Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene

© 2019 The Authors. Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum b-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes bla TEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids

Balancing carrots and sticks: incentives for sustainable hilsa fishery management in Bangladesh

Mihir Kanti Majumder, Md Mokammel Hossain, Atiq Rahman, Belayet Hussei

Potential of a cyclone prototype spacer to improve in vitro dry powder delivery

Copyright The Author(s) 2013. This article is published with open access at Springerlink.com. This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are creditedPurpose: Low inspiratory force in patients with lung disease is associated with poor deagglomeration and high throat deposition when using dry powder inhalers (DPIs). The potential of two reverse flow cyclone prototypes as spacers for commercial carrierbased DPIs was investigated. Methods: Cyclohaler®, Accuhaler® and Easyhaler® were tested with and without the spacers between 30-60 Lmin-1. Deposition of particles in the next generation impactor and within the devices was determined by high performance liquid chromatography. Results: Reduced induction port deposition of the emitted particles from the cyclones was observed due to the high retention of the drug within the spacers (e.g. salbutamol sulphate (SS): 67.89 ± 6.51 % at 30 Lmin-1 in Cheng 1). Fine particle fractions of aerosol as emitted from the cyclones were substantially higher than the DPIs alone. Moreover, the aerodynamic diameters of particles emitted from the cyclones were halved compared to the DPIs alone (e.g. SS from the Cyclohaler® at 4 kPa: 1.08 ± 0.05 μm vs. 3.00 ± 0.12 μm, with and without Cheng 2, respectively) and unaltered with increased flow rates. Conclusion: This work has shown the potential of employing a cyclone spacer for commercial carrier-based DPIs to improve inhaled drug delivery.Peer reviewe

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

Peer reviewedPublisher PD

Culture-independent molecular analysis of bacterial diversity in uranium-ore/-mine waste-contaminated and non-contaminated sites from uranium mines

Soil, water and sediment samples collected from in and around Jaduguda, Bagjata and Turamdih mines were analyzed for physicochemical parameters and cultured, and yet to be cultured microbial diversity. Culturable fraction of microbial community measured as Colony Forming Unit (CFU) on R2A medium revealed microbes between 104 and 109 CFU/g sample. Community DNA was extracted from all the samples; 16S rRNA gene amplified, cloned and subject to Amplified Ribosomal DNA Restriction Analysis. Clones representing each OTU were selected and sequenced. Sequence analyses revealed that non-contaminated samples were mostly represented by Acidobacteria, Bacteroidetes, Firmicutes and Proteobacteria (β-, γ-, and/or δ-subdivisions) along with less frequent phyla Nitrospira, Deferribacteres, Chloroflexi. In contrast, samples obtained from highly contaminated samples showed distinct abundance of β-,γ- and α-Proteobacteria along with Acidobacteria,Bacteroidetes and members of Firmicutes, Chloroflexi, Candidate division, Planctomycete, Cyanobacteria and Actinobacteria as minor groups. Our data represented the baseline information on bacterial community composition within non-contaminated samples which could potentially be useful for assessing the impact of metal and radionuclides contamination due to uranium mine activities

Number crunching in the cancer stem cell market

Like their normal counterparts, many tumours are thought to have a hierarchical organization, albeit a disorganized one. Accordingly, the concept of cancer stem cells has emerged, and that these cells are responsible for perpetuating tumour existence. Operationally, cancer stem cells are regarded as prospectively purified cells that are the most effective at tumour initiation in an in vivo assay, usually after xenotransplantation to NOD/SCID mice. The conventional wisdom is that such tumour-initiating cells are rare based upon having to xenotransplant large numbers of human tumour cells into immunodeficient mice to propagate the tumour, but new evidence indicates that perhaps these cells are not so rare, at least in malignant melanoma, if a supportive soil is provided for the transplanted cells along with further restriction of the murine host's immune response

Interleukin-6 gene (IL-6): a possible role in brain morphology in the healthy adult brain

Background: Cytokines such as interleukin 6 (IL-6) have been implicated in dual functions in neuropsychiatric disorders. Little is known about the genetic predisposition to neurodegenerative and neuroproliferative properties of cytokine genes. In this study the potential dual role of several IL-6 polymorphisms in brain morphology is investigated. Methodology: In a large sample of healthy individuals (N = 303), associations between genetic variants of IL-6 (rs1800795; rs1800796, rs2069833, rs2069840) and brain volume (gray matter volume) were analyzed using voxel-based morphometry (VBM). Selection of single nucleotide polymorphisms (SNPs) followed a tagging SNP approach (e.g., Stampa algorigthm), yielding a capture 97.08% of the variation in the IL-6 gene using four tagging SNPs. Principal findings/results: In a whole-brain analysis, the polymorphism rs1800795 (−174 C/G) showed a strong main effect of genotype (43 CC vs. 150 CG vs. 100 GG; x = 24, y = −10, z = −15; F(2,286) = 8.54, puncorrected = 0.0002; pAlphaSim-corrected = 0.002; cluster size k = 577) within the right hippocampus head. Homozygous carriers of the G-allele had significantly larger hippocampus gray matter volumes compared to heterozygous subjects. None of the other investigated SNPs showed a significant association with grey matter volume in whole-brain analyses. Conclusions/significance: These findings suggest a possible neuroprotective role of the G-allele of the SNP rs1800795 on hippocampal volumes. Studies on the role of this SNP in psychiatric populations and especially in those with an affected hippocampus (e.g., by maltreatment, stress) are warranted.Bernhard T Baune, Carsten Konrad, Dominik Grotegerd, Thomas Suslow, Eva Birosova, Patricia Ohrmann, Jochen Bauer, Volker Arolt, Walter Heindel, Katharina Domschke, Sonja Schöning, Astrid V Rauch, Christina Uhlmann, Harald Kugel and Udo Dannlowsk

Prevalence of Chlamydia trachomatis infection among women in a Middle Eastern community

BACKGROUND: Common vaginal infections that manifest in women are usually easily diagnosed. However, Chlamydia infection is often asymptomatic, leading to infertility before it is detected. If it occurs in pregnancy, it could lead to significant neonatal morbidity. It may also play a role with other viral infections for e.g. Human Papilloma Virus in the development of cervical cancer. The objective of this study was to determine the prevalence of Chlamydia infection in women undergoing screening for cervical abnormalities as a part of a research project in primary and secondary care institutions in the United Arab Emirates. METHODS: In this cross sectional study married women attending primary and secondary care participating in a large nationwide cervical abnormalities screening survey were offered Chlamydia testing using a commercially available test kit. This kit uses a rapid immunoassay for the direct detection of Chlamydia trachomatis antigen in endocervical swab specimens. As this study was performed in a traditional Islamic country, unmarried women were excluded from testing, as the management of any positive cases would create legal and social problems. All married women consenting to take part in the study were included irrespective of age. RESULTS: Of 1039 women approached over a period of eight months 919 (88.5%) agreed to participate. The number of women in the 16 to 19 years was small (0.01%) and 30% were aged over 40 years. The prevalence of Chlamydia infection in this study was 2.6% (95% confidence interval 1.2–3.3%), which was marginally higher in women screened in secondary care (p = 0.05). CONCLUSION: This is one of the few reports on the prevalence of Chlamydia infection in women from the Middle East. Due to cultural and social constraints this study excluded a large proportion of women aged less than 19 years of age. Hence no direct comparisons on prevalence could be made with studies from the West, which all included younger women at high risk of Chlamydia. However this study emphasizes the importance of cultural factors while interpreting results of studies from different cultures and communities