scholarly journals Natural Merodiploidy of the lux-rib Operon of Photobacterium leiognathi from Coastal Waters of Honshu, Japan

2007 ◽  
Vol 189 (17) ◽  
pp. 6148-6158 ◽  
Author(s):  
Jennifer C. Ast ◽  
Henryk Urbanczyk ◽  
Paul V. Dunlap
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Coastal Waters ◽  
Efflux Pump ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Multidrug Efflux Pump ◽  
Photobacterium Leiognathi ◽  
Content Organization ◽  
Luminous Bacteria

ABSTRACT Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib 1 and lux-rib 2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib 1 and lux-rib 2, whereas ATCC 25521T apparently carries only lux-rib 1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib 1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib 2 of lnuch.13.1, and the chromosomal location of lux-rib 2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib 1 and lux-rib 2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib 2 in P. leiognathi; lux-rib 2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.

scholarly journals Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

2013 ◽  
Vol 94 (9) ◽  
pp. 1995-2004 ◽  
Author(s):  
Rafal Tokarz ◽  
Saddef Haq ◽  
Stephen Sameroff ◽  
Stephen R. C. Howie ◽  
W. Ian Lipkin
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Genomic Analysis ◽  
The Other ◽  
High Rate ◽  
Structural Genes ◽  
Genome Sequences ◽  
Capsid Region ◽  
High Degree ◽  
Degree Of Similarity

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.

Global distribution, dissemination and overexpression of potent multidrug efflux pump RE-CmeABC in Campylobacter jejuni

2020 ◽  
Author(s):  
Hong Yao ◽  
Wenbo Zhao ◽  
Dian Jiao ◽  
Stefan Schwarz ◽  
Rongmin Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Campylobacter Jejuni ◽  
Promoter Region ◽  
Spanning Trees ◽  
Efflux Pump ◽  
Global Distribution ◽  
Multidrug Efflux ◽  
Rt Pcr ◽  
Multidrug Efflux Pump ◽  
Close Relationship

Abstract Objectives To investigate the global distribution, dissemination and overexpression of RE-CmeABC in Campylobacter jejuni. Methods WGS information for 433 RE-cmeABC-positive C. jejuni isolates (including 18 isolates sequenced in this study and 415 isolates from GenBank) was used for the generation of minimum-spanning trees with STs. WGS information for 95 representative RE-cmeABC-positive C. jejuni isolates was used for phylogenetic analysis. RT–PCR was conducted to evaluate the association between inverted repeat (IR) sequence diversity in the RE-CmeABC promoter region and RE-cmeABC gene expression. Results WGS analysis revealed the global distribution of RE-cmeABC among C. jejuni from more than 10 countries. MLST results indicated that various STs were involved in the dissemination of RE-cmeABC, with ST2109 being the most predominant ST. Phylogenetic analysis revealed the close relationship between RE-cmeABC-carrying C. jejuni isolates from poultry and humans. The IR polymorphism in the RE-CmeABC promoter region is associated with the overexpression of RE-cmeABC, which was demonstrated experimentally by RT–PCR. Conclusions To the best of our knowledge, our analysis represents the first view of the global distribution of RE-CmeABC, which is horizontally transferable and diffused regionally in a clonal manner. The close relationship of RE-cmeABC-positive C. jejuni from poultry and humans supports the potential of these isolates for zoonotic transmission. Overexpressed RE-CmeABC in C. jejuni will increase the fitness of the corresponding bacteria and be of advantage under antimicrobial selection.

scholarly journals Evidence of Horizontal Gene Transfer of 50S Ribosomal Genes rplB, rplD, and rplY in Neisseria gonorrhoeae

2021 ◽  
Vol 12 ◽  
Author(s):  
Sheeba Santhini Manoharan-Basil ◽  
Jolein Gyonne Elise Laumen ◽  
Christophe Van Dijck ◽  
Tessa De Block ◽  
Irith De Baetselier ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Neisseria Gonorrhoeae ◽  
Ribosomal Proteins ◽  
Efflux Pump ◽  
Bacterial Species ◽  
23S Rrna ◽  
Comparative Genomic ◽  
Multidrug Efflux ◽  
Multidrug Efflux Pump

Horizontal gene transfer (HGT) in the penA and multidrug efflux pump genes has been shown to play a key role in the genesis of antimicrobial resistance in Neisseria gonorrhoeae. In this study, we evaluated if there was evidence of HGT in the genes coding for the ribosomal proteins in the Neisseria genus. We did this in a collection of 11,659 isolates of Neisseria, including N. gonorrhoeae and commensal Neisseria species (N. cinerea, N. elongata, N. flavescens, N. mucosa, N. polysaccharea, and N. subflava). Comparative genomic analyses identified HGT events in three genes: rplB, rplD, and rplY coding for ribosomal proteins L2, L4 and L25, respectively. Recombination events were predicted in N. gonorrhoeae and N. cinerea, N. subflava, and N. lactamica were identified as likely progenitors. In total, 2,337, 2,355, and 1,127 isolates possessed L2, L4, and L25 HGT events. Strong associations were found between HGT in L2/L4 and the C2597T 23S rRNA mutation that confers reduced susceptibility to macrolides. Whilst previous studies have found evidence of HGT of entire genes coding for ribosomal proteins in other bacterial species, this is the first study to find evidence of HGT-mediated chimerization of ribosomal proteins.

scholarly journals AbeM, an H+-Coupled Acinetobacter baumannii Multidrug Efflux Pump Belonging to the MATE Family of Transporters

2005 ◽  
Vol 49 (10) ◽  
pp. 4362-4364 ◽  
Author(s):  
Xian-Zhong Su ◽  
Jing Chen ◽  
Tohru Mizushima ◽  
Teruo Kuroda ◽  
Tomofusa Tsuchiya
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Acinetobacter Baumannii ◽  
Efflux Pump ◽  
Multidrug Efflux ◽  
Multidrug Efflux Pump ◽  
Unique Member

ABSTRACT We cloned a gene, abeM, for a multidrug efflux pump from Acinetobacter baumannii using Escherichia coli as the host. Sequence analysis revealed that AbeM is a member of the MATE family of pumps. AbeM was found to be an H+-coupled multidrug efflux pump and a unique member of the MATE family.

scholarly journals Nearly Identical Plasmids Encoding VIM-1 and Mercury Resistance in Enterobacteriaceae from North-Eastern Germany

2021 ◽  
Vol 9 (7) ◽  
pp. 1345
Author(s):  
Stefan E. Heiden ◽  
Katharina Sydow ◽  
Stephan Schaefer ◽  
Ingo Klempien ◽  
Veronika Balau ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Public Health Problem ◽  
Multidrug Resistant ◽  
Mercury Resistance ◽  
Major Public Health Problem ◽  
Eastern Germany ◽  
North Eastern ◽  
Resistance Plasmids

The emergence of carbapenemase-producing Enterobacteriaceae limits therapeutic options and presents a major public health problem. Resistances to carbapenems are mostly conveyed by metallo-beta-lactamases (MBL) including VIM, which are often encoded on resistance plasmids. We characterized four VIM-positive isolates that were obtained as part of a routine diagnostic screening from two laboratories in north-eastern Germany between June and August 2020. Whole-genome sequencing was performed to address (a) phylogenetic properties, (b) plasmid content, and (c) resistance gene carriage. In addition, we performed phenotypic antibiotic and mercury resistance analyses. The genomic analysis revealed three different bacterial species including C. freundii, E. coli and K. oxytoca with four different sequence types. All isolates were geno- and phenotypically multidrug-resistant (MDR) and the phenotypic profile was explained by the underlying resistance gene content. Three isolates of four carried nearly identical VIM-1-resistance plasmids, which in addition encoded a mercury resistance operon and showed some similarity to two publicly available plasmid sequences from sources other than the two laboratories above. Our results highlight the circulation of a nearly identical IncN-type VIM-1-resistance plasmid in different Enterobacteriaceae in north-eastern Germany.

scholarly journals Molecular Insights into an Antibiotic Enhancer Action of New Morpholine-Containing 5-Arylideneimidazolones in the Fight against MDR Bacteria

2021 ◽  
Vol 22 (4) ◽  
pp. 2062
Author(s):  
Aneta Kaczor ◽  
Karolina Witek ◽  
Sabina Podlewska ◽  
Veronique Sinou ◽  
Joanna Czekajewska ◽  
...  
Keyword(s):  
Molecular Modelling ◽  
Efflux Pump ◽  
Gram Negative Bacteria ◽  
Potential Mechanism ◽  
Multidrug Efflux ◽  
Aromatic Rings ◽  
Allosteric Site ◽  
Multidrug Efflux Pump ◽  
Dual Action

In the search for an effective strategy to overcome antimicrobial resistance, a series of new morpholine-containing 5-arylideneimidazolones differing within either the amine moiety or at position five of imidazolones was explored as potential antibiotic adjuvants against Gram-positive and Gram-negative bacteria. Compounds (7–23) were tested for oxacillin adjuvant properties in the Methicillin-susceptible S. aureus (MSSA) strain ATCC 25923 and Methicillin-resistant S. aureus MRSA 19449. Compounds 14–16 were tested additionally in combination with various antibiotics. Molecular modelling was performed to assess potential mechanism of action. Microdilution and real-time efflux (RTE) assays were carried out in strains of K. aerogenes to determine the potential of compounds 7–23 to block the multidrug efflux pump AcrAB-TolC. Drug-like properties were determined experimentally. Two compounds (10, 15) containing non-condensed aromatic rings, significantly reduced oxacillin MICs in MRSA 19449, while 15 additionally enhanced the effectiveness of ampicillin. Results of molecular modelling confirmed the interaction with the allosteric site of PBP2a as a probable MDR-reversing mechanism. In RTE, the compounds inhibited AcrAB-TolC even to 90% (19). The 4-phenylbenzylidene derivative (15) demonstrated significant MDR-reversal “dual action” for β-lactam antibiotics in MRSA and inhibited AcrAB-TolC in K. aerogenes. 15 displayed also satisfied solubility and safety towards CYP3A4 in vitro.

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

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