Biology subjects

Weitzel, T.

Publications and source records attributed to Weitzel, T..

3 recordsLinked to original sources

bioRxiv2020

Genomic analysis of the diversity, antimicrobial resistance and virulence potential of Campylobacter jejuni and Campylobacter coli strains from a private health care center in Central Chile

Campylobacter jejuni and Campylobacter coli 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 C. jejuni and C. coli strains from Chile available to date (n=81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for over a third of the genome sequences available of clinical strains from South America. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. 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. AUTHOR SUMMARYCampylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. In this study, we performed an in-depth analysis of the genome sequences of 69 C. jejuni and 12 C. coli clinical strains isolated from Chile, which account for over a third of the sequences from clinical strains available from South America. We identified a high genetic diversity among C. jejuni strains and the unexpected identification of clade 3 C. coli strains, which are infrequently isolated from humans in other regions of the world. Most strains harbored the virulence factors described for Campylobacter. While [~]40% of strains harbored mutation in the gyrA gene described to confer fluoroquinolone resistance, very few strains encoded the determinants linked to macrolide resistance, currently used for the treatment of campylobacteriosis. Our study contributes to our knowledge of this important foodborne pathogen providing valuable data from South America.

microbiology↗

bioRxiv2020

Head-to-head comparison of four antigen-based rapid detection tests for the diagnosis of SARS-CoV-2 in respiratory samples

In the context of the Covid-19 pandemic, the development and validation of rapid and easy-to-perform diagnostic methods are of high priority. We compared the performance of four rapid antigen detection tests for SARS-CoV-2 in respiratory samples. Immunochromatographic SARS-CoV-2 assays from RapiGEN, Liming bio, Savant, and Bioeasy were evaluated using universal transport medium containing naso-oropharyngeal swabs from suspected Covid-19 cases. The diagnostic accuracy was determined in comparison to SARS-CoV-2 RT-PCR. A total of 111 samples were included; 80 were RT-PCR positive. Median patients age was 40 years, 55% were female, and 88% presented within the first week after symptom onset. The evaluation of the Liming bio assay was discontinued due to insufficient performance. The overall sensitivity values of RapiGEN, Liming bio, and Bioeasy tests were 62.0% (CI95% 51.0-71.9), 16.7% (CI95% 10.0-26.5), and 85.0% (CI95% 75.6-91.2), respectively, with specificities of 100%. Sensitivity was significantly higher in samples with high viral loads (RapiGEN, 84.9%; Bioeasy, 100%). The study highlighted the significant heterogeneity of test performance among evaluated assays, which might have been influenced by the use of a non-validated sample material. The high sensitivity of some tests demonstrated that rapid antigen detection has the potential to serve as an alternative diagnostic method, especially in patients presenting with high viral loads in early phases of infection. This is particularly important in situations with limited access to RT-PCR or prolonged turnaround time. Further comparative evaluations are necessary to select products with high performance among the growing market of diagnostic tests for SARS-CoV-2.

microbiology↗

bioRxiv2019

First identification of trombiculid mites (Acari: Trombiculidae) on rodents captured on Chiloe Island, an endemic region of scrub typhus in southern Chile

BackgroundScrub typhus in an emerging vector-borne zoonosis, caused by Orientia spp. and transmitted by larvae of trombiculid mites, called chiggers. It mainly occurs within a certain region of the Asia-Pacific, called tsutsugamushi triangle, where rodents are known as the most relevant hosts for the trombiculid vector. The disease has recently been discovered on Chiloe Island in southern Chile. Still, the reservoir(s) and vector(s) of the scrub typhus outside Asia-Pacific are unknown. The aim of the present work was to study the prevalence of chiggers on different rodent species captured in sites identified as probably hot spots of scrub typhus on Chiloe Island in southern Chile.\n\nMethodology/Principal FindingsDuring austral summer 2018, rodents were live-trapped in six sites and examined for chigger infestation. During a total of 4,713 trap-nights, 244 rodents of seven species were captured: the most abundant was Abrothrix olivacea. All study sites were rural areas on Chiloe Island, previously identified as localities of probable human infection with scrub typhus. Chiggers were detected on all seven rodent species with a 55% prevalence rate. Chiggers showed low host specificity and varied according to site specific host abundance. We identified trombiculids of three genera. Colicus was the most abundant chigger (93%), prevalent in five of six sites, followed by Quadraseta (7%) and Paratrombicula (7%), which were in only one site. Infestation rates showed site specific differences, which were statistically different using a GLM model with binomial errors.\n\nConclusions/SignificanceThis study firstly reports the presence of different rodent-associated chigger mites in a region with endemic scrub typhus in southern Chile. Colicus and two other genera of mites were found with high infestation rates in sites previously identified as hot spots of scrub typhus, suggesting their role as vectors and reservoirs of this emerging zoonosis in South America.\n\nAuthor SummaryScrub typhus is a chigger-transmitted zoonotic infection, which is endemic in the tsutsugamushi triangle in Asia-Pacific. Recently, a first focus of scrub typhus in South America has been confirmed on Chiloe Island in southern Chile. Still, the vectors of scrub typhus in this region remain unknown. We undertook a survey to study the prevalence of chiggers on different rodent species in areas identified as probable hot spots of scrub typhus on Chiloe Island. The study showed that 55% of rodents were infested by trombiculids. Three chigger genera were identified, of which Colicus was the most abundant. Chiggers showed low host specificity, but spatial differences. This first demonstration of rodent-associated chigger mites in hot spots of scrub typhus suggests their possible role as vectors of this infection in Chile.

zoology↗