Emergence of an Empedobacter falsenii strain harbouring a tet(X)-variant-bearing novel plasmid conferring resistance to tigecycline

2019 ◽  
Vol 75 (3) ◽  
pp. 531-536 ◽  
Author(s):  
Yu Zeng ◽  
Ning Dong ◽  
Rong Zhang ◽  
Congcong Liu ◽  
Qiaoling Sun ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Carbapenem Resistance ◽  
Chinese Patient ◽  
Phenotypic Characteristics ◽  
Species Identity ◽  
Gene Encoding ◽  
Resistance Determinants ◽  
Variant Gene ◽  
The Usa ◽  
Tof Ms

Abstract Objectives To investigate the genomic and phenotypic characteristics of an MDR Empedobacter falsenii strain isolated from a Chinese patient, which was phenotypically resistant to all last-line antibiotics (carbapenems, colistin and tigecycline). Methods Species identity was determined by MALDI-TOF MS analysis. The complete genome sequence of the isolate was determined by WGS and the genetic elements conferring antimicrobial resistance were determined. The origin of this strain was tracked by phylogenetic analysis. Results The E. falsenii strain was genetically most closely related to an Empedobacter sp. strain isolated from the USA. Members of E. falsenii are speculated to be intrinsically resistant to colistin. The carbapenem resistance of this strain was conferred by a chromosomal blaEBR-2 variant gene. Phylogenetic analysis indicated that the gene encoding the EBR β-lactamase was widely distributed in Empedobacter spp. Tigecycline resistance was mediated by a tet(X) variant gene encoded by a non-conjugative and non-typeable plasmid. Conclusions The MDR phenotype of the E. falsenii isolate was conferred by different mechanisms. Findings from us and others indicate that E. falsenii may serve as a reservoir for carbapenem and tigecycline resistance determinants.

scholarly journals Gene Sequencing and Phylogenetic Analysis: Powerful Tools for an Improved Diagnosis of Fish Mycobacteriosis Caused by Mycobacterium fortuitum Group Members

2021 ◽  
Vol 9 (4) ◽  
pp. 797
Author(s):  
Davide Mugetti ◽  
Mattia Tomasoni ◽  
Paolo Pastorino ◽  
Giuseppe Esposito ◽  
Vasco Menconi ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Sequencing ◽  
Diagnostic Techniques ◽  
Individual Species ◽  
Identification System ◽  
Mycobacterium Fortuitum ◽  
Biochemical Tests ◽  
Species Determination ◽  
Gene Encoding ◽  
The Individual

The Mycobacterium fortuitum group (MFG) consists of about 15 species of fast-growing nontuberculous mycobacteria (NTM). These globally distributed microorganisms can cause diseases in humans and animals, especially fish. The increase in the number of species belonging to MFG and the diagnostic techniques panel do not allow to clarify their real clinical significance. In this study, biomolecular techniques were adopted for species determination of 130 isolates derived from fish initially identified through biochemical tests as NTM belonging to MFG. Specifically, gene sequencing and phylogenetic analysis were used based on a fragment of the gene encoding the 65 KDa heat shock protein (hsp65). The analyzes made it possible to confirm that all the isolates belong to MFG, allowing to identify the strains at species level. Phylogenetic analysis substantially confirmed what was obtained by gene sequencing, except for six strains; this is probably due to the sequences present in NCBI database. Although the methodology used cannot represent a univocal identification system, this study has allowed us to evaluate its effectiveness as regards the species of MFG. Future studies will be necessary to apply these methods with other gene fragments and to clarify the real pathogenic significance of the individual species of this group of microorganisms.

scholarly journals Structure, expression and phylogenetic analysis of the gene encoding actin I in Pneumocystis carinii.

Genetics ◽  
1994 ◽  
Vol 137 (3) ◽  
pp. 743-750 ◽  
Author(s):  
L D Fletcher ◽  
J M McDowell ◽  
R R Tidwell ◽  
R B Meagher ◽  
C C Dykstra
Keyword(s):  
Phylogenetic Analysis ◽  
Essential Gene ◽  
Pneumocystis Carinii ◽  
Comparative Sequence Analysis ◽  
Cdna Clones ◽  
Actin Gene ◽  
Gene Encoding ◽  
Actin Protein ◽  
Relationship Of ◽  
High Degree

Abstract Actin is a major component of the cytoskeleton and one of the most abundant proteins found in eukaryotic cells. Comparative sequence analysis shows that this essential gene has been highly conserved throughout eukaryotic evolution making it useful for phylogenetic analysis. Complete cDNA clones for the actin-encoding gene were isolated and characterized from Pneumocystis carinii purified from immunosuppressed rat lungs. The nucleotide sequence encodes a protein of 376 amino acids. The predicted actin protein of P. carinii shares a high degree of conservation to other known actins. Only one major actin gene was found in P. carinii. The P. carinii actin sequence was compared with 30 other actin sequences. Gene phylogenies constructed using both neighbor-joining and protein parsimony methods places the P. carinii actin sequence closest to the majority of the fungi. Since the phylogenetic relationship of P. carinii to fungi and protists has been questioned, these data on the actin gene phylogeny support the grouping of P. carinii with the fungi.

scholarly journals Marinomonas mangrovi sp. nov., isolated from mangrove sediment

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1537-1541 ◽  
Author(s):  
De-Chao Zhang ◽  
Rosa Margesin
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Content Sharing ◽  
Link Type ◽  
Curved Rods ◽  
Sequence Similarities

A Gram-stain-negative, Na+-requiring bacterial strain, designated B20-1T, was isolated from soil of the root system of mangrove forest. Cells were curved rods and motile by means of a polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain B20-1T belonged to the genus Marinomonas , sharing highest sequence similarities with Marinomonas rhizomae IVIA-Po-145T (97.6 %), Marinomonas dokdonensis DSW10-10T (97.0 %) and Marinomonas foliarum IVIA-Po-155T (96.9 %). The predominant cellular fatty acids of strain B20-1T were C10 : 0 3-OH, C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. The predominant ubiquinone was Q-8. The genomic DNA G+C content of strain B20-1T was 46.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas mangrovi sp. nov., is proposed with B20-1T ( = DSM 28136T = LMG 28077T) as the type strain.

scholarly journals The use of MALDI-TOF MS as a rapid test to detect carbapenem resistance in Bacteroides fragilis

2019 ◽  
Vol 1 (7) ◽  
Author(s):  
Sarah Copsey-Mawer ◽  
Selina Scotford ◽  
Bethan Copsey-Mawer ◽  
Carol Davis ◽  
Michael Perry ◽  
...  
Keyword(s):  
Bacteroides Fragilis ◽  
Rapid Test ◽  
Carbapenem Resistance ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals Complete Nucleotide Sequence of pK245, a 98-Kilobase Plasmid Conferring Quinolone Resistance and Extended-Spectrum-β-Lactamase Activity in a Clinical Klebsiella pneumoniae Isolate

2006 ◽  
Vol 50 (11) ◽  
pp. 3861-3866 ◽  
Author(s):  
Ying-Tsong Chen ◽  
Hung-Yu Shu ◽  
Ling-Hui Li ◽  
Tsai-Lien Liao ◽  
Keh-Ming Wu ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Shigella Flexneri ◽  
Quinolone Resistance ◽  
Gene Encoding ◽  
Modification System ◽  
Resistance Determinants ◽  
Restriction Modification System ◽  
Extended Spectrum ◽  
Sequence Elements

ABSTRACT A plasmid containing the qnrS quinolone resistance determinant and the gene encoding the SHV-2 β-lactamase has been discovered from a clinical Klebsiella pneumoniae strain isolated in Taiwan. The complete 98-kb sequence of this plasmid, designated pK245, was determined by using a whole-genome shotgun approach. Transfer of pK245 conferred low-level resistance to fluoroquinolones in electroporant Escherichia coli epi300. The sequence of the immediate region surrounding qnrS in pK245 is nearly identical (>99% identity) to those of pAH0376 from Shigella flexneri and pINF5 from Salmonella enterica serovar Infantis, the two other qnrS-carrying plasmids reported to date, indicating a potential common origin. Other genes conferring resistance to aminoglycosides (aacC2, strA, and strB), chloramphenicol (catA2), sulfonamides (sul2), tetracycline (tetD), and trimethoprim (dfrA14) were also detected in pK245. The dfrA14 gene is carried on a class I integron. Several features of this plasmid, including three separate regions containing putative replicons, a partitioning-control system, and a type II restriction modification system, suggest that it may be able to replicate and adapt in a variety of hosts. Although no critical conjugative genes were detected, multiple insertion sequence elements were found scattered throughout pK245, and these may facilitate the dissemination of the antimicrobial resistance determinants. We conclude that pK245 is a chimera which acquired its multiple antimicrobial resistance determinants horizontally from different sources. The identification of pK245 plasmid expands the repertoire of the coexistence of quinolone and extended-spectrum-β-lactam resistance determinants in plasmids carried by various species of the family Enterobacteriaceae in different countries.

scholarly journals Sequencing, Cloning, and High-Level Expression of the pfp Gene, Encoding a PPi-Dependent Phosphofructokinase from the Extremely Thermophilic EubacteriumDictyoglomus thermophilum

2000 ◽  
Vol 182 (16) ◽  
pp. 4661-4666 ◽  
Author(s):  
Yan-Huai R. Ding ◽  
Ron S. Ronimus ◽  
Hugh W. Morgan
Keyword(s):  
Phylogenetic Analysis ◽  
Cloning And Expression ◽  
High Level Expression ◽  
Gene Encoding ◽  
Thermoproteus Tenax ◽  
High Level ◽  
High Degree ◽  
Dictyoglomus Thermophilum ◽  
Degree Of Similarity

ABSTRACT The sequencing, cloning, and expression of the pfp gene from Dictyoglomus thermophilum, which consists of 1,041 bp and encodes a pyrophosphate-dependent phosphofructokinase, are described. A phylogenetic analysis indicates that the enzyme is closely related to the pyrophosphate-dependent enzyme from Thermoproteus tenax. The recombinant and native enzymes share a high degree of similarity for most properties examined.

scholarly journals Phylogenetic Characterization of the Palyam Serogroup Orbiviruses

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 446 ◽  
Author(s):  
Karen Ebersohn ◽  
Peter Coetzee ◽  
Louwrens P. Snyman ◽  
Robert Swanepoel ◽  
Estelle H. Venter
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Full Genome Sequence ◽  
African Horse Sickness Virus ◽  
Gene Encoding ◽  
Phylogenetic Characterization ◽  
Next Generation Sequencing Ngs ◽  
High Degree

The Palyam serogroup orbiviruses are associated with abortion and teratogenesis in cattle and other ruminants. Of the 13 different serotypes that have been identified, the full genome sequence of only one, Kasba, has been published. We undertook to perform Next Generation Sequencing (NGS) and phylogenetic analysis on 12 Palyam serotypes plus field isolates of the African serotypes in our possession. The Palyam serogroup was found to be most closely related to the African horse sickness virus group and showed the most distant evolutionary relationship to the equine encephalosis viruses (EEV). Amino acid sequence analysis revealed that the gene encoding VP7 was the most conserved within serotypes and VP2 and VP5 showed the highest degree of variation. A high degree of sequence identity was found for isolates from the same geographical region. The phylogenetic analysis revealed two clades where the African serotypes were all very closely related in one clade and the other clade contained the Australian and Asian serotypes and one African serotype, Petevo. It was evident from the sequence data that the geographical origin of Palyam serogroup viruses played an important role in the development of the different serotypes.

scholarly journals Genetic analysis of antibiotic-resistance determinants in multidrug-resistant Shigella strains isolated from Chilean children

2004 ◽  
Vol 133 (1) ◽  
pp. 81-86 ◽  
Author(s):  
C. S. TORO ◽  
M. FARFÁN ◽  
I. CONTRERAS ◽  
O. FLORES ◽  
N. NAVARRO ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Rural Community ◽  
Tetracycline Resistance ◽  
Multidrug Resistant ◽  
Genetic Determinants ◽  
Gene Encoding ◽  
Ampicillin Resistance ◽  
Resistance Determinants ◽  
Gene Coding ◽  
Class 1

A total of 162 clinical isolates of Shigella collected from children in a semi-rural community of Chile were examined for the presence of genetic determinants of resistance to ampicillin, chloramphenicol, tetracycline, and trimethoprim. Ampicillin resistance was most frequently associated with the presence of blaOXA in S. flexneri and with blaTEM in S. sonnei. The blaOXA gene but not blaTEM was located in class 1 integrons. The dhfrIa gene encoding for resistance to trimethoprim was associated to class 2 integrons and detected exclusively in S. flexneri, whereas dhfrIIIc was found in all S. sonnei strains and in 10% of the S. flexneri isolates. Cat, coding for choramphenicol resistance, and blaOXA genes were located in the chromosome in all cases, whereas tetA gene, coding for tetracycline resistance, and blaTEM, dhfrIa and dhfrIIIc genes were found either in the chromosome or in conjugative plasmids. Our results show a heterogenous distribution of antibiotic-resistance determinants between S. flexneri and S. sonnei.

A phylogenetic analysis based on the gene encoding phosphoglycerate kinase

1992 ◽  
Vol 34 (5) ◽  
pp. 383-395 ◽  
Author(s):  
Geeta B. Vohra ◽  
G. Brian Golding ◽  
Nora Tsao ◽  
Ronald E. Pearlman
Keyword(s):  
Phylogenetic Analysis ◽  
Phosphoglycerate Kinase ◽  
Gene Encoding
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