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Ghazisaeedi F, Ciesinski L, Bednorz C, Johanns V, Pieper L, Tedin K, Wieler LH, Günther S. Phenotypic zinc resistance does not correlate with antimicrobial multi-resistance in fecal E. coli isolates of piglets. Gut Pathog 2020; 12:4. [PMID: 31988666 PMCID: PMC6972033 DOI: 10.1186/s13099-019-0342-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
Background Following the ban on antimicrobial usage for growth promotion in animal husbandry in the EU, non-antimicrobial agents including heavy metal ions (e.g. zinc and copper), prebiotics or probiotics have been suggested as alternatives. Zinc has extensively been used in pig farming, particularly during weaning of piglets to improve animal health and growth rates. Recent studies, however, have suggested that high dietary zinc feeding during weaning of piglets increases the proportion of multi-drug resistant E. coli in the gut, contraindicating the appropriateness of zinc as an alternative. The underlying mechanisms of zinc effects on resistant bacteria remains unclear, but co-selection processes could be involved. In this study, we determined whether E. coli isolates from intestinal contents of piglets that had been supplemented with high concentrations of zinc acquired a higher tolerance towards zinc, and whether multi-drug resistant isolates tolerated higher zinc concentrations. In addition, we compared phenotypic zinc and copper resistance of E. coli isolates for possible correlation between phenotypic resistance/tolerance to different bivalent ionic metals. Results We screened phenotypic zinc/copper tolerance of 210 isolates (including antimicrobial resistant, multi-drug resistant, and non-resistant E. coli) selected from two, independent zinc-feeding animal trials by determining a zinc/copper minimal inhibitory concentration (Merlin, Bornheim-Hersel, Germany). In both trials, groups of piglets were supplemented either with high dietary zinc (> 2000 ppm) or control (50–70 ppm, background) concentrations. Our observations showed that high concentration zinc exposure did not have an effect on either zinc or copper phenotypic tolerance of E. coli isolates from the animals. No significant association was found between antimicrobial resistance and phenotypic zinc/copper tolerance of the same isolates. Conclusion Our findings argue against a co-selection mechanism of antimicrobial drug-resistance and zinc tolerance after dietary zinc supplementation in weaning piglets. An explanation for an increase in multi-drug resistant isolates from piglets with high zinc dietary feeding could be that resistant bacteria to antimicrobial agents are more persistent to stresses such as zinc or copper exposure.
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Marbach-Breitrück E, Kutzner L, Rothe M, Gurke R, Schreiber Y, Reddanna P, Schebb NH, Stehling S, Wieler LH, Heydeck D, Kuhn H. Functional Characterization of Knock-In Mice Expressing a 12/15-Lipoxygenating Alox5 Mutant Instead of the 5-Lipoxygenating Wild-Type Enzyme. Antioxid Redox Signal 2020; 32:1-17. [PMID: 31642348 DOI: 10.1089/ars.2019.7751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aims: Most mammalian genomes involve several genes encoding for functionally distinct arachidonate lipoxygenase (ALOX isoforms). Proinflammatory leukotrienes are formed via the ALOX5 pathway, but 12/15-lipoxygenating ALOX isoforms have been implicated in the biosynthesis of pro-resolving mediators. In vitro mutagenesis of the triad determinants abolished the leukotriene synthesizing activity of ALOX5, but the biological consequences of these alterations have not been studied. To fill this gap, we created Alox5 knock-in mice, which express the 12/15-lipoxygenating Phe359Trp + Ala424Ile + Asn425Met Alox5 triple mutant and characterized its phenotypic alterations. Results: The mouse Alox5 triple mutant functions as arachidonic acid 15-lipoxygenating enzyme, which also forms 12S-hydroxy and 8S-hydroxy arachidonic acid. In contrast to the wild-type enzyme, the triple mutant effectively oxygenates linoleic acid to 13S-hydroxy linoleic acid (13S-HODE), which functions as activating ligand of the type-2 nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ). Knock-in mice expressing the mutant enzyme are viable, fertile, and develop normally. The mice cannot synthesize proinflammatory leukotrienes but show significantly attenuated plasma levels of lipolytic endocannabinoids. When aging, the animals gained significantly more body weight, which may be related to the fivefold higher levels of 13-HODE in the adipose tissue. Innovation: These data indicate for the first time that in vivo mutagenesis of the triad determinants of mouse Alox5 abolished the biosynthetic capacity of the enzyme for proinflammatory leukotrienes and altered the catalytic properties of the protein favoring the formation of 13-HODE. Conclusion:In vivo triple mutation of the mouse Alox5 gene impacts the body weight homeostasis of aging mice via augmented formation of the activating PPARγ ligand 13-HODE.
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Epping L, Golz JC, Knüver MT, Huber C, Thürmer A, Wieler LH, Stingl K, Semmler T. Comparison of different technologies for the decipherment of the whole genome sequence of Campylobacter jejuni BfR-CA-14430. Gut Pathog 2019; 11:59. [PMID: 31890037 PMCID: PMC6913002 DOI: 10.1186/s13099-019-0340-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/05/2019] [Indexed: 01/31/2023] Open
Abstract
Background Campylobacter jejuni is a zoonotic pathogen that infects the human gut through the food chain mainly by consumption of undercooked chicken meat, raw chicken cross-contaminated ready-to-eat food or by raw milk. In the last decades, C. jejuni has increasingly become the most common bacterial cause for food-born infections in high income countries, costing public health systems billions of euros each year. Currently, different whole genome sequencing techniques such as short-read bridge amplification and long-read single molecule real-time sequencing techniques are applied for in-depth analysis of bacterial species, in particular, Illumina MiSeq, PacBio and MinION. Results In this study, we analyzed a recently isolated C. jejuni strain from chicken meat by short- and long-read data from Illumina, PacBio and MinION sequencing technologies. For comparability, this strain is used in the German PAC-CAMPY research consortium in several studies, including phenotypic analysis of biofilm formation, natural transformation and in vivo colonization models. The complete assembled genome sequence most likely consists of a chromosome of 1,645,980 bp covering 1665 coding sequences as well as a plasmid sequence with 41,772 bp that encodes for 46 genes. Multilocus sequence typing revealed that the strain belongs to the clonal complex CC-21 (ST-44) which is known to be involved in C. jejuni human infections, including outbreaks. Furthermore, we discovered resistance determinants and a point mutation in the DNA gyrase (gyrA) that render the bacterium resistant against ampicillin, tetracycline and (fluoro-)quinolones. Conclusion The comparison of Illumina MiSeq, PacBio and MinION sequencing and analyses with different assembly tools enabled us to reconstruct a complete chromosome as well as a circular plasmid sequence of the C. jejuni strain BfR-CA-14430. Illumina short-read sequencing in combination with either PacBio or MinION can substantially improve the quality of the complete chromosome and epichromosomal elements on the level of mismatches and insertions/deletions, depending on the assembly program used.
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Hussain A, Shaik S, Ranjan A, Suresh A, Sarker N, Semmler T, Wieler LH, Alam M, Watanabe H, Chakravortty D, Ahmed N. Genomic and Functional Characterization of Poultry Escherichia coli From India Revealed Diverse Extended-Spectrum β-Lactamase-Producing Lineages With Shared Virulence Profiles. Front Microbiol 2019; 10:2766. [PMID: 31849903 PMCID: PMC6901389 DOI: 10.3389/fmicb.2019.02766] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/13/2019] [Indexed: 01/16/2023] Open
Abstract
Extended-spectrum β-lactamases (ESBLs) form the most important resistance determinants prevalent worldwide. Data on ESBL-producing Escherichia coli from poultry and livestock are scarce in India. We present data on the functional and genomic characterization of ESBL-producing E. coli obtained from poultry in India. The whole genome sequences of 28 ESBL-producing E. coli were analyzed comprising of 12 broiler chicken E. coli isolates, 11 free-range chicken E. coli isolates, and 5 human extraintestinal pathogenic E. coli. All of the 28 ESBL-producing E. coli isolates were tested for antibiotic susceptibilities, in vitro conjugation, and virulence-associated phenotypic characteristics. A total of 13 sequence types were identified from the poultry E. coli, which included globally successful sequence types such as ST117 (9%), ST131 (4.3%), and ST10 (4.3%). The most common ESBL gene detected in poultry E. coli genomes was blaCTX-M-15 (17%). Also, FIB (73%) and FII (73%) were the most common plasmid replicons identified. Conjugation experiments demonstrated 54 (7/13), 30 (3/10), and 40% (2/5) of broiler, free-range, and human ExPEC E. coli to be able to transfer their ESBL genes, respectively. The in vitro virulence-associated phenotypic tests revealed the broiler, free-range, and human ExPEC isolates to be comparable in biofilm formation, resistance to serum bactericidal activity, adherence, and invasion capabilities. Our overall results showed prevalence of virulence phenotypes among the diverse ESBL-producing E. coli from poultry; while certain E. coli clones from broiler-poultry may indeed have the potential to cause infection in humans.
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Johanns VC, Ghazisaeedi F, Epping L, Semmler T, Lübke-Becker A, Pfeifer Y, Bethe A, Eichhorn I, Merle R, Walther B, Wieler LH. Effects of a Four-Week High-Dosage Zinc Oxide Supplemented Diet on Commensal Escherichia coli of Weaned Pigs. Front Microbiol 2019; 10:2734. [PMID: 31849886 PMCID: PMC6892955 DOI: 10.3389/fmicb.2019.02734] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022] Open
Abstract
Strategies to reduce economic losses associated with post-weaning diarrhea in pig farming include high-level dietary zinc oxide supplementation. However, excessive usage of zinc oxide in the pig production sector was found to be associated with accumulation of multidrug resistant bacteria in these animals, presenting an environmental burden through contaminated manure. Here we report on zinc tolerance among a random selection of intestinal Escherichia coli comprising of different antibiotic resistance phenotypes and sampling sites isolated during a controlled feeding trial from 16 weaned piglets: In total, 179 isolates from "pigs fed with high zinc concentrations" (high zinc group, [HZG]: n = 99) and a corresponding "control group" ([CG]: n = 80) were investigated with regard to zinc tolerance, antimicrobial- and biocide susceptibilities by determining minimum inhibitory concentrations (MICs). In addition, in silico whole genome screening (WGSc) for antibiotic resistance genes (ARGs) as well as biocide- and heavy metal tolerance genes was performed using an in-house BLAST-based pipeline. Overall, porcine E. coli isolates showed three different ZnCl2 MICs: 128 μg/ml (HZG, 2%; CG, 6%), 256 μg/ml (HZG, 64%; CG, 91%) and 512 μg/ml ZnCl2 (HZG, 34%, CG, 3%), a unimodal distribution most likely reflecting natural differences in zinc tolerance associated with different genetic lineages. However, a selective impact of the zinc-rich supplemented diet seems to be reasonable, since the linear mixed regression model revealed a statistically significant association between "higher" ZnCl2 MICs and isolates representing the HZG as well as "lower ZnCl2 MICs" with isolates of the CG (p = 0.005). None of the zinc chloride MICs was associated with a particular antibiotic-, heavy metal- or biocide- tolerance/resistance phenotype. Isolates expressing the 512 μg/ml MIC were either positive for ARGs conferring resistance to aminoglycosides, tetracycline and sulfamethoxazole-trimethoprim, or harbored no ARGs at all. Moreover, WGSc revealed a ubiquitous presence of zinc homeostasis and - detoxification genes, including zitB, zntA, and pit. In conclusion, we provide evidence that zinc-rich supplementation of pig feed selects for more zinc tolerant E. coli, including isolates harboring ARGs and biocide- and heavy metal tolerance genes - a putative selective advantage considering substances and antibiotics currently used in industrial pork production systems.
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Kauter A, Epping L, Semmler T, Antao EM, Kannapin D, Stoeckle SD, Gehlen H, Lübke-Becker A, Günther S, Wieler LH, Walther B. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. Anim Microbiome 2019; 1:14. [PMID: 33499951 PMCID: PMC7807895 DOI: 10.1186/s42523-019-0013-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/09/2019] [Indexed: 12/26/2022] Open
Abstract
Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components.Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter".This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.
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Schneider S, Salm F, Vincze S, Moeser A, Petruschke I, Schmücker K, Ludwig N, Hanke R, Schröder C, Gropmann A, Behnke M, Lübke-Becker A, Wieler LH, Hagel S, Pletz MW, Gensichen J, Gastmeier P. Perceptions and attitudes regarding antibiotic resistance in Germany: a cross-sectoral survey amongst physicians, veterinarians, farmers and the general public. J Antimicrob Chemother 2019; 73:1984-1988. [PMID: 29590400 DOI: 10.1093/jac/dky100] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 03/02/2018] [Indexed: 11/14/2022] Open
Abstract
Background Drivers of antibiotic (AB) resistance (ABR) include outpatient treatment, hospital care and animal husbandry. During the first phase of the One Health project RAI (Responsible Antibiotic Use via Information and Communication) surveys were conducted in these sectors. Objectives To compare perceptions and attitudes towards ABR among general practitioners (GPs), hospital physicians, veterinarians, pig farmers and the general public. Methods Cross-sectional questions on AB use and ABR were integrated in group-specific surveys of GPs, hospital physicians, veterinarians, pig farmers and the German general population. Results A total of 1789 participants (340 GPs, 170 hospital physicians, 215 pig farmers, 60 veterinarians and 1004 members of the public) responded. Each group tended to identify drivers of ABR as being from outside its own area of activity. Guidelines were shown to be an important information source for AB therapy for all prescriber groups, but the frequency of routine use differed (39% of GPs, 65% of hospital physicians and 53% of veterinarians). Regarding further information sources, hospital physicians preferred smartphone apps and e-learning, GPs preferred non-sponsored training and veterinarians preferred multidisciplinary networks and e-learning. Farmers were predominantly satisfied with existing solutions. Farmers had three times better basic knowledge of ABR and knew twice as many people with MDR organism problems than the general public. They also received information on ABR more often from their veterinarians than patients did from their doctors. Conclusions This study reveals considerable differences in perceptions and attitudes to ABR among the groups investigated. The results can help to tailor future interventions. Furthermore, they promote mutual understanding and thus support the One Health approach.
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Kumar N, Browne HP, Viciani E, Forster SC, Clare S, Harcourt K, Stares MD, Dougan G, Fairley DJ, Roberts P, Pirmohamed M, Clokie MRJ, Jensen MBF, Hargreaves KR, Ip M, Wieler LH, Seyboldt C, Norén T, Riley TV, Kuijper EJ, Wren BW, Lawley TD. Adaptation of host transmission cycle during Clostridium difficile speciation. Nat Genet 2019; 51:1315-1320. [PMID: 31406348 DOI: 10.1038/s41588-019-0478-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/04/2019] [Indexed: 12/20/2022]
Abstract
Bacterial speciation is a fundamental evolutionary process characterized by diverging genotypic and phenotypic properties. However, the selective forces that affect genetic adaptations and how they relate to the biological changes that underpin the formation of a new bacterial species remain poorly understood. Here, we show that the spore-forming, healthcare-associated enteropathogen Clostridium difficile is actively undergoing speciation. Through large-scale genomic analysis of 906 strains, we demonstrate that the ongoing speciation process is linked to positive selection on core genes in the newly forming species that are involved in sporulation and the metabolism of simple dietary sugars. Functional validation shows that the new C. difficile produces spores that are more resistant and have increased sporulation and host colonization capacity when glucose or fructose is available for metabolism. Thus, we report the formation of an emerging C. difficile species, selected for metabolizing simple dietary sugars and producing high levels of resistant spores, that is adapted for healthcare-mediated transmission.
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Antão EM, Vincze S, Hanke R, Klimmek L, Suchecka K, Lübke-Becker A, Wieler LH. Antibiotic resistance, the 3As and the road ahead. Gut Pathog 2018; 10:52. [PMID: 30598701 PMCID: PMC6303944 DOI: 10.1186/s13099-018-0280-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance is by far one of the most important health threats of our time. Only a global concerted effort of several disciplines based on the One-Health concept will help in slowing down this process and potentially mitigate the ruin of healthcare we have come to enjoy. In this review, we attempt to summarize the most basic and important topics that serve as good information tools to create Awareness. The Availability of antibiotics or the lack thereof is another significant factor that must be given thought, and finally because antibiotic resistance is a problem that will not go away, it is important to have Alternatives. Together, we have the 3As, essential concepts, in dealing with this growing and complex problem.
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Suresh A, Ranjan A, Jadhav S, Hussain A, Shaik S, Alam M, Baddam R, Wieler LH, Ahmed N. Molecular Genetic and Functional Analysis of pks-Harboring, Extra-Intestinal Pathogenic Escherichia coli From India. Front Microbiol 2018; 9:2631. [PMID: 30498477 PMCID: PMC6249908 DOI: 10.3389/fmicb.2018.02631] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/16/2018] [Indexed: 01/08/2023] Open
Abstract
Colibactin, a genotoxin, encoded by the pks pathogenicity island of Escherichia coli belonging to the B2 phylogroup has been reported as a determinant of bacterial pathogenicity. The present study was carried out to detect the pks pathogenicity island in extraintestinal pathogenic E. coli (ExPEC) isolated from a tertiary hospital in Pune, India. Of 462 isolates analyzed, the pks genomic island was detected in 35 (7.6%) isolates, which predominantly belonged to pathogenic phylogroup B2 (97%), and harbored virulence genes such as fimH, sfaD/E, and usp. Biofilm formation assay revealed 21 of the 35 pks-carrying isolates to be strong (SBF > 1.0), 10 isolates to be moderate (SBF = 0.5–1.0), and 4 as weak (SBF < 0.5) biofilm formers. All of the pks-carrying isolates proved resistant against bactericidal activity of human serum. Assays carried out to detect antimicrobial susceptibility revealed 11% of these isolates to be multidrug resistant, 37% producing ESBL and 25% were positive for blaCTX-M-15. The observed prevalence of multidrug resistance and colibactin producing characteristics among pathogenic E. coli belonging to phylogenetic group B2 advocate urgent need for broader surveillance in order to understand and prevent transmission of these ExPEC in community and hospital settings.
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Saile N, Schuh E, Semmler T, Eichhorn I, Wieler LH, Bauwens A, Schmidt H. Determination of virulence and fitness genes associated with the pheU, pheV and selC integration sites of LEE-negative food-borne Shiga toxin-producing Escherichia coli strains. Gut Pathog 2018; 10:43. [PMID: 30337962 PMCID: PMC6174562 DOI: 10.1186/s13099-018-0271-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/01/2018] [Indexed: 01/22/2023] Open
Abstract
Background In the current study, nine foodborne “Locus of Enterocyte Effacement” (LEE)-negative Shiga toxin-producing Escherichia coli (STEC) strains were selected for whole genome sequencing and analysis for yet unknown genetic elements within the already known LEE integration sites selC, pheU and pheV. Foreign DNA ranging in size from 3.4 to 57 kbp was detected and further analyzed. Five STEC strains contained an insertion of foreign DNA adjacent to the selC tRNA gene and five and seven strains contained foreign DNA adjacent to the pheU and pheV tRNA genes, respectively. We characterized the foreign DNA insertion associated with selC (STEC O91:H21 strain 17584/1), pheU (STEC O8:H4 strain RF1a and O55:Hnt strain K30) and pheV (STEC O91:H21 strain 17584/1 and O113:H21 strain TS18/08) as examples. Results In total, 293 open reading frames partially encoding putative virulence factors such as TonB-dependent receptors, DNA helicases, a hemolysin activator protein precursor, antigen 43, anti-restriction protein KlcA, ShiA, and phosphoethanolamine transferases were detected. A virulence type IV toxin-antitoxin system was detected in three strains. Additionally, the ato system was found in one strain. In strain 17584/1 we were able to define a new genomic island which we designated GIselC17584/1. The island contained integrases and mobile elements in addition to genes for increased fitness and those playing a putative role in pathogenicity. Conclusion The data presented highlight the important role of the three tRNAs selC, pheU, and pheV for the genomic flexibility of E. coli. Electronic supplementary material The online version of this article (10.1186/s13099-018-0271-8) contains supplementary material, which is available to authorized users.
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Eichhorn I, Heidemanns K, Ulrich RG, Schmidt H, Semmler T, Fruth A, Bethe A, Goulding D, Pickard D, Karch H, Wieler LH. Lysogenic conversion of atypical enteropathogenic Escherichia coli (aEPEC) from human, murine, and bovine origin with bacteriophage Φ3538 Δstx 2::cat proves their enterohemorrhagic E. coli (EHEC) progeny. Int J Med Microbiol 2018; 308:890-898. [PMID: 29937391 DOI: 10.1016/j.ijmm.2018.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/04/2018] [Accepted: 06/16/2018] [Indexed: 10/28/2022] Open
Abstract
Bacteriophages play an important role in the evolution of bacterial pathogens. A phage-mediated transfer of stx-genes to atypical enteropathogenic E. coli (aEPEC) which are prevalent in different hosts, would convert them to enterohemorrhagic E. coli (EHEC). We decided to confirm this hypothesis experimentally to provide conclusive evidence that aEPEC isolated from different mammalian hosts are indeed progenitors of typical EHEC which gain the ability to produce Shiga-Toxin by lysogeny with stx-converting bacteriophages, utilizing the model phage Φ3538 Δstx2::cat. We applied a modified in vitro plaque-assay, using a high titer of a bacteriophage carrying a deletion in the stx2 gene (Φ3538 Δstx2::cat) to increase the detection of lysogenic conversion events. Three wild-type aEPEC strains were chosen as acceptor strains: the murine aEPEC-strain IMT14505 (sequence type (ST)28, serotype Ont:H6), isolated from a striped field mouse (Apodemus agrarius) in the surrounding of a cattle shed, and the human aEPEC-strain 910#00 (ST28, Ont:H6). The close genomic relationship of both strains implies a high zoonotic potential. A third strain, the bovine aEPEC IMT19981, was of serotype O26:H11 and ST21 (STC29). All three aEPEC were successfully lysogenized with phage Φ3538 Δstx2::cat. Integration of the bacteriophage DNA into the aEPEC host genomes was confirmed by amplification of chloramphenicol transferase (cat) marker gene and by Southern-Blot hybridization. Analysis of the whole genome sequence of each of the three lysogens showed that the bacteriophage was integrated into the known tRNA integration site argW, which is highly variable among E. coli. In conclusion, the successful lysogenic conversion of aEPEC with a stx-phage in vitro underlines the important role of aEPEC as progenitors of EHEC. Given the high prevalence and the wide host range of aEPEC acceptors, their high risk of zoonotic transmission should be recognized in infection control measures.
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Wieler LH, Broich K. Antibiotikaresistenzen: Große Herausforderungen erfordern komplexe Lösungen. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2018; 61:495-498. [DOI: 10.1007/s00103-018-2732-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Baddam R, Kumar N, Wieler LH, Lankapalli AK, Ahmed N, Peacock SJ, Semmler T. Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis. Sci Rep 2018; 8:4628. [PMID: 29545614 PMCID: PMC5854631 DOI: 10.1038/s41598-018-22883-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/01/2018] [Indexed: 02/06/2023] Open
Abstract
Pyrazinamide (PZA) is an important first-line anti-tuberculosis drug, resistance to which occurs primarily due to mutations in pncA (Rv2043c) that encodes the pyrazinamidase enzyme responsible for conversion of pro-drug PZA into its active form. Previous studies have reported numerous resistance-conferring mutations distributed across the entire length of pncA without any hotspot regions. As different lineages of Mycobacterium tuberculosis display a strong geographic association, we sought to understand whether the genetic background influenced the distribution of mutations in pncA. We analyzed the whole genome sequence data of 1,480 clinical isolates representing four major M. tuberculosis lineages to identify the distribution of mutations in the complete operon (Rv2044c-pncA-Rv2042c) and its upstream promoter region. We observed a non-overlapping pattern of mutations among various lineages and identified a lineage 3-specific frame-shift deletion in gene Rv2044c upstream of pncA that disrupted the stop codon and led to its fusion with pncA. This resulted in the addition of a novel domain of unknown function (DUF2784) to the pyrazinamidase enzyme. The variant molecule was computationally modelled and physico-chemical parameters determined to ascertain stability. Although the functional impact of this mutation remains unknown, its lineage specific nature highlights the importance of genetic background and warrants further study.
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Rabold D, Espelage W, Abu Sin M, Eckmanns T, Schneeberg A, Neubauer H, Möbius N, Hille K, Wieler LH, Seyboldt C, Lübke-Becker A. The zoonotic potential of Clostridium difficile from small companion animals and their owners. PLoS One 2018; 13:e0193411. [PMID: 29474439 PMCID: PMC5825086 DOI: 10.1371/journal.pone.0193411] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/10/2018] [Indexed: 01/24/2023] Open
Abstract
Background Clostridium difficile infections (CDI) in humans range from asymptomatic carriage to life-threatening intestinal disease. Findings on C. difficile in various animal species and an overlap in ribotypes (RTs) suggest potential zoonotic transmission. However, the impact of animals for human CDI remains unclear. Methods In a large-scale survey we collected 1,447 fecal samples to determine the occurrence of C. difficile in small companion animals (dogs and cats) and their owners and to assess potential epidemiological links within the community. The Germany-wide survey was conducted from July 2012-August 2013. PCR ribotyping, Multilocus VNTR Analysis (MLVA) and PCR detection of toxin genes were used to characterize isolated C. difficile strains. A database was defined and logistic regression used to identify putative factors associated with fecal shedding of C. difficile. Results In total, 1,418 samples met the inclusion criteria. The isolation rates for small companion animals and their owners within the community were similarly low with 3.0% (25/840) and 2.9% (17/578), respectively. PCR ribotyping revealed eight and twelve different RTs in animals and humans, respectively, whereas three RTs were isolated in both, humans and animals. RT 014/0, a well-known human hospital-associated lineage, was predominantly detected in animal samples. Moreover, the potentially highly pathogenic RTs 027 and 078 were isolated from dogs. Even though, C. difficile did not occur simultaneously in animals and humans sharing the same household. The results of the epidemiological analysis of factors associated with fecal shedding of C. difficile support the hypothesis of a zoonotic potential. Conclusions Molecular characterization and epidemiological analysis revealed that the zoonotic risk for C. difficile associated with dogs and cats within the community is low but cannot be excluded.
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Schaufler K, Nowak K, Düx A, Semmler T, Villa L, Kourouma L, Bangoura K, Wieler LH, Leendertz FH, Guenther S. Clinically Relevant ESBL-Producing K. pneumoniae ST307 and E. coli ST38 in an Urban West African Rat Population. Front Microbiol 2018; 9:150. [PMID: 29479341 PMCID: PMC5812336 DOI: 10.3389/fmicb.2018.00150] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/23/2018] [Indexed: 01/22/2023] Open
Abstract
High-risk ESBL-producing Enterobacteriaceae (ESBL-E) have been described in wild birds and rodents worldwide. Rats are of special interest not only due to their indicator role for environmental pollution with multi-resistant bacteria but also as possible infection source. Data on the presence of high-risk ESBL-E in urban wildlife from Africa remain scarce, however. Twenty-nine animals from three different rat (Rattus) species were captured in the city of Conakry (Guinea, West Africa) in 2015. Rectal swabs were analyzed for ESBL-E using selective media. Species typing and phenotypic antimicrobial resistance analysis to broad-spectrum beta-lactams and other classes of antimicrobials was performed for Enterobacteriaceae-like isolates using the VITEK®2 system (BioMérieux, Germany). Confirmed ESBL-producing E. coli and K. pneumoniae were whole-genome sequenced and resistance genes, phylogenetic background and genes related to bacterial fitness and virulence were analyzed. In total, six of twenty-nine rats (20%) carried ESBL-E (K. pneumoniae and E. coli). All ESBL-producers were multi-drug resistant with blaCTX−M−15 as the dominating ESBL-type. Interestingly, ESBL-associated clonal lineages E. coli ST38 and K. pneumoniae ST307 were found. The ESBL-plasmid in K. pneumoniae ST307 revealed high sequence similarities to pKPN3-307_TypeC, a >200 kbp IncFII plasmid originating from a human clinical ST307 isolate. This was in contrast to the core genome: the rat isolate was distantly related to the human clinical ST307 isolate (27 SNPs/Mbp). In addition, we identified π-fimbrial, capsule 2, and glycogen synthesis clusters in the rodent ST307 isolate, whose involvement in the adaptation to survival outside the host and in human urinary tracts has been suggested. Our results demonstrate the presence of clinically relevant, ESBL-producing K. pneumoniae ST307 and E. coli ST38 clonal lineages in an urban West African rat population. The human community is likely the initial source of ESBL-E however, rats might function as infection source and transmission hub, accelerated by frequent interactions at a human-wildlife interface.
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Ciesinski L, Guenther S, Pieper R, Kalisch M, Bednorz C, Wieler LH. High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut. PLoS One 2018; 13:e0191660. [PMID: 29373597 PMCID: PMC5786291 DOI: 10.1371/journal.pone.0191660] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
High levels of zinc oxide are used frequently as feed additive in pigs to improve gut health and growth performance and are still suggested as an alternative to antimicrobial growth promoters. However, we have recently described an increase of multi-resistant E. coli in association to zinc feeding in piglets. This previous study focused on clonal diversity of E. coli, observing the effect on multi-resistant strains by chance. To shed further light into this highly important topic and falsify our previous findings, we performed a zinc pig feeding trial where we specifically focused on in-depth analysis of antimicrobial resistant E. coli. Under controlled experimental conditions, piglets were randomly allocated to a high dietary zinc (zinc group) and a background zinc feeding group (control group). At different ages samples were taken from feces, digesta, and mucosa and absolute E. coli numbers were determined. A total of 2665 E. coli isolates were than phenotypically tested for antimicrobial resistance and results were confirmed by minimum inhibitory concentration testing for random samples. In piglets fed with high dietary zinc, we detected a substantial increase of multi-resistant E. coli in all gut habitats tested, ranging from 28.9–30.2% multi-resistant E. coli compared to 5.8–14.0% in the control group. This increase was independent of the total number of E. coli. Interestingly, the total amount of the E. coli population decreased over time. Thus, the increase of the multi-resistant E. coli populations seems to be linked with persistence of the resistant population, caused by the influence of high dietary zinc feeding. In conclusion, these findings corroborate our previous report linking high dietary zinc feeding of piglets with the occurrence of antimicrobial resistant E. coli and therefore question the feeding of high dietary zinc oxide as alternative to antimicrobial growth promoters.
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Guenther S, Semmler T, Stubbe A, Stubbe M, Wieler LH, Schaufler K. Chromosomally encoded ESBL genes in Escherichia coli of ST38 from Mongolian wild birds. J Antimicrob Chemother 2018; 72:1310-1313. [PMID: 28158613 DOI: 10.1093/jac/dkx006] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/04/2017] [Indexed: 01/16/2023] Open
Abstract
Objectives ESBL genes in Escherichia coli are mainly plasmid encoded, although recent studies have also shown chromosomal integration, e.g. in clinical E. coli isolates of ST38. As ESBL-producing E. coli are also found in non-clinical settings, we were interested in determining whether chromosomally integrated ESBL genes occur in ST38 isolates from non-clinical habitats, e.g. wildlife. Methods Four ESBL-producing E. coli isolates of ST38 originating from Mongolian birds of prey sampled in 2015 were subjected to a detailed analysis in terms of phenotypic resistance, plasmid profiling and WGS, followed by the determination of genotypic resistance factors including the chromosomal integration of ESBL and carbapenemase genes. Results Results based on phenotypic and genotypic plasmid profiling, contiguous sequence (contig) sizes and PCR analysis of flanking insertion site regions showed that three of four ST38 isolates harboured chromosomally encoded bla CTX-M genes of three different types ( bla CTX-M-14 , bla CTX-M-15 and bla CTX-M-24 ) that were inserted into three different chromosomal locations. A comparison of WGS data with ST38 isolates from a clinical outbreak in the UK indicated only low numbers of core-genome SNPs detected among one Mongolian wild bird isolate and eight clinical isolates from the UK. Conclusions The chromosomal integration of bla CTX-M genes in E. coli isolates of ST38 appears to be common and is likely independent of antimicrobial selective pressure in clinical environments. Our data corroborate the zoonotic potential of environmental isolates of ESBL-producing E. coli , which harbour stably integrated, chromosomally encoded resistance factors.
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Hussain A, Shaik S, Ranjan A, Nandanwar N, Tiwari SK, Majid M, Baddam R, Qureshi IA, Semmler T, Wieler LH, Islam MA, Chakravortty D, Ahmed N. Risk of Transmission of Antimicrobial Resistant Escherichia coli from Commercial Broiler and Free-Range Retail Chicken in India. Front Microbiol 2017; 8:2120. [PMID: 29180984 PMCID: PMC5694193 DOI: 10.3389/fmicb.2017.02120] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/18/2017] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant Escherichia coli infections are a growing public health concern. This study analyzed the possibility of contamination of commercial poultry meat (broiler and free-range) with pathogenic and or multi-resistant E. coli in retail chain poultry meat markets in India. We analyzed 168 E. coli isolates from broiler and free-range retail poultry (meat/ceca) sampled over a wide geographical area, for their antimicrobial sensitivity, phylogenetic groupings, virulence determinants, extended-spectrum-β-lactamase (ESBL) genotypes, fingerprinting by Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR and genetic relatedness to human pathogenic E. coli using whole genome sequencing (WGS). The prevalence rates of ESBL producing E. coli among broiler chicken were: meat 46%; ceca 40%. Whereas, those for free range chicken were: meat 15%; ceca 30%. E. coli from broiler and free-range chicken exhibited varied prevalence rates for multi-drug resistance (meat 68%; ceca 64% and meat 8%; ceca 26%, respectively) and extraintestinal pathogenic E. coli (ExPEC) contamination (5 and 0%, respectively). WGS analysis confirmed two globally emergent human pathogenic lineages of E. coli, namely the ST131 (H30-Rx subclone) and ST117 among our poultry E. coli isolates. These results suggest that commercial poultry meat is not only an indirect public health risk by being a possible carrier of non-pathogenic multi-drug resistant (MDR)-E. coli, but could as well be the carrier of human E. coli pathotypes. Further, the free-range chicken appears to carry low risk of contamination with antimicrobial resistant and extraintestinal pathogenic E. coli (ExPEC). Overall, these observations reinforce the understanding that poultry meat in the retail chain could possibly be contaminated by MDR and/or pathogenic E. coli.
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Thomas P, Semmler T, Eichhorn I, Lübke-Becker A, Werckenthin C, Abdel-Glil MY, Wieler LH, Neubauer H, Seyboldt C. First report of two complete Clostridium chauvoei genome sequences and detailed in silico genome analysis. INFECTION GENETICS AND EVOLUTION 2017; 54:287-298. [PMID: 28720440 DOI: 10.1016/j.meegid.2017.07.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/28/2022]
Abstract
Clostridium (C.) chauvoei is a Gram-positive, spore forming, anaerobic bacterium. It causes black leg in ruminants, a typically fatal histotoxic myonecrosis. High quality circular genome sequences were generated for the C. chauvoei type strain DSM 7528T (ATCC 10092T) and a field strain 12S0467 isolated in Germany. The origin of replication (oriC) was comparable to that of Bacillus subtilis in structure with two regions containing DnaA boxes. Similar prophages were identified in the genomes of both C. chauvoei strains which also harbored hemolysin and bacterial spore formation genes. A CRISPR type I-B system with limited variations in the repeat number was identified. Sporulation and germination process related genes were homologous to that of the Clostridia cluster I group but novel variations for regulatory genes were identified indicative for strain specific control of regulatory events. Phylogenomics showed a higher relatedness to C. septicum than to other so far sequenced genomes of species belonging to the genus Clostridium. Comparative genome analysis of three C. chauvoei circular genome sequences revealed the presence of few inversions and translocations in locally collinear blocks (LCBs). The species genome also shows a large number of genes involved in proteolysis, genes for glycosyl hydrolases and metal iron transportation genes which are presumably involved in virulence and survival in the host. Three conserved flagellar genes (fliC) were identified in each of the circular genomes. In conclusion this is the first comparative analysis of circular genomes for the species C. chauvoei, enabling insights into genome composition and virulence factor variation.
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Nowak K, Fahr J, Weber N, Lübke-Becker A, Semmler T, Weiss S, Mombouli JV, Wieler LH, Guenther S, Leendertz FH, Ewers C. Highly diverse and antimicrobial susceptible Escherichia coli display a naïve bacterial population in fruit bats from the Republic of Congo. PLoS One 2017; 12:e0178146. [PMID: 28700648 PMCID: PMC5507484 DOI: 10.1371/journal.pone.0178146] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 05/09/2017] [Indexed: 01/30/2023] Open
Abstract
Bats are suspected to be a reservoir of several bacterial and viral pathogens relevant to animal and human health, but studies on Escherichia coli in these animals are sparse. We investigated the presence of E. coli in tissue samples (liver, lung and intestines) collected from 50 fruit bats of five different species (Eidolon helvum, Epomops franqueti, Hypsignathus monstrosus, Myonycteris torquata, Rousettus aegyptiacus) of two different areas in the Republic of Congo between 2009 and 2010. To assess E. coli pathotypes and phylogenetic relationships, we determined the presence of 59 virulence associated genes and multilocus sequence types (STs). Isolates were further tested for their susceptibility to several antimicrobial substances by agar disk diffusion test and for the presence of an Extended-Spectrum Beta-Lactamase phenotype. E. coli was detected in 60% of the bats analysed. The diversity of E. coli strains was very high, with 37 different STs within 40 isolates. Occasionally, we detected sequence types (e.g. ST69, ST127, and ST131) and pathotypes (e.g. ExPEC, EPEC and atypical EPEC), which are known pathogens in human and/or animal infections. Although the majority of strains were assigned to phylogenetic group B2 (46.2%), which is linked with the ExPEC pathovar, occurrence of virulence-associated genes in these strains were unexpectedly low. Due to this, and as only few of the E. coli isolates showed intermediate resistance to certain antimicrobial substances, we assume a rather naïve E. coli population, lacking contact to humans or domestic animals. Future studies featuring in depth comparative whole genome sequence analyses will provide insights into the microevolution of this interesting strain collection.
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Lodemann U, Amasheh S, Radloff J, Kern M, Bethe A, Wieler LH, Pieper R, Zentek J, Aschenbach JR. Effects of Ex Vivo Infection with ETEC on Jejunal Barrier Properties and Cytokine Expression in Probiotic-Supplemented Pigs. Dig Dis Sci 2017; 62:922-933. [PMID: 27995406 DOI: 10.1007/s10620-016-4413-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 12/06/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIM Enterotoxigenic Escherichia coli (ETEC) strains are involved in piglet post-weaning diarrhea. Prophylactic measures including probiotics have been examined in infection experiments with live piglets. In the present study, we have tested whether the early effects of ETEC infection can also be evoked and studied in a model in which ETEC is added to whole mucosal tissues ex vivo, and whether this response can be modulated by prior supplementation of the piglets with probiotics. METHODS Jejunal barrier and transport properties of Enterococcus faecium-supplemented or control piglets were assessed in Ussing chambers. Part of the epithelia was challenged with an ETEC strain at the mucosal side. Fluxes of fluorescein as a marker of paracellular permeability, and the expression of selected tight junction (TJ) proteins and of proinflammatory cytokines were measured. RESULTS The addition of ETEC ex vivo induced an increase in transepithelial resistance peaking in the first 2 h with a concomitant reduction in fluorescein fluxes, indicating tightening effects on barrier function. The response of short-circuit current after stimulation with PGE2 or glucose was reduced in epithelia treated with ETEC. ETEC induced a decrease in the TJ protein claudin-4 in the control diet group after 280 min and an increase in the mRNA expression of the proinflammatory cytokines interleukin-8 and TNF-α in both groups after 180 min. CONCLUSIONS The addition of ETEC ex vivo affected barrier function and transport properties of the jejunal tissues and enhanced cytokine expression. The differences in claudin-4 expression in the jejunum might indicate a beneficial effect of E. faecium prefeeding.
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Dadi TH, Renard BY, Wieler LH, Semmler T, Reinert K. SLIMM: species level identification of microorganisms from metagenomes. PeerJ 2017; 5:e3138. [PMID: 28367376 PMCID: PMC5372838 DOI: 10.7717/peerj.3138] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out using whole genome shotgun sequences with less bias than when using 16S-rDNA sequences. However, shared regions of DNA among reference genomes and taxonomic units pose a significant challenge in assigning reads correctly to their true origins. The existing microbial community profiling tools commonly deal with this problem by either preparing signature-based unique references or assigning an ambiguous read to its least common ancestor in a taxonomic tree. The former method is limited to making use of the reads which can be mapped to the curated regions, while the latter suffer from the lack of uniquely mapped reads at lower (more specific) taxonomic ranks. Moreover, even if the tools exhibited good performance in calling the organisms present in a sample, there is still room for improvement in determining the correct relative abundance of the organisms. We present a new method Species Level Identification of Microorganisms from Metagenomes (SLIMM) which addresses the above issues by using coverage information of reference genomes to remove unlikely genomes from the analysis and subsequently gain more uniquely mapped reads to assign at lower ranks of a taxonomic tree. SLIMM is based on a few, seemingly easy steps which when combined create a tool that outperforms state-of-the-art tools in run-time and memory usage while being on par or better in computing quantitative and qualitative information at species-level.
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Geue L, Menge C, Eichhorn I, Semmler T, Wieler LH, Pickard D, Berens C, Barth SA. Evidence for Contemporary Switching of the O-Antigen Gene Cluster between Shiga Toxin-Producing Escherichia coli Strains Colonizing Cattle. Front Microbiol 2017; 8:424. [PMID: 28377748 PMCID: PMC5359238 DOI: 10.3389/fmicb.2017.00424] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/28/2017] [Indexed: 11/13/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) comprise a group of zoonotic enteric pathogens with ruminants, especially cattle, as the main reservoir. O-antigens are instrumental for host colonization and bacterial niche adaptation. They are highly immunogenic and, therefore, targeted by the adaptive immune system. The O-antigen is one of the most diverse bacterial cell constituents and variation not only exists between different bacterial species, but also between individual isolates/strains within a single species. We recently identified STEC persistently infecting cattle and belonging to the different serotypes O156:H25 (n = 21) and O182:H25 (n = 15) that were of the MLST sequence types ST300 or ST688. These STs differ by a single nucleotide in purA only. Fitness-, virulence-associated genome regions, and CRISPR/CAS (clustered regularly interspaced short palindromic repeats/CRISPR associated sequence) arrays of these STEC O156:H25 and O182:H25 isolates were highly similar, and identical genomic integration sites for the stx converting bacteriophages and the core LEE, identical Shiga toxin converting bacteriophage genes for stx1a, identical complete LEE loci, and identical sets of chemotaxis and flagellar genes were identified. In contrast to this genomic similarity, the nucleotide sequences of the O-antigen gene cluster (O-AGC) regions between galF and gnd and very few flanking genes differed fundamentally and were specific for the respective serotype. Sporadic aEPEC O156:H8 isolates (n = 5) were isolated in temporal and spatial proximity. While the O-AGC and the corresponding 5' and 3' flanking regions of these aEPEC isolates were identical to the respective region in the STEC O156:H25 isolates, the core genome, the virulence associated genome regions and the CRISPR/CAS elements differed profoundly. Our cumulative epidemiological and molecular data suggests a recent switch of the O-AGC between isolates with O156:H8 strains having served as DNA donors. Such O-antigen switches can affect the evaluation of a strain's pathogenic and virulence potential, suggesting that NGS methods might lead to a more reliable risk assessment.
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