scholarly journals The Novel CTX-M-116 β-Lactamase Gene Discovered in Proteus mirabilis Is Composed of Parts of the CTX-M-22 and CTX-M-23 Genes

2013 ◽  
Vol 57 (3) ◽  
pp. 1552-1555 ◽  
Author(s):  
N. Fursova ◽  
S. Pryamchuk ◽  
A. Kruglov ◽  
I. Abaev ◽  
E. Pecherskikh ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Retrospective Analysis ◽  
Dna Sequence ◽  
Proteus Mirabilis ◽  
Hybrid Structure ◽  
The Novel ◽  
Hybrid Gene ◽  
Content Type ◽  
Putative Site ◽  
Lactamase Gene

ABSTRACTThe novel β-lactamase geneblaCTX-M-116was identified in aProteus mirabilisnosocomial isolate recovered from the urine of a patient in Moscow in 2005. DNA sequence analysis showedblaCTX-M-116to be a hybrid gene consisting of 5′blaCTX-M-23(nucleotides 1 to 278) and 3′blaCTX-M-22(nucleotides 286 to 876) moieties separated by an intervening putative site of recombination (GTTAAAT). A retrospective analysis of availableblaCTX-Mgenes in the GenBank database revealed 19blaCTX-Mgenes that display the same hybrid structure.

scholarly journals Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African Great Lakes region

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 23-29 ◽  
Author(s):  
Dominique Gueule ◽  
Gérard Fourny ◽  
Elisabeth Ageron ◽  
Anne Le Flèche-Matéos ◽  
Mathias Vandenbogaert ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Gene Sequencing ◽  
Great Lakes Region ◽  
The Novel ◽  
Content Type ◽  
African Great Lakes ◽  
Link Type

Six isolates recovered from coffee seeds giving off a potato-like flavour were studied. Gene sequencing (rrs and rpoB) showed they belong to the genus Pantoea . By DNA–DNA hybridization, the isolates constituted a genomic species with less than 17 % relatedness to 96 strains representing enterobacterial species. Multilocus sequence analysis (gyrB, rpoB, atpD and infB genes) showed the isolates to represent a discrete species of the genus Pantoea . Nutritional versatility of the novel species was poor. The novel species is proposed as Pantoea coffeiphila sp.nov. and its type strain is Ca04T ( = CIP 110718T = DSM 28482T).

scholarly journals Characterization of a Novel SXT/R391 Integrative and Conjugative Element Carrying cfr, blaCTX-M-65, fosA3, and aac(6′)-Ib-cr in Proteus mirabilis

2018 ◽  
Vol 62 (9) ◽  
Author(s):  
Chang-Wei Lei ◽  
Yan-Peng Chen ◽  
Zhuang-Zhuang Kang ◽  
Ling-Han Kong ◽  
Hong-Ning Wang
Keyword(s):  
Resistance Gene ◽  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Hot Spot ◽  
Fluoroquinolone Resistance ◽  
Content Type ◽  
Antimicrobial Resistance Genes ◽  
Methyltransferase Gene ◽  
Lactamase Gene ◽  
Integrative And Conjugative Element

ABSTRACT A novel 139,487-bp SXT/R391 integrative and conjugative element, ICEPmiChnBCP11, was characterized in Proteus mirabilis of swine origin in China. ICEPmiChnBCP11 harbors 20 different antimicrobial resistance genes, including the clinically important rRNA methyltransferase gene cfr, the extended-spectrum β-lactamase gene blaCTX-M-65, fosfomycin resistance gene fosA3, and fluoroquinolone resistance gene aac(6′)-Ib-cr. An ISPpu12-mediated composite transposon containing various resistance genes and 10 copies of IS26 is inserted in hot spot 4. ICEPmiChnBCP11 was successfully transferred to Escherichia coli.

scholarly journals Proposal to rename Carnobacterium inhibens as Carnobacterium inhibens subsp. inhibens subsp. nov. and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a psychrotolerant bacterium isolated from Siberian permafrost

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 556-561 ◽  
Author(s):  
Wayne L. Nicholson ◽  
Kateryna Zhalnina ◽  
Rafael R. de Oliveira ◽  
Eric W. Triplett
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Fatty Acid Content ◽  
Optimal Growth ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Positive Staining ◽  
The Novel ◽  
Content Type ◽  
Link Type

A novel, psychrotolerant facultative anaerobe, strain WN1359T, was isolated from a permafrost borehole sample collected at the right bank of the Kolyma River in Siberia, Russia. Gram-positive-staining, non-motile, rod-shaped cells were observed with sizes of 1–2 µm long and 0.4–0.5 µm wide. Growth occurred in the range of pH 5.8–9.0 with optimal growth at pH 7.8–8.6 (pH optimum 8.2). The novel isolate grew at temperatures from 0–37 °C and optimal growth occurred at 25 °C. The novel isolate does not require NaCl; growth was observed between 0 and 8.8 % (1.5 M) NaCl with optimal growth at 0.5 % (w/v) NaCl. The isolate was a catalase-negative, facultatively anaerobic chemo-organoheterotroph that used sugars but not several single amino acids or dipeptides as substrates. The major metabolic end-product was lactic acid in the ratio of 86 % l-lactate : 14 % d-lactate. Strain WN1359T was sensitive to ampicillin, chloramphenicol, fusidic acid, lincomycin, monocycline, rifampicin, rifamycin SV, spectinomycin, streptomycin, troleandomycin and vancomycin, and resistant to nalidixic acid and aztreonam. The fatty acid content was predominantly unsaturated (70.2 %), branched-chain unsaturated (11.7 %) and saturated (12.5 %). The DNA G+C content was 35.3 mol% by whole genome sequence analysis. 16S rRNA gene sequence analysis showed 98.7 % sequence identity between strain WN1359T and Carnobacterium inhibens . Genome relatedness was computed using both Genome-to-Genome Distance Analysis (GGDA) and Average Nucleotide Identity (ANI), which both strongly supported strain WN1359T belonging to the species C. inhibens . On the basis of these results, the permafrost isolate WN1359T represents a novel subspecies of C. inhibens , for which the name Carnobacterium inhibens subsp. gilichinskyi subsp. nov. is proposed. The type strain is WN1359T ( = ATCC BAA-2557T = DSM 27470T). The subspecies Carnobacterium inhibens subsp. inhibens subsp. nov. is created automatically. An emended description of C. inhibens is also provided.

scholarly journals OXA-207, a Novel OXA-24 Variant with Reduced Catalytic Efficiency against Carbapenems in Acinetobacter pittii from Spain

2014 ◽  
Vol 58 (8) ◽  
pp. 4944-4948 ◽  
Author(s):  
Rodrigo Cayô ◽  
María Merino ◽  
Belén Ruiz del Castillo ◽  
María Eliecer Cano ◽  
Jorge Calvo ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Binding Sites ◽  
Catalytic Efficiency ◽  
The Novel ◽  
Northern Spain ◽  
Site Specific ◽  
Content Type ◽  
Noticeable Increase ◽  
Carbapenem Resistant ◽  
Acinetobacter Pittii

ABSTRACTA carbapenem-resistantAcinetobacter pittiistrain carrying an OXA-24-like enzyme was isolated in northern Spain in 2008. Sequence analysis confirmed the presence of the novelblaOXA-207gene flanked by the site-specific XerC/XerD-like recombination binding sites and showing a unique Gly222Val substitution compared to OXA-24. Cloning and kinetic analysis showed that OXA-207 presents a reduction in the catalytic efficiency against carbapenems and a noticeable increase for oxacillin.

scholarly journals Analysis ofblaCTX-M-Carrying Plasmids from Escherichia coli Isolates Collected in the BfT-GermVet Study

2011 ◽  
Vol 77 (20) ◽  
pp. 7142-7146 ◽  
Author(s):  
Anne-Kathrin Schink ◽  
Kristina Kadlec ◽  
Stefan Schwarz
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Multilocus Sequence Typing ◽  
Farm Animals ◽  
Insertion Sequences ◽  
The Novel ◽  
Content Type ◽  
E Coli ◽  
Structural Differences ◽  
Mlst Type

ABSTRACTIn this study, 417Escherichia coliisolates from defined disease conditions of companion and farm animals collected in the BfT-GermVet study were investigated for the presence of extended-spectrum β-lactamase (ESBL) genes. Three ESBL-producingE. coliisolates were identified among the 100 ampicillin-resistant isolates. TheE. coliisolates 168 and 246, of canine and porcine origins, respectively, harboredblaCTX-M-1, and the canine isolate 913 harboredblaCTX-M-15, as confirmed by PCR and sequence analysis. The isolates 168 and 246 belonged to the novel multilocus sequence typing (MLST) types ST1576 and ST1153, respectively, while isolate 913 had the MLST type ST410. The ESBL genes were located on structurally related IncN plasmids in isolates 168 and 246 and on an IncF plasmid in isolate 913. TheblaCTX-M-1upstream regions of plasmids pCTX168 and pCTX246 were similar, whereas the downstream regions showed structural differences. The genetic environment of theblaCTX-M-15gene on plasmid pCTX913 differed distinctly from that of bothblaCTX-M-1genes. Detailed sequence analysis showed that the integration of insertion sequences, as well as interplasmid recombination events, accounted for the structural variability in theblaCTX-Mgene regions.

scholarly journals Culture-Based and Culture-Independent Bacteriologic Analysis of Cystic Fibrosis Respiratory Specimens

2015 ◽  
Vol 54 (3) ◽  
pp. 613-619 ◽  
Author(s):  
Mona A. Mahboubi ◽  
Lisa A. Carmody ◽  
Bridget K. Foster ◽  
Linda M. Kalikin ◽  
Donald R. VanDevanter ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Sequence Analysis ◽  
Dna Sequence ◽  
Bacterial Species ◽  
Bacterial Load ◽  
Considerable Proportion ◽  
Content Type ◽  
Culture Independent ◽  
Respiratory Specimens

Cystic fibrosis (CF) is characterized by chronic infection and inflammation of the airways.In vitroculture of select bacterial species from respiratory specimens has been used to guide antimicrobial therapy in CF for the past few decades. More recently, DNA sequence-based, culture-independent approaches have been used to assess CF airway microbiology, although the role that these methods will (or should) have in routine microbiologic analysis of CF respiratory specimens is unclear. We performed DNA sequence analyses to detect bacterial species in 945 CF sputum samples that had been previously analyzed by selective CF culture. We determined the concordance of results based on culture and sequence analysis, highlighting the comparison of the results for the most prevalent genera. Although overall prevalence rates were comparable between the two methods, results varied by genus. While sequence analysis was more likely to detectAchromobacter,Stenotrophomonas, andBurkholderia, it was less likely to detectStaphylococcus.Streptococcusspp. were rarely reported in culture results but were the most frequently detected species by sequence analysis. A variety of obligate and facultative anaerobic species, not reported by culture, was also detected with high prevalence by sequence analysis. Sequence analysis indicated that in a considerable proportion of samples, taxa not reported by selective culture constituted a relatively high proportion of the total bacterial load, suggesting that routine CF culture may underrepresent significant segments of the bacterial communities inhabiting CF airways.

scholarly journals IMP-27, a Unique Metallo-β-Lactamase Identified in Geographically Distinct Isolates of Proteus mirabilis

2016 ◽  
Vol 60 (10) ◽  
pp. 6418-6421 ◽  
Author(s):  
Nyssa Dixon ◽  
Randal C. Fowler ◽  
A. Yoshizumi ◽  
Tsukasa Horiyama ◽  
Y. Ishii ◽  
...  
Keyword(s):  
United States ◽  
Antimicrobial Susceptibility ◽  
Proteus Mirabilis ◽  
Susceptibility Testing ◽  
Gene Cassette ◽  
The United States ◽  
Antimicrobial Susceptibility Testing ◽  
Content Type ◽  
Lactamase Gene

ABSTRACTA novel metallo-β-lactamase gene,blaIMP-27, was identified in unrelatedProteus mirabilisisolates from two geographically distinct locations in the United States. Both isolates harborblaIMP-27as part of the first gene cassette in a class 2 integron. Antimicrobial susceptibility testing indicated susceptibility to aztreonam, piperacillin-tazobactam, and ceftazidime but resistance to ertapenem. However, hydrolysis assays indicated that ceftazidime was a substrate for IMP-27.

scholarly journals Pseudomonas baetica sp. nov., a fish pathogen isolated from wedge sole, Dicologlossa cuneata (Moreau)

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 874-882 ◽  
Author(s):  
Jose R. López ◽  
Ana L. Diéguez ◽  
Alejandra Doce ◽  
Elena De la Roca ◽  
Roberto De la Herran ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Related Species ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Sequence Similarities

Five Gram-negative bacterial isolates, recovered from an outbreak that occurred in March 2006 in Huelva, Spain, affecting adult diseased cultured wedge sole [Dicologlossa cuneata (Moreau)], were characterized phenotypically and genotypically in order to clarify their taxonomic position. On the basis of 16S rRNA gene sequence analysis, the isolates were included in the genus Pseudomonas , within the Pseudomonas fluorescens -related species group, their closest relatives being the Pseudomonas jessenii and Pseudomonas koreensis subgroups. The highest sequence similarities were recorded with the type strains of Pseudomonas reinekei , P. moorei , P. umsongensis , P. jessenii and P. mohnii (99.4–99.3 % similarity). Sequence analysis of the housekeeping genes gyrB and rpoD clearly differentiated the isolates from currently described Pseudomonas species, the highest sequence similarities recorded to type strains being below 95 % for both genes. Phylogenetic analysis using concatenated sequences of the three genes showed Pseudomonas moraviensis DSM 16007T and P. koreensis DSM 16610T as the closest reference strains. DNA–DNA hybridization assays with related strains confirmed that these isolates belong to a novel species of the genus Pseudomonas , for which the name Pseudomonas baetica sp. nov. is proposed. The type strain is strain a390T ( = CECT 7720T  = LMG 25716T). The novel species could be easily distinguished from phylogenetically related species by several phenotypic characteristics, including gelatin hydrolysis, acid production from glucose and growth at 6 % NaCl. Virulence assays revealed that the novel species is pathogenic for wedge sole.

scholarly journals Sphingobacterium detergens sp. nov., a surfactant-producing bacterium isolated from soil

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3036-3041 ◽  
Author(s):  
Ana M. Marqués ◽  
César Burgos-Díaz ◽  
Francisco José Aranda ◽  
José Antonio Teruel ◽  
Àngels Manresa ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Genotypic Characteristics ◽  
Sequence Similarities

A novel Gram-negative-staining strain, designated 6.2ST, was isolated from a soil sample and identified as a biosurfactant producer. Its taxonomic position was investigated using a polyphasic approach. The cells were non-motile, non-spore-forming rods. The organism grew optimally at 30-37 °C, with 0–3 % (w/v) NaCl, and at pH 7.0. Based on 16S rRNA gene sequence analysis, strain 6.2ST was found to be a member of the genus Sphingobacterium and was most closely related to four type species of the genus, showing sequence similarities of 96.8–98.9 %. Partial chaperonin 60 (cpn60) gene sequence analysis was useful in resolving the phylogenetic relationships between strain 6.2ST and closely related taxa, with similarities ranging from 85.5 % (with Sphingobacterium thalpophilum DSM 11723T) to 90.3 % (with Sphingobacterium canadense CR11T and Sphingobacterium multivorum JCM 21156T). The results of DNA–DNA hybridization experiments between the novel strain and its closest relatives gave a DNA–DNA relatedness value of less than 70 %, and consequently confirmed that this new strain did not belong to a previously described species of the genus Sphingobacterium . The major fatty acids were summed feature 3 (iso-C15 : 0 2 OH and/or C16 : 1ω7c); iso-C15 : 0; iso-C17 : 0 3-OH and C16 : 0. The G+C content of the genomic DNA was 40.0 mol%. According to its phenotypic and genotypic characteristics and the phylogenetic data, strain 6.2ST represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium detergens sp. nov. is proposed. The type strain is 6.2ST ( = CECT 7938T = LMG 26465T).

scholarly journals Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3950-3957 ◽  
Author(s):  
Jerri E. Zilli ◽  
Alexandre C. Baraúna ◽  
Krisle da Silva ◽  
Sofie E. De Meyer ◽  
Eliane N. C. Farias ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
23S Rrna ◽  
Physiological Data ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Link Type

Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247T, BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6 %) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S–23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05T ( = LMG 24129T) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium . Results of DNA–DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium . Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus Bradyrhizobium . Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247T ( = HAMBI 3599T).

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