scholarly journals Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan

2020 ◽  
Author(s):  
Farhan Rasheed ◽  
Muhammad Saeed ◽  
Nabil-Fareed Alikhan ◽  
David Baker ◽  
Mohsin Khurshid ◽  
...  
Keyword(s):  
Typhoid Fever ◽  
Food Chain ◽  
Sequence Data ◽  
Treatment Options ◽  
Added Value ◽  
Future Research ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Nucleotide Sequence Data ◽  
Sindh Province

AbstractBackgroundExtensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterisation of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan.MethodsIsolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby-Bauer method. These findings were confirmed using Illumina whole genome nucleotide sequence data. All sequences were compared to the outbreak strain from southern Pakistan and typed using the S. Typhi genotyping scheme.FindingsTwenty-seven XDR S. Typhi isolates were identified from patients at Jinnah Hospital in Lahore between January and April 2019. All isolates were confirmed by sequence analysis to harbour an IncY plasmid and the CTX-M-15 ceftriaxone resistance determinant. All isolates were of the same genotypic background as the outbreak strain from Sindh province.SummaryWe report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing.FundingThis work was supported by the BBSRC-funded QIB Institute Strategic Programme “Microbes in the Food Chain” BB/R012504/1 and its constituent projects Microbial Survival in the Food Chain (BBS/E/F/000PR10349) and Research Infrastructure (BBS/E/F/000PR10352), and the BBSRC funded Core Capability Grant (project number BB/CCG1860/1).Research in contextEvidence before this studyTyphoid fever is endemic in Pakistan, with widespread resistance to first line drugs: ampicillin, co-trimoxazole, and chloramphenicol, and to fluoroquinolones. In 2017 the first report of additional resistance to ceftriaxone was published as XDR typhoid fever from southern Pakistan. Treatment of XDR typhoid fever has been a clinical challenge; options are scarce, and the level of chronic carriage is unknown. Current treatment is dependent upon azithromycin and this represents a major threat for the community as resistance has been reported from Bangladesh.Added value of this studyThis study is the first genomic report of XDR typhoid fever in a central part of Pakistan, describing the same genetic background as strains responsible for XDR typhoid in Sindh province. We have confirmed that the outbreak strain of XDR S. Typhi is now present in the most populated province and second largest city of Pakistan.Implications of all the available evidenceThe present study highlights the gravity of the situation - the spread of this strain is of serious concern. The clinical situation remains unchanged since this study was performed; we believe it is imperative that future research focuses upon the biology, transmission and control of this strain.

scholarly journals Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan

2020 ◽  
Vol 8 (9) ◽  
pp. 1336
Author(s):  
Farhan Rasheed ◽  
Muhammad Saeed ◽  
Nabil-Fareed Alikhan ◽  
David Baker ◽  
Mohsin Khurshid ◽  
...  
Keyword(s):  
Sequence Data ◽  
Treatment Options ◽  
Salmonella Typhi ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Nucleotide Sequence Data ◽  
Sindh Province ◽  
Genome Nucleotide Sequence ◽  
Emergence Of Resistance

Extensively drug-resistant (XDR) Salmonella Typhi has been reported in Sindh province of Pakistan since 2016. The potential for further spread is of serious concern as remaining treatment options are severely limited. We report the phenotypic and genotypic characterization of 27 XDR S. Typhi isolated from patients attending Jinnah Hospital, Lahore, Pakistan. Isolates were identified by biochemical profiling; antimicrobial susceptibility was determined by a modified Kirby–Bauer method. These findings were confirmed using Illumina whole genome nucleotide sequence data. All sequences were compared to the outbreak strain from Southern Pakistan and typed using the S. Typhi genotyping scheme. All isolates were confirmed by a sequence analysis to harbor an IncY plasmid and the CTX-M-15 ceftriaxone resistance determinant. All isolates were of the same genotypic background as the outbreak strain from Sindh province. We report the first emergence of XDR S. Typhi in Punjab province of Pakistan confirmed by whole genome sequencing.

scholarly journals Genome Sequence Data of the Soybean Pathogen Stagonosporopsis vannaccii: A Resource for Studies on Didymellaceae Evolution

2020 ◽  
Vol 33 (8) ◽  
pp. 1022-1024
Author(s):  
Giovanni Cafà ◽  
Thaís Regina Boufleur ◽  
Renata Rebellato Linhares de Castro ◽  
Nelson Sidnei Massola ◽  
Riccardo Baroncelli
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Gene Prediction ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Associated Species

The genus Stagonosporopsis is classified within the Didymellaceae family and has around 40 associated species. Among them, several species are important plant pathogens responsible for significant losses in economically important crops worldwide. Stagonosporopsis vannaccii is a newly described species pathogenic to soybean. Here, we present the draft whole-genome sequence, gene prediction, and annotation of S. vannaccii isolate LFN0148 (also known as IMI 507030). To our knowledge, this is the first genome sequenced of this species and represents a new useful source for future research on fungal comparative genomics studies.

scholarly journals Whole genome sequence and gene annotation resource for Didymella bellidis, associated with tea leaf spot

Plant Disease ◽  
2020 ◽  
Author(s):  
Xue Wang ◽  
Xian Wu ◽  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Leaf Spot ◽  
Sequence Data ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Whole Genome

Didymella bellidis is a phytopathogenic fungus that causes leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in Guizhou Province, China. D. bellidis isolate GZYQYQX2B was sequenced using Pacific Biosciences and Illumina technologies, and assembled into a whole genome of 35.5 Mbp. Transcripts of D. bellidis isolate GZYQYQX2B were predicted from the assembled genome and were further validated by RNA sequence data. In total, 10,731 genes were predicted by integrating three approaches, namely ab initio and homology-based gene prediction, as well as transcriptomics data. The whole-genome sequence of D. bellidis will provide a resource for future research on trait-specific genes of the pathogen and host-pathogen interactions.

scholarly journals The Gathering Storm: Is Untreatable Typhoid Fever on the Way?

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
Author(s):  
Myron M. Levine ◽  
Raphael Simon
Keyword(s):  
Typhoid Fever ◽  
Salmonella Enterica ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antibiotic Sensitivity ◽  
Public Health Importance ◽  
Outbreak Strain ◽  
Content Type ◽  
Extensively Drug Resistant ◽  
Antimicrobial Resistance Genes

ABSTRACT Klemm et al. (mBio 9:e00105-18, 2018, https://doi.org/10.1128/mBio.00105-18 ) present comprehensive antibiotic sensitivity patterns and genomic sequence data on Salmonella enterica serovar Typhi blood culture isolates from typhoid fever cases during an epidemic in Pakistan. Microbiologic and genomic data pinpoint the identities and locations of the antimicrobial resistance genes and the outbreak strain’s lineage. They propose that Salmonella enterica serovar Typhi be added to the list of bacterial pathogens of public health importance that have become extensively drug resistant (XDR). This paper portends possible dire scenarios for typhoid fever control if XDR strains disseminate globally. Since the outbreak strain is of the H58 haplotype, known for its ability to spread worldwide and displace endemic S . Typhi, this concern is well-founded. The report of Klemm et al. forewarns the global community to address control of typhoid fever more aggressively through prevention, should therapeutic options disappear. This Commentary frames the Klemm et al. findings within a historic perspective.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Decision Making from the Experience of Orthognathic Surgery Patients: A Grounded Theory Approach

2021 ◽  
pp. 238008442110144
Author(s):  
N.R. Paul ◽  
S.R. Baker ◽  
B.J. Gibson
Keyword(s):  
Decision Making ◽  
Grounded Theory ◽  
Treatment Options ◽  
Study Data ◽  
Primary Objective ◽  
Major Surgery ◽  
Future Research ◽  
Decision Making Process ◽  
Theory Approach

Introduction: Patients’ decisions to undergo major surgery such as orthognathic treatment are not just about how the decision is made but what influences the decision. Objectives: The primary objective of the study was to identify the key processes involved in patients’ experience of decision making for orthognathic treatment. Methods: This study reports some of the findings of a larger grounded theory study. Data were collected through face-to-face interviews of patients who were seen for orthognathic treatment at a teaching hospital in the United Kingdom. Twenty-two participants were recruited (age range 18–66 y), of whom 12 (male = 2, female = 10) were 6 to 8 wk postsurgery, 6 (male = 2, female = 4) were in the decision-making stage, and 4 (male = 0, female = 4) were 1 to 2 y postsurgery. Additional data were also collected from online blogs and forums on jaw surgery. The data analysis stages of grounded theory methodology were undertaken, including open and selective coding. Results: The study identified the central role of dental care professionals (DCPs) in several underlying processes associated with decision making, including legitimating, mediating, scheduling, projecting, and supporting patients’ decisions. Six categories were related to key aspects of decision making. These were awareness about their underlying dentofacial problems and treatment options available, the information available about the treatment, the temporality of when surgery would be undertaken, the motivations and expectation of patients, social support, and fear of the surgery, hospitalization, and potentially disliking their new face. Conclusion: The decision-making process for orthognathic treatment is complex, multifactorial, and heavily influenced by the role of DCPs in patient care. Understanding the magnitude of this role will enable DCPs to more clearly participate in improving patients’ decision-making process. The findings of this study can inform future quantitative studies. Knowledge Transfer Statement: The results of this study can be used both for informing clinical practice around enabling decision making for orthognathic treatment and also for designing future research. The findings can better inform clinicians about the importance of their role in the patients’ decision-making process for orthognathic treatment and the means to improve the patient experience. It is suggested that further research could be conducted to measure some of the key constructs identified within our grounded theory and assess how these change during the treatment process.

scholarly journals The Bioactive Potential of Trawl Discard: Case Study from a Crinoid Bed Off Blanes (North-Western Mediterranean)

Marine Drugs ◽  
2021 ◽  
Vol 19 (2) ◽  
pp. 83
Author(s):  
Alfredo García-de-Vinuesa ◽  
Montserrat Demestre ◽  
Arnau Carreño ◽  
Josep Lloret
Keyword(s):  
Bioactive Compounds ◽  
Fish Habitat ◽  
Antibacterial Properties ◽  
Marine Species ◽  
Western Mediterranean ◽  
Bioactive Molecules ◽  
Added Value ◽  
Future Research ◽  
Trawl Survey ◽  
Bioactive Potential

Although knowledge of the bioactive compounds produced by species inhabiting coastal waters is increasing, little is known about the bioactive potential produced by marine species occupying deeper habitats with high biodiversity and productivity. Here, we investigate about the bioactive potential of molecules produced by species that inhabit the crinoid beds, a poorly known essential fish habitat affected by trawling, wherein large amounts of commercial and noncommercial species are discarded. Based on a trawl survey conducted in 2019, 14% of the 64 species discarded on crinoid beds produce molecules with some type of bioactive potential, including; soft corals (Alcyonium palmatum); tunicates (Ascidia mentula); bony fish, such as horse mackerel (Trachurus trachurus); European hake (Merluccius merluccius); and chondrichthyans, such as small-spotted catshark (Scyliorhinus canicula). In addition, 16% of the discarded species had congeneric species that produce compounds with bioactive potential, indicating that such species might also possess similar types of bioactive molecules. Molecules with antioxidant, antitumour, antihypertensive, and antibacterial properties were the most frequent, which could provide the basis for future research aiming to discover new marine-based drugs and compounds for other human uses. Among all species or genera that produce compounds with bioactive potential, 68% presented medium or high vulnerability to trawling. Results show that the discarded catch contains many species, which produce different bioactive compounds that represent an added-value resource. These results highlight the importance of manage properly crinoid beds, to ensure that species that produce molecules with bioactive potential inhabiting these habitats are protected.

First encounter effects in testing of highly automated vehicles during two experimental occasions – The need for recurrent testing

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Jonas Andersson ◽  
Azra Habibovic ◽  
Daban Rizgary
Keyword(s):  
Driver Behavior ◽  
Added Value ◽  
Future Research ◽  
Gaze Behavior ◽  
Repeated Testing ◽  
Automated Vehicles ◽  
Automated Driving ◽  
Perceived Safety ◽  
Repeated Interaction ◽  
Over Time

Abstract To explore driver behavior in highly automated vehicles (HAVs), independent researchers are mainly conducting short experiments. This limits the ability to explore drivers’ behavioral changes over time, which is crucial when research has the intention to reveal human behavior beyond the first-time use. The current paper shows the methodological importance of repeated testing in experience and behavior related studies of HAVs. The study combined quantitative and qualitative data to capture effects of repeated interaction between drivers and HAVs. Each driver ( n = 8 n=8 ) participated in the experiment on two different occasions (∼90 minutes) with one-week interval. On both occasions, the drivers traveled approximately 40 km on a rural road at AstaZero proving grounds in Sweden and encountered various traffic situations. The participants could use automated driving (SAE level 4) or choose to drive manually. Examples of data collected include gaze behavior, perceived safety, as well as interviews and questionnaires capturing general impressions, trust and acceptance. The analysis shows that habituation effects were attenuated over time. The drivers went from being exhilarated on the first occasion, to a more neutral behavior on the second occasion. Furthermore, there were smaller variations in drivers’ self-assessed perceived safety on the second occasion, and drivers were faster to engage in non-driving related activities and become relaxed (e. g., they spent more time glancing off road and could focus more on non-driving related activities such as reading). These findings suggest that exposing drivers to HAVs on two (or more) successive occasions may provide more informative and realistic insights into driver behavior and experience as compared to only one occasion. Repeating an experiment on several occasions is of course a balance between the cost and added value, and future research should investigate in more detail which studies need to be repeated on several occasions and to what extent.

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