scholarly journals Lineage-Specific Distribution of Insertion Sequence Excision Enhancer in Enterotoxigenic Escherichia coli Isolated from Swine

2013 ◽  
Vol 80 (4) ◽  
pp. 1394-1402 ◽  
Author(s):  
Masahiro Kusumoto ◽  
Dai Fukamizu ◽  
Yoshitoshi Ogura ◽  
Eiji Yoshida ◽  
Fumiko Yamamoto ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Enterotoxigenic Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Genomic Deletions ◽  
Specific Distribution ◽  
Multiple Copies ◽  
Genomic Locations

ABSTRACTInsertion sequences (ISs) are the simplest transposable elements and are widely distributed in bacteria; however, they also play important roles in genome evolution. We recently identified a protein called IS excision enhancer (IEE) in enterohemorrhagicEscherichia coli(EHEC) O157. IEE promotes the excision of IS elements belonging to the IS3family, such as IS629, as well as several other families. IEE-mediated IS excision generates various genomic deletions that lead to the diversification of the bacterial genome. IEE has been found in a broad range of bacterial species; however, among sequencedE. colistrains, IEE is primarily found in EHEC isolates. In this study, we investigated non-EHEC pathogenicE. colistrains isolated from domestic animals and found that IEE is distributed in specific lineages of enterotoxigenicE. coli(ETEC) strains of serotypes O139 or O149 isolated from swine. Theieegene is located within integrative elements that are similar to SpLE1 of EHEC O157. Alliee-positive ETEC lineages also contained multiple copies of IS629, a preferred substrate of IEE, and their genomic locations varied significantly between strains, as observed in O157. These data suggest that IEE may have been transferred among EHEC and ETEC in swine via SpLE1 or SpLE1-like integrative elements. In addition, IS629is actively moving in the ETEC O139 and O149 genomes and, as in EHEC O157, is promoting the diversification of these genomes in combination with IEE.

scholarly journals Phylogenetic Grouping and Virulence Potential of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains in Cattle

2012 ◽  
Vol 78 (13) ◽  
pp. 4677-4682 ◽  
Author(s):  
Charlotte Valat ◽  
Frédéric Auvray ◽  
Karine Forest ◽  
Véronique Métayer ◽  
Emilie Gay ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Virulence Determinants ◽  
Phylogenetic Groups ◽  
Content Type ◽  
E Coli ◽  
Extended Spectrum ◽  
Specific Distribution ◽  
Extended Spectrum Beta Lactamases ◽  
Phylogenetic Grouping ◽  
Almost All

ABSTRACTIn line with recent reports of extended-spectrum beta-lactamases (ESBLs) inEscherichia coliisolates of highly virulent serotypes, such as O104:H4, we investigated the distribution of phylogroups (A, B1, B2, D) and virulence factor (VF)-encoding genes in 204 ESBL-producingE. coliisolates from diarrheic cattle. ESBL genes, VFs, and phylogroups were identified by PCR and a commercial DNA array (Alere, France). ESBL genes belonged mostly to the CTX-M-1 (65.7%) and CTX-M-9 (27.0%) groups, whereas those of the CTX-M-2 and TEM groups were much less represented (3.9% and 3.4%, respectively). One ESBL isolate wasstx1andeaepositive and belonged to a major enterohemorrhagicE. coli(EHEC) serotype (O111:H8). Two other isolates wereeaepositive butstxnegative; one of these had serotype O26:H11. ESBL isolates belonged mainly to phylogroup A (55.4%) and, to lesser extents, to phylogroups D (25.5%) and B1 (15.6%), whereas B2 strains were quasi-absent (1/204). The number of VFs was significantly higher in phylogroup B1 than in phylogroups A (P= 0.04) and D (P= 0.02). Almost all of the VFs detected were found in CTX-M-1 isolates, whereas only 64.3% and 33.3% of them were found in CTX-M-9 and CTX-M-2 isolates, respectively. These results indicated that the widespread dissemination of theblaCTX-Mgenes within theE. colipopulation from cattle still spared the subpopulation of EHEC/Shiga-toxigenicE. coli(STEC) isolates. In contrast to other reports on non-ESBL-producing isolates from domestic animals, B1 was not the main phylogroup identified. However, B1 was found to be the most virulent phylogroup, suggesting host-specific distribution of virulence determinants among phylogenetic groups.

scholarly journals Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

2016 ◽  
Vol 55 (2) ◽  
pp. 616-623 ◽  
Author(s):  
Marie A. Chattaway ◽  
Ulf Schaefer ◽  
Rediat Tewolde ◽  
Timothy J. Dallman ◽  
Claire Jenkins
Keyword(s):  
Escherichia Coli ◽  
Clonal Complex ◽  
Shigella Flexneri ◽  
Bacterial Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Shigella Species ◽  
Close Phylogenetic Relationship ◽  
Initial Identification

ABSTRACTEscherichia coliandShigellaspecies are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species ofShigellaare therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982Escherichia coliandShigellasp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasiveE. coliisolates that were misidentified asShigella flexneriorS. boydiiby the kmer ID, and 8 wereS. flexneriisolates misidentified by TB&S asS. boydiidue to nonfunctionalS. flexneriO antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising bothS. boydiiandS. dysenteriaestrains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data.Shigellacan be differentiated fromE. coliand accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species ofShigella, and identified emerging pathoadapted lineages.

scholarly journals Simultaneous Presence of Insertion Sequence Excision Enhancer and Insertion Sequence IS629Correlates with Increased Diversity and Virulence in Shiga Toxin-Producing Escherichia coli

2015 ◽  
Vol 53 (11) ◽  
pp. 3466-3473 ◽  
Author(s):  
M. Toro ◽  
L. V. Rump ◽  
G. Cao ◽  
J. Meng ◽  
E. W. Brown ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Insertion Sequence ◽  
Family Members ◽  
Simultaneous Presence ◽  
Content Type ◽  
E Coli ◽  
Genomic Deletions ◽  
Human Illness ◽  
Hostile Environments

Although new serotypes of enterohemorrhagicEscherichia coli(EHEC) emerge constantly, the mechanisms by which these new pathogens arise and the reasons emerging serotypes tend to carry more virulence genes than otherE. coliare not understood. An insertion sequence (IS) excision enhancer (IEE) was discovered in EHEC O157:H7 that promoted the excision of IS3family members and generating various genomic deletions. One IS3family member, IS629, actively transposes and proliferates in EHEC O157:H7 and enterotoxigenicE. coli(ETEC) O139 and O149. The simultaneous presence of the IEE and IS629(and other IS3family members) may be part of a system promoting not only adaptation and genome diversification inE. coliO157:H7 but also contributing to the development of pathogenicity among predominant serotypes. Prevalence comparisons of these elements in 461 strains, representing 72 different serotypes and 5 preassigned seropathotypes (SPT) A to E, showed that the presence of these two elements simultaneously was serotype specific and associated with highly pathogenic serotypes (O157 and top non-O157 Shiga toxin-producing Escherichia coli [STEC]) implicated in outbreaks and sporadic cases of human illness (SPT A and B). Serotypes lacking one or both elements were less likely to have been isolated from clinical cases. Our comparisons of IEE sequences showed sequence variations that could be divided into at least three clusters. Interestingly, the IEE sequences from O157 and the top 10 non-O157 STEC serotypes fell into clusters I and II, while less commonly isolated serotypes O5 and O174 fell into cluster III. These results suggest that IS629and IEE elements may be acting synergistically to promote genome plasticity and genetic diversity among STEC strains, enhancing their abilities to adapt to hostile environments and rapidly take up virulence factors.

scholarly journals TleA, a Tsh-Like Autotransporter Identified in a Human Enterotoxigenic Escherichia coli Strain

2015 ◽  
Vol 83 (5) ◽  
pp. 1893-1903 ◽  
Author(s):  
Daniela Gutiérrez ◽  
Mirka Pardo ◽  
David Montero ◽  
Angel Oñate ◽  
Mauricio J. Farfán ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genomic Library ◽  
Coli Strain ◽  
Enterotoxigenic Escherichia Coli ◽  
Watery Diarrhea ◽  
Temperature Sensitive ◽  
Content Type ◽  
E Coli ◽  
Colonization Factor ◽  
Adhesion Level

EnterotoxigenicEscherichia coli(ETEC), a leading cause of acute diarrhea, colonizes the intestine by means of adhesins. However, 15 to 50% of clinical isolates are negative for known adhesins, making it difficult to identify antigens for broad-coverage vaccines. The ETEC strain 1766a, obtained from a child with watery diarrhea in Chile, harbors the colonization factor CS23 but is negative for other known adhesins. One clone, derived from an ETEC 1766a genomic library (clone G10), did not produce CS23 yet was capable of adhering to Caco-2 cells. The goal of this study was to identify the gene responsible for this capacity. Random transposon-based mutagenesis allowed the identification of a 4,110-bp gene that codes for a homologue of the temperature-sensitive hemagglutinin (Tsh) autotransporter described in avianE. colistrains (97% identity, 90% coverage) and that is called TleA (Tsh-like ETEC autotransporter) herein. An isogenic ETEC 1766a strain with atleAmutation showed an adhesion level similar to that of the wild-type strain, suggesting that the gene does not direct attachment to Caco-2 cells. However, expression oftleAconferred the capacity for adherence to nonadherentE. coliHB101. This effect coincided with the detection of TleA on the surface of nonpermeabilized bacteria, while, conversely, ETEC 1766a seems to secrete most of the produced autotransporter to the medium. On the other hand, TleA was capable of degrading bovine submaxillary mucin and leukocyte surface glycoproteins CD45 and P-selectin glycoprotein ligand 1 (PSGL-1). These results suggest that TleA promotes colonization of the intestinal epithelium and that it may modulate the host immune response.

scholarly journals Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes

2021 ◽  
Vol 7 (8) ◽  
Author(s):  
Marie Petitjean ◽  
Bénédicte Condamine ◽  
Charles Burdet ◽  
Erick Denamur ◽  
Etienne Ruppé
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Type Species ◽  
Antibiotic Resistance Genes ◽  
Resistance Pattern ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Specific Distribution

Escherichia coli is a ubiquitous bacterium that has been widely exposed to antibiotics over the last 70 years. It has adapted by acquiring different antibiotic-resistance genes (ARGs), the census of which we aim to characterize here. To do so, we analysed 70 301 E. coli genomes obtained from the EnteroBase database and detected 1 027 651 ARGs using the AMRFinder, Mustard and ResfinderFG ARG databases. We observed a strong phylogroup and clonal lineage specific distribution of some ARGs, supporting the argument for epistasis between ARGs and the strain genetic background. However, each phylogroup had ARGs conferring a similar antibiotic class resistance pattern, indicating phenotypic adaptive convergence. The G+C content or the type of ARG was not associated with the frequency of the ARG in the database. In addition, we identified ARGs from anaerobic, non- Proteobacteria bacteria in four genomes of E. coli , supporting the hypothesis that the transfer between anaerobic bacteria and E. coli can spontaneously occur but remains exceptional. In conclusion, we showed that phylum barrier and intra-species phylogenetic history are major drivers of the acquisition of a resistome in E. coli .

scholarly journals Tumble Suppression Is a Conserved Feature of Swarming Motility

mBio ◽  
2020 ◽  
Vol 11 (3) ◽  
Author(s):  
Jonathan D. Partridge ◽  
Nguyen T. Q. Nhu ◽  
Yann S. Dufour ◽  
Rasika M. Harshey
Keyword(s):  
Escherichia Coli ◽  
Bacterial Species ◽  
Behavioral Adaptation ◽  
Diverse Group ◽  
Swarming Motility ◽  
Gram Negative ◽  
Content Type ◽  
E Coli ◽  
Surfactant Secretion ◽  
Motility Parameters

ABSTRACT Many bacteria use flagellum-driven motility to swarm or move collectively over a surface terrain. Bacterial adaptations for swarming can include cell elongation, hyperflagellation, recruitment of special stator proteins, and surfactant secretion, among others. We recently demonstrated another swarming adaptation in Escherichia coli, wherein the chemotaxis pathway is remodeled to decrease tumble bias (increase run durations), with running speeds increased as well. We show here that the modification of motility parameters during swarming is not unique to E. coli but is shared by a diverse group of bacteria we examined—Proteus mirabilis, Serratia marcescens, Salmonella enterica, Bacillus subtilis, and Pseudomonas aeruginosa—suggesting that increasing run durations and speeds are a cornerstone of swarming. IMPORTANCE Bacteria within a swarm move characteristically in packs, displaying an intricate swirling motion in which hundreds of dynamic rafts continuously form and dissociate as the swarm colonizes an increasing expanse of territory. The demonstrated property of E. coli to reduce its tumble bias and hence increase its run duration during swarming is expected to maintain and promote side-by-side alignment and cohesion within the bacterial packs. In this study, we observed a similar low tumble bias in five different bacterial species, both Gram positive and Gram negative, each inhabiting a unique habitat and posing unique problems to our health. The unanimous display of an altered run-tumble bias in swarms of all species examined in this investigation suggests that this behavioral adaptation is crucial for swarming.

scholarly journals Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli: TABLE 1

2015 ◽  
Vol 198 (1) ◽  
pp. 7-11 ◽  
Author(s):  
Regine Hengge ◽  
Michael Y. Galperin ◽  
Jean-Marc Ghigo ◽  
Mark Gomelsky ◽  
Jeffrey Green ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Mechanisms ◽  
Bacterial Species ◽  
Content Type ◽  
E Coli ◽  
Diguanylate Cyclases ◽  
Genes Encoding ◽  
Systematic Nomenclature ◽  
K 12 ◽  
Encoding Genes

In recent years,Escherichia colihas served as one of a few model bacterial species for studying cyclic di-GMP (c-di-GMP) signaling. The widely usedE. coliK-12 laboratory strains possess 29 genes encoding proteins with GGDEF and/or EAL domains, which include 12 diguanylate cyclases (DGC), 13 c-di-GMP-specific phosphodiesterases (PDE), and 4 “degenerate” enzymatically inactive proteins. In addition, six new GGDEF and EAL (GGDEF/EAL) domain-encoding genes, which encode two DGCs and four PDEs, have recently been found in genomic analyses of commensal and pathogenicE. colistrains. As a group of researchers who have been studying the molecular mechanisms and the genomic basis of c-di-GMP signaling inE. coli, we now propose a general and systematicdgcandpdenomenclature for the enzymatically active GGDEF/EAL domain-encoding genes of this model species. This nomenclature is intuitive and easy to memorize, and it can also be applied to additional genes and proteins that might be discovered in various strains ofE. coliin future studies.

scholarly journals Unexpected Diversity of Escherichia coli SialateO-Acetyl Esterase NanS

2016 ◽  
Vol 198 (20) ◽  
pp. 2803-2809 ◽  
Author(s):  
Ariel Rangel ◽  
Susan M. Steenbergen ◽  
Eric R. Vimr
Keyword(s):  
Escherichia Coli ◽  
Sialic Acid ◽  
Bacterial Species ◽  
Sialic Acids ◽  
Host Bacterium ◽  
Acetyl Esterase ◽  
Content Type ◽  
E Coli ◽  
Host Microbe Interactions ◽  
K 12

ABSTRACTThe sialic acids (N-acylneuraminates) are a group of nine-carbon keto-sugars existing mainly as terminal residues on animal glycoprotein and glycolipid carbohydrate chains. Bacterial commensals and pathogens exploit host sialic acids for nutrition, adhesion, or antirecognition, whereN-acetyl- orN-glycolylneuraminic acids are the two predominant chemical forms of sialic acids. Each form may be modified by acetyl esters at carbon position 4, 7, 8, or 9 and by a variety of less-common modifications. Modified sialic acids produce challenges for colonizing bacteria, because the chemical alterations toN-acetylneuraminic acid (Neu5Ac) confer increased resistance to sialidase and aldolase activities essential for the catabolism of host sialic acids. Bacteria withO-acetyl sialate esterase(s) utilize acetylated sialic acids for growth, thereby gaining a presumed metabolic advantage over competitors lacking this activity. Here, we demonstrate the esterase activity ofEscherichia coliNanS after purifying it as a C-terminal HaloTag fusion. Using a similar approach, we show thatE. colistrain O157:H7 Stx prophage or prophage remnants invariably include paralogs ofnanSoften located downstream of the Shiga-like toxin genes. These paralogs may include sequences encoding N- or C-terminal domains of unknown function where the NanS domains can act as sialateO-acetyl esterases, as shown by complementation of anE. colistrain K-12nanSmutant and the unimpaired growth of anE. coliO157nanSmutant onO-acetylated sialic acid. We further demonstrate thatnanShomologs inStreptococcusspp. also encode active esterase, demonstrating an unexpected diversity of bacterial sialateO-acetyl esterase.IMPORTANCEThe sialic acids are a family of over 40 naturally occurring 9-carbon keto-sugars that function in a variety of host-bacterium interactions. These sugars occur primarily as terminal carbohydrate residues on host glycoproteins and glycolipids. Available evidence indicates that diverse bacterial species use host sialic acids for adhesion or as sources of carbon and nitrogen. Our results show that the catabolism of the diacetylated form of host sialic acid requires a specialized esterase, NanS. Our results further show thatnanShomologs exist in bacteria other thanEscherichia coli, as well as part of toxigenicE. coliprophage. The unexpected diversity of these enzymes suggests new avenues for investigating host-bacterium interactions. Therefore, these original results extend our previous studies ofnanSto include mucosal pathogens, prophage, and prophage remnants. This expansion of thenanSsuperfamily suggests important, although as-yet-unknown, functions in host-microbe interactions.

scholarly journals Impact of Metazooplankton Filter Feeding on Escherichia coli under Variable Environmental Conditions

2019 ◽  
Vol 85 (23) ◽  
Author(s):  
Niveen S. Ismail ◽  
Brittney M. Blokker ◽  
Tyler R. Feeney ◽  
Ruby H. Kohn ◽  
Jingyi Liu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Water Quality ◽  
Surface Waters ◽  
Environmental Variables ◽  
Bacterial Species ◽  
Clearance Rates ◽  
Filter Feeding ◽  
Fecal Indicator ◽  
Content Type ◽  
E Coli

ABSTRACT The fecal indicator bacterial species Escherichia coli is an important measure of water quality and a leading cause of impaired surface waters. We investigated the impact of the filter-feeding metazooplankton Daphnia magna on the inactivation of E. coli. The E. coli clearance rates of these daphnids were calculated from a series of batch experiments conducted under variable environmental conditions. Batch system experiments of 24 to 48 h in duration were completed to test the impacts of bacterial concentration, organism density, temperature, and water type. The maximum clearance rate for adult D. magna organisms was 2 ml h−1 organism−1. Less than 5% of E. coli removed from water by daphnids was recoverable from excretions. Sorption of E. coli on daphnid carapaces was not observed. As a comparison, the clearance rates of the freshwater rotifer Branchionus calyciflorus were also calculated for select conditions. The maximum clearance rate for B. calyciflorus was 6 × 10−4 ml h−1 organism−1. This research furthers our understanding of the impacts of metazooplankton predation on E. coli inactivation and the effects of environmental variables on filter feeding. Based on our results, metazooplankton can play an important role in the reduction of E. coli in natural treatment systems under environmentally relevant conditions. IMPORTANCE Escherichia coli is a fecal indicator bacterial species monitored by the U.S. Environmental Protection Agency to assess microbial water quality. Due to the potential human health implications linked to high levels of E. coli, it is important to understand the inactivation or reduction mechanisms in surface waters. Our research examines the capacities of two types of widespread filter-feeding freshwater metazooplankton, Daphnia magna and Brachionus calyciflorus, to reduce E. coli concentrations. We examine the impacts of different environmentally relevant conditions on the clearance rates. Our results contribute to a better understanding of the importance of metazooplankton in controlling E. coli concentrations and what conditions will reduce or increase grazing. These results provide baseline data to support future efforts to develop a quantitative model relating zooplankton uptake rates to relevant environmental variables.

scholarly journals Emergence of a Multidrug-Resistant Shiga Toxin-Producing Enterotoxigenic Escherichia coli Lineage in Diseased Swine in Japan

2016 ◽  
Vol 54 (4) ◽  
pp. 1074-1081 ◽  
Author(s):  
Masahiro Kusumoto ◽  
Yuna Hikoda ◽  
Yuki Fujii ◽  
Misato Murata ◽  
Hirotsugu Miyoshi ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Significant Risk ◽  
Multidrug Resistant ◽  
Limited Range ◽  
Enterotoxigenic Escherichia Coli ◽  
Content Type ◽  
E Coli ◽  
Shigella Boydii ◽  
High Level

EnterotoxigenicEscherichia coli(ETEC) and Shiga toxin-producingE. coli(STEC) are important causes of diarrhea and edema disease in swine. The majority of swine-pathogenicE. colistrains belong to a limited range of O serogroups, including O8, O138, O139, O141, O147, O149, and O157, which are the most frequently reported strains worldwide. However, the circumstances of ETEC and STEC infections in Japan remain unknown; there have been few reports on the prevalence or characterization of swine-pathogenicE. coli. In the present study, we determined the O serogroups of 967E. coliisolates collected between 1991 and 2014 from diseased swine in Japan, and we found that O139, O149, O116, and OSB9 (O serogroup ofShigella boydiitype 9) were the predominant serogroups. We further analyzed these four O serogroups using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing, and virulence factor profiling. Most of the O139 and O149 strains formed serogroup-specific PFGE clusters (clusters I and II, respectively), whereas the O116 and OSB9 strains were grouped together in the same cluster (cluster III). All of the cluster III strains belonged to a single sequence type (ST88) and carried genes encoding both enterotoxin and Shiga toxin. This PFGE cluster III/ST88 lineage exhibited a high level of multidrug resistance (to a median of 10 antimicrobials). Notably, these bacteria were resistant to fluoroquinolones. Thus, this lineage should be considered a significant risk to animal production due to the toxigenicity and antimicrobial resistance of these bacteria.

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