scholarly journals Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Andreina I. Castillo ◽  
Chi-Wei Tsai ◽  
Chiou-Chu Su ◽  
Ling-Wei Weng ◽  
Yu-Chen Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Type Species ◽  
Xylella Fastidiosa ◽  
Content Type ◽  
Link Type ◽  
Genome Recombination ◽  
Haplotype Networks ◽  
The Usa ◽  
Multiple Regions ◽  
Central Taiwan

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce’s disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis , which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.

scholarly journals Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan

2021 ◽  
Author(s):  
Andreina I. Castillo ◽  
Chi-Wei Tsai ◽  
Chiou-Chu Su ◽  
Ling-Wei Weng ◽  
Yu-Chen Lin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Xylella Fastidiosa ◽  
Haplotype Network ◽  
The United States ◽  
Genome Recombination ◽  
Taichung City ◽  
The Us ◽  
Multiple Regions ◽  
Southeast Us ◽  
Central Taiwan

The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of crops and industries. Xylella fastidiosa subspecies fastidiosa causes disease in grapevines (Pierce's disease of grapevines, PD), a current problem in the United States (US), Spain, and Taiwan. We studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the US and two from Spain. Phylogenetic relationships, haplotype network, and genetic diversity analyses confirm that subsp. fastidiosa was recently introduced into Taiwan from the Southeast US (i.e., the PD-I lineage in Georgia based on available data). Recent core genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity, particularly in the Houli District of Taichung City in Central Taiwan. Unexpectedly, despite comprehensive sampling of all regions with high PD incidences in Taiwan, the genetic diversity observed include contributions through recombination from unknown donors, suggesting that higher diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis. In summary, this study improved our understanding of the genetic diversity of PD-causing subsp. fastidiosa after invasion to a new region.

Kerstersia similis sp. nov., isolated from human clinical samples

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2156-2159 ◽  
Author(s):  
Peter Vandamme ◽  
Evie De Brandt ◽  
Kurt Houf ◽  
Thierry De Baere
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Clinical Samples ◽  
Content Type ◽  
Biochemical Characteristics ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
The Usa ◽  
Kerstersia Gyiorum

Analysis of gyrB gene sequences, (GTG)5-primed PCR fingerprinting and biochemical characteristics determined in the Biolog GEN III microtest system were used to differentiate an unnamed Kerstersia species from Kerstersia gyiorum , the type and only named species in this genus. The inability to oxidize d-galacturonic and d-glucuronic acids and the ability to oxidize d-serine, along with gyrB gene sequence analysis and (GTG)5-PCR fingerprints, readily differentiated the unnamed taxon from the type species. Therefore, we propose to formally classify this unnamed taxon as Kerstersia similis sp. nov. with strain LMG 5890T ( = CCUG 46999T), isolated from a leg wound in the USA in 1983, as the type strain.

scholarly journals Sneathia amnii bacteraemia and chorioamnionitis leading to second trimester abortion: a case report

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Lien Gruwier ◽  
Aaron Sprenkels ◽  
Sofie Hulsbosch ◽  
Anne Vankeerberghen ◽  
Reinoud Cartuyvels
Keyword(s):  
Type Species ◽  
Culture Broth ◽  
Second Trimester ◽  
Trimester Abortion ◽  
Content Type ◽  
Link Type ◽  
First Case ◽  
Gene Sequence Analysis ◽  
The Usa ◽  
Septic Abortion

Background. Sneathia amnii (formerly designated as Leptotrichia amnionii ) was first described in 2002 in the USA. Members of the genus Sneathia can be part of the normal flora of the genitourinary tract, but have been implicated in invasive (mostly gynaecological) infections. Case presentation. To the best of our knowledge, here we present the first case of S. amnii infection in Belgium, in a young woman presenting with fever leading to second trimester septic abortion. Conclusions. Despite its pathogenicity, S. amnii remains an underrated cause of infections due to inherent difficulties with conventional laboratory methods. By extracting the bacterial DNA directly from the blood culture broth and performing a 16S ribosomal RNA gene sequence analysis we succeeded in identifying S. amnii as the most probable cause of the septic abortion in our patient.

scholarly journals Microbe Profile: Xylella fastidiosa – a devastating agricultural pathogen with an endophytic lifestyle

Microbiology ◽  
2021 ◽  
Vol 167 (10) ◽  
Author(s):  
Lindsey P. Burbank ◽  
M. Caroline Roper
Keyword(s):  
Type Species ◽  
Xylella Fastidiosa ◽  
Xylem Sap ◽  
Disease Outbreaks ◽  
Plant Tissues ◽  
Content Type ◽  
Link Type ◽  
Quarantine Pathogen ◽  
Sap Feeding ◽  
Vector Borne

Xylella fastidiosa is a vector-borne plant vascular pathogen that has caused devastating disease outbreaks in diverse agricultural crops worldwide. A major global quarantine pathogen, X. fastidiosa can infect hundreds of plant species and can be transmitted by many different xylem sap-feeding insects. Several decades of research have revealed a complex lifestyle dependent on adaptation to the xylem and insect environments and interactions with host plant tissues.

scholarly journals Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Lin Zhao ◽  
Hongyou Chen ◽  
Xavier Didelot ◽  
Zhenpeng Li ◽  
Yinghui Li ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Vibrio Parahaemolyticus ◽  
Type Species ◽  
Genomic Islands ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Gene Segregation ◽  
Strain Collection ◽  
The Usa

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

scholarly journals Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile

2020 ◽  
Vol 2 (7) ◽  
Author(s):  
Yuta Okada ◽  
Shu Okugawa ◽  
Mahoko Ikeda ◽  
Tatsuya Kobayashi ◽  
Ryoichi Saito ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
In Silico ◽  
Type Species ◽  
Clinical Samples ◽  
Pcr Analysis ◽  
Accessory Gene ◽  
Content Type ◽  
Link Type ◽  
Accessory Gene Regulator ◽  
Clostridioides Difficile

Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining Clostridioides difficile show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and C. difficile isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133 C . difficile isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in C. difficile . These findings provide a foundation for further functional and clinical research of the agr loci.

Molecular mechanisms of macrolide and fluoroquinolone resistance among Korean isolates of Mycoplasma genitalium over a period of five years 2014–2019

2021 ◽  
Vol 70 (11) ◽  
Author(s):  
Yumi Seo ◽  
Heeyoon Park ◽  
Gilho Lee
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Type Species ◽  
Mycoplasma Genitalium ◽  
Quinolone Resistance ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
23S Rrna Gene

Antimicrobial resistance in Mycoplasma genitalium has become a global issue, and certain groups have a higher probability of acquiring resistant strains. Little is known about the genetic diversity and characteristics of the antimicrobial resistance-determining sites (ARDSs) of M. genitalium in the Korean population. Therefore, we examined the genetic diversity of the ARDSs of M. genitalium-positive urogenital samples obtained from Korean females (G1) and males (G2) visiting primary care clinics and DNA samples from referred males (G3) with persistent urethritis. From 2014 to 2019, 54 patients from G1, 86 patients from G2, and 68 patients from G3 were included in the study. Sanger sequencing was performed on the 2058/2059 sites in the 23S rRNA gene and quinolone resistance-determining regions (QRDRs) of M. genitalium . The rates of mutation in G1, G2, and G3 were 1.85, 5.81, and 48.53 %, respectively, for A2059G in the 23S rRNA gene (P<0.001); 1.85, 0, and 17.78 %, respectively, for M95R or I in gyrA (P<0.001); 0, 0, and 31.11 %, respectively, for D99N or G in gyrA (P<0.001); and 7.41, 16.28, and 30 %, respectively, for S83R or N or I in parC (P=0.015). A2059G significantly increased the risk of mutations at the gyrA95, gyrA99, and parC83 sites (all P<0.01). In conclusion, although the genetic diversity of the ARDSs of M. genitalium was variable among the groups, it was generally lower in isolates with macrolide resistance and higher in isolates with quinolone resistance in Korea compared with the isolates in other countries. The G3 group demonstrated increased genetic diversity at the A2059G, gyrA95, gyrA99, and parC83 sites.

scholarly journals High frequency of colonization by diverse clones of beta-lactam-resistant Gram-negative bacilli in haemodialysis: different sources of transmission outside the renal unit?

2020 ◽  
Vol 69 (9) ◽  
pp. 1132-1144
Author(s):  
Johanna M. Vanegas ◽  
Lorena Salazar-Ospina ◽  
Daniela Montoya-Urrego ◽  
Julián Builes ◽  
Gustavo E. Roncancio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Type Species ◽  
Molecular Characteristics ◽  
Renal Unit ◽  
Beta Lactam ◽  
High Genetic Diversity ◽  
Gram Negative ◽  
Content Type ◽  
Link Type ◽  
Stool Samples

Introduction. While colonization by Staphylococcus aureus in haemodialysis patients has been assessed, knowledge about colonization by beta-lactam-resistant Gram-negative bacilli is still limited. Aim. To describe clinical and molecular characteristics in haemodialysis patients colonized by S. aureus (MSSA-MRSA) and beta-lactam-resistant Gram-negative bacilli in an ambulatory renal unit. Methodology. The study included patients with central venous catheters in an outpatient haemodialysis facility in Medellín, Colombia (October 2017–October 2018). Swab specimens were collected from the nostrils and skin around vascular access to assess colonization by S. aureus (MSSA-MRSA). Stool samples were collected from each patient to evaluate beta-lactam-resistant Gram-negative bacilli colonization. Molecular typing included PFGE, multilocus sequence typing (MLST), spa typing and enterobacterial repetitive intergenic consensus-PCR (ERIC). Clinical information was obtained from medical records and personal interview. Results. A total of 210 patients were included in the study. S. aureus colonization was observed in 33.8 % (n=71) of the patients, 4.8 % (n=10) of which were colonized by methicillin-resistant S. aureus . Stool samples were collected from 165 patients and of these 41.2 % (n=68) and 11.5 % (n=19) were colonized by extended-spectrum-beta-lactamase-producing (ESBL) and carbapenem-resistant bacilli, respectively. Typing methods revealed high genetic diversity among S. aureus and ESBL-producing Gram-negative bacilli (ESBL-GNB). Antibiotic use and hospitalization in the previous 6 months were observed in more than half of the studied population. Conclusion. The high colonization by ESBL-GNB in haemodialysis patients shows evidence for the need for stronger surveillance, not only for S. aureus but also for multidrug-resistant bacilli in order to avoid their spread. Additionally, the high genetic diversity suggests other sources of transmission outside the renal unit instead of horizontal transmission between patients.

scholarly journals Cryptic prophages within a Streptococcus pyogenes genotype emm4 lineage

2020 ◽  
Author(s):  
Alex Remmington ◽  
Samuel Haywood ◽  
Julia Edgar ◽  
Luke R. Green ◽  
Thushan de Silva ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Type Species ◽  
Gene Loss ◽  
Content Type ◽  
Regulatory Modules ◽  
Link Type ◽  
Genes Encoding ◽  
Variable Extent ◽  
The Usa ◽  
The Uk

The major human pathogen Streptococcus pyogenes shares an intimate evolutionary history with mobile genetic elements, which in many cases carry genes encoding bacterial virulence factors. During recent whole-genome sequencing of a longitudinal sample of S. pyogenes isolates in England, we identified a lineage within emm4 that clustered with the reference genome MEW427. Like MEW427, this lineage was characterized by substantial gene loss within all three prophage regions, compared to MGAS10750 and isolates outside of the MEW427-like lineage. Gene loss primarily affected lysogeny, replicative and regulatory modules, and to a lesser and more variable extent, structural genes. Importantly, prophage-encoded superantigen and DNase genes were retained in all isolates. In isolates where the prophage elements were complete, like MGAS10750, they could be induced experimentally, but not in MEW427-like isolates with degraded prophages. We also found gene loss within the chromosomal island SpyCIM4 of MEW427-like isolates, although surprisingly, the SpyCIM4 element could not be experimentally induced in either MGAS10750-like or MEW427-like isolates. This did not, however, appear to abolish expression of the mismatch repair operon, within which this element resides. The inclusion of further emm4 genomes in our analyses ratified our observations and revealed an international emm4 lineage characterized by prophage degradation. Intriguingly, the USA population of emm4 S. pyogenes appeared to constitute predominantly MEW427-like isolates, whereas the UK population comprised both MEW427-like and MGAS10750-like isolates. The degraded and cryptic nature of these elements may have important phenotypic and fitness ramifications for emm4 S. pyogenes , and the geographical distribution of this lineage raises interesting questions on the population dynamics of the genotype.

scholarly journals Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 286-292 ◽  
Author(s):  
Daniel Weller ◽  
Alexis Andrus ◽  
Martin Wiedmann ◽  
Henk C. den Bakker
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
Eastern Usa ◽  
The Usa ◽  
Genotypic Identification

Sampling of seafood and dairy processing facilities in the north-eastern USA produced 18 isolates of Listeria spp. that could not be identified at the species-level using traditional phenotypic and genotypic identification methods. Results of phenotypic and genotypic analyses suggested that the isolates represent two novel species with an average nucleotide blast identity of less than 92 % with previously described species of the genus Listeria . Phylogenetic analyses based on whole genome sequences, 16S rRNA gene and sigB gene sequences confirmed that the isolates represented by type strain FSL M6-0635T and FSL A5-0209 cluster phylogenetically with Listeria cornellensis . Phylogenetic analyses also showed that the isolates represented by type strain FSL A5-0281T cluster phylogenetically with Listeria riparia . The name Listeria booriae sp. nov. is proposed for the species represented by type strain FSL A5-0281T ( = DSM 28860T = LMG 28311T), and the name Listeria newyorkensis sp. nov. is proposed for the species represented by type strain FSL M6-0635T ( = DSM 28861T = LMG 28310T). Phenotypic and genotypic analyses suggest that neither species is pathogenic.

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