scholarly journals Identification of a Type IV CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae

2019 ◽  
Author(s):  
Enas Newire ◽  
Alp Aydin ◽  
Samina Juma ◽  
Virve I Enne ◽  
Adam P. Roberts
Keyword(s):  
Sequence Analysis ◽  
Klebsiella Pneumoniae ◽  
Drug Resistant ◽  
Rt Pcr ◽  
Chromosome Type ◽  
Bacterial Host ◽  
Type Iv ◽  
Transfer Genes ◽  
The Uk ◽  
The Relationship

AbstractDuring an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a novel CRISPR-Cas system (which we have designated Type IV-B) was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the UK (isolated in 2017). Sequence analysis of other genomes available in GenBank revealed that this novel Type IV-B CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on the chromosome. Type IV-B is found exclusively on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Type IV-B has a single repeat-spacer array (CRISPR1) upstream of the cas loci with some spacers matching regions of conjugal transfer genes of IncFIIK/IncFIB(K) plasmids suggesting a role in plasmid incompatibility. Expression of the cas loci was confirmed in available clinical isolates by RT-PCR; indicating the system is active. To our knowledge, this is the first report describing a new subtype within Type IV CRISPR-Cas systems exclusively associated with IncHI1B/IncFIB plasmids.ImportanceHere, we report the identification of a novel subtype of Type IV CRISPR-Cas that is expressed and exclusively carried by IncHI1B/IncFIB plasmids in Enterobacteriaceae, demonstrating unique evolutionarily juxtaposed connections between CRISPR-Cas and mobile genetic elements (MGEs). Type IV-B encodes a variety of spacers showing homology to DNA from various sources, including plasmid specific spacers and is therefore thought to provide specific immunity against plasmids of other incompatible groups (IncFIIK/IncFIB(K)). The relationship between Type IV-B CRISPR-Cas and MGEs that surround and interrupt the system is likely to promote rearrangement and be responsible for the observed variability of this type. Finally, the Type IV-B CRISPR-Cas is likely to co-operate with other cas loci within the bacterial host genome during spacer acquisition.

scholarly journals Molecular Epidemiology of Peste Des Petits Ruminants Cases Associated with Abortion in Sheep and Goat in Marmara Region of Turkey, 2018

2020 ◽  
Vol 40 (04) ◽  
pp. 494-498
Author(s):  
Zuleyha Pestil
Keyword(s):  
Sequence Analysis ◽  
Molecular Epidemiology ◽  
Experimental Infection ◽  
Epidemiological Data ◽  
Marmara Region ◽  
Peste Des Petits Ruminants ◽  
Rt Pcr ◽  
Etiologic Agents ◽  
The Relationship ◽  
Lineage Iv

The aim of this study was to investigate the molecular epidemiology of peste des petits ruminants (PPR) infections associated with abortion in sheep and goat samples from the Marmara region of Turkey during 2018. The study was carried out from 116 sheep and 26 goat abortion cases. PPR virus (PPRV) detection in these samples was performed using real-time RT-PCR (Q-RT-PCR). Then, sequence analysis was performed from PPRV positive samples. Q-RT-PCR results demonstrated that 12 (10.34%) out of 116 sheep abortion samples and 3 (11.53%) out of 26 goat abortion samples were positive for PPRV genome. The sequence results of RT-PCR positive products revealed that the viruses causing the cases belong to lineage IV. Furthermore, molecular analysis showed that present cases were not related to PPRV vaccine strains or its mutants. Marmara region, where this study was conducted, is a neighbour of European countries such as Bulgaria and Greece. The first PPR cases in Europe were reported from Bulgaria at the beginning of 2018 and subsequently, other cases also reported before are mentioned in the present study. This study provides valuable information to understand the epidemiology of recently emerged PPRV cases in Europe and Turkey. Furthermore, because of the prevalence of PPRV in abortion samples in this study, these results suggest that PPRV may be one of the possible etiologic agents of abortions in sheep and goat. However, for clarification of the relationship between abortion and PPRV, there is need more robust epidemiological data and experimental infection studies

scholarly journals An unequivocal superbug: PDR Klebsiella pneumoniae with an arsenal of resistance and virulence factor genes

2021 ◽  
Vol 15 (03) ◽  
pp. 404-414
Author(s):  
Ahmad Sleiman ◽  
Bassel Awada ◽  
Michele Mocadie ◽  
Nour Sherri ◽  
Louis-Patrick Haraoui ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Virulence Factor ◽  
Molecular Mechanisms ◽  
Whole Genome Sequence ◽  
Drug Resistant ◽  
Type Iv ◽  
Antimicrobial Resistance Genes ◽  
Life Threatening ◽  
High Level ◽  
Virulence Factor Genes

Introduction: Infections caused by extensively-drug resistant (XDR) and pan-drug resistant (PDR) Klebsiella pneumoniae represent an emerging threat due to the high associated mortality. This study aimed to characterize two carbapenem resistant K. pneumoniae strains from the same patient, the first being PDR (referred to as IMP 1078b) and the second being XDR (referred to IMP 1078s) isolated from the same patient. Methodology: Antimicrobial susceptibility testing was done for the 2 K. pneumoniae isolates, followed by carbapenem/β-lactamase inhibitor combination assay, and fitness cost against cefepime and meropenem. Then, whole-genome sequence analysis was performed to decipher the molecular mechanisms behind the high level of resistance recorded in both isolates. Finally, qRT-PCR was done for β-lactam resistant genes. Results: This is the first report about a K. pneumoniae isolate harboring 47 antimicrobial resistance genes and having type IV pilli (Yersinia) and the fimbrial adherence determinant Stb (Salmonella) as virulence factors. Further analysis on both isolates are discussed within the article. Conclusion: The co-existence of a high number of antimicrobial resistant (AMR) genes and virulence factor genes may lead to a life threatening invasive and untreatable infection.

Thromboplastin Related Differences in the Determination of International Normalised Ratio: A Cause for Concern?

1994 ◽  
Vol 72 (03) ◽  
pp. 426-429 ◽  
Author(s):  
S Kitchen ◽  
I D Walker ◽  
T A L Woods ◽  
F E Preston
Keyword(s):  
Patient Management ◽  
External Quality Assessment ◽  
Oral Anticoagulant Therapy ◽  
Warfarin Dosage ◽  
External Quality ◽  
External Quality Assessment Scheme ◽  
International Normalised Ratio ◽  
The Uk ◽  
The Relationship

SummaryWhen the International Normalised Ratio (INR) is used for control of oral anticoagulant therapy the same result should be obtained irrespective of the laboratory reagent used. However, in the UK National External Quality Assessment Scheme (NEQAS) for Blood Coagulation INRs determined using different reagents have been significantly different.For 18 NEQAS samples Manchester Reagent (MR) was associated with significantly lower INRs than those obtained using Diagen Activated (DA, p = 0.0004) or Instrumentation Laboratory PT-Fib HS (IL, p = 0.0001). Mean INRs for this group were 3.15, 3.61, and 3.65 for MR, DA, and IL respectively. For 61 fresh samples from warfarin-ised patients with INRs of greater than 3.0 the relationship between thromboplastins in respect of INR was similar to that observed for NEQAS data. Thus INRs obtained with MR were significantly lower than with DA or IL (p <0.0001). Mean INRs for this group were 4.01, 4.40, and 4.59 for MR, DA, and IL respectively.We conclude that the differences between INRs measured with the thromboplastins studied here are sufficiently great to influence patient management through warfarin dosage schedules, particularly in the upper therapeutic range of INR. There is clearly a need to address the issues responsible for the observed discrepancies.

Researching (with) Major Food Retailers

2015 ◽  
Vol 15 (3) ◽  
pp. 33-39 ◽  
Author(s):  
David Evans
Keyword(s):  
Food Systems ◽  
Academic Research ◽  
Social Scientists ◽  
Major Food ◽  
Food Retailers ◽  
Food Retailer ◽  
The One ◽  
The Uk ◽  
The Relationship ◽  
Opening Up

This paper considers the relationship between social science and the food industry, and it suggests that collaboration can be intellectually productive and morally rewarding. It explores the middle ground that exists between paid consultancy models of collaboration on the one hand and a principled stance of nonengagement on the other. Drawing on recent experiences of researching with a major food retailer in the UK, I discuss the ways in which collaborating with retailers can open up opportunities for accessing data that might not otherwise be available to social scientists. Additionally, I put forward the argument that researchers with an interest in the sustainability—ecological or otherwise—of food systems, especially those of a critical persuasion, ought to be empirically engaging with food businesses. I suggest that this is important in terms of generating better understandings of the objectionable arrangements that they seek to critique, and in terms of opening up conduits through which to affect positive changes. Cutting across these points is the claim that while resistance to commercial engagement might be misguided, it is nevertheless important to acknowledge the power-geometries of collaboration and to find ways of leveling and/or leveraging them. To conclude, I suggest that universities have an important institutional role to play in defining the terms of engagement as well as maintaining the boundaries between scholarship and consultancy—a line that can otherwise become quite fuzzy when the worlds of commerce and academic research collide.

Monitoring the marine environment for small round structured viruses (SRSVS): a new approach to combating the transmission of these viruses by molluscan shellfish

1998 ◽  
Vol 38 (12) ◽  
pp. 51-56 ◽  
Author(s):  
K. Henshilwood ◽  
J. Green ◽  
D. N. Lees
Keyword(s):  
Enteric Virus ◽  
Winter Period ◽  
Rt Pcr ◽  
Cloning And Sequencing ◽  
New Approach ◽  
Human Enteric Virus ◽  
Different Strains ◽  
The Uk ◽  
Public Health Protection

This study investigates human enteric virus contamination of a shellfish harvesting area. Samples were analysed over a 14-month period for Small Round Structured Viruses (SRSVs) using a previously developed nested RT-PCR. A clear seasonal difference was observed with the largest numbers of positive samples obtained during the winter period (October to March). This data concurs with the known winter association of gastroenteric illness due to oyster consumption in the UK and also with the majority of the outbreaks associated with shellfish harvested from this area during the study period. RT-PCR positive amplicons were further characterised by cloning and sequencing. Sequence analysis of the positive samples identified eleven SRSV strains, of both Genogroup I and Genogroup II, occurring throughout the study period. Many shellfish samples contained a mixture of strains with a few samples containing up to three different strains with both Genogroups represented. The observed common occurrence of strain mixtures may have implications for the role of shellfish as a vector for dissemination of SRSV strains. These results show that nested RT-PCR can identify SRSV contamination in shellfish harvesting areas. Virus monitoring of shellfish harvesting areas by specialist laboratories using RT-PCR is a possible approach to combating the transmission of SRSVs by molluscan shellfish and could potentially offer significantly enhanced levels of public health protection.

Archaeologists and the Dead

2016 ◽  
Keyword(s):  
Historical Context ◽  
Ethical Considerations ◽  
International Context ◽  
The Public ◽  
The Us ◽  
The Dead ◽  
The Many ◽  
The Uk ◽  
The Relationship ◽  
Experience Effect

This volume addresses the relationship between archaeologists and the dead, through the many dimensions of their relationships: in the field (through practical and legal issues), in the lab (through their analysis and interpretation), and in their written, visual and exhibitionary practice--disseminated to a variety of academic and public audiences. Written from a variety of perspectives, its authors address the experience, effect, ethical considerations, and cultural politics of working with mortuary archaeology. Whilst some papers reflect institutional or organizational approaches, others are more personal in their view: creating exciting and frank insights into contemporary issues that have hitherto often remained "unspoken" among the discipline. Reframing funerary archaeologists as "death-workers" of a kind, the contributors reflect on their own experience to provide both guidance and inspiration to future practitioners, arguing strongly that we have a central role to play in engaging the public with themes of mortality and commemoration, through the lens of the past. Spurred by the recent debates in the UK, papers from Scandinavia, Austria, Italy, the US, and the mid-Atlantic, frame these issues within a much wider international context that highlights the importance of cultural and historical context in which this work takes place.

scholarly journals Genomic insights into multi-drug and extensively drug resistant Klebsiella pneumoniae from India

2020 ◽  
Vol 101 ◽  
pp. 12-13
Author(s):  
C. Shankar ◽  
P. Mathur ◽  
J.J. Jacob ◽  
C. Rodrigues ◽  
K. Walia ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Drug Resistant ◽  
Extensively Drug Resistant

scholarly journals 1675. Epidemiology of Urinary Tract Infections in the United States, 2009 - 2018

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S823-S823
Author(s):  
Kendra Foster ◽  
Linnea A Polgreen ◽  
Brett Faine ◽  
Philip M Polgreen
Keyword(s):  
United States ◽  
Urinary Tract ◽  
Klebsiella Pneumoniae ◽  
Urinary Tract Infections ◽  
Proteus Mirabilis ◽  
Antibiotic Use ◽  
The United States ◽  
Drug Resistant ◽  
E Coli ◽  
Tract Infections

Abstract Background Urinary tract infections (UTIs) are one of the most common bacterial infections. There is a lack of large epidemiologic studies evaluating the etiologies of UTIs in the United States. This study aimed to determine the prevalence of different UTI-causing organisms and their antimicrobial susceptibility profiles among patients being treated in a hospital setting. Methods We used the Premier Healthcare Database. Patients with a primary diagnosis code of cystitis, pyelonephritis, or urinary tract infection and had a urine culture from 2009- 2018 were included in the study. Both inpatients and patients who were only treated in the emergency department (ED) were included. We calculated descriptive statistics for uropathogens and their susceptibilities. Multi-drug-resistant pathogens are defined as pathogens resistant to 3 or more antibiotics. Resistance patterns are also described for specific drug classes, like resistance to fluoroquinolones. We also evaluated antibiotic use in this patient population and how antibiotic use varied during the hospitalization. Results There were 640,285 individuals who met the inclusion criteria. Females make up 82% of the study population and 45% were age 65 or older. The most common uropathogen was Escherichia Coli (64.9%) followed by Klebsiella pneumoniae (8.3%), and Proteus mirabilis (5.7%). 22.2% of patients were infected with a multi-drug-resistant pathogen. We found that E. Coli was multi-drug resistant 23.8% of the time; Klebsiella pneumoniae was multi-drug resistant 7.4%; and Proteus mirabilis was multi-drug resistant 2.8%. The most common antibiotics prescribed were ceftriaxone, levofloxacin, and ciprofloxacin. Among patients that were prescribed ceftriaxone, 31.7% of them switched to a different antibiotic during their hospitalization. Patients that were prescribed levofloxacin and ciprofloxacin switched to a different antibiotic 42.8% and 41.5% of the time, respectively. Conclusion E. Coli showed significant multidrug resistance in this population of UTI patients that were hospitalized or treated within the ED, and antibiotic switching is common. Disclosures All Authors: No reported disclosures

scholarly journals The labour of place: Memory and extended reality (XR) in migration museums

2021 ◽  
Vol 14 (3) ◽  
pp. 606-621
Author(s):  
Anna Reading ◽  
Jim Bjork ◽  
Jack Hanlon ◽  
Neil Jakeman
Keyword(s):  
Web 2.0 ◽  
Innovative Approach ◽  
Place Making ◽  
Place Memory ◽  
Museum Exhibitions ◽  
Global Mapping ◽  
The Uk ◽  
The Relationship

How do we understand the relationship between memory and place in the context of Extended Reality (XR) migration museum exhibitions? The study combines a global mapping of XR within migration museums, a user analysis of Cologne’s virtual migration museum, and practice-led research with the UK Migration Museum to argue that XR places in Web 2.0 constitute a multiplication of memory’s significant localities. These include a migration memory’s place of beginning (the location of a migrant experience), the place of production (where the memory is transformed into representation) and the place of consumption (where the mediated memory is engaged with, looked at, heard). Mnemonic labour involving digital frictions at each of these sites constitutes a form of multiple place-making with complex feelings, meanings, and (dis)connections. This points to an innovative approach to understanding and curating XR experiences with museums that recognises the significance of the labour of place.

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