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Katarzyna Baldy-chudzik - One of the best experts on this subject based on the ideXlab platform.

  • Extended Phylogeny and Extraintestinal Virulence Potential of Commensal Escherichia Coli from Piglets and Sows
    International journal of environmental research and public health, 2020
    Co-Authors: Ewa Bok, Aleksandra Kożańska, Justyna Mazurek-popczyk, Magdalena Wojciech, Katarzyna Baldy-chudzik
    Abstract:

    Commensal Escherichia Coli, naturally occurring in the intestinal tract, can be the origin of extraintestinal pathogenic E. Coli (ExPEC) strains. ExPEC causes high mortality and significant economic losses in the swine industry in several countries and poses a serious threat to public health worldwide. The aim of this study was to analyze the extended phylogenetic structure and extraintestinal virulence potential in two groups of Commensal E. Coli isolates from post-weaning piglets and sows. The phylogenetic assignment to eight groups was determined using the revised Clermont phylogenetic typing method in quadruplex PCR. Identification of extraintestinal virulence genes (VGs) and adhesin operon genes was performed using multiplex or simplex PCR. The revised phylogenetic assignment allowed us to distinguish E. Coli with significantly higher (groups C and F) or lower (group E) virulence potential in isolates from piglets. The majority of the tested VGs occurred more frequently in isolates from piglets than from sows, with statistically significant differences for seven genes: fimH, papAH, iutA, iroN, ompT, traT, and iss. Complete operons for type I and P fimbriae significantly prevailed among E. Coli from piglets. This study provides insight into the extended phylogenetic structure of porcine Commensal E. Coli and showed that these strains, particularly from piglets, constitute a considerable reservoir of extraintestinal VGs and may increase the potential risk of extraintestinal infections.

  • Comparison of Commensal Escherichia Coli Isolates from Adults and Young Children in Lubuskie Province, Poland: Virulence Potential, Phylogeny and Antimicrobial Resistance.
    International journal of environmental research and public health, 2018
    Co-Authors: Ewa Bok, Magdalena Wojciech, Justyna Mazurek, Andrzej Myc, M. Stosik, Katarzyna Baldy-chudzik
    Abstract:

    Commensal Escherichia Coli population is a dynamic structure which may be important in the pathogenesis of extraintestinal infections. The aim of this study was the comparison of genetic diversity of Commensal E. Coli isolates from two age group—adults and young children. E. Coli strains were isolated on MacConkey agar and identified by biochemical tests. Determination of four major phylogenetic groups, identification of virulence genes and antimicrobial resistance determinants were performed by using multiplex or simplex PCR. Phenotypic analysis of resistance was based on disc-diffusion method. The prevalence of virulence genes was significantly higher among isolates from adults than from young children. Phylogroup B2 predominated among E. Coli from adults, whereas phylogroup A was the most common in isolates from young children. The analyses of antimicrobial resistance revealed that resistance to at least one antimicrobial agent and multidrug-resistance were detected significantly more frequent in the isolates from adults than from young children. This study documented that the Commensal E. Coli isolates from adults showed greater genetic diversity than from young children and constitutes a substantial reservoir of the virulence genes typical for extraintestinal pathogenic E. Coli.

  • Phylogenetic background, virulence gene profiles, and genomic diversity in Commensal Escherichia Coli isolated from ten mammal species living in one zoo.
    Veterinary microbiology, 2008
    Co-Authors: Katarzyna Baldy-chudzik, Paweł Mackiewicz, Michał Stosik
    Abstract:

    Three hundred Commensal Escherichia Coli recovered from healthy herbivorous, carnivorous, and omnivorous mammals from one zoo were characterized for their phylogenetic origin, intestinal virulence gene (VG) prevalence, and genomic diversity. The phylogenetic structure of the E. Coli (groups A, B1, B2, and D) from the herbivores was homogenous, with a prevailing representation of group B1. In the carnivores and omnivores, the phylogenetic diversity was species specific with a higher representation of group A compared to the herbivores. Of 16 intestinal VGs in the whole set, 8 were detected and they formed 13 VG profiles. In the herbivores, all the VG-positive isolates belonged to group B1 and harboured the genes eaeA, eastI, ehxA, stx1, and stx2, which separately or in combination formed 8 VG profiles. In the carnivores and omnivores, the VG-positive isolates frequently belonged to group A and harboured the estI and estII genes or a combination of eastI and estI, forming three VG profiles. Single genes cnf2, in group B2, and eastI, in group D, were found. Similarity analysis of pulsed-field gel electrophoresis (PFGE) patterns revealed closer relatedness between the isolates from carnivores and omnivores than those from herbivores. The comparison between the prevalence of phylogenetic groups and the phylogenetic origin of VG-positive isolates in the examined E. Coli suggested, that E. Coli from group B1 in herbivores and E. Coli from group A rather than B1 in carnivores and omnivores are "best adapted" to the host organism. The groups revealed different preferences in the acquisition and maintenance of intestinal VGs.

Maia A Rabaa - One of the best experts on this subject based on the ideXlab platform.

  • Commensal Escherichia Coli are a reservoir for the transfer of XDR plasmids into epidemic fluoroquinolone-resistant Shigella sonnei
    Nature Microbiology, 2020
    Co-Authors: Pham Thanh Duy, Felicity Alcock, Christine J Boinett, Guy E Thwaites, To Nguyen Nguyen, Duong Thuy, Hao Chung The, Ho Ngoc Thanh, Ha Thanh Tuyen, Maia A Rabaa
    Abstract:

    Despite the sporadic detection of fluoroquinolone-resistant Shigella in Asia in the early 2000s and the subsequent global spread of ciprofloxacin-resistant (cipR) Shigella sonnei from 2010, fluoroquinolones remain the recommended therapy for shigellosis^ 1 – 7 . The potential for cipR S. sonnei to develop resistance to alternative second-line drugs may further limit future treatment options^ 8 . Here, we aim to understand the evolution of novel antimicrobial resistant (AMR) S. sonnei variants after introduction into Vietnam. We found that cipR S. sonnei displaced the resident ciprofloxacin-susceptible (cipS) lineage while rapidly acquiring additional resistance to multiple alternative antimicrobial classes. We identified several independent acquisitions of extensively drug-resistant/multidrug-resistant-inducing plasmids, probably facilitated by horizontal transfer from Commensals in the human gut. By characterizing Commensal Escherichia Coli from Shigella- infected and healthy children, we identified an extensive array of AMR genes and plasmids, including an identical multidrug-resistant plasmid isolated from both S. sonnei and E. Coli in the gut of a single child. We additionally found that antimicrobial usage may impact plasmid transfer between Commensal E. Coli and S. sonnei . These results suggest that, in a setting with high antimicrobial use and a high prevalence of AMR Commensals, cipR S. sonnei may be propelled towards pan-resistance by adherence to outdated international treatment guidelines. This study tracks emergent ciprofloxacin-resistant Shigella sonnei in Vietnam, showing displacement of sensitive strains by others that acquired beta-lactam-antibiotic-resistance plasmids from Commensal E. Coli in infected individuals.

  • Commensal Escherichia Coli are a reservoir for the transfer of xdr plasmids into epidemic fluoroquinolone resistant shigella sonnei
    Nature microbiology, 2020
    Co-Authors: Pham Thanh Duy, To Nguyen Thi Nguyen, Duong Vu Thuy, Felicity Alcock, Christine J Boinett, Ho Ngoc Dan Thanh, Ha Thanh Tuyen, Guy E Thwaites, Maia A Rabaa, Stephen Baker
    Abstract:

    Despite the sporadic detection of fluoroquinolone-resistant Shigella in Asia in the early 2000s and the subsequent global spread of ciprofloxacin-resistant (cipR) Shigella sonnei from 2010, fluoroquinolones remain the recommended therapy for shigellosis1-7. The potential for cipR S. sonnei to develop resistance to alternative second-line drugs may further limit future treatment options8. Here, we aim to understand the evolution of novel antimicrobial resistant (AMR) S. sonnei variants after introduction into Vietnam. We found that cipR S. sonnei displaced the resident ciprofloxacin-susceptible (cipS) lineage while rapidly acquiring additional resistance to multiple alternative antimicrobial classes. We identified several independent acquisitions of extensively drug-resistant/multidrug-resistant-inducing plasmids, probably facilitated by horizontal transfer from Commensals in the human gut. By characterizing Commensal Escherichia Coli from Shigella-infected and healthy children, we identified an extensive array of AMR genes and plasmids, including an identical multidrug-resistant plasmid isolated from both S. sonnei and E. Coli in the gut of a single child. We additionally found that antimicrobial usage may impact plasmid transfer between Commensal E. Coli and S. sonnei. These results suggest that, in a setting with high antimicrobial use and a high prevalence of AMR Commensals, cipR S. sonnei may be propelled towards pan-resistance by adherence to outdated international treatment guidelines.

Muna F Anjum - One of the best experts on this subject based on the ideXlab platform.

  • Use of whole genome sequencing of Commensal Escherichia Coli in pigs for antimicrobial resistance surveillance, United Kingdom, 2018.
    Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 2019
    Co-Authors: Emma Stubberfield, Manal Abuoun, Roderick M Card, Ellie Sayers, Heather M O’connor, Muna F Anjum
    Abstract:

    Background Surveillance of Commensal Escherichia Coli, a possible reservoir of antimicrobial resistance (AMR) genes, is important as they pose a risk to human and animal health. Most surveillance activities rely on phenotypic characterisation, but whole genome sequencing (WGS) presents an alternative. Aim In this retrospective study, we tested 515 E. Coli isolated from pigs to evaluate the use of WGS to predict resistance phenotype. Methods Minimum inhibitory concentration (MIC) was determined for nine antimicrobials of clinical and veterinary importance. Deviation from wild-type, fully-susceptible MIC was assessed using European Committee on Antimicrobial Susceptibility Testing (EUCAST) epidemiological cut-off (ECOFF) values. Presence of AMR genes and mutations were determined using APHA SeqFinder. Statistical two-by-two table analysis and Cohen’s kappa (k) test were applied to assess genotype and phenotype concordance. Results Overall, correlation of WGS with susceptibility to the nine antimicrobials was 98.9% for test specificity, and 97.5% for the positive predictive value of a test. The overall kappa score (k = 0.914) indicated AMR gene presence was highly predictive of reduced susceptibility and showed excellent correlation with MIC. However, there was variation for each antimicrobial; five showed excellent correlation; four very good and one moderate. Suggested ECOFF adjustments increased concordance between genotypic data and kappa values for four antimicrobials. Conclusion WGS is a powerful tool for accurately predicting AMR that can be used for national surveillance purposes. Additionally, it can detect resistance genes from a wider panel of antimicrobials whose phenotypes are currently not monitored but may be of importance in the future.

  • an in vitro chicken gut model demonstrates transfer of a multidrug resistance plasmid from salmonella to Commensal Escherichia Coli
    Mbio, 2017
    Co-Authors: Roderick M Card, Martin J Woodward, Shaun Cawthraw, Javier Nunezgarcia, Richard J Ellis, Gemma L Kay, Mark J Pallen, Muna F Anjum
    Abstract:

    The chicken gastrointestinal tract is richly populated by Commensal bacteria that fulfill various beneficial roles for the host, including helping to resist colonization by pathogens. It can also facilitate the conjugative transfer of multidrug resistance (MDR) plasmids between Commensal and pathogenic bacteria which is a significant public and animal health concern as it may affect our ability to treat bacterial infections. We used an in vitro chemostat system to approximate the chicken cecal microbiota, simulate colonization by an MDR Salmonella pathogen, and examine the dynamics of transfer of its MDR plasmid harboring several genes, including the extended-spectrum beta-lactamase blaCTX-M1 We also evaluated the impact of cefotaxime administration on plasmid transfer and microbial diversity. Bacterial community profiles obtained by culture-independent methods showed that Salmonella inoculation resulted in no significant changes to bacterial community alpha diversity and beta diversity, whereas administration of cefotaxime caused significant alterations to both measures of diversity, which largely recovered. MDR plasmid transfer from Salmonella to Commensal Escherichia Coli was demonstrated by PCR and whole-genome sequencing of isolates purified from agar plates containing cefotaxime. Transfer occurred to seven E. Coli sequence types at high rates, even in the absence of cefotaxime, with resistant strains isolated within 3 days. Our chemostat system provides a good representation of bacterial interactions, including antibiotic resistance transfer in vivo It can be used as an ethical and relatively inexpensive approach to model dissemination of antibiotic resistance within the gut of any animal or human and refine interventions that mitigate its spread before employing in vivo studies.IMPORTANCE The spread of antimicrobial resistance presents a grave threat to public health and animal health and is affecting our ability to respond to bacterial infections. Transfer of antimicrobial resistance via plasmid exchange is of particular concern as it enables unrelated bacteria to acquire resistance. The gastrointestinal tract is replete with bacteria and provides an environment for plasmid transfer between Commensals and pathogens. Here we use the chicken gut microbiota as an exemplar to model the effects of bacterial infection, antibiotic administration, and plasmid transfer. We show that transfer of a multidrug-resistant plasmid from the zoonotic pathogen Salmonella to Commensal Escherichia Coli occurs at a high rate, even in the absence of antibiotic administration. Our work demonstrates that the in vitro gut model provides a powerful screening tool that can be used to assess and refine interventions that mitigate the spread of antibiotic resistance in the gut before undertaking animal studies.

  • genome scale reconstruction of a salmonella metabolic model comparison of similarity and differences with a Commensal Escherichia Coli strain
    Journal of Biological Chemistry, 2009
    Co-Authors: Manal Abuoun, Patrick F Suthers, Gareth Jones, Ben Carter, Mark P Saunders, Costas D Maranas, Martin J Woodward, Muna F Anjum
    Abstract:

    Salmonella are closely related to Commensal Escherichia Coli but have gained virulence factors enabling them to behave as enteric pathogens. Less well studied are the similarities and differences that exist between the metabolic properties of these organisms that may contribute toward niche adaptation of Salmonella pathogens. To address this, we have constructed a genome scale Salmonella metabolic model (iMA945). The model comprises 945 open reading frames or genes, 1964 reactions, and 1036 metabolites. There was significant overlap with genes present in E. Coli MG1655 model iAF1260. In silico growth predictions were simulated using the model on different carbon, nitrogen, phosphorous, and sulfur sources. These were compared with substrate utilization data gathered from high throughput phenotyping microarrays revealing good agreement. Of the compounds tested, the majority were utilizable by both Salmonella and E. Coli. Nevertheless a number of differences were identified both between Salmonella and E. Coli and also within the Salmonella strains included. These differences provide valuable insight into differences between a Commensal and a closely related pathogen and within different pathogenic strains opening new avenues for future explorations.

  • The effect of chlortetracycline treatment and its subsequent withdrawal on multi-resistant Salmonella enterica serovar Typhimurium DT104 and Commensal Escherichia Coli in the pig.
    Journal of applied microbiology, 2003
    Co-Authors: Anne A. Delsol, Martin J Woodward, Muna F Anjum, Julie Sunderland, John M. Roe
    Abstract:

    Aims: To investigate the effect of a therapeutic and sub-therapeutic chlortetracycline treatment on tetracycline-resistant Salmonella enterica serovar Typhimurium DT104 and on the Commensal Escherichia Coli in pig. Methods and Results:Salmonella Typhimurium DT104 was orally administered in all pigs prior to antibiotic treatment, and monitored with the native E. Coli. Higher numbers of S. Typhimurium DT104 were shed from treated pigs than untreated pigs. This lasted up to 6 weeks post-treatment in the high-dose group. In this group, there was a 30% increase in E. Coli with a chlortetracycline minimal inhibitory concentration (MIC) > 16 mg l−1 and a 10% increase in E. Coli with an MIC > 50 mg l−1 during and 2 weeks post-treatment. This effect was less-pronounced in the low-dose group. PCR identified the predominant tetracycline resistance genes in the E. Coli as tetA, tetB and tetC. The concentration of chlortetracycline in the pig faeces was measured by HPLC and levels reached 80 μg g−1 faeces during treatment. Conclusion: Chlortetracycline treatment increases the proportion of resistant enteric bacteria beyond the current withdrawal time. Significance and Impact of the Study: Treated pigs are more likely to enter abattoirs with higher levels of resistant bacteria than untreated pigs promoting the risk of these moving up the food chain and infecting man.

David M. Gordon - One of the best experts on this subject based on the ideXlab platform.

  • functional genotypes are associated with Commensal Escherichia Coli strain abundance within host individuals and populations
    Molecular Ecology, 2013
    Co-Authors: Michaela D. J. Blyton, Sam C. Banks, Rod Peakall, David M. Gordon
    Abstract:

    The selective pressures that determine genotype abundance and distribution frequently vary between ecological levels. Thus, it is often unclear whether the same functional genotypes will become abundant at different levels and how selection acting at these different scales is linked. In this study, we examined whether particular functional genotypes, defined by the presence or absence of 34 genes, of Commensal Escherichia Coli strains were associated with within-host abundance and/or host population abundance in a wild population of 54 adult mountain brushtail possums (Trichosurus cunninghami). Our results revealed that there was a positive correlation between a strain's relative abundance within individuals and the strain's abundance in the host population. We also found that strain abundance at both ecological levels was predicted by the same group of functional genes (agn43, focH, micH47, iroN, ygiL, ompT, kspmT2 and K1) that had associated patterns of occurrence. We propose that direct selection on the same functional genes at both levels may in part be responsible for the observed correlation between the ecological levels. However, a potential link between abundance within the host and excretion rate may also contribute.

  • Functional genotypes are associated with Commensal Escherichia Coli strain abundance within‐host individuals and populations
    Molecular ecology, 2013
    Co-Authors: Michaela D. J. Blyton, Sam C. Banks, Rod Peakall, David M. Gordon
    Abstract:

    The selective pressures that determine genotype abundance and distribution frequently vary between ecological levels. Thus, it is often unclear whether the same functional genotypes will become abundant at different levels and how selection acting at these different scales is linked. In this study, we examined whether particular functional genotypes, defined by the presence or absence of 34 genes, of Commensal Escherichia Coli strains were associated with within-host abundance and/or host population abundance in a wild population of 54 adult mountain brushtail possums (Trichosurus cunninghami). Our results revealed that there was a positive correlation between a strain's relative abundance within individuals and the strain's abundance in the host population. We also found that strain abundance at both ecological levels was predicted by the same group of functional genes (agn43, focH, micH47, iroN, ygiL, ompT, kspmT2 and K1) that had associated patterns of occurrence. We propose that direct selection on the same functional genes at both levels may in part be responsible for the observed correlation between the ecological levels. However, a potential link between abundance within the host and excretion rate may also contribute.

Stephen Baker - One of the best experts on this subject based on the ideXlab platform.

  • Commensal Escherichia Coli are a reservoir for the transfer of xdr plasmids into epidemic fluoroquinolone resistant shigella sonnei
    Nature microbiology, 2020
    Co-Authors: Pham Thanh Duy, To Nguyen Thi Nguyen, Duong Vu Thuy, Felicity Alcock, Christine J Boinett, Ho Ngoc Dan Thanh, Ha Thanh Tuyen, Guy E Thwaites, Maia A Rabaa, Stephen Baker
    Abstract:

    Despite the sporadic detection of fluoroquinolone-resistant Shigella in Asia in the early 2000s and the subsequent global spread of ciprofloxacin-resistant (cipR) Shigella sonnei from 2010, fluoroquinolones remain the recommended therapy for shigellosis1-7. The potential for cipR S. sonnei to develop resistance to alternative second-line drugs may further limit future treatment options8. Here, we aim to understand the evolution of novel antimicrobial resistant (AMR) S. sonnei variants after introduction into Vietnam. We found that cipR S. sonnei displaced the resident ciprofloxacin-susceptible (cipS) lineage while rapidly acquiring additional resistance to multiple alternative antimicrobial classes. We identified several independent acquisitions of extensively drug-resistant/multidrug-resistant-inducing plasmids, probably facilitated by horizontal transfer from Commensals in the human gut. By characterizing Commensal Escherichia Coli from Shigella-infected and healthy children, we identified an extensive array of AMR genes and plasmids, including an identical multidrug-resistant plasmid isolated from both S. sonnei and E. Coli in the gut of a single child. We additionally found that antimicrobial usage may impact plasmid transfer between Commensal E. Coli and S. sonnei. These results suggest that, in a setting with high antimicrobial use and a high prevalence of AMR Commensals, cipR S. sonnei may be propelled towards pan-resistance by adherence to outdated international treatment guidelines.