scholarly journals Genetic Characterization of Plasmid-Borne blaOXA-58 in Distinct Acinetobacter Species

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Adriana P. Matos ◽  
Rodrigo Cayô ◽  
Luiz G. P. Almeida ◽  
Ana Paula Streling ◽  
Carolina S. Nodari ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
South American ◽  
Acinetobacter Species ◽  
Content Type ◽  
Clinical Strains ◽  
Carbapenem Resistant ◽  
Encoding Genes ◽  
Reading Frames ◽  
Over Time

ABSTRACT We characterize by whole-plasmid-sequence (WPS) two-plasmid-borne blaOXA-58 obtained from Acinetobacter seifertii (Asp-1069) and A. baumannii (Acb-45063) clinical strains recovered 17 years apart from distinct Brazilian regions. Multilocus sequence type (MLST) analysis showed that the Asp-1069 and Acb-45063 strains belong to ST551 and ST15/CC15, respectively. WPS analysis demonstrated that blaOXA-58 was located in two distinct plasmids named pAs1069_a (24,672 bp/44 open reading frames [ORFs]) and pAb45063_b (19,808 bp/24 ORFs), which belong to the GR8/GR23 (repAci23) and GR4 (repAci4) incompatibility groups, respectively. The genetic environments surrounding blaOXA-58 revealed that it was flanked by two intact ISAba3 copies on pAb45063_b, which differed from pAs1069_a. In the latter, the upstream ISAba3 copy was truncated by insertion of ISAba825 element. Although Re27-specific recombination sites were found adjacent to ISAba3-blaOXA-58-ISAba3 arrangement on pAb45063_b, such structures were absent on pAs1069_a. The conserved ISAba125-araC1-lysE arrangement was disrupted by TnaphA6 harboring the aminoglycosides resistance gene aphA6 on pAs1069_a, while an IS26-blaTEM-1-aac(3)-IIa-IS26 genetic structure was found upstream from ISAba3-blaOXA-58-ISAba3 on pAb45063_b. Other two plasmids, pAb45063_a (183,767 bp/209 ORFs) and pAs1069_b (13,129 bp/14 ORFs), were also found in the OXA-58-producing Acinetobacter species strains, harboring the strA and strB genes and the sul2 gene, which confer resistance to streptomycin and sulfonamides, respectively. The plasmid-mediated virulence factors corresponding to genes tonB, spl, glmM, ppa, sulP, and map were found in both strains, as well distinct toxin-antitoxin system-encoding genes stbD and relE (pAs1069_a), brnT and brnA (pAb45063_b), and xreE (pAb45063_a). Although infrequently reported in Brazil, plasmid-borne blaOXA-58 showed a complex and diverse genetic backbone that confers stability in different Acinetobacter species that have been isolated from nosocomial settings over time. IMPORTANCE Although the blaOXA-58 gene has been infrequently described in Brazil, contrasting with other bordering South American countries, we verified the maintenance of this resistance determinant over time among carbapenem-resistant Acinetobacter species isolates, not only in nosocomial settings but also in the environment. In addition, to the best of our knowledge, this is the first study to have used WPS analysis to evaluate the genetic surroundings of blaOXA-58 in Brazil. Moreover, the A. seifertii and A. baumannii clinical strains evaluated in this study were recovered 17 years apart in hospitals located in distinct Brazilian geographic regions.

scholarly journals Characterization of Two Virulent Phages of Lactobacillus plantarum

2012 ◽  
Vol 78 (24) ◽  
pp. 8719-8734 ◽  
Author(s):  
Mariángeles Briggiler Marcó ◽  
Josiane E. Garneau ◽  
Denise Tremblay ◽  
Andrea Quiberoni ◽  
Sylvain Moineau
Keyword(s):  
Lactobacillus Plantarum ◽  
Corn Silage ◽  
Open Reading Frames ◽  
High Identity ◽  
Content Type ◽  
Defense Systems ◽  
Double Stranded Dna ◽  
Type Phage ◽  
Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

scholarly journals Characterization of the Enterobacter Phage vB_EclM_CIP9

2020 ◽  
Vol 9 (13) ◽  
Author(s):  
Klara Wang ◽  
Marielou G. Tamayo ◽  
Tiffany V. Penner ◽  
Bradley W. M. Cook ◽  
Deborah A. Court ◽  
...  
Keyword(s):  
Enterobacter Cloacae ◽  
Opportunistic Pathogen ◽  
Multidrug Resistant ◽  
Open Reading Frames ◽  
Resistant Isolate ◽  
Content Type ◽  
Hospital Acquired Infections ◽  
Hospital Acquired ◽  
Reading Frames

Enterobacter cloacae is an opportunistic pathogen that causes hospital-acquired infections in immunocompromised patients. Here, we describe vB_EclM_CIP9, a novel Enterobacter phage that infects a multidrug-resistant isolate of E. cloacae. Phage vB_EclM_CIP9 is a myovirus that has a 174,924-bp genome, with 296 predicted open reading frames.

scholarly journals Characterization of a Novel Panton-Valentine Leukocidin (PVL)-Encoding Staphylococcal Phage and Its Naturally PVL-Lacking Variant

2013 ◽  
Vol 79 (8) ◽  
pp. 2828-2832 ◽  
Author(s):  
Lynn El Haddad ◽  
Sylvain Moineau
Keyword(s):  
Raw Milk ◽  
Open Reading Frames ◽  
Direct Repeats ◽  
Content Type ◽  
Genes Encoding ◽  
Tail Protein ◽  
Reading Frames ◽  
Panton Valentine Leukocidin ◽  
Valentine Leukocidin

ABSTRACTA new siphophage (LH1) was isolated from raw milk using aStaphylococcus aureusST352 host. Its genome (46,048 bp, 57 open reading frames) includes the two genes encoding Panton-Valentine leukocidin (PVL), a virulence factor usually harbored byS. aureusprophages. Nine structural proteins were identified, including a tail protein generated through a +1 frameshift. A phage lytic mutant was isolated, and its analysis revealed the deletion of genes coding for the PVL and an integrase. The deletion likely occurred through recombination between direct repeats.

scholarly journals Characterization of the AggR Regulon in Enteroaggregative Escherichia coli

2012 ◽  
Vol 81 (1) ◽  
pp. 122-132 ◽  
Author(s):  
Nicholas Morin ◽  
Araceli E. Santiago ◽  
Robert K. Ernst ◽  
Stacey J. Guillot ◽  
James P. Nataro
Keyword(s):  
Escherichia Coli ◽  
Open Reading Frames ◽  
Virulence Plasmid ◽  
Type Vi Secretion System ◽  
Content Type ◽  
Bacterial Surface ◽  
Reverse Transcription Pcr ◽  
Type Vi Secretion ◽  
Reading Frames

AggR is a transcriptional regulator of enteroaggregativeEscherichia coli(EAEC) and has been proposed as the defining factor for typical EAEC strains. Expression of multiple putative virulence factors, including the aggregative adherence fimbriae (AAF), dispersin, the dispersin translocator Aat, and the Aai type VI secretion system, have been found to be regulated by AggR. Here, we confirm the existence of at least 44 AggR-regulated genes using DNA microarray and real-time quantitative reverse transcription-PCR (qRT-PCR); these genes include chromosomal and plasmid-borne loci and 19 previously unsuspected genes. Two previously uncharacterized virulence plasmid-encoded open reading frames (ORFs) (designated ORF3 and ORF4) exhibit significant identity with isoprenoid biosynthesis genes ofBacteriaandArchaea. The predicted ORF4 product is closely related to isopentenyl isomerase (IDI) enzymes, whereas the predicted product of the adjacent ORF3 exhibits an aspartate-rich region that is common amongtrans-isoprenyl phosphate synthases. We show that mutations in these ORFs confer changes in bacterial surface properties. AggR coordinately controls expression of a large number of EAEC genes.

scholarly journals Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalis

2021 ◽  
Vol 10 (12) ◽  
Author(s):  
Alexia Bordigoni ◽  
Sonia Bouchard ◽  
Christelle Desnues
Keyword(s):  
Bacterial Vaginosis ◽  
Gc Content ◽  
Open Reading Frames ◽  
Gardnerella Vaginalis ◽  
Clinical Strain ◽  
Content Type ◽  
Isolation And Characterization ◽  
Double Stranded Dna ◽  
Reading Frames

ABSTRACT Gardnerella vaginalis is the presumed causative agent of bacterial vaginosis. Here, we describe the complete genome sequence of Gardnerella phage vB_Gva_AB1, induced from a vaginal bacterial strain from a woman suffering with bacterial vaginosis. The phage double-stranded DNA (dsDNA) genome is 50,268 bp long with a GC content of 39.55% and contains 62 predicted open reading frames.

scholarly journals Genetic Characterization of 2,4,6-Trichlorophenol Degradation in Cupriavidus necator JMP134

2007 ◽  
Vol 73 (9) ◽  
pp. 2769-2776 ◽  
Author(s):  
M. A. Sánchez ◽  
B. González
Keyword(s):  
Ralstonia Eutropha ◽  
Degradation Pathway ◽  
Cupriavidus Necator ◽  
Open Reading Frames ◽  
Aerobic Bacterium ◽  
Gene Encoding ◽  
Encoding Genes ◽  
Genetic Context ◽  
Reading Frames

ABSTRACT The degradation pathway of 2,4,6-trichlorophenol (2,4,6-TCP), a hazardous pollutant, in the aerobic bacterium Cupriavidus necator JMP134(pJP4) (formerly Ralstonia eutropha JMP134) is encoded by the tcp genes. These genes are located in a genetic context, tcpRXABCYD, which resembles a putative catabolic operon. In this work, these gene sequences were individually disrupted and mutant strains were evaluated for their ability to grow on or degrade 2,4,6-TCP. The tcpX and tcpA mutants completely failed to degrade this compound. Although the tcpC mutant was also unable to grow on 2,4,6-TCP, it still transformed this chlorophenol to 6-chlorohydroquinol. In contrast, the tcpD mutant grew on 2,4,6-TCP, suggesting the presence of additional maleylacetate reductase-encoding genes. Five other open reading frames encoding maleylacetate reductases, in addition to the tcpD gene, were found in the genome of C. necator, and two of them provide this function in the tcpD mutant. The tcpR gene, encoding a putative LysR-type transcriptional regulator, was disrupted, and this mutant strain completely failed to grow on 2,4,6-TCP. Transcriptional fusion studies demonstrated that TcpR activates the expression of the tcp genes, responding specifically to 2,4,6-TCP. The transcriptional start of the tcp operon was mapped, and a putative σ70-type promoter was identified.

scholarly journals DeORFanizing Candida albicans Genes using Coexpression

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Teresa R. O’Meara ◽  
Matthew J. O’Meara
Keyword(s):  
Cell Cycle ◽  
Candida Albicans ◽  
Gene Function ◽  
Fungal Pathogen ◽  
Large Scale ◽  
Open Reading Frames ◽  
Coexpression Network ◽  
Content Type ◽  
Reading Frames

ABSTRACT Functional characterization of open reading frames in nonmodel organisms, such as the common opportunistic fungal pathogen Candida albicans, can be labor-intensive. To meet this challenge, we built a comprehensive and unbiased coexpression network for C. albicans, which we call CalCEN, from data collected from 853 RNA sequencing runs from 18 large-scale studies deposited in the NCBI Sequence Read Archive. Retrospectively, CalCEN is highly predictive of known gene function annotations and can be synergistically combined with sequence similarity and interaction networks in Saccharomyces cerevisiae through orthology for additional accuracy in gene function prediction. To prospectively demonstrate the utility of the coexpression network in C. albicans, we predicted the function of underannotated open reading frames (ORFs) and identified CCJ1 as a novel cell cycle regulator in C. albicans. This study provides a tool for future systems biology analyses of gene function in C. albicans. We provide a computational pipeline for building and analyzing the coexpression network and CalCEN itself at http://github.com/momeara/CalCEN. IMPORTANCE Candida albicans is a common and deadly fungal pathogen of humans, yet the genome of this organism contains many genes of unknown function. By determining gene function, we can help identify essential genes, new virulence factors, or new regulators of drug resistance, and thereby give new targets for antifungal development. Here, we use information from large-scale RNA sequencing (RNAseq) studies and generate a C. albicans coexpression network (CalCEN) that is robust and able to predict gene function. We demonstrate the utility of this network in both retrospective and prospective testing and use CalCEN to predict a role for C4_06590W/CCJ1 in cell cycle. This tool will allow for a better characterization of underannotated genes in pathogenic yeasts.

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

scholarly journals Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

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