scholarly journals Population structure, virulence factors and resistance determinants of invasive, non-invasive and colonizing Streptococcus agalactiae in Poland

2010 ◽  
Vol 65 (9) ◽  
pp. 1907-1914 ◽  
Author(s):  
E. Sadowy ◽  
B. Matynia ◽  
W. Hryniewicz
Keyword(s):  
Population Structure ◽  
Virulence Factors ◽  
Streptococcus Agalactiae ◽  
Non Invasive ◽  
Resistance Determinants

Distribution of virulence genes and the molecular epidemiology of Streptococcus pyogenes clinical isolates by emm and multilocus sequence typing methods

2020 ◽  
Author(s):  
Siti Nur Adila Hamzah ◽  
Mohd Nasir Mohd Desa ◽  
Azmiza Syawani Jasni ◽  
Niazlin Mohd Taib ◽  
Siti Norbaya Masri ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Virulence Factors ◽  
Streptococcus Pyogenes ◽  
Multilocus Sequence Typing ◽  
Virulence Genes ◽  
Clinical Samples ◽  
Pcr Analysis ◽  
Gold Standard Method ◽  
Non Invasive ◽  
Typing Methods

Abstract Background: Streptococcus pyogenes has a variety of virulence factors and the predominant invasive strains differ according to specific emm types and geographical orientation. Although emm typing is commonly used as the gold standard method for the molecular characterization, multilocus sequence typing (MLST) has become an important tool for comparing the genetic profiles globally. This study aimed to screen selected virulence genes from invasive and non-invasive clinical samples and to characterize the molecular epidemiology by emm typing and MLST methods. Methods: A total of 42 S. pyogenes isolates from invasive and non-invasive samples collected from 2014 to 2015 from two different tertiary hospitals were investigated for the distribution of virulence factors and their molecular epidemiology by emm and multilocus sequence typing methods. Detection of five virulence genes (speA , speB , speJ , ssa and sdaB) was performed using multiplex polymerase chain reaction (PCR) using the standard primers and established protocol. Results: Multiplex PCR analysis revealed that sdaB/speF (78.6%) and speB (61.9%) were the predominant virulence genes. Regardless of the type of invasiveness, diverse distribution of emm types/subtypes was noted which comprised of 27 different emm types/subtypes. The predominant emm types/subtypes were emm63 and emm18 with each gene accounted for 11.8% whereas 12% for each gene was noted for emm28, emm97.4 and emm91. The MLST revealed that the main sequence type (ST) in invasive samples was ST402 (17.7%) while ST473 and ST318 (12% for each ST) were the major types in non-invasive samples. Out of 18 virulotypes, Virulotype A (five genes, 55.6%) and Virulotype B (two genes, 27.8%) were the major virulotypes found in this study. Phylogenetic analysis indicated the presence of seven different clusters of S. pyogenes. Interestingly, Cluster VI showed that selected emm/ST types such as emm71/ST318 (n=2), emm70.1/ST318 (n=1), emm44/ST31 (n=1) and emm18/ST442 (n=1) have clustered within a common group (Virulotype A) for both hospitals studied. Conclusion: The present study showed that group A streptococci (GAS) are genetically diverse and possess virulence genes regardless of their invasiveness. Majority of the GAS exhibited no restricted pattern of virulotypes except for a few distinct clusters. Therefore, it can be concluded that virulotyping is partially useful for characterizing a heterogeneous population of GAS in hospitals.

scholarly journals Phylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Lang Yang ◽  
Bing Lü ◽  
Quanyi Wang ◽  
Kaiying Wang ◽  
Yanfeng Lin ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Bacillary Dysentery ◽  
Shigella Flexneri ◽  
Content Type ◽  
Phylogenetic Characterization ◽  
Local Expansion ◽  
Resistance Determinants ◽  
Genetic Features ◽  
Beijing China

ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that S. flexneri epidemics in Beijing were caused by both local expansion and interregional transmission. IMPORTANCE Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing of 93 S. flexneri isolates revealed that S. flexneri epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of S. flexneri in Beijing.

scholarly journals Population Structure of Human Isolates of Streptococcus agalactiae from Dakar and Bangui

2008 ◽  
Vol 47 (3) ◽  
pp. 800-803 ◽  
Author(s):  
M. Brochet ◽  
E. Couve ◽  
R. Bercion ◽  
J.-M. Sire ◽  
P. Glaser
Keyword(s):  
Population Structure ◽  
Streptococcus Agalactiae

scholarly journals Describing the population structure of Rhincodon typus occurring in the waters of Oslob– Cebu, Philippines– between March 2012 and June 2013, during the provisioning interaction hours.

2013 ◽  
Author(s):  
Gonzalo Araujo ◽  
Alessandro Ponzo ◽  
Daniel Geary ◽  
Samantha Craven ◽  
Sally J Snow ◽  
...  
Keyword(s):  
Population Structure ◽  
The Philippines ◽  
First Year ◽  
Systematic Data ◽  
Rhincodon Typus ◽  
Non Invasive ◽  
Monthly Average ◽  
Whale Sharks ◽  
The Impact ◽  
Systematic Data Collection

Background: Prior to this study, the aggregation of whale sharks in the waters of Oslob had never been described. Provisioning (Orams, 2002) activities started in late 2011, and systematic data collection in March 2012, attracting over 100,000 tourists in the first year, and is currently the most reliable aggregation of R. typus in the Philippines. Methods: Daily in-­‐water photographic identification was used as a non-­‐invasive means to describe the population throughout the study period. A total of 135 sharks were identified, and IDs were independently matched by three researchers to minimize error. Photogrammetry (Rohner, 2011) was adopted to complement population description. Results: Daily sightings ranged from 2 to 23 different animals in the interaction area (mean=11.14). A total of 109 males, 15 females and 11 R. typus of undetermined sex were described. The size was estimated for 73.3% of the population, with an average of 5.36m ±1.3m. Photogrammetry posed a mean of 5.63m ±0.59m on 14 sharks, 6.75% >than researchers’ estimates. Resighting (>1d) was observed in 66.7% of the population. Five individuals were present for >300d (n=443) in the interaction area, with a maximum of 420d. Nine individuals were successfully matched across regional hotspots including Donsol and Southern Leyte. Conclusion: Despite the presence of animals in Oslob year round and the influence of the provisioning, there appears to be a seasonal influx of animals, with a maximum of 46 different animals present in the month of June 2012 and again in May 2013, contrasting with a monthly average of 28.9. It appears these waters are important to the species and it’s paramount to fully investigate the impact of the provisioning on the population of R. typus in the Philippines.

scholarly journals 728. Genomic Characterization of Burkholderia pseudomallei Isolates in Colombia

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S463-S463
Author(s):  
Catalina Espitia-Acero ◽  
Rafael Rios ◽  
Monica Gabriela huertas ◽  
Sandra Vargas ◽  
Carolina Duarte Valderrama ◽  
...  
Keyword(s):  
Population Structure ◽  
Rural Areas ◽  
Burkholderia Pseudomallei ◽  
Virulence Determinants ◽  
Secretion Systems ◽  
Research Support ◽  
Middle Income ◽  
Resistance Determinants ◽  
Low Middle Income Countries ◽  
Genomic Characterization

Abstract Background Melioidosis is a serious infection caused by Burkholderia pseudomallei (Bps), an opportunistic organism, highly adaptable and with a wide array of intrinsic virulence factors and antimicrobial resistance determinants. Bps is underdiagnosed due to its slow growth on routine laboratory media and the lack of robust diagnostic infrastructure in rural areas of low/middle income countries. Recent data indicates that Bps infections are increasing in Colombia (COL). However, the understanding of the genomic epidemiology and population structure of the emerging Bps isolates in COL is unknown. Here we characterize the genomic features of Bps isolates from infected patients in COL. Methods We identified 13 Bps clinical isolates recovered in 5 Colombian cities between 2018 and 2020. We performed WGS and phylogenomic analyses using Bayesian methods. For comparisons, we included 82 publicly available genomes from Bps recovered worldwide (including 10 additional isolates from COL). Additionally, we characterized the resistome, virulome and MLST of all isolates. Results 12 out of the 13 isolates were confirmed as Bps and 1 belonged to the B. cepacia complex. The Bps population structure was divided in two main clades: clade 1 with isolates from Asia and Australia, and clade 2 with isolates from Africa, America, and the Caribbean (Figure 1). We found two groups of Colombian isolates, the first was related to ST518 and the second, highly diverse including 11 different STs (1742, 1748, 92, among others). Genomic characterization showed the presence of β-lactamases PenA (n=11) and OXA-57 (n=1). We also identified a T584A substitution in PBP3 (n=11). All genomes contained virulence determinants of motility (BimA), invasion (Flagella), signaling (CdpA) and adherence (Type IV pili). Type III and VI secretion systems, were also found in all isolates resembling Bps from other parts of the world. Figure 1. Maximum clade credibility tree of 82 genomes of Bps. The inner ring shows the ST for each genome, while the outer ring shows the geographical region associated with them. Groups highlighted in red show the location of the Colombian genomes and those related to them. Conclusion Bps is an emerging pathogen in COL and its population structure seems highly diverse, predominantly of the American lineage and absence of Australasians strains. A high prevalence ( >90%) of resistance determinants, particularly related to β-lactams, suggest that active surveillance of these emergent pathogens is needed in countries like COL. Disclosures Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support) Lorena Diaz, PhD , Nothing to disclose

scholarly journals A Newly Discovered Forest of the Whip Coral Viminella flagellum (Anthozoa, Alcyonacea) in the Mediterranean Sea: A Non-Invasive Method to Assess Its Population Structure

Biology ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 39
Author(s):  
Giovanni Chimienti ◽  
Ricardo Aguilar ◽  
Michela Maiorca ◽  
Francesco Mastrototaro
Keyword(s):  
Population Structure ◽  
Ad Hoc ◽  
Anthropogenic Impacts ◽  
Tyrrhenian Sea ◽  
Non Invasive ◽  
The Status ◽  
Conservation Actions ◽  
Population Structures ◽  
Invasive Method ◽  
Southern Tyrrhenian Sea

Coral forests are vulnerable marine ecosystems formed by arborescent corals (e.g., Anthozoa of the orders Alcyonacea and Antipatharia). The population structure of the habitat-forming corals can inform on the status of the habitat, representing an essential aspect to monitor. Most Mediterranean corals live in the mesophotic and aphotic zones, and their population structures can be assessed by analyzing images collected by underwater vehicles. This is still not possible in whip-like corals, whose colony lengths and flexibilities impede the taking of direct length measurements from images. This study reports on the occurrence of a monospecific forest, of the whip coral Viminella flagellum in the Aeolian Archipelago (Southern Tyrrhenian Sea; 149 m depth), and the assessment of its population structure through an ad-hoc, non-invasive method to estimate a colony height based on its width. The forest of V. flagellum showed a mean density of 19.4 ± 0.2 colonies m−2 (up to 44.8 colonies m−2) and no signs of anthropogenic impacts. The population was dominated by young colonies, with the presence of large adults and active recruitment. The new model proved to be effective for non-invasive monitoring of this near threatened species, representing a needed step towards appropriate conservation actions.

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