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.

scholarly journals Molecular Investigation of hemolytic phospholipase C Encoding Genes in Clinical Isolates of Pseudomonas aeruginosa

2018 ◽  
Vol 9 (SPL1) ◽  
Author(s):  
Rasha Hadi Saleh ◽  
Habeeb S Naher ◽  
Mohammed AK Al-saadi
Keyword(s):  
Phospholipase C ◽  
Virulence Genes ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Burn Wound ◽  
Molecular Investigation ◽  
Genes Encoding ◽  
Stool Samples ◽  
Polymerase Chain ◽  
Encoding Genes

This study is aimed to isolate P.aeruginosa from different clinical cases and to detect the prevalence of virulence genes encoding hemolytic phospholipase C(plcH)in these clinical isolates. In this study a total of 422 clinical samples including burn,wound,ear,urine,abscess and stool were aseptically taken from out- and inpatients who admitted into two hospitals in Hilla City (Teaching Al-Hilla Hospital and Babylon Hospital for Maternity and children during a period of three months. All samples were subjected to bacterial cultivation for the isolation of P.aeruginosa. The isolated P.aeruginosa was diagnosed depended on morphological,biochemical and molecular standard characteristics. Hemolytic phospholipase Cencoding genes(plcH) were detected by PCR and the amplification products were separated in 1% agarose gels containing ethidium bromide. Out of 422 samples,P.aeruginosa was isolated from 54 samples (12.8%). The distribution of these isolates were: 22 (55%) from burn samples,2; (50%) from diabitics foot samples,8 (14.8%) from wound samples, 8 (32%) from ear samples,3 (11%) from abscess samples, 7 (4%) from stool samples,4 (4%) from urine samples and 0 sputum samples. The genotypic properties of hemolytic phospholipase C (plcH )toxins was detected by polymerase chain reaction (PCR). The results of this study revealed that(plcH )gene found in 13/20 (65%)of isolates.

scholarly journals An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

2019 ◽  
Author(s):  
Mohireh Taei ◽  
Mostafa Chadeganipour ◽  
Rasoul Mohammadi
Keyword(s):  
Candida Species ◽  
Systemic Infection ◽  
Molecular Techniques ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Molecular Tests ◽  
Yeast Strains ◽  
Etiologic Agents ◽  
Pcr Multiplex ◽  
Pcr Rflp

Abstract Objective: Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. Results: A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR-RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non-albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non-Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.

scholarly journals Antibiotic susceptibility and genetic relatedness of Shigella species isolated from food and human stool samples in Qazvin, Iran

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Babak Pakbin ◽  
Abdollah Didban ◽  
Yousef Khazaye Monfared ◽  
Razzagh Mahmoudi ◽  
Amir Peymani ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Cross Sectional Study ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Sectional Study ◽  
Cross Sectional ◽  
Shigella Species ◽  
Rapd Pcr ◽  
Stool Samples ◽  
Human Stool

Abstract Objective The aim of this study was to investigate the genetic relatedness and antimicrobial resistance among Shigella species isolated from food and stool samples. Using cross sectional study method, Shigella spp. were isolated from food and clinical samples using culture-based, biochemical and serological methods. Antimicrobial susceptibility and genetic relatedness among the isolates were evaluated using disk diffusion and RAPD-PCR methods respectively. Results The prevalence of Shigella spp. were 4.84 and 7.7% in food and stool samples respectively. All food isolates were Sh. sonnei. 91.42% of the Shigella stool isolates were Sh. sonnei. 62.5% of food isolates were resistant to tetracycline. 46.8, 50 and 65.8% of clinical isolates were resistant to imipenem, amikacin and azithromycin respectively. 50 and 85.7% of the food and clinical isolates respectively were MDR. Dendrogram generated by RAPD-PCR showed that the isolates from food and stool samples were categorized in a same group. Close genetic relatedness between MDR Shigella isolates from food and clinical samples indicate that foods can be considered as one of the main vehicles for transmission of MDR Shigella to human causing acute diseases. Survey of MDR Shigella among food and clinical samples is strongly suggested to be implemented.

scholarly journals An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Monireh Taei ◽  
Mostafa Chadeganipour ◽  
Rasoul Mohammadi
Keyword(s):  
Systemic Infection ◽  
Molecular Techniques ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Molecular Tests ◽  
Yeast Strains ◽  
Etiologic Agents ◽  
Pcr Multiplex ◽  
Pcr Rflp ◽  
First Time

Abstract Objective Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. Results A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR–RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non-albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non-Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.

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 An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

2019 ◽  
Author(s):  
Mohireh Taei ◽  
Mostafa Chadeganipour ◽  
Rasoul Mohammadi
Keyword(s):  
Candida Species ◽  
Systemic Infection ◽  
Molecular Techniques ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Molecular Tests ◽  
Yeast Strains ◽  
Etiologic Agents ◽  
Pcr Multiplex ◽  
Pcr Rflp

Abstract Objective: Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. Results: A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR-RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non- albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non- Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.

scholarly journals An alarming rise of non-albicans Candida species and uncommon yeasts in the clinical samples; a combination of various molecular techniques for identification of etiologic agents

2019 ◽  
Author(s):  
Mohireh Taei ◽  
Mostafa Chadeganipour ◽  
Rasoul Mohammadi
Keyword(s):  
Candida Species ◽  
Systemic Infection ◽  
Molecular Techniques ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Molecular Tests ◽  
Yeast Strains ◽  
Etiologic Agents ◽  
Pcr Multiplex ◽  
Pcr Rflp

Abstract Objective: Yeasts are unicellular microorganisms may cause systemic infection in immunocompromised patients. The aim of this study was to identify yeast strains isolated from clinical specimens using molecular techniques. Results: A total of 202 yeast strains isolated from 341 clinical samples between February 2017 and May 2019. All clinical isolates were identified using phenotypic and molecular tests including PCR-RFLP, duplex-PCR, multiplex-PCR, and PCR-sequencing. The most yeast fungal isolates were obtained from urine (66.8%), nail (9.4%), skin lesion (7.9%), bronchoalveolar lavage (5.9%), and blood (3.9%). One hundred and twenty-one Candida species were identified as non- albicans versus 76 Candida albicans. Trichosporon asahii, and Pichia terricola were uncommon non- Candida yeasts isolated from urine samples. For the first time, we isolated P. terricola as etiological agent of urinary tract infection in a pregnant female. Since Candida species show different levels of resistance to antifungal agents, precise identification of clinical isolates is critical for better treatment of infection.

scholarly journals Emergence of clinical isolates of Pseudomonas asiatica and Pseudomonas monteilii from Japan harbouring an acquired gene encoding a carbapenemase VIM-2

2020 ◽  
Author(s):  
Mari Tohya ◽  
Kohei Uechi ◽  
Tatsuya Tada ◽  
Tomomi Hishinuma ◽  
Takeshi Kinjo ◽  
...  
Keyword(s):  
Type Species ◽  
Clinical Isolates ◽  
Pulse Field ◽  
Clinical Samples ◽  
Pfge Analysis ◽  
Content Type ◽  
Link Type ◽  
Carbapenem Resistant ◽  
Pseudomonas Monteilii ◽  
Stool Samples

Pseudomonas asiatica and Pseudomonas monteilii , belonging to the Pseudomonas putida phylogenetic group, are occasionally isolated from clinical samples, partly because they are often misidentified as P. putida in clinical laboratories. There are five reports describing carbapenem-resistant clinical isolates of these species. Carbapenem-resistant strains of P. asiatica and P. monteilii were isolated from stool samples. These isolates were sequenced using Illumina MiSeq and reidentified using average nucleotide identity (ANI) based on comparisons of their whole-genome sequences using the OrthoANI algorithm. The clonal relatedness of the isolates was assessed by pulse-field gel electrophoresis (PFGE). The size of plasmids conveying bla VIM-2 was examined by Southern blotting. A total of six carbapenem-resistant clinical isolates of P. asiatica (two isolates) and P. monteilii (four isolates) were obtained from stool samples from five patients in a Japanese hospital. All isolates harboured blaVIM-2 . The two isolates of P. asiatica had a different pattern in the PFGE analysis, with both having a 23 kb plasmid. Of the four isolates of P. monteilii with similar patterns in the PFGE analysis, three had 320 kb plasmids and one had a 240 kb plasmid. The genetic environments of the 320/240 kb and 23 kb plasmids differed. The results strongly indicated that carbapenem-resistant P. asiatica and P. monteilii producing metallo-β-lactamase are emerging in Japan. This is the first report of carbapenem-resistant P. asiatica and P. monteilii in Japan.

scholarly journals A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India

2016 ◽  
Vol 54 (6) ◽  
pp. 1500-1511 ◽  
Author(s):  
Pavitra N. Rao ◽  
Swapna Uplekar ◽  
Sriti Kayal ◽  
Prashant K. Mallick ◽  
Nabamita Bandyopadhyay ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Plasmodium Falciparum ◽  
Artemisinin Combination Therapy ◽  
Amplicon Sequencing ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Ion Torrent ◽  
Content Type ◽  
Ion Torrent Pgm ◽  
Reference Strains

A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of sixPlasmodium falciparumgenes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverseP. falciparumreference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy.

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