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Author: search.filters.author.Carmen Varela

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      6Scopus© Citations 2
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    Performance of the VITEK® MS system for the identification of filamentous fungi in a microbiological laboratory in Chile
    (Public Library of Science (PLoS), 2024-12-23)
    PORTE TORRE, LORENA ISABEL  
    ;
    Rodrigo Cruz
    ;
    Pérez Villa, Inia
    ;
    Carmen Varela
    ;
    Cristina Díaz
    <jats:p>Filamentous fungi are an emergent cause of severe infections in immunocompromised patients. Timely and accurate identification is crucial to initiate appropriate therapy. Traditional identification methods are time-consuming, labor-intensive, and operator-dependent. Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry is a rapid and easy-to-perform identification method. The effectiveness of a commercial MALDI-TOF MS platform to identify filamentous fungi in a clinical laboratory was evaluated. The study included 67 fungal isolates from 35 species/species complexes, which were identified and confirmed in mycology reference laboratories; 32 derived from clinical samples, 34 from strain collections and one was an ATCC strain. The study used the VITEK<jats:sup>®</jats:sup> MS system (v3.2.0 database), after sample extraction by VITEK<jats:sup>®</jats:sup> MS Mould Kit. Results were classified as “correct species”, “correct species complex”, “correct genus”and “no identification”. VITEK<jats:sup>®</jats:sup> MS correctly identified 91.0% of isolates (58.2% to species, 29.9% to species complex, and 1.5% to genus level only). In 82%, the result matched the species/species complex identified by reference methods. No misidentifications were observed. The kit was rapid and easy to use. In conclusion, the VITEK<jats:sup>®</jats:sup> MS system showed a high capability to accurately identify filamentous fungi in a clinical laboratory.</jats:p>
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    Whole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains
    (2023)
    Assaf Katz
    ;
    Lorena Porte  
    ;
    WEITZEL, THOMAS  
    ;
    Carmen Varela
    ;
    Cristina Muñoz-Rehbein
    <jats:p><jats:italic>Campylobacter</jats:italic> is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of <jats:italic>Campylobacter</jats:italic> spp. isolated from patients with acute gastrointestinal disease at ‘Clinica Alemana’, Santiago de Chile. The study considered the isolation of <jats:italic>Campylobacter</jats:italic> spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 <jats:italic>Campylobacter jejuni</jats:italic> and 2 <jats:italic>Campylobacter</jats:italic> coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. je<jats:italic>juni</jats:italic> strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barré syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen. In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.</jats:p>
      29Scopus© Citations 8
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    Head-to-head comparison of CAMPYAIR aerobic culture medium versus standard microaerophilic culture for Campylobacter isolation from clinical samples
    (2023)
    Arturo Levican
    ;
    Carmen Varela
    ;
    Lorena Porte  
    ;
    WEITZEL, THOMAS  
    ;
    Isabel Briceño
    <jats:p><jats:italic>Campylobacter</jats:italic> spp. are considered the most frequent cause of acute gastroenteritis worldwide. However, outside high-income countries, its burden is poorly understood. Limited published data suggest that <jats:italic>Campylobacter</jats:italic> prevalence in low- and middle-income countries is high, but their reservoirs and age distribution are different. Culturing <jats:italic>Campylobacter</jats:italic> is expensive due to laboratory equipment and supplies needed to grow the bacterium (e.g., selective culture media, microaerophilic atmosphere, and a 42°C incubator). These requirements limit the diagnostic capacity of clinical laboratories in many resource-poor regions, leading to significant underdiagnosis and underreporting of isolation of the pathogen. CAMPYAIR, a newly developed selective differential medium, permits <jats:italic>Campylobacter</jats:italic> isolation without the need for microaerophilic incubation. The medium is supplemented with antibiotics to allow <jats:italic>Campylobacter</jats:italic> isolation in complex matrices such as human feces. The present study aims to evaluate the ability of the medium to recover <jats:italic>Campylobacter</jats:italic> from routine clinical samples. A total of 191 human stool samples were used to compare the ability of CAMPYAIR (aerobic incubation) and a commercial <jats:italic>Campylobacter</jats:italic> medium (CASA, microaerophilic incubation) to recover <jats:italic>Campylobacter</jats:italic>. All <jats:italic>Campylobacter</jats:italic> isolates were then identified by MALDI-TOF MS. CAMPYAIR showed sensitivity and specificity values of 87.5% (95% CI 47.4%–99.7%) and 100% (95% CI 98%–100%), respectively. The positive predictive value of CAMPYAIR was 100% and its negative predictive value was 99.5% (95% CI 96.7%–99.9%); Kappa Cohen coefficient was 0.93 (95% CI 0.79–1.0). The high diagnostic performance and low technical requirements of the CAMPYAIR medium could permit <jats:italic>Campylobacter</jats:italic> culture in countries with limited resources.</jats:p>
    Scopus© Citations 3  1
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    Genomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile
    (2021)
    Veronica Bravo
    ;
    Assaf Katz
    ;
    PORTE TORRE, LORENA ISABEL  
    ;
    WEITZEL, THOMAS  
    ;
    Carmen Varela
    <jats:p><jats:italic>Campylobacter jejuni</jats:italic> and <jats:italic>Campylobacter coli</jats:italic> are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical <jats:italic>C</jats:italic>. <jats:italic>jejuni</jats:italic> and <jats:italic>C</jats:italic>. <jats:italic>coli</jats:italic> strains from Chile available to date (n = 81), collected in 2017–2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both <jats:italic>C</jats:italic>. <jats:italic>jejuni</jats:italic> and <jats:italic>C</jats:italic>. <jats:italic>coli</jats:italic>. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.</jats:p>
    Scopus© Citations 23  4
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    Campylobacter spp. Prevalence in Santiago, Chile: A Study Based on Molecular Detection in Clinical Stool Samples from 2014 to 2019
    (2023)
    PORTE TORRE, LORENA ISABEL  
    ;
    Caricia Pérez
    ;
    Mario Barbé
    ;
    Carmen Varela
    ;
    Valeska Vollrath
    <jats:p>Campylobacter spp. is an emerging cause of infectious diarrhea worldwide. In South American countries such as Chile, its prevalence is underestimated due to inadequate detection methods. Gastrointestinal multiplex PCR panels (GMP) permit rapid and sensitive detection of bacterial pathogens and provide important epidemiological information. This study aimed to analyze Campylobacter epidemiology using the results of molecular methods and to compare molecular detection results to those of culture methods. We performed a retrospective, descriptive analysis of Campylobacter spp. detected in clinical stool samples between 2014–2019 by GMP and culture. Within 16,582 specimens examined by GMP, Campylobacter was the most prevalent enteropathogenic bacteria (8.5%), followed by Salmonella spp. (3.9%), Shigella spp./enteroinvasive Escherichia coli (EIEC) (1.9%), and Yersinia enterocolitica (0.8%). The highest Campylobacter prevalence occurred in 2014/2015. Campylobacteriosis affected more males (57.2%) and adults from 19–65 years (47.9%) and showed a bimodal seasonality with summer and winter peaks. In 11,251 routine stool cultures, Campylobacter spp. was detected in 4.6%, mostly C. jejuni (89.6%). Among 4533 samples tested by GMP and culture in parallel, GMP showed a superior sensitivity (99.1% versus 50%, respectively). The study suggests that Campylobacter spp. is the most frequent bacterial enteropathogen in Chile.</jats:p>
      1Scopus© Citations 6  1
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    Draft Whole-Genome Sequences of 51 Campylobacter jejuni and 12 Campylobacter coli Clinical Isolates from Chile
    (2020)
    Verónica Bravo
    ;
    Carmen Varela
    ;
    PORTE TORRE, LORENA ISABEL  
    ;
    WEITZEL, THOMAS  
    ;
    George J. Kastanis
    <jats:p> <jats:italic>Campylobacter</jats:italic> species are the leading cause of gastroenteritis worldwide and an emerging threat in developing countries. Here, we report the draft whole-genome sequences of 51 <jats:named-content content-type="genus-species">Campylobacter jejuni</jats:named-content> and 12 <jats:named-content content-type="genus-species">Campylobacter coli</jats:named-content> strains isolated from patients with gastroenteritis in Santiago, Chile. </jats:p>
      17Scopus© Citations 4
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    Scopus© Citations 11  2
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      10Scopus© Citations 12
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    Scopus© Citations 1  1