scholarly journals High Rates of Genome Rearrangements and Pathogenicity of Shigella spp.

2021 ◽  
Vol 12 ◽  
Author(s):  
Zaira Seferbekova ◽  
Alexey Zabelkin ◽  
Yulia Yakovleva ◽  
Robert Afasizhev ◽  
Natalia O. Dranenko ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Synteny Block ◽  
Genome Rearrangements ◽  
Genomic Islands ◽  
E Coli ◽  
Coding Regions ◽  
Shigella Spp ◽  
High Level ◽  
Protein Ligases

Shigella are pathogens originating within the Escherichia lineage but frequently classified as a separate genus. Shigella genomes contain numerous insertion sequences (ISs) that lead to pseudogenisation of affected genes and an increase of non-homologous recombination. Here, we study 414 genomes of E. coli and Shigella strains to assess the contribution of genomic rearrangements to Shigella evolution. We found that Shigella experienced exceptionally high rates of intragenomic rearrangements and had a decreased rate of homologous recombination compared to pathogenic and non-pathogenic E. coli. The high rearrangement rate resulted in independent disruption of syntenic regions and parallel rearrangements in different Shigella lineages. Specifically, we identified two types of chromosomally encoded E3 ubiquitin-protein ligases acquired independently by all Shigella strains that also showed a high level of sequence conservation in the promoter and further in the 5′-intergenic region. In the only available enteroinvasive E. coli (EIEC) strain, which is a pathogenic E. coli with a phenotype intermediate between Shigella and non-pathogenic E. coli, we found a rate of genome rearrangements comparable to those in other E. coli and no functional copies of the two Shigella-specific E3 ubiquitin ligases. These data indicate that the accumulation of ISs influenced many aspects of genome evolution and played an important role in the evolution of intracellular pathogens. Our research demonstrates the power of comparative genomics-based on synteny block composition and an important role of non-coding regions in the evolution of genomic islands.

scholarly journals Molecular survey of mcr1 and mcr2 plasmid mediated colistin resistance genes in Escherichia coli isolates of animal origin in Iran

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Kayhan Ilbeigi ◽  
Mahdi Askari Badouei ◽  
Hossein Vaezi ◽  
Hassan Zaheri ◽  
Sina Aghasharif ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Genes ◽  
Companion Animals ◽  
Multidrug Resistant ◽  
Animal Origin ◽  
Colistin Resistance ◽  
E Coli ◽  
High Level ◽  
Farming Industry

Abstract Objectives The emergence of colistin-resistant Enterobacteriaceae from human and animal sources is one of the major public health concerns as colistin is the last-resort antibiotic for treating infections caused by multidrug-resistant Gram-negative bacteria. We aimed to determine the prevalence of the prototype widespread colistin resistance genes (mcr-1 and mcr-2) among commensal and pathogenic Escherichia coli strains isolated from food-producing and companion animals in Iran. Results A total of 607 E. coli isolates which were previously collected from different animal sources between 2008 and 2016 used to uncover the possible presence of plasmid-mediated colistin resistance genes (mcr-1 and mcr-2) by PCR. Overall, our results could not confirm the presence of any mcr-1 or mcr-2 positive E. coli among the studied isolates. It is concluded that despite the important role of food-producing animals in transferring the antibiotic resistance, they were not the main source for carriage of mcr-1 and mcr-2 in Iran until 2016. This study suggests that the other mcr variants (mcr-3 to mcr-9) might be responsible for conferring colistin resistance in animal isolates in Iran. The possible linkage between pig farming industry and high level of mcr carriage in some countries needs to be clarified in future prospective studies.

scholarly journals Longitudinal Study of Escherichia coli O157:H7 in a Beef Cattle Feedlot and Role of High-Level Shedders in Hide Contamination

2009 ◽  
Vol 75 (20) ◽  
pp. 6515-6523 ◽  
Author(s):  
Terrance M. Arthur ◽  
James E. Keen ◽  
Joseph M. Bosilevac ◽  
Dayna M. Brichta-Harhay ◽  
Norasak Kalchayanand ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Longitudinal Study ◽  
Beef Cattle ◽  
Intervention Studies ◽  
High Density ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
High Level ◽  
Cattle Feedlot

ABSTRACT The objectives of the study described here were (i) to investigate the dynamics of Escherichia coli O157:H7 fecal and hide prevalence over a 9-month period in a feedlot setting and (ii) to determine how animals shedding E. coli O157:H7 at high levels affect the prevalence and levels of E. coli O157:H7 on the hides of other animals in the same pen. Cattle (n = 319) were distributed in 10 adjacent pens, and fecal and hide levels of E. coli O157:H7 were monitored. When the fecal pen prevalence exceeded 20%, the hide pen prevalence was usually (25 of 27 pens) greater than 80%. Sixteen of 19 (84.2%) supershedder (>104 CFU/g) pens had a fecal prevalence greater than 20%. Significant associations with hide and high-level hide (≥40 CFU/100 cm2) contamination were identified for (i) a fecal prevalence greater than 20%, (ii) the presence of one or more high-density shedders (≥200 CFU/g) in a pen, and (iii) the presence of one or more supershedders in a pen. The results presented here suggest that the E. coli O157:H7 fecal prevalence should be reduced below 20% and the levels of shedding should be kept below 200 CFU/g to minimize the contamination of cattle hides. Also, large and unpredictable fluctuations within and between pens in both fecal and hide prevalence of E. coli O157:H7 were detected and should be used as a guide when preharvest studies, particularly preharvest intervention studies, are designed.

scholarly journals Saccharomyces cerevisiae histone Chaperones FACT and Spt6 modulate Pol II and histone occupancy genome-wide

2018 ◽  
Author(s):  
Rakesh Pathak ◽  
Priyanka Singh ◽  
Sudha Ananthakrishnan ◽  
Sarah Adamczyk ◽  
Olivia Schimmel ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Critical Role ◽  
Histone Chaperones ◽  
Strongly Correlated ◽  
Pol Ii ◽  
Chromatin Remodelers ◽  
Coding Regions ◽  
Genome Wide ◽  
High Level

ABSTRACTHistone chaperones, chromatin remodelers, and histone modifying complexes play a critical role in alleviating the nucleosomal barrier. Here, we have examined the role of two highly conserved yeast (Saccharomyces cerevisiae) histone chaperones, FACT and Spt6, in regulating transcription and histone occupancy. We show that the H3 tail contributes to the recruitment of FACT to coding sequences in a manner dependent on acetylation. We found that deleting a H3 HAT Gcn5 or mutating lysines on the H3 tail impairs FACT recruitment at ADH1 and ARG1 genes. However, deleting the H4 tail or mutating the H4 lysines failed to dampen FACT occupancy in coding regions. Additionally, we show that FACT-depletion greatly reduces Pol II occupancy in the 5’ ends genome-wide. By contrast, Spt6-depletion led to reduction in Pol II occupancy towards the 3’ end, in a manner dependent on the gene-length. Severe transcription and histone eviction defects were also observed in a strain that was impaired for Spt6 recruitment (spt6Δ202) and depleted of FACT. Importantly, the severity of the defect strongly correlated with WT Pol II occupancies at these genes, indicating critical roles of Spt6 and Spt16 in promoting high-level transcription. Collectively, our study shows cooperation, as well as redundancy between chaperones, FACT and Spt6, in regulating transcription and chromatin in coding regions of transcribed genes.

scholarly journals Low-Density Macroarray Targeting Non-Locus of Enterocyte Effacement Effectors (nle Genes) and Major Virulence Factors of Shiga Toxin-Producing Escherichia coli (STEC): a New Approach for Molecular Risk Assessment of STEC Isolates

2009 ◽  
Vol 76 (1) ◽  
pp. 203-211 ◽  
Author(s):  
Marie Bugarel ◽  
Lothar Beutin ◽  
Patrick Fach
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Genomic Islands ◽  
Low Density ◽  
Healthy Children ◽  
E Coli ◽  
Health Authorities ◽  
Public Health Authorities ◽  
Enterocyte Effacement ◽  
High Level

ABSTRACT Rapid and specific detection of Shiga toxin-producing Escherichia coli (STEC) strains with a high level of virulence for humans has become a priority for public health authorities. This study reports on the development of a low-density macroarray for simultaneously testing the genes stx 1, stx 2, eae, and ehxA and six different nle genes issued from genomic islands OI-122 (ent, nleB, and nleE) and OI-71 (nleF, nleH1-2, and nleA). Various strains of E. coli isolated from the environment, food, animals, and healthy children have been compared with clinical isolates of various seropathotypes. The eae gene was detected in all enteropathogenic E. coli (EPEC) strains as well as in enterohemorrhagic E. coli (EHEC) strains, except in EHEC O91:H21 and EHEC O113:H21. The gene ehxA was more prevalent in EHEC (90%) than in STEC (42.66%) strains, in which it was unequally distributed. The nle genes were detected only in some EPEC and EHEC strains but with various distributions, showing that nle genes are strain and/or serotype specific, probably reflecting adaptation of the strains to different hosts or environmental niches. One characteristic nle gene distribution in EHEC O157:[H7], O111:[H8], O26:[H11], O103:H25, O118:[H16], O121:[H19], O5:H−, O55:H7, O123:H11, O172:H25, and O165:H25 was ent/espL2, nleB, nleE, nleF, nleH1-2, nleA. (Brackets indicate genotyping of the flic or rfb genes.) A second nle pattern (ent/espL2, nleB, nleE, nleH1-2) was characteristic of EHEC O103:H2, O145:[H28], O45:H2, and O15:H2. The presence of eae, ent/espL2, nleB, nleE, and nleH1-2 genes is a clear signature of STEC strains with high virulence for humans.

scholarly journals Phenotypic and Biochemical Comparison of the Carbapenem-Hydrolyzing Activities of Five Plasmid-Borne AmpC β-Lactamases

2010 ◽  
Vol 54 (11) ◽  
pp. 4556-4560 ◽  
Author(s):  
Hedi Mammeri ◽  
Hélène Guillon ◽  
François Eb ◽  
Patrice Nordmann
Keyword(s):  
Biochemical Analysis ◽  
Carbapenem Resistance ◽  
Catalytic Efficiency ◽  
Wild Type ◽  
E Coli ◽  
Genes Encoding ◽  
High Level ◽  
Biochemical Comparison ◽  
Outer Membrane Permeability

ABSTRACT The CMY-2, ACT-1, DHA-1, ACC-1, and FOX-1 enzymes are representative of five plasmid-mediated AmpC (pAmpC) β-lactamase clusters. Resistance to imipenem has been reported in Enterobacteriaceae as a result of pAmpC expression combined with decreased outer membrane permeability. The aim of this study was to determine the role of different pAmpCs in carbapenem resistance and to define the structure/activity relationship supporting carbapenemase activity. The ampC genes encoding the five pAmpCs and the chromosomal AmpC of Escherichia coli EC6, which was used as a reference cephalosporinase, were cloned and introduced into wild-type E. coli TOP10 and OmpC/OmpF porin-deficient E. coli HB4 strains. The MICs of β-lactams for the recombinant strains revealed that CMY-2, ACT-1, and DHA-1 β-lactamases conferred a high level of resistance to ceftazidime and cefotaxime once expressed in E. coli TOP10 and reduced significantly the susceptibility to imipenem once expressed in E. coli HB4. In contrast, FOX-1 and ACC-1 enzymes did not confer resistance to imipenem. Biochemical analysis showed that CMY-2 β-lactamase and, to a lesser extent, ACT-1 exhibited the highest catalytic efficiency toward imipenem and showed low Km values. A modeling study revealed that the large R2 binding site of these two enzymes may support the carbapenemase activity. Therefore, CMY-2-type, ACT-1-type, and DHA-1-type β-lactamases may promote the emergence of carbapenem resistance in porin-deficient clinical isolates.

scholarly journals Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci

2019 ◽  
Vol 116 (29) ◽  
pp. 14740-14748 ◽  
Author(s):  
Veronika Tchesnokova ◽  
Matthew Radey ◽  
Sujay Chattopadhyay ◽  
Lydia Larson ◽  
Jamie Lee Weaver ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Homologous Recombination ◽  
Multidrug Resistant ◽  
Fluoroquinolone Resistance ◽  
Resistance Mutations ◽  
Chromosomal Dna ◽  
Topoisomerase Iv ◽  
E Coli ◽  
Naturally Occurring ◽  
High Level

Global growth in antibiotic resistance is a major social problem. A high level of resistance to fluoroquinolones requires the concurrent presence of at least 3 mutations in the target proteins—2 in DNA gyrase (GyrA) and 1 in topoisomerase IV (ParC), which occur in a stepwise manner. In the Escherichia coli chromosome, the gyrA and parC loci are positioned about 1 Mb away from each other. Here we show that the 3 fluoroquinolone resistance mutations are tightly associated genetically in naturally occurring strains. In the latest pandemic uropathogenic and multidrug-resistant E. coli clonal group ST1193, the mutant variants of gyrA and parC were acquired not by a typical gradual, stepwise evolution but all at once. This happened as part of 11 simultaneous homologous recombination events involving 2 phylogenetically distant strains of E. coli, from an uropathogenic clonal complex ST14 and fluoroquinolone-resistant ST10. The gene exchanges swapped regions between 0.5 and 139 Kb in length (183 Kb total) spread along 976 Kb of chromosomal DNA around and between gyrA and parC loci. As a result, all 3 fluoroquinolone resistance mutations in GyrA and ParC have simultaneously appeared in ST1193. Based on molecular clock estimates, this potentially happened as recently as <12 y ago. Thus, naturally occurring homologous recombination events between 2 strains can involve numerous chromosomal gene locations simultaneously, resulting in the transfer of distant but tightly associated genetic mutations and emergence of a both highly pathogenic and antibiotic-resistant strain with a rapid global spread capability.

scholarly journals The Saccharomyces cerevisiae DNA Recombination and Repair Functions of the RAD52 Epistasis Group Inhibit Ty1 Transposition

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 543-556 ◽  
Author(s):  
Alison J Rattray ◽  
Brenda K Shafer ◽  
David J Garfinkel
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Homologous Recombination ◽  
Dna Recombination ◽  
Recombinational Repair ◽  
Repair Pathway ◽  
Low Frequencies ◽  
Double Stranded Dna ◽  
High Level ◽  
In Cells

Abstract RNA transcribed from the Saccharomyces cerevisiae retrotransposon Ty1 accumulates to a high level in mitotically growing haploid cells, yet transposition occurs at very low frequencies. The product of reverse transcription is a linear double-stranded DNA molecule that reenters the genome by either Ty1-integrase-mediated insertion or homologous recombination with one of the preexisting genomic Ty1 (or δ) elements. Here we examine the role of the cellular homologous recombination functions on Ty1 transposition. We find that transposition is elevated in cells mutated for genes in the RAD52 recombinational repair pathway, such as RAD50, RAD51, RAD52, RAD54, or RAD57, or in the DNA ligase I gene CDC9, but is not elevated in cells mutated in the DNA repair functions encoded by the RAD1, RAD2, or MSH2 genes. The increase in Ty1 transposition observed when genes in the RAD52 recombinational pathway are mutated is not associated with a significant increase in Ty1 RNA or proteins. However, unincorporated Ty1 cDNA levels are markedly elevated. These results suggest that members of the RAD52 recombinational repair pathway inhibit Ty1 post-translationally by influencing the fate of Ty1 cDNA.

scholarly journals Prc Contributes to Escherichia coli Evasion of Classical Complement-Mediated Serum Killing

2012 ◽  
Vol 80 (10) ◽  
pp. 3399-3409 ◽  
Author(s):  
Chin-Ya Wang ◽  
Shainn-Wei Wang ◽  
Wen-Chun Huang ◽  
Kwang Sik Kim ◽  
Nan-Shan Chang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Infections ◽  
Membrane Attack Complex ◽  
Gram Negative ◽  
Content Type ◽  
E Coli ◽  
Serum Killing ◽  
High Level ◽  
Classical Complement

ABSTRACTEscherichia coliis a common Gram-negative organism that causes bacteremia. Prc, a bacterial periplasmic protease, and its homologues are known to be involved in the pathogenesis of Gram-negative bacterial infections. The present study examined the role of Prc inE. colibacteremia and characterized the ability of theprcmutant of the pathogenicE. colistrain RS218 to cause bacteremia and survive in human serum. Theprcmutant of RS218 exhibited a decreased ability to cause a high level of bacteremia and was more sensitive to serum killing than strain RS218. This sensitivity was due to the mutant's decreased ability to avoid the activation of the antibody-dependent and -independent classical complement cascades as well as its decreased resistance to killing mediated by the membrane attack complex, the end product of complement system activation. The demonstration of Prc in the evasion of classical complement-mediated serum killing of pathogenicE. colimakes this factor a potential target for the development of therapeutic and preventive measures againstE. colibacteremia.

scholarly journals The dual role of HOP2 in mammalian meiotic homologous recombination

2013 ◽  
Vol 42 (4) ◽  
pp. 2346-2357 ◽  
Author(s):  
Roberto J. Pezza ◽  
Oleg N. Voloshin ◽  
Alexander A. Volodin ◽  
Kingsley A. Boateng ◽  
Marina A. Bellani ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Homologous Chromosome ◽  
Strand Break ◽  
Dsb Repair ◽  
Chromosome Synapsis ◽  
Homologous Chromosome Pairing ◽  
Strand Invasion ◽  
High Level

Abstract Deletion of Hop2 in mice eliminates homologous chromosome synapsis and disrupts double-strand break (DSB) repair through homologous recombination. HOP2 in vitro shows two distinctive activities: when it is incorporated into a HOP2–MND1 complex it stimulates DMC1 and RAD51 recombination activities and the purified HOP2 alone is proficient in promoting strand invasion. We observed that a fraction of Mnd1−/− spermatocytes, which express HOP2 but apparently have inactive DMC1 and RAD51 due to lack of the HOP2–MND1 complex, exhibits a high level of chromosome synapsis and that most DSBs in these spermatocytes are repaired. This suggests that DSB repair catalyzed solely by HOP2 supports homologous chromosome pairing and synapsis. In addition, we show that in vitro HOP2 promotes the co-aggregation of ssDNA with duplex DNA, binds to ssDNA leading to unstacking of the bases, and promotes the formation of a three-strand synaptic intermediate. However, HOP2 shows distinctive mechanistic signatures as a recombinase. Namely, HOP2-mediated strand exchange does not require ATP and, in contrast to DMC1, joint molecules formed by HOP2 are more sensitive to mismatches and are efficiently dissociated by RAD54. We propose that HOP2 may act as a recombinase with specific functions in meiosis.

scholarly journals Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Jean-Emmanuel Hugonnet ◽  
Dominique Mengin-Lecreulx ◽  
Alejandro Monton ◽  
Tanneke den Blaauwen ◽  
Etienne Carbonnelle ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Broad Spectrum ◽  
Cell Walls ◽  
Cross Linking ◽  
Penicillin Binding Proteins ◽  
E Coli ◽  
Class A ◽  
Cross Links ◽  
High Level

The target of β-lactam antibiotics is the D,D-transpeptidase activity of penicillin-binding proteins (PBPs) for synthesis of 4→3 cross-links in the peptidoglycan of bacterial cell walls. Unusual 3→3 cross-links formed by L,D-transpeptidases were first detected in Escherichia coli more than four decades ago, however no phenotype has previously been associated with their synthesis. Here we show that production of the L,D-transpeptidase YcbB in combination with elevated synthesis of the (p)ppGpp alarmone by RelA lead to full bypass of the D,D-transpeptidase activity of PBPs and to broad-spectrum β-lactam resistance. Production of YcbB was therefore sufficient to switch the role of (p)ppGpp from antibiotic tolerance to high-level β-lactam resistance. This observation identifies a new mode of peptidoglycan polymerization in E. coli that relies on an unexpectedly small number of enzyme activities comprising the glycosyltransferase activity of class A PBP1b and the D,D-carboxypeptidase activity of DacA in addition to the L,D-transpeptidase activity of YcbB.

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