scholarly journals Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Graça Pinto ◽  
Marta Sampaio ◽  
Oscar Dias ◽  
Carina Almeida ◽  
Joana Azeredo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Shiga Toxin ◽  
Genetic Material ◽  
High Genetic Diversity ◽  
Vast Number ◽  
Coding Regions ◽  
Regulatory Systems ◽  
Geographical Regions ◽  
Lytic System

Abstract Background A total of 179 Shiga toxin-producing Escherichia coli (STEC) complete genomes were analyzed in terms of serotypes, prophage coding regions, and stx gene variants and their distribution. We further examined the genetic diversity of Stx-converting phage genomes (Stx phages), focusing on the lysis-lysogeny decision and lytic cassettes. Results We show that most STEC isolates belong to non-O157 serotypes (73 %), regardless the sources and geographical regions. While the majority of STEC genomes contain a single stx gene (61 %), strains containing two (35 %), three (3 %) and four (1 %) stx genes were also found, being stx2 the most prevalent gene variant. Their location is exclusively found in intact prophage regions, indicating that they are phage-borne. We further demonstrate that Stx phages can be grouped into four clusters (A, B, C and D), three subclusters (A1, A2 and A3) and one singleton, based on their shared gene content. This cluster distribution is in good agreement with their predicted virion morphologies. Stx phage genomes are highly diverse with a vast number of 1,838 gene phamilies (phams) of related sequences (of which 677 are orphams i.e. unique genes) and, although having high mosaicism, they are generally organized into three major transcripts. While the mechanisms that guide lysis–lysogeny decision are complex, there is a strong selective pressure to maintain the stx genes location close to the lytic cassette composed of predicted SAR-endolysin and pin-holin lytic proteins. The evolution of STEC Stx phages seems to be strongly related to acquiring genetic material, probably from horizontal gene transfer events. Conclusions This work provides novel insights on the genetic structure of Stx phages, showing a high genetic diversity throughout the genomes, where the various lysis-lysogeny regulatory systems are in contrast with an uncommon, but conserved, lytic system always adjacent to stx genes.

scholarly journals Comparative Genomics and Characterization of the Late Promoter pR’ from Shiga Toxin Prophages in Escherichia coli

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 595 ◽  
Author(s):  
Ling Zhang ◽  
David Simpson ◽  
Lynn McMullen ◽  
Michael Gänzle
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Toxin Production ◽  
Late Promoter ◽  
Regulatory Systems ◽  
Human Illness ◽  
Late Transcription ◽  
Native Strains ◽  
Native Host

Shiga-toxin producing Escherichia coli (STEC) causes human illness ranging from mild diarrhea to death. The bacteriophage encoded stx genes are located in the late transcription region, downstream of the antiterminator Q. The transcription of the stx genes is directly under the control of the late promoter pR’, thus the sequence diversity of the region between Q and stx, here termed the pR’ region, may affect Stx toxin production. Here, we compared the gene structure of the pR’ region and the stx subtypes of nineteen STECs. The sequence alignment and phylogenetic analysis suggested that the pR’ region tends to be more heterogeneous than the promoter itself, even if the prophages harbor the same stx subtype. Furthermore, we established and validated transcriptional fusions of the pR’ region to the DsRed reporter gene using mitomycin C (MMC) induction. Finally, these constructs were transformed into native and non-native strains and examined with flow cytometry. The results showed that induction levels changed when pR’ regions were placed under different regulatory systems. Moreover, not every stx gene could be induced in its native host bacteria. In addition to the functional genes, the diversity of the pR’ region plays an important role in determining the level of toxin induction.

scholarly journals Genetic diversity of the enterohaemolysin gene (ehxA) in non-O157 Shiga toxin-producing Escherichia coli strains in China

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Shanshan Fu ◽  
Xiangning Bai ◽  
Ruyue Fan ◽  
Hui Sun ◽  
Yanmei Xu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Shiga Toxin

scholarly journals High genetic diversity of nitrofurantoin- or mecillinam-resistant Escherichia coli indicates low propensity for clonal spread

2013 ◽  
Vol 68 (9) ◽  
pp. 1974-1977 ◽  
Author(s):  
Hanna O. Poulsen ◽  
Anders Johansson ◽  
Susanne Granholm ◽  
Gunnar Kahlmeter ◽  
Martin Sundqvist
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
High Genetic Diversity ◽  
Clonal Spread

Isolation and Characterization of Non-O157 Shiga Toxin–Producing Escherichia coli in Foods Sold at Retail Markets in China

2019 ◽  
Vol 83 (3) ◽  
pp. 460-466
Author(s):  
GUANGZHU YANG ◽  
SHUHONG ZHANG ◽  
YUANBIN HUANG ◽  
QINGHUA YE ◽  
JUMEI ZHANG ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Foodborne Pathogens ◽  
Shiga Toxin ◽  
Multidrug Resistant ◽  
Food Samples ◽  
High Genetic Diversity ◽  
Retail Markets ◽  
Republic Of China ◽  
Isolation And Characterization ◽  
High Prevalence

ABSTRACT Non-O157 Shiga toxin–producing Escherichia coli (STEC) strains are significant foodborne pathogens that can cause acute diarrhea in humans. This study was conducted to investigate the contamination by non-O157 STEC in different types of food sold at retail markets in the People's Republic of China and to characterize non-O157 STEC strains. From May 2012 to April 2014, 1,200 retail food samples were collected from markets in 24 cities in China. Forty-four non-O157 isolates were recovered from 43 STEC-positive samples. Of the isolates, 22 and 19 carried the stx1 and stx2 genes, respectively, and 3 harbored both stx1 and stx2. stx1a and stx2a were the most prevalent stx subtypes. Other virulence genes, ent, hlyA, astA, eae, espB, iha, subAB, and tia, were commonly detected. Diverse O serogroups were identified among these isolates. Multilocus sequence typing indicated the high genetic diversity of the isolates. Thirty-two sequence types (STs) were identified among the 44 isolates, with ST383 (9.09%), ST134 (6.82%), and ST91 (6.82%) the most prevalent. Nine new STs were found. The isolates had a high prevalence of resistance to cephalothin, ampicillin, tetracycline, trimethoprim-sulfamethoxazole, nalidixic acid, streptomycin, and chloramphenicol. Twenty isolates (45.45%) were resistant to at least three antibiotics. This study provides updated surveillance data for non-O157 STEC isolates from foods sold at retail markets. Virulent and multidrug-resistant non-O57 STEC strains were isolated from all types of food. Our findings highlight the need for increased monitoring of non-O157 STEC in retail foods. HIGHLIGHTS

scholarly journals Transmission of IncN Plasmids Carrying blaCTX-M-1 between Commensal Escherichia coli in Pigs and Farm Workers

2009 ◽  
Vol 53 (4) ◽  
pp. 1709-1711 ◽  
Author(s):  
Arshnee Moodley ◽  
Luca Guardabassi
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Farm Workers ◽  
High Genetic Diversity ◽  
Air Samples ◽  
E Coli ◽  
Pig Farms ◽  
Cephalosporin Resistance ◽  
Human Animal

ABSTRACT CTX-M-1-producing Escherichia coli were isolated from 56 pigs, three farm personnel, two manure samples, and two air samples from two Danish pig farms where an association between prophylactic ceftiofur use and the occurrence of cephalosporin resistance was previously demonstrated. Human, animal, and environmental strains displayed high genetic diversity but harbored indistinguishable or closely related IncN plasmids carrying bla CTX-M-1, indicating that IncN plasmids mediating cephalosporin resistance were transmitted between pigs and farm workers across multiple E. coli lineages.

scholarly journals DETERMINATION OF GENETIC DIVERSITY IN PORTUNUS PELAGICUS (LINNAEUS, 1758) COLLECTED FROM GULF OF MANNAR

2021 ◽  
Vol 9 (03) ◽  
pp. 409-420
Author(s):  
C. Shibana ◽  
◽  
P. Subavathy ◽  
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Gulf Of Mannar ◽  
High Genetic Diversity ◽  
Portunus Pelagicus ◽  
Specific Level ◽  
Main Emphasis ◽  
Geographical Regions ◽  
High Level

In the present study, the marine crab Portunuspelagicus was screened with 17 primers and made to score polymorphism. The main emphasis of the present study was to assess the genetic diversity at intra specific level among the 3 accessions of P. pelagicus species of Gulf of Mannarusing RAPD markers. RAPD analysis shows that there is a high level of polymorphism among different accessions. From this study, it was understood that each location varied with respect to environmental factors and genetic parameters. The OPB-18, OPB-19, OPC-07 and OPN-06 primers produced distinct, highly reproducible amplification profile for all the screened samples. In the present study, amplification bands ranged between 250 and 663 bp. Maximum numbers of bands were produced by OPN-06 and least by OPB-19. Moderate to high genetic diversity was observed in all geographic samples of P. pelagicus from RAPD analysis. RAPD analysis from three different geographical regions shows clear polymorphic patterns. Thoothukudi and Rameshwaram populations appear in one cluster, while the Kanyakumari populations formed the other cluster indicating a genetic variability and diversity in samples collected from different places.

Virulence genes and genetic diversity assessment of Shiga toxin-producing Escherichia coli O91 strains from cattle, beef and poultry products

2018 ◽  
Vol 125 ◽  
pp. 463-467
Author(s):  
Luciana Belén Hernandez ◽  
Jimena Soledad Cadona ◽  
Martín Christensen ◽  
Daniel Fernández ◽  
Nora Lía Padola ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genetic Diversity ◽  
Shiga Toxin ◽  
Virulence Genes ◽  
Poultry Products ◽  
Diversity Assessment
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