scholarly journals Serological Survey and Molecular Typing Reveal New Leptospira Serogroup Pomona Strains among Pigs of Northern Italy

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 332 ◽  
Author(s):  
Cristina Bertasio ◽  
Alice Papetti ◽  
Erika Scaltriti ◽  
Silvia Tagliabue ◽  
Mario D’Incau ◽  
...  
Keyword(s):  
Serological Test ◽  
Variable Number Tandem Repeat ◽  
16S Rrna Gene Sequencing ◽  
Variable Number ◽  
Northern Italy ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Pathogenic Leptospira ◽  
Rrna Gene Sequencing

Swine act as both maintenance and incidental hosts of pathogenic Leptospira spp. Here, a serological test was performed on 131,660 pig sera collected between 2002 and 2017 from 4715 farms in Northern Italy. A positivity rate of 13.05% was determined. Australis was the most frequently identified serogroup (77.29%), followed by Pomona (18.47%), Tarassovi (1.51%) and Icterohaemorrhagie (1.40%). Culture isolation and real-time Polymerase chain reaction (PCR) were carried out on 347 kidneys and 470 clinical samples, respectively. Overall, 133 strains were cultured successfully and 43 randomly chosen isolates were identified as serogroup Pomona. Multi-locus sequence typing (MLST) revealed that 41 isolates and 8 DNA extracted from biological samples belonged to sequence type 140. Using a multiple-locus, variable-number tandem repeat analysis, 43 samples produced identical profiles but, after 2014, three new Leptospira interrogans serogroup Pomona genotypes were observed. Interestingly, two isolates showed new MLST profiles and an unclassified identification by monoclonal antibodies. The 16S rRNA gene sequencing clustered them into L. kirschneri species and a core genome MLST analysis revealed an allelic identity of 96% compared with Mozdok strains. Genotyping allowed us to discriminate leptospires and to identify new emerging strains. The accurate identification of infective strains is required for formulating preventive methods and intervention strategies.

scholarly journals Adaptation of Microbial Communities to Environmental Arsenic and Selection of Arsenite-Oxidizing Bacteria From Contaminated Groundwaters

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarah Zecchin ◽  
Simona Crognale ◽  
Patrizia Zaccheo ◽  
Stefano Fazi ◽  
Stefano Amalfitano ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Inorganic Arsenic ◽  
16S Rrna Gene Sequencing ◽  
Northern Italy ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Main Driver ◽  
Rrna Gene Sequencing ◽  
Arsenite Oxidizing Bacteria ◽  
Card Fish

Arsenic mobilization in groundwater systems is driven by a variety of functionally diverse microorganisms and complex interconnections between different physicochemical factors. In order to unravel this great ecosystem complexity, groundwaters with varying background concentrations and speciation of arsenic were considered in the Po Plain (Northern Italy), one of the most populated areas in Europe affected by metalloid contamination. High-throughput Illumina 16S rRNA gene sequencing, CARD-FISH and enrichment of arsenic-transforming consortia showed that among the analyzed groundwaters, diverse microbial communities were present, both in terms of diversity and functionality. Oxidized inorganic arsenic [arsenite, As(III)] was the main driver that shaped each community. Several uncharacterized members of the genus Pseudomonas, putatively involved in metalloid transformation, were revealed in situ in the most contaminated samples. With a cultivation approach, arsenic metabolisms potentially active at the site were evidenced. In chemolithoautotrophic conditions, As(III) oxidation rate linearly correlated to As(III) concentration measured at the parental sites, suggesting that local As(III) concentration was a relevant factor that selected for As(III)-oxidizing bacterial populations. In view of the exploitation of these As(III)-oxidizing consortia in biotechnology-based arsenic bioremediation actions, these results suggest that contaminated aquifers in Northern Italy host unexplored microbial populations that provide essential ecosystem services.

scholarly journals SPDB: a specialized database and web-based analysis platform for swine pathogens

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Xiaoru Wang ◽  
Zongbao Liu ◽  
Xiaoying Li ◽  
Danwei Li ◽  
Jiayu Cai ◽  
...  
Keyword(s):  
Related Species ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Swine Pathogen ◽  
Negative Impacts ◽  
Rrna Gene Sequencing ◽  
Swine Disease ◽  
Swine Diseases ◽  
Analysis Platform

Abstract The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research. Database URL: http://spdatabase.com:2080/

scholarly journals Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi)

2006 ◽  
Vol 56 (11) ◽  
pp. 2671-2676 ◽  
Author(s):  
Ana I. Vela ◽  
María C. Gutiérrez ◽  
Enevold Falsen ◽  
Eduardo Rollán ◽  
Isabel Simarro ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Molecular Genetic ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Sequencing Studies ◽  
Rrna Gene Sequencing ◽  
Callithrix Geoffroyi

An unusual Gram-negative, catalase- and oxidase-positive, rod-shaped bacterium isolated from different clinical samples from two monkeys (Callithrix geoffroyi) was characterized by phenotypic and molecular genetic methods. The micro-organism was tentatively identified as a Pseudomonas species on the basis of the results of cellular morphological and biochemical tests. Fatty acid studies confirmed this generic placement and comparative 16S rRNA gene sequencing studies demonstrated that the unknown isolates were phylogenetically closely related to each other (100 % sequence similarity) and were part of the ‘Pseudomonas fluorescens intrageneric cluster’. The novel bacterium, however, was distinguished from other phylogenetically related species of Pseudomonas by DNA–DNA hybridization studies and biochemical tests. On the basis of both phenotypic and phylogenetic findings, it is proposed that the novel Pseudomonas isolates are classified as Pseudomonas simiae sp. nov. The type strain of P. simiae is OLiT (=CCUG 50988T=CECT 7078T).

scholarly journals McKay agar enables routine quantification of the ‘Streptococcus milleri’ group in cystic fibrosis patients

2010 ◽  
Vol 59 (5) ◽  
pp. 534-540 ◽  
Author(s):  
Christopher D. Sibley ◽  
Margot E. Grinwis ◽  
Tyler R. Field ◽  
Michael D. Parkins ◽  
Jens C. Norgaard ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Clinical Laboratory ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Columbia Blood Agar ◽  
Streptococcus Anginosus ◽  
Streptococcus Milleri ◽  
Streptococcus Milleri Group ◽  
Rrna Gene Sequencing

The ‘Streptococcus milleri’ group (SMG) has recently been recognized as a contributor to bronchopulmonary disease in cystic fibrosis (CF). Routine detection and quantification is limited by current CF microbiology protocols. McKay agar was developed previously for the semi-selective isolation of this group. Here, McKay agar was validated against a panel of clinical SMG isolates, which revealed improved SMG recovery compared with Columbia blood agar. The effectiveness of this medium was evaluated by appending it to the standard CF sputum microbiology protocols in a clinical laboratory for a 6-month period. All unique colony types were isolated and identified by 16S rRNA gene sequencing. Whilst a wide variety of organisms were isolated, members of the SMG were the most prevalent bacteria cultured, and McKay agar allowed routine quantification of the SMG from 103 to >108 c.f.u. ml−1 directly from sputum. All members of the SMG were detected [Streptococcus anginosus (40.7 %), Streptococcus intermedius (34.3 %) and Streptococcus constellatus (25 %)] with an overall prevalence rate of 40.6 % in our adult CF population. Without exception, samples where SMG isolates were cultured at 107 c.f.u. ml−1 or greater were associated with pulmonary exacerbations. This study demonstrates that McKay agar can be used routinely to quantify the SMG from complex clinical samples.

Comparison of the automated Phoenix with the Vitek 2 for the identification of Streptococcus pneumoniaePortions of this study were presented at the 2007 American Society of Microbiology 107th General Meeting in Toronto, Ontario, Canada.

2010 ◽  
Vol 56 (4) ◽  
pp. 326-332 ◽  
Author(s):  
Scott A. Mittman ◽  
Richard C. Huard ◽  
Phyllis Della-Latta ◽  
Susan Whittier
Keyword(s):  
General Meeting ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Diagnostic Systems ◽  
Accurate Identification ◽  
Significant Difference ◽  
Vitek 2 ◽  
Rrna Gene Sequencing ◽  
American Society ◽  
The Phoenix

Rapid and accurate identification of Streptococcus pneumoniae is a critical component in the optimal management of infected patients. The performance of the BD Phoenix Automated Microbiology System (BD Diagnostic Systems, Sparks, Md.) was evaluated for identification of S. pneumoniae (n = 311) and was compared to the Vitek 2 (bioMérieux, Marcy l’Étoile, France). Strains with discordant identification between methods were resolved with 16S rRNA gene sequencing as the gold standard. The Phoenix and the Vitek 2 correctly identified 96.8% (n = 301) and 95.2% (n = 296) of S. pneumoniae strains, respectively. Overall, there was no statistically significant difference in the performance of the 2 automated systems for the identification of S. pneumoniae in this study. The Vitek 2 mean time-to-results for all streptococcal identification was 1.5 h faster than that for the Phoenix. We conclude that the automated Phoenix and the Vitek 2 systems are comparable in their ability to identify S. pneumoniae and are preferable to the use of routine biochemical assays, which have delayed time-to-results and are not dependably accurate.

scholarly journals Variable-number tandem repeat markers for Mycobacterium intracellulare genotyping: comparison to the 16S rRNA gene sequencing

2017 ◽  
Vol 11 (02) ◽  
pp. 158-165 ◽  
Author(s):  
Kaisen Chen ◽  
Yangyi Zhang ◽  
Yiping Peng
Keyword(s):  
16S Rrna ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Point Mutations ◽  
Allelic Diversity ◽  
Variable Number ◽  
Clinical Samples ◽  
Group Method ◽  
Rrna Gene ◽  
Mycobacterium Intracellulare

Introduction: Characterizing Mycobacterium intracellulare responsible for nontuberculous mycobacterial (NTM) infections may aid in controlling outbreaks. This study aimed to compare 16S ribosomal ribonucleic acid (rRNA) sequencing and variable-number tandem repeat (VNTR) genotyping of M. intracellulare strains isolated from clinical samples, and to characterize VNTR clusters associated with NTM infections or cavity formation. Methodology: Sputum samples were obtained from 77 HIV-negative patients with pulmonary disease between 2009 and 2013. One M. intracellulare strain was isolated from each patient and genotyped using 16S rRNA and eight loci VNTR sequencing. Results: Single nucleotide polymorphism (SNP) genotyping identified seven point mutations at nucleotide positions 101, 178, 190, 252, 382, 443, and 490 in 16S rRNA, and four SNP patterns were identified: type 1 (16 strains), 2 (41 strains), 3 (11 strains), and 4 (1 strain); 5 strains had unique SNP patterns. VNTR genotyping identified VNTR12 as the most discriminating marker (allelic diversity 0.692). VNTR3 was the most homogeneous marker (allelic diversity 0.518), but each locus had high discriminating ability. The 77 strains were clustered according to the unpaired group method using arithmetic averages: cluster 1 (17 strains), 2 (43 strains), 3 (9 strains), and 4 (4 strains); 4strains had unique SNP patterns. Overall, over 90% strains were matched to similar SNP and VNTR groupings. VNTR clusters were associated with NTM infection (p =0.007) and presence of a cavity (p =0.042). Both methods distinguished four subtypes of M. intracellulare, which corresponded. Conclusions: VNTRs may represent an effective, user-friendly, low-cost typing technique.

scholarly journals Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens

2006 ◽  
Vol 56 (6) ◽  
pp. 1413-1418 ◽  
Author(s):  
Joann L. Cloud ◽  
Jay J. Meyer ◽  
June I. Pounder ◽  
Kenneth C. Jost ◽  
Amy Sweeney ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Several Mycobacterium-like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99.6 % to Mycobacterium nonchromogenicum ATCC 19530T. Sequencing of the nearly full-length 16S rRNA gene, the 16S–23S internal transcribed spacer region and the hsp65 gene did not reveal genotypic identity with the type strains of M. nonchromogenicum, M. terrae or Mycobacterium triviale. Although sequence analysis suggested that these clinical isolates represented a novel species, mycolic acid analysis by HPLC failed to distinguish them from M. nonchromogenicum. Therefore, phenotypic analysis including growth characterization, antibiotic susceptibility testing and biochemical testing was performed. These strains from clinical samples should be recognized as representing a novel species of the genus Mycobacterium, for which the name Mycobacterium arupense sp. nov. is proposed. The type strain is AR30097T (=ATCC BAA-1242T=DSM 44942T).

scholarly journals Detection and identification of bacteria in clinical samples by 16S rRNA gene sequencing: comparison of two different approaches in clinical practice

2012 ◽  
Vol 61 (4) ◽  
pp. 483-488 ◽  
Author(s):  
Claire Jenkins ◽  
Clare L. Ling ◽  
Holly L. Ciesielczuk ◽  
Julianne Lockwood ◽  
Susan Hopkins ◽  
...  
Keyword(s):  
Clinical Practice ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Detection And Identification ◽  
Identification Of Bacteria ◽  
Rrna Gene Sequencing

scholarly journals Comparison of Illumina Versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota

2020 ◽  
Author(s):  
Astrid. P. Heikema ◽  
Deborah Horst-Kreft ◽  
Stefan A. Boers ◽  
Rick Jansen ◽  
Saskia D. Hiltemann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Single Species ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Nanopore Sequencing ◽  
Accurate Identification ◽  
Rrna Gene Sequencing

Illumina and nanopore sequencing technologies are powerful tools that can be used to determine the bacterial composition of complex microbial communities. In this study, we compared nasal microbiota results at genus level using both Illumina and nanopore 16S rRNA gene sequencing. We also monitored the progression of nanopore sequencing in the accurate identification of species, using pure, single species cultures, and evaluated the performance of the nanopore EPI2ME 16S data analysis pipeline. Fifty-nine nasal swabs were sequenced using Illumina MiSeq and Oxford Nanopore 16S rRNA gene sequencing technologies. In addition, five pure cultures of relevant bacterial species were sequenced with the nanopore sequencing technology. The Illumina MiSeq sequence data were processed using bioinformatics modules present in the Mothur software package. Albacore and Guppy base calling, a workflow in nanopore EPI2ME and an in house developed bioinformatics script were used to analyze the nanopore data. At genus level, similar bacterial diversity profiles were found, and five main and established genera were identified by both platforms. However, probably due to mismatching of the nanopore sequence primers, the nanopore sequencing platform identified Corynebacterium in much lower abundance compared to Illumina sequencing. Further, when using default settings in the EPI2ME workflow, almost all sequence reads that seem to belong to the bacterial genus Dolosigranulum and a considerable part to the genus Haemophilus were only identified at family level. Nanopore sequencing of single species cultures demonstrated at least 88% accurate identification of the species at genus and species level for 4/5 strains tested, including improvements in accurate sequence read identification when the basecaller Guppy and Albacore, and when flowcell versions R9.4 and R9.2 were compared.

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