scholarly journals Occurrence of Putative Pathogenicity Islands in Enterococci from Distinct Species and of Differing Origins

2009 ◽  
Vol 75 (22) ◽  
pp. 7271-7274 ◽  
Author(s):  
Teresa Semedo-Lemsaddek ◽  
Maria Teresa Barreto-Crespo ◽  
Rog�rio Tenreiro
Keyword(s):  
Enterococcus Faecalis ◽  
Pcr Amplification ◽  
Pathogenicity Island ◽  
Distinct Species ◽  
Clinical Isolates ◽  
Pathogenicity Islands ◽  
Culture Collections ◽  
Ewe's Milk ◽  
Reference Strains

ABSTRACT Enterococci isolated from ewe's milk and cheese, clinical isolates of human and veterinary origins, and reference strains obtained from culture collections were screened for the occurrence of putative pathogenicity island (PAIs). Results obtained after PCR amplification and hybridization point toward PAI dissemination among enterococci of diverse origins (food/clinical) and species (Enterococcus faecalis/non-E. faecalis).

scholarly journals Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae

2004 ◽  
Vol 54 (5) ◽  
pp. 1543-1551 ◽  
Author(s):  
C. Y. Turenne ◽  
V. J. Cook ◽  
T. V. Burdz ◽  
R. J. Pauls ◽  
L. Thibert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Great Part ◽  
16S Rrna Gene Sequencing ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Culture Collections ◽  
Clinical Specimens ◽  
Mycobacterium Simiae ◽  
Reference Strains

A group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (=ATCC BAA-614T=DSM 44648T).

scholarly journals Evaluation of Two Commercial Kits and Arbitrarily Primed PCR for Identification and Differentiation ofActinobacillus actinomycetemcomitans,Haemophilus aphrophilus, and Haemophilus paraphrophilus

1999 ◽  
Vol 37 (3) ◽  
pp. 742-747 ◽  
Author(s):  
Başak Doğan ◽  
Sirkka Asikainen ◽  
Hannele Jousimies-Somer
Keyword(s):  
Pcr Amplification ◽  
Clinical Isolates ◽  
Species Differentiation ◽  
Oral Microbiota ◽  
Closely Related Species ◽  
Haemophilus Aphrophilus ◽  
Consistent Performance ◽  
Commercial Kits ◽  
Arbitrarily Primed Pcr ◽  
Reference Strains

The closely related species Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, andHaemophilus paraphrophilus are common findings in oral microbiota. The aims of this study were to evaluate the applicability of the Rapid NH and API ZYM kits and arbitrarily primed PCR (AP-PCR) in the identification and differentiation of the three species from each other. The material included 62 clinical isolates and three reference strains of A. actinomycetemcomitans representing the 5 serotypes and 18 AP-PCR genotypes. Haemophilus species included 12 clinical isolates and 11 reference strains of H. aphrophilus, H. paraphrophilus, and 5 other species. For the PCR amplification, the oligonucleotide 5′-CAGCACCCAC-3′ was used as a primer. Contrary to the consistent performance of API ZYM, the Rapid NH system was able to identify only 10 of 65 (15%) A. actinomycetemcomitans isolates, whereas allHaemophilus species were correctly identified. The API ZYM test differentiated A. actinomycetemcomitans from H. aphrophilus and H. paraphrophilus by negative β-galactosidase and α-glucosidase reactions and a positive esterase lipase reaction. However, the API ZYM test was unable to differentiateH. aphrophilus from H. paraphrophilus, it also could not differentiate A. actinomycetemcomitans serotypes from each other. Among the H. aphrophilus isolates three AP-PCR genotypes and among H. paraphrophilus isolates only one AP-PCR genotype, distinct from those of A. actinomycetemcomitans, were found. The Rapid NH test showed poor ability to identify clinical isolates of all A. actinomycetemcomitans serotypes. Moreover, AP-PCR genotyping proved to be a rapid method for the species differentiation of A. actinomycetemcomitans, H. aphrophilus, and H. paraphrophilus.

scholarly journals Intestinal Spirochaetes of the Genus Brachyspira Share a Partially Conserved 26 Kilobase Genomic Region with Enterococcus faecalis and Escherichia coli

2008 ◽  
Vol 1 ◽  
pp. MBI.S762 ◽  
Author(s):  
Yair Motro ◽  
David S. Dunn ◽  
Tom La ◽  
Nyree D. Phillips ◽  
David J. Hampson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Enterococcus Faecalis ◽  
Repeat Unit ◽  
Bacterial Species ◽  
Pcr Amplification ◽  
Genomic Analysis ◽  
Distinct Species ◽  
Genomic Region ◽  
Sequence Conservation ◽  
Comparative Genomic

Anaerobic intestinal spirochaetes of the genus Brachyspira include both pathogenic and commensal species. The two best-studied members are the pathogenic species B. hyodysenteriae (the aetiological agent of swine dysentery) and B. pilosicoli (a cause of intestinal spirochaetosis in humans and other species). Analysis of near-complete genome sequences of these two species identified a highly conserved 26 kilobase (kb) region that was shared, against a background of otherwise very little sequence conservation between the two species. PCR amplification was used to identify sets of contiguous genes from this region in the related Brachyspira species B. intermedia, B. innocens, B. murdochii, B. alvinipulli, and B. aalborgi, and demonstrated the presence of at least part of this region in species from throughout the genus. Comparative genomic analysis with other sequenced bacterial species revealed that none of the completely sequenced spirochaete species from different genera contained this conserved cluster of coding sequences. In contrast, Enterococcus faecalis and Escherichia coli contained high gene cluster conservation across the 26 kb region, against an expected background of little sequence conservation between these phylogenetically distinct species. The conserved region in B. hyodysenteriae contained five genes predicted to be associated with amino acid transport and metabolism, four with energy production and conversion, two with nucleotide transport and metabolism, one with ion transport and metabolism, and four with poorly characterised or uncertain function, including an ankyrin repeat unit at the 5’ end. The most likely explanation for the presence of this 26 kb region in the Brachyspira species and in two unrelated enteric bacterial species is that the region has been involved in horizontal gene transfer.

scholarly journals Distribution of pathogenicity islands among Colombian isolates of Salmonella

2010 ◽  
Vol 4 (09) ◽  
pp. 555-559 ◽  
Author(s):  
Miryan Margot Sánchez-Jiménez ◽  
Nora María Cardona-Castro ◽  
Nunzia Canu ◽  
Sergio Uzzau ◽  
Salvatore Rubino
Keyword(s):  
Systemic Infection ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Pathogenicity Islands ◽  
Gastrointestinal Infection ◽  
Heterogeneous Distribution ◽  
Geographical Regions ◽  
Stool Samples ◽  
Salmonella Pathogenicity Islands ◽  
Reference Strains

Introduction: Salmonella pathogenicity islands (SPIs) are regions scattered along the bacterial chromosome, with an acknowledged pivotal role during gastrointestinal and systemic infection. The distribution of SPIs has been investigated in reference strains. However, there is a lack of studies on their presence and/or assortment within the genomes of Salmonella enterica (S. enterica) serovars that circulate in different geographical regions. Therefore, in this study, we aimed to determine the presence of genes of the pathogenicity islands 1 to 5 (SPI-1 to 5), in Salmonella clinical isolates from Colombian patients with systemic and enteric outcomes. Methodology: A total of 125 strains of S. enterica belonging to different serovars were isolated from various clinical samples. Strains were identified and screened for the presence of various genes located in pathogenicity islands. The genes tested were selected according to the attributed pathogenic function and detected by PCR for the SPI-1 hilA and invA; for SPI-2 spiC and ttrC; for SPI-3 misL and mgtC; for SPI-4 orfL and SPI-4R; and for SPI-5 pipD and sopB. Results: Salmonella pathogenicity islands 1 to 5 were detected in isolates from patients with systemic and gastrointestinal infection. All the systemic isolates possessed all the genes tested; in contrast, 16 isolates from stool samples lacked one or more sequences encoded by the SPI-3 and SPI-4 (p < 0.000001). Conclusions: These results describe the heterogeneous distribution of SPIs-encoded sequences within the genomes of Colombian clinical isolates, and reveal important differences among systemic and stool sample isolates.

Azole resistance among clinical isolates of Aspergillus fumigatus in Lima-Peru

2019 ◽  
Vol 58 (1) ◽  
pp. 54-60 ◽  
Author(s):  
Beatriz Bustamante ◽  
Luis Ricardo Illescas ◽  
Andrés Posadas ◽  
Pablo E Campos
Keyword(s):  
Aspergillus Fumigatus ◽  
Latin American ◽  
Pcr Amplification ◽  
Sensu Stricto ◽  
Clinical Isolates ◽  
Azole Resistance ◽  
Molecular Testing ◽  
Naive Patient ◽  
In Vitro Susceptibility

Abstract Azole resistance among Aspergillus fumigatus isolates, which is mainly related to mutations in the cyp51A gene, is a concern because it is rising, worldwide disseminated, and associated with treatment failure and death. Data on azole resistance of aspergillus from Latin American countries is very scarce and do not exist for Peru. Two hundred and seven Aspergillus clinical isolates collected prospectively underwent mycology and molecular testing for specie identification, and 143 isolates were confirmed as A. fumigatus sensu stricto (AFSS). All AFSS were tested for in vitro azole susceptibility, and resistant isolates underwent PCR amplification and sequencing of the whole cyp51A gene and its promoter. The in vitro susceptibility showed a minimal inhibitory concentration (MIC) range, MIC50 and MIC90 of 0.125 to &gt;16, 0.25, and 0.5 μg/ml for itraconazole; 0.25 to 2, 0.5, and 0.5 μg/ml for voriconazole; and 0.003 to 1, 0.06, and 0.125 μg/ml for posaconazole. Three isolates (2%) showed resistance to itraconazole and exhibited different mutations of the cyp51A gene. One isolate harbored the mutation M220K, while a second one exhibited the G54 mutation plus a modification in the cyp51A gene promoter. The third isolate, from an azole naive patient, presented an integration of a 34-bp tandem repeat (TR34) in the promoter region of the gene and a substitution of leucine 98 by histidine (L98H). The three source patients had a diagnosis or suspicion of chronic pulmonary aspergillosis.

scholarly journals Structures, Locations, and Transfer Frequencies of Genetic Elements Conferring High-Level Gentamicin Resistance in Enterococcus faecalis Isolates in Greece

2003 ◽  
Vol 47 (12) ◽  
pp. 3950-3953 ◽  
Author(s):  
George L. Daikos ◽  
George Bamias ◽  
Christos Kattamis ◽  
Marcus J. Zervos ◽  
Joseph W. Chow ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Restriction Enzyme ◽  
Plasmid Dna ◽  
Strong Association ◽  
Hybridization Analysis ◽  
Clinical Isolates ◽  
Genetic Elements ◽  
Transfer Characteristics ◽  
Gentamicin Resistance ◽  
High Level

ABSTRACT The elements conferring high-level gentamicin resistance in 64 clinical isolates of Enterococcus faecalis were characterized by PCR and by restriction enzyme hybridization analysis of genomic and plasmid DNA. There was a strong association between gentamicin resistance and the aac(6′)-aph(2") gene carried on IS256-based elements with different structures, locations, and transfer characteristics.

Phylogenetic Diversity and Mycotoxin Potential of Emergent Phytopathogens within the Fusarium tricinctum Species Complex

2022 ◽  
Author(s):  
Imane Laraba ◽  
Mark Busman ◽  
David M. Geiser ◽  
Kerry O'Donnell
Keyword(s):  
Species Complex ◽  
Phylogenetic Diversity ◽  
Agricultural Research ◽  
Distinct Species ◽  
Culture Collections ◽  
Strain Collection ◽  
Food And Feed ◽  
Feed Safety ◽  
Large Survey ◽  
Fusarium Tricinctum

Recent studies on multiple continents indicate members of the Fusarium tricinctum species complex (FTSC) are emerging as prevalent pathogens of small-grain cereals, pulses, and other economically important crops. These understudied fusaria produce structurally diverse mycotoxins, among which enniatins (ENNs) and moniliformin (MON) are the most frequent and of greatest concern to food and feed safety. Herein a large survey of fusaria in the Fusarium Research Center and Agricultural Research Service culture collections was undertaken to assess species diversity and mycotoxin potential within the FTSC. A 151-strain collection originating from diverse hosts and substrates from different agroclimatic regions throughout the world was selected from 460 FTSC strains to represent the breadth of FTSC phylogenetic diversity. Evolutionary relationships inferred from a 5-locus dataset, using maximum likelihood and parsimony, resolved the 151 strains as 24 phylogenetically distinct species, including nine that are new to science. Of the five genes analyzed, nearly full-length phosphate permease sequences contained the most phylogenetically informative characters, establishing its suitability for species-level phylogenetics within the FTSC. Fifteen of the species produced ENNs, MON, the sphingosine analog 2-amino-14,16- dimethyloctadecan-3-ol (AOD), and the toxic pigment aurofusarin (AUR) on a cracked corn kernel substrate. Interestingly, the five earliest diverging species in the FTSC phylogeny (i.e., F. iranicum, F. flocciferum, F. torulosum, Fusarium spp. FTSC 8 and 24) failed to produce AOD and MON, but synthesized ENNs and/or AUR. Moreover, our reassessment of nine published phylogenetic studies on the FTSC identified 11 additional novel taxa, suggesting this complex comprises at least 36 species.

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