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  1. Article: The role of genetic sequencing and analysis in the polio eradication programme.

    Jorgensen, David / Pons-Salort, Margarita / Shaw, Alexander G / Grassly, Nicholas C

    Virus evolution

    2020  Volume 6, Issue 2, Page(s) veaa040

    Abstract: Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical ... ...

    Abstract Genetic sequencing of polioviruses detected through clinical and environmental surveillance is used to confirm detection, identify their likely origin, track geographic patterns of spread, and determine the appropriate vaccination response. The critical importance of genetic sequencing and analysis to the Global Polio Eradication Initiative has grown with the increasing incidence of vaccine-derived poliovirus (VDPV) infections in Africa specifically (470 reported cases in 2019), and globally, alongside persistent transmission of serotype 1 wild-type poliovirus in Pakistan and Afghanistan (197 reported cases in 2019). Adapting what has been learned about the virus genetics and evolution to address these threats has been a major focus of recent work. Here, we review how phylogenetic and phylogeographic methods have been used to trace the spread of wild-type polioviruses and identify the likely origins of VDPVs. We highlight the analysis methods and sequencing technology currently used and the potential for new technologies to speed up poliovirus detection and the interpretation of genetic data. At a pivotal point in the eradication campaign with the threat of anti-vaccine sentiment and donor and public fatigue, innovation is critical to maintain drive and overcome the last remaining circulating virus.
    Language English
    Publishing date 2020-05-20
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veaa040
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Time Taken to Detect and Respond to Polio Outbreaks in Africa and the Potential Impact of Direct Molecular Detection and Nanopore Sequencing.

    Shaw, Alexander G / Cooper, Laura V / Gumede, Nicksy / Bandyopadhyay, Ananda S / Grassly, Nicholas C / Blake, Isobel M

    The Journal of infectious diseases

    2022  Volume 226, Issue 3, Page(s) 453–462

    Abstract: Background: Detection of poliovirus outbreaks relies on a complex laboratory algorithm of cell-culture, polymerase chain reaction (PCR), and sequencing to distinguish wild-type and vaccine-derived polioviruses (VDPV) from Sabin-like strains. We ... ...

    Abstract Background: Detection of poliovirus outbreaks relies on a complex laboratory algorithm of cell-culture, polymerase chain reaction (PCR), and sequencing to distinguish wild-type and vaccine-derived polioviruses (VDPV) from Sabin-like strains. We investigated the potential for direct molecular detection and nanopore sequencing (DDNS) to accelerate poliovirus detection.
    Methods: We analyzed laboratory data for time required to analyze and sequence serotype-2 VDPV (VDPV2) in stool collected from children with acute flaccid paralysis in Africa (May 2016-February 2020). Impact of delayed detection on VDPV2 outbreak size was assessed through negative binomial regression.
    Results: VDPV2 confirmation in 525 stools required a median of 49 days from paralysis onset (10th-90th percentile, 29-74), comprising collection and transport (median, 16 days), cell-culture (7 days), intratypic differentiation quantitative reverse transcription PCR (3 days), and sequencing, including shipping if required (15 days). New VDPV2 outbreaks were confirmed a median of 35 days (27-60) after paralysis onset, which we estimate could be reduced to 16 days by DDNS (9-37). Because longer delays in confirmation and response were positively associated with more cases (P < .001), we estimate that DDNS could reduce the number of VDPV2 cases before a response by 28% (95% credible interval, 12%-42%).
    Conclusions: DDNS could accelerate poliovirus outbreak response, reducing their size and the cost of eradication.
    MeSH term(s) Africa ; Child ; Disease Outbreaks ; Humans ; Nanopore Sequencing ; Paralysis ; Poliomyelitis ; Poliovirus ; Poliovirus Vaccine, Oral
    Chemical Substances Poliovirus Vaccine, Oral
    Language English
    Publishing date 2022-09-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiab518
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Automated detection and classification of polioviruses from nanopore sequencing reads using piranha.

    O'Toole, Áine / Colquhoun, Rachel / Ansley, Corey / Troman, Catherine / Maloney, Daniel / Vance, Zoe / Akello, Joyce / Bujaki, Erika / Majumdar, Manasi / Khurshid, Adnan / Arshad, Yasir / Alam, Muhammad Masroor / Martin, Javier / Shaw, Alexander G / Grassly, Nicholas C / Rambaut, Andrew

    Virus evolution

    2024  Volume 10, Issue 1, Page(s) veae023

    Abstract: Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies' MinION, the time from ... ...

    Abstract Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies' MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We developed piranha (poliovirus investigation resource automating nanopore haplotype analysis), a 'sequencing reads-to-report' solution to aid routine poliovirus testing of both stool and environmental samples and alleviate the bioinformatic bottleneck that often exists for laboratories adopting novel NGS approaches. Piranha can be used for efficient intratypic differentiation of poliovirus serotypes, for classification of Sabin-like polioviruses, and for detection of wild-type and vaccine-derived polioviruses. It produces interactive, distributable reports, as well as summary comma-separated values files and consensus poliovirus FASTA sequences. Piranha optionally provides phylogenetic analysis, with the ability to incorporate a local database, processing from raw sequencing reads to an interactive, annotated phylogeny in a single step. The reports describe each nanopore sequencing run with interpretable plots, enabling researchers to easily detect the presence of poliovirus in samples and quickly disseminate their results. Poliovirus eradication efforts are hindered by the lack of real-time detection and reporting, and piranha can be used to complement direct detection sequencing approaches.
    Language English
    Publishing date 2024-02-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veae023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Wastewater Surveillance in Europe for Non-Polio Enteroviruses and Beyond.

    Bubba, Laura / Benschop, Kimberley S M / Blomqvist, Soile / Duizer, Erwin / Martin, Javier / Shaw, Alexander G / Bailly, Jean-Luc / Rasmussen, Lasse D / Baicus, Anda / Fischer, Thea K / Harvala, Heli

    Microorganisms

    2023  Volume 11, Issue 10

    Abstract: Wastewater surveillance (WWS) was developed in the early 1960s for the detection of poliovirus (PV) circulation in the population. It has been used to monitor several pathogens, including non-polio enteroviruses (NPEVs), which are increasingly recognised ...

    Abstract Wastewater surveillance (WWS) was developed in the early 1960s for the detection of poliovirus (PV) circulation in the population. It has been used to monitor several pathogens, including non-polio enteroviruses (NPEVs), which are increasingly recognised as causes of morbidity in children. However, when applying WWS to a new pathogen, it is important to consider the purpose of such a study as well as the suitability of the chosen methodology. With this purpose, the European Non-Polio Enterovirus Network (ENPEN) organised an expert webinar to discuss its history, methods, and applications; its evolution from a culture-based method to molecular detection; and future implementation of next generation sequencing (NGS). The first simulation experiments with PV calculated that a 400 mL sewage sample is sufficient for the detection of viral particles if 1:10,000 people excrete poliovirus in a population of 700,000 people. If the method is applied correctly, several NPEV types are detected. Despite culture-based methods remaining the gold standard for WWS, direct methods followed by molecular-based and sequence-based assays have been developed, not only for enterovirus but for several pathogens. Along with case-based sentinel and/or syndromic surveillance, WWS for NPEV and other pathogens represents an inexpensive, flexible, anonymised, reliable, population-based tool for monitoring outbreaks and the (re)emergence of these virus types/strains within the general population.
    Language English
    Publishing date 2023-10-05
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11102496
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Comparison of Eleven RNA Extraction Methods for Poliovirus Direct Molecular Detection in Stool Samples.

    Akello, Joyce Odeke / Bujaki, Erika / Shaw, Alexander G / Khurshid, Adnan / Arshad, Yasir / Troman, Catherine / Majumdar, Manasi / O'Toole, Áine / Rambaut, Andrew / Alam, Muhammad Masroor / Martin, Javier / Grassly, Nicholas C

    Microbiology spectrum

    2023  , Page(s) e0425222

    Abstract: Direct detection by PCR of poliovirus RNA in stool samples provides a rapid diagnostic and surveillance tool that can replace virus isolation by cell culture in global polio surveillance. The sensitivity of direct detection methods is likely to depend on ...

    Abstract Direct detection by PCR of poliovirus RNA in stool samples provides a rapid diagnostic and surveillance tool that can replace virus isolation by cell culture in global polio surveillance. The sensitivity of direct detection methods is likely to depend on the choice of RNA extraction method and sample volume. We report a comparative analysis of 11 nucleic acid extraction methods (7 manual and 4 semiautomated) for poliovirus molecular detection using stool samples (
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.04252-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Noninvasive Fecal Cytokine and Microbiota Profiles Predict Commencement of Necrotizing Enterocolitis in a Proof-of-Concept Study.

    Zenner, Christian / Chalklen, Lisa / Adjei, Helena / Dalby, Matthew J / Mitra, Suparna / Cornwell, Emma / Shaw, Alexander G / Sim, Kathleen / Kroll, J Simon / Hall, Lindsay J

    Gastro hep advances

    2023  Volume 2, Issue 5, Page(s) 666–675

    Abstract: Background and aims: Necrotizing enterocolitis (NEC) is a life-threatening disease and the most common gastrointestinal emergency in premature infants. Accurate early diagnosis is challenging. Modified Bell's staging is routinely used to guide diagnosis, ...

    Abstract Background and aims: Necrotizing enterocolitis (NEC) is a life-threatening disease and the most common gastrointestinal emergency in premature infants. Accurate early diagnosis is challenging. Modified Bell's staging is routinely used to guide diagnosis, but early diagnostic signs are nonspecific, potentially leading to unobserved disease progression, which is problematic given the often rapid deterioration observed. We investigated fecal cytokine levels, coupled with gut microbiota profiles, as a noninvasive method to discover specific NEC-associated signatures that can be applied as potential diagnostic markers.
    Methods: Premature babies born below 32 weeks of gestation were admitted to the 2-site neonatal intensive care unit (NICU) of Imperial College hospitals (St. Mary's or Queen Charlotte's & Chelsea) between January 2011 and December 2012. During the NICU stay, expert neonatologists grouped individuals by modified Bell's staging (healthy, NEC1, NEC2/3) and fecal samples from diapers were collected consecutively. Microbiota profiles were assessed by 16S rRNA gene amplicon sequencing and cytokine concentrations were measured by V-Plex multiplex assays.
    Results: Early evaluation of microbiota profiles revealed only minor differences. However, at later time points, significant changes in microbiota composition were observed for Bacillota (adj.
    Conclusion: Differences in certain fecal cytokine profiles in patients with NEC indicate their potential use as diagnostic biomarkers to facilitate earlier diagnosis. Additionally, associations between microbial and cytokine profiles contribute to improving knowledge about NEC pathogenesis.
    Language English
    Publishing date 2023-07-19
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2772-5723
    ISSN (online) 2772-5723
    DOI 10.1016/j.gastha.2023.03.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Defining a research agenda for environmental wastewater surveillance of pathogens.

    Shaw, Alexander G / Troman, Catherine / Akello, Joyce Odeke / O'Reilly, Kathleen M / Gauld, Jillian / Grow, Stephanie / Grassly, Nicholas / Steele, Duncan / Blazes, David / Kumar, Supriya

    Nature medicine

    2023  Volume 29, Issue 9, Page(s) 2155–2157

    MeSH term(s) Wastewater ; Wastewater-Based Epidemiological Monitoring ; Sewage ; Environmental Monitoring
    Chemical Substances Wastewater ; Sewage
    Language English
    Publishing date 2023-08-01
    Publishing country United States
    Document type Letter
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-023-02457-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis.

    Shaw, Alexander G / Sim, Kathleen / Rose, Graham / Wooldridge, David J / Li, Ming-Shi / Misra, Raju V / Gharbia, Saheer / Kroll, J Simon

    BMC microbiology

    2021  Volume 21, Issue 1, Page(s) 225

    Abstract: Background: Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements ... ...

    Abstract Background: Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data.
    Results: We found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation.
    Conclusions: The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.
    MeSH term(s) Bayes Theorem ; DNA, Bacterial/genetics ; Enterocolitis, Necrotizing/immunology ; Enterocolitis, Necrotizing/microbiology ; Epithelial Cells/immunology ; Epithelial Cells/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/immunology ; Infant, Premature, Diseases/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Toll-Like Receptor 4/genetics ; Toll-Like Receptor 4/immunology
    Chemical Substances DNA, Bacterial ; RNA, Ribosomal, 16S ; TLR4 protein, human ; Toll-Like Receptor 4
    Language English
    Publishing date 2021-08-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1471-2180
    ISSN (online) 1471-2180
    DOI 10.1186/s12866-021-02285-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Gastrointestinal, vaginal, nasopharyngeal, and breast milk microbiota profiles and breast milk metabolomic changes in Gambian infants over the first two months of lactation: A prospective cohort study.

    Karampatsas, Konstantinos / Faal, Amadou / Jaiteh, Mustapha / Garcia-Perez, Isabel / Aller, Sean / Shaw, Alexander G / Kopytek, Aleksandra / Witney, Adam A / Le Doare, Kirsty

    Medicine

    2022  Volume 101, Issue 46, Page(s) e31419

    Abstract: Microbiota composition in breast milk affects intestinal and respiratory microbiota colonization and the mucosal immune system's development in infants. The metabolomic content of breast milk is thought to interact with the microbiota and may influence ... ...

    Abstract Microbiota composition in breast milk affects intestinal and respiratory microbiota colonization and the mucosal immune system's development in infants. The metabolomic content of breast milk is thought to interact with the microbiota and may influence developing infant immunity. One hundred seven Gambian mothers and their healthy, vaginally delivered, exclusively breastfed infants were included in our study. We analyzed 32 breast milk samples, 51 maternal rectovaginal swabs and 30 infants' rectal swabs at birth. We also analyzed 9 breast milk samples and 18 infants' nasopharyngeal swabs 60 days post-delivery. We used 16S rRNA gene sequencing to determine the microbiota composition. Metabolomic profiling analysis was performed on colostrum and mature breast milk samples using a multiplatform approach combining 1-H Nuclear Magnetic Resonance Spectroscopy and Gas Chromatography-Mass Spectrometry. Bacterial communities were distinct in composition and diversity across different sample types. Breast milk composition changed over the first 60 days of lactation. α-1,4- and α-1,3-fucosylated human milk oligosaccharides, and other 33 key metabolites in breast milk (monosaccharides, sugar alcohols and fatty acids) increased between birth and day 60 of life. This study's results indicate that infant gut and respiratory microbiota are unique bacterial communities, distinct from maternal gut and breast milk, respectively. Breast milk microbiota composition and metabolomic profile change throughout lactation. These changes may contribute to the infant's immunological, metabolic, and neurological development and could consist the basis for future interventions to correct disrupted early life microbial colonization.
    MeSH term(s) Humans ; Infant ; Infant, Newborn ; Female ; Milk, Human/chemistry ; Breast Feeding ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 16S/analysis ; Prospective Studies ; Gambia ; Lactation ; Microbiota ; Bacteria
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2022-11-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 80184-7
    ISSN 1536-5964 ; 0025-7974
    ISSN (online) 1536-5964
    ISSN 0025-7974
    DOI 10.1097/MD.0000000000031419
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  10. Article ; Online: Dynamics of toxigenic Clostridium perfringens colonisation in a cohort of prematurely born neonatal infants.

    Shaw, Alexander G / Cornwell, Emma / Sim, Kathleen / Thrower, Hannah / Scott, Hannah / Brown, Joseph C S / Dixon, Ronald A / Kroll, J Simon

    BMC pediatrics

    2020  Volume 20, Issue 1, Page(s) 75

    Abstract: Background: Clostridium perfringens forms part of the human gut microbiota and has been associated with life-threatening necrotising enterocolitis (NEC) in premature infants. Whether specific toxigenic strains are responsible is unknown, as is the ... ...

    Abstract Background: Clostridium perfringens forms part of the human gut microbiota and has been associated with life-threatening necrotising enterocolitis (NEC) in premature infants. Whether specific toxigenic strains are responsible is unknown, as is the extent of diversity of strains in healthy premature babies. We investigated the C. perfringens carrier status of premature infants in the neonatal intensive care unit, factors influence this status, and the toxic potential of the strains.
    Methods: C. perfringens was isolated by culture from faecal samples from 333 infants and their toxin gene profiles analysed by PCR. A survival analysis was used to identify factors affecting probability of carriage. Competitive growth experiments were used to explore the results of the survival analysis.
    Results: 29.4% of infants were colonized with C. perfringens before they left hospital. Three factors were inversely associated with probability of carriage: increased duration of maternal milk feeds, CPAP oxygen treatment and antibiotic treatment. C. perfringens grew poorly in breast milk and was significantly outperformed by Bifidobacterium infantis, whether grown together or separately. Toxin gene screening revealed that infants carried isolates positive for collagenase, perfringolysin O, beta 2, beta, becA/B, netB and enterotoxin toxin genes, yet none were observed to be associated with the development of NEC.
    Conclusions: Approximately a third of preterm infants are colonised 3 weeks after birth with toxin gene-carrying C. perfringens. We speculate that increased maternal breast milk, oxygen and antibiotic treatment creates an environment in the gut hostile to growth of C. perfringens. Whilst potentially toxigenic C. perfringens isolates were frequent, no toxin type was associated with NEC.
    Trial registration: clinicaltrials.gov NCT01102738, registered 13th April 2010.
    MeSH term(s) Clostridium Infections/diagnosis ; Clostridium Infections/microbiology ; Clostridium perfringens/pathogenicity ; Enterotoxins ; Feces ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Male ; Pregnancy
    Chemical Substances Enterotoxins
    Language English
    Publishing date 2020-02-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2041342-7
    ISSN 1471-2431 ; 1471-2431
    ISSN (online) 1471-2431
    ISSN 1471-2431
    DOI 10.1186/s12887-020-1976-7
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