Ten patients had an HBeAg positive status in plasma, all were detected positive using DBS. HBV genotyping and mutation detection were successfully performed on DBS, with full concordance between the 10 paired DBS and plasma samples.

Conclusion

This study shows DBS is a reliable alternative to plasma specimens for quantifying and detecting HBsAg, anti-HBs, HBeAg and genotyping. DBS may increase the opportunities for HBV testing and treatment follow-up in hard-to-reach individuals.     

Male Urinary Incontinence: Prevalence,Risk Factors,and Preventive Interventions

Urinary incontinence (UI) in community-dwelling men affects quality of life and increases the risk of institutionalization. Observational studies and randomized, controlled trials published in English from 1990 to November 2007 on the epidemiology and prevention of UI were identified in several databases to abstract rates and adjusted odds ratios (OR) of incontinence, calculate absolute risk difference (ARD) after clinical interventions, and synthesize evidence with random-effects models. Of 1083 articles identified, 126 were eligible for analysis. Pooled prevalence of UI increased with age to 21% to 32% in elderly men. Poor general health, comorbidities, severe physical limitations, cognitive impairment, stroke (pooled OR 1.54; 95% confidence interval [CI], 1.14–2.1), urinary tract infections (pooled OR 3.49; 95% CI, 2.33–5.23), prostate diseases, and diabetes (pooled OR 1.36; 95% CI, 1.14–1.61) were associated with UI. Treatment with tolterodine alone (ARD 0.17; 95% CI, 0.02–0.32) or combined with tamsulosin (ARD 0.17; 95% CI, 0.08–0.25) resulted in greater self-reported benefit compared with placebo. Radical prostatectomy or radiotherapy for prostate cancer compared with watchful waiting increased UI. Short-term prevention of UI with pelvic floor muscle rehabilitation after prostatectomy was not consistently seen across randomized, controlled trials. The prevalence of incontinence increased with age and functional dependency. Stroke, diabetes, poor general health, radiation, and surgery for prostate cancer were associated with UI in community-dwelling men. Men reported overall benefit from drug treatments. Limited evidence of preventive effects of pelvic floor rehabilitation requires future investigation.Key words: Urinary incontinence, Risk factors, Rehabilitation, Drug therapyUrinary incontinence (UI) affects substantial proportions of men¹; the estimated prevalence of UI varied from 11% among those aged 60 to 64 years to 31% in older men, and from 16% among white men to 21% among African American men.² Daily UI was reported by 30% to 47% and weekly UI by 15% to 37% of community-dwelling men.² A small proportion (22%) of men with weekly UI episodes ever sought medical care for this problem, whereas 40% of treated men reported moderate to great frustration with continued urine leakage.³Baseline mechanisms of UI include overactive bladder that may result in urge UI and poor urethral sphincter function that can result in primary urethral incompetence and stress UI.^4,5 Baseline mechanisms of incontinence lead to variable definitions, risk factors, and effective interventions to prevent and treat UI.⁵This review was commissioned as background material for a National Institutes of Health Office of Medical Applications of Research State of the Science Conference on Incontinence. We aimed to synthesize evidence of the effectiveness of different clinical interventions to prevent the occurrence and progression of UI in community-dwelling men.     

Polymicrobial Bloodstream Infection in Neonates: Microbiology,Clinical Characteristics,and Risk Factors

Background

Polymicrobial bloodstream infections (PBSIs) have been associated with complex underlying medical conditions and a high incidence of specific microorganisms in several settings, but the relevant data are scarce in neonates.

Methods

Positive blood cultures from January 2004 to December 2011 in the neonatal intensive care unit (NICU) of Chang Gung Memorial Hospital (CGMH) were reviewed. Each neonate with PBSI (case episode) was matched to two episodes of monomicrobial BSI (control episode) by birth weight, gestational age and gender. Records were reviewed to compare their underlying medical conditions, organisms isolated, adequacy of therapy, clinical characteristics and outcomes.

Results

Forty-five episodes of PBSI (4.4% of all neonatal BSIs) were identified in 43 neonates. Gram-negative organisms constituted 59.8% of all PBSI pathogens, and 33 (73.3%) of PBSIs were caused by at least one Gram-negative organism. PBSIs were significantly more likely to be the recurrent episode and have endotracheal tube in place. No significant difference was found between PBSIs and controls in terms of demographics and most chronic conditions. PBSIs were significantly associated with a higher severity of illness, a longer duration of septic symptoms, and a higher rate of modification of antimicrobial regimens than monomicrobial BSIs. However, the sepsis-attributable mortality rates were comparable between these two groups.

Conclusions

In the NICU, PBSIs were more often caused by Gram-negative bacilli, and often occurred in neonates without any chronic conditions. The clinical significance of PBSIs included a more severe illness, longer duration of septic symptoms and a higher rate of modification of antimicrobial regimens.     

Molecular genetic analysis of Wanggu remains, Inner Mongolia, China

The Wanggu tribe, which contributed significantly to the foundation of the Yuan Dynasty, was one of the groups living on the Mongolian steppes during the Jin-Yuan period (AD 1127-1368) of Chinese history. However, there has been both archaeological and historical dispute regarding the origin of the ancient tribe. Recently, we discovered human remains of the Wanggu tribe in the Chengbozi cemetery in the Siziwang Banner of Inner Mongolia, China. To investigate the genetic structure of the Wanggu tribe and to trace the origins of the tribe at a molecular level, we analyzed the control-region sequences and coding regions of mitochondrial DNA (mtDNA) from the remains by direct sequencing and restriction-fragment length polymorphism analysis. In combination with mtDNA data of 15 extant Eurasian populations, we performed phylogenetic analysis and multidimensional scaling analysis. Our results show that the genetic structure of the Wanggu tribe in the Jin-Yuan period is a complex matriline, containing admixture from both Asian and European populations. In addition, we reveal that on the basis of mtDNA data, the ancient tribe may share a recent common ancestor with the Turkic-speaking Uzbeks and Uighurs.     

Clinical and Molecular Attributes and Evaluation of Pancreatic Cystic Neoplasm

Intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs) are all considered “Pancreatic cystic neoplasms (PCNs)” and show a varying risk of developing into pancreatic ductal adenocarcinoma (PDAC). These lesions display different molecular characteristics, mutations, and clinical manifestations. A lack of detailed understanding of PCN subtype characteristics and their molecular mechanisms limits the development of efficient diagnostic tools and therapeutic strategies for these lesions. Proper in vivo mouse models that mimic human PCNs are also needed to study the molecular mechanisms and for therapeutic testing. A comprehensive understanding of the current status of PCN biology, mechanisms, current diagnostic methods, and therapies will help in the early detection and proper management of patients with these lesions and PDAC. This review aims to describe all these aspects of PCNs, specifically IPMNs, by describing the future perspectives.     

Primary Drug-Resistant Tuberculosis in Hanoi,Viet Nam: Present Status and Risk Factors

Introduction

Resistance of Mycobacterium tuberculosis (MTB) to anti-tuberculosis (TB) drugs presents a serious challenge to TB control worldwide. We investigated the status of drug resistance, including multidrug-resistant (MDR) TB, and possible risk factors among newly diagnosed TB patients in Hanoi, the capital of Viet Nam.

Methods

Clinical and epidemiological information was collected from 506 newly diagnosed patients with sputum smear- and culture-positive TB, and 489 (96.6%) MTB isolates were subjected to conventional drug susceptibility testing, spoligotyping, and 15-locus variable numbers of tandem repeats typing. Adjusted odds ratios (aORs) were calculated to analyze the risk factors for primary drug resistance.

Results

Of 489 isolates, 298 (60.9%) were sensitive to all drugs tested. Resistance to isoniazid, rifampicin, streptomycin, ethambutol, and MDR accounted for 28.2%, 4.9%, 28.2%, 2.9%, and 4.5%, respectively. Of 24 isolates with rifampicin resistance, 22 (91.7%) were MDR and also resistant to streptomycin, except one case. Factors associated with isoniazid resistance included living in old urban areas, presence of the Beijing genotype, and clustered strains [aOR = 2.23, 95% confidence interval (CI) 1.15–4.35; 1.91, 1.18–3.10; and 1.69, 1.06–2.69, respectively). The Beijing genotype was also associated with streptomycin resistance (aOR = 2.10, 95% CI 1.29–3.40). Human immunodeficiency virus (HIV) coinfection was associated with rifampicin resistance and MDR (aOR = 5.42, 95% CI 2.07–14.14; 6.23, 2.34–16.58, respectively).

Conclusion

Isoniazid and streptomycin resistance was observed in more than a quarter of TB patients without treatment history in Hanoi. Transmission of isoniazid-resistant TB among younger people should be carefully monitored in urban areas, where Beijing strains and HIV coinfection are prevalent. Choosing an optimal treatment regimen on the basis of the results of drug susceptibility tests and monitoring of treatment adherence would minimize further development of drug resistance strains.     

No-Reflow Phenomenon in Central Retinal Artery Occlusion: Incidence,Risk Factors,and Clinical Implications

Purpose

To investigate the incidence and risk factors of the no-reflow phenomenon in central retinal artery occlusion (CRAO) patients and to determine its effects on visual and anatomic outcomes.

Methods

In 102 eyes with CRAO in which arterial recanalization was obtained within 1 week from baseline, fluorescein angiography images obtained at baseline and 1 week were retrospectively reviewed. The no-reflow phenomenon in the retina was defined as macular capillary nonperfusion following arterial recanalization on fluorescein angiographs. We investigated the incidence and risk factors for the no-reflow phenomenon and compared the anatomical and visual outcomes between eyes with and without the phenomenon.

Results

Among the 102 CRAO eyes with arterial recanalization, 39 exhibited the no-reflow phenomenon, resulting in an incidence of 38.2%. The incidence among the eyes with treatment-induced and spontaneous recanalization was 43.4% and 15.8%, respectively, and it increased with the CRAO stage. CRAO stage and increased central macular thickness were risk factors for the phenomenon, with an odds ratio of 4.47 [95% confidence interval (CI), 1.19–16.8; P = 0.027] and 1.69 (95% CI, 1.12–2.55; P = 0.012) per 100-μm increase, respectively. The visual outcome was significantly poorer and retinal atrophy and photoreceptor disruption was greater in eyes with the no-reflow phenomenon than in those without.

Conclusions

The no-reflow phenomenon may occur after arterial recanalization in approximately one-third of CRAO patients and can affect anatomical and visual outcomes. This phenomenon may provide an additional explanation regarding the permanent retinal damage and vision loss in eyes with CRAO.     

Genetic Variation in the Base Excision Repair Pathway,Environmental Risk Factors,and Colorectal Adenoma Risk

Cigarette smoking, high alcohol intake, and low dietary folate levels are risk factors for colorectal adenomas. Oxidative damage caused by these three factors can be repaired through the base excision repair pathway (BER). We hypothesized that genetic variation in BER might modify colorectal adenoma risk. In a sigmoidoscopy-based study, we examined associations between 182 haplotype tagging SNPs in 14 BER genes, and colorectal adenoma risk, and examined their potential role as modifiers of the effect cigarette smoking, alcohol intake, and dietary folate levels. Among all individuals, no statistically significant associations between BER SNPs and adenoma risk persisted after correction for multiple comparisons. However, among Asian-Pacific Islanders we observed two SNPs in FEN1 and one in NTHL1, and among African-Americans one SNP in APEX1 that were associated with colorectal adenoma risk. Significant associations were also observed between SNPs in the NEIL2 gene and rectal adenoma risk. Three SNPS modified the effect of smoking (MUTYH interaction p = 0.002; OGG1 interaction p = 0.013); FEN1 interaction p = 0.013)), one SNP in LIG3 modified the effect of alcohol consumption (interaction p = 0.024) and two SNPs in LIG3 modified the effect of dietary folate (interaction p = 0.001 and p = 0.08) on colorectal adenoma risk. These findings support a role for genetic variants in the BER pathway as potential modifiers of colorectal adenoma risk. Our findings strengthen the role of oxidative damage induced by key lifestyle and dietary risk factors in colorectal adenoma formation.     

直肠癌的淋巴结转移的危险因素

目的:本研究主要目的为确定直肠癌的淋巴结转移的危险因素。方法:通过对1250例于2004年-2008年行直肠癌根治性切除的患者进行单因素和多因素分析,以确定淋巴结转移相关的危险因素,同时对PT分期和肿瘤大小之间的关系进行了相关性分析。结果:直肠癌患者淋巴结转移发生率为41%。在单因素分析中,患者年龄(P=0.008)、肿瘤大小(P=0.003)、PT分期(P<0.0019)以及分化程度(P<0.001)和淋巴结转移相关。在多因素分析中,年龄(P=0.017,OR=0.988,95%可信区间:0.978-0.998)、PT分期(P<0.001,OR=1.952,95%可信区间:1.656-2.302)和分化程度(P<0.001,OR=3.697,95%可信区间:2.112-6.472)是淋巴结转移的独立因素。结论:在直肠癌相关分析中,肿瘤的大小和PT分期呈正相关。年龄、PT分期和肿瘤分化程度是淋巴结转移的独立因素。在直肠癌中,肿瘤的大小和PT分期呈正相关。     

Fluconazole-Resistant Candida: Mechanisms and Risk Factor Identification

The extensive use of fluconazole in the previous two decades has fostered the emergence of azole-resistant strains, including non-albicans species such as C. glabrata. The main mechanisms of fluconazole resistance described involve alteration of the quality or quantity of 14-alpha-demethylase enzyme or reduced access of the drug to the target enzyme by upregulation of efflux pumps. Fluconazole prophylaxis has been used successfully to prevent fungal infections in high-risk neonates, neutropenic patients, individuals with HIV infection, recipients of solid organ (eg, liver) transplants and bone marrow transplants, and patients in intensive care units, with a small increase in the risk of colonization, but not infection, with fluconazole-resistant Candida isolates. Among other risk factors, recent fluconazole exposure is associated with fluconazole-resistant candidemia.     

进口奶牛犬新孢子虫病血清学抗体及流产胎儿病原分子生物学检测

采用间接免疫荧光抗体试验对随机抽取的3批进口奶牛1 238份奶牛血样进行牛新孢子虫病的流行病调查.随后用乳胶凝集对牛新孢子虫抗体阳性样品进行弓形虫抗体检测.并用已建立的牛新孢子虫病巢式PCR(Nested-PCR)对第一批进口奶牛的数十头流产胎儿进行牛新孢子虫病的病原分子生物学检测.结果表明,3批进口奶牛的新孢子虫整体感染率为6.54%,所有奶牛犬新孢子虫抗体阳性血清的弓形虫抗体全部为阴性.新孢子虫血清抗体阳性母牛流产的胎儿经Nested-PCR检测,60%胎儿为阳性,而抗体阴性母牛流产的胎儿经Nested-PCR检测均为阴性.     

Genetic Variation in a4GnT in Relation to Helicobacter pylori Serology and Gastric Cancer Risk

Background:  Helicobacter pylori, a known risk factor of gastric cancer, rarely colonize the deeper portion of normal gastric glands, where the mucus is rich in α-1,4-linked N -acetylglucosamine capped O -glycans, that strongly inhibit H. pylori growth in vitro .
Materials and methods:  We investigated the association between genetic variation in the O -glycan transferase encoding gene ( a4GnT ) and H. pylori infection and gastric cancer risk using a Polish population-based case–control study (273 gastric cancer patients and 377 controls).
Results:  A haplotype at the rs2622694–rs397266 locus was associated with H. pylori infection, with the A-A haplotype associated with a higher risk compared with the most frequent G-G haplotype (odds ratio 2.30; 95% confidence interval 1.35–3.92). The association remained significant after correction for multiple tests (global p value: nominal 0.002, empirical 0.045). Neither this haplotype nor the tagSNPs were associated with overall gastric cancer risk.
Conclusion:  a4GnT genetic variation may be relevant to H. pylori infection, but not to gastric cancer risk.