Is Multilocus Sequence Typing Approach Useful in Identification of Commensal Neisseria from Clinical Samples?

2018 ◽  
Vol 33 (4) ◽  
pp. 248-253
Author(s):  
Arij Mechergui ◽  
Wafa Achour ◽  
Dario Giorgini ◽  
Rekaya Baaboura ◽  
Muhamed-Kheir Taha ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Clinical Samples ◽  
Commensal Neisseria

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 An Extended Multilocus Sequence Typing (MLST) Scheme for Rapid Direct Typing of Leptospira from Clinical Samples

2016 ◽  
Vol 10 (9) ◽  
pp. e0004996 ◽  
Author(s):  
Sabrina Weiss ◽  
Angela Menezes ◽  
Kate Woods ◽  
Anisone Chanthongthip ◽  
Sabine Dittrich ◽  
...  
Keyword(s):  
Multilocus Sequence Typing ◽  
Clinical Samples ◽  
Mlst Scheme

scholarly journals Multilocus Sequence Typing of Pneumocystis jirovecii from Clinical Samples: How Many and Which Loci Should Be Used?

2013 ◽  
Vol 51 (9) ◽  
pp. 2843-2849 ◽  
Author(s):  
C. Maitte ◽  
M. Leterrier ◽  
P. Le Pape ◽  
M. Miegeville ◽  
F. Morio
Keyword(s):  
Multilocus Sequence Typing ◽  
Pneumocystis Jirovecii ◽  
Clinical Samples

scholarly journals High-resolution multilocus sequence typing for Chlamydia trachomatis: improved results for clinical samples with low amounts of C. trachomatis DNA

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shlomo Pilo ◽  
Gal Zizelski Valenci ◽  
Mor Rubinstein ◽  
Lea Pichadze ◽  
Yael Scharf ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Multilocus Sequence Typing ◽  
Phylogenetic Trees ◽  
Melting Curve ◽  
Pcr Amplification ◽  
Clinical Samples ◽  
Melting Curve Analysis ◽  
Whole Genome ◽  
Mlst Scheme ◽  
Low Concentrations

Abstract Background Several Multilocus Sequence Typing (MLST) schemes have been developed for Chlamydia trachomatis. Bom’s MLST scheme for MLST is based on nested PCR amplification and sequencing of five hypervariable genes and ompA. In contrast to other Chlamydia MLST schemes, Bom’s MLST scheme gives higher resolution and phylogenetic trees that are comparable to those from whole genome sequencing. However, poor results have been obtained with Bom’s MLST scheme in clinical samples with low concentrations of Chlamydia DNA. Results In this work, we present an improved version of the scheme that is based on the same genes and MLST database as Bom’s MLST scheme, but with newly designed primers for nested-1 and nested-2 steps under stringent conditions. Furthermore, we introduce a third primer set for the sequencing step, which considerably improves the performance of the assay. The improved primers were tested in-silico using a dataset of 141 Whole Genome Sequences (WGS) and in a comparative analysis of 32 clinical samples. Based on cycle threshold and melting curve analysis values obtained during Real-Time PCR of nested-1 & 2 steps, we developed a simple scoring scheme and flow chart that allow identification of reaction inhibitors as well as to predict with high accuracy amplification success. The improved MLST version was used to obtain a genovars distribution in patients attending an STI clinic in Tel Aviv. Conclusions The newly developed MLST version showed great improvement of assay results for samples with very low concentrations of Chlamydia DNA. A similar concept could be applicable to other MLST schemes.

scholarly journals Markedly Reduced Azithromycin and Ceftriaxone Susceptibility in Commensal Neisseria Species in Clinical Samples From Belgian Men Who Have Sex With Men

2020 ◽  
Author(s):  
Jolein G E Laumen ◽  
Christophe Van Dijck ◽  
Said Abdellati ◽  
Sheeba S Manoharan-Basil ◽  
Irith De Baetselier ◽  
...  
Keyword(s):  
Clinical Samples ◽  
Neisseria Species ◽  
Sex With Men ◽  
Commensal Neisseria

scholarly journals Molecular Characteristics of Carbapenem-resistant Klebsiella pneumoniae Isolates Producing blaVIM, blaNDM, and blaIMP in Clinical Centers in Isfahan, Iran

2021 ◽  
Vol 14 (2) ◽  
Author(s):  
Houri Alizadeh ◽  
Alireza Khodavandi ◽  
Fahimeh Alizadeh ◽  
Nima Bahador
Keyword(s):  
Klebsiella Pneumoniae ◽  
Multilocus Sequence Typing ◽  
Antibiotic Resistance Genes ◽  
Carbapenem Resistance ◽  
Detection Methods ◽  
Clinical Samples ◽  
Molecular Characteristics ◽  
Beta Lactamase ◽  
Global Public Health ◽  
Genes Encoding

Background: The emergence and spread of metallo-beta-lactamase (MBL)-producing Klebsiella pneumoniae are growing global public health concerns. One of the most common mechanisms of carbapenem resistance is the production of MBLs, including Verona Integron-encoded Metallo-beta-lactamase (VIM), imipenemase (IMP), and New Delhi metallo-beta-lactamase (NDM). Objectives: This study aimed to investigate MBLs production among K. pneumoniae isolates. Methods: In this study, 240 K. pneumoniae isolates were collected from clinical samples in three clinical centers of Isfahan, Iran, during February 2017 and November 2018. All isolates were identified using biochemical, microbiological, and molecular methods, and then antimicrobial susceptibility tests were performed to find MBL-producing isolates via phenotypic and genotypic detection methods. Moreover, the minimum inhibitory concentration (MIC) of antibiotics against MBL-positive strains was determined by E-test. Eventually, the clonal relatedness of the MBL-positive strains was analyzed using both multilocus sequence typing (MLST) and rep-PCR. Results: Overall, 33.7% (81/240) of the isolates were resistant to carbapenems, among which 25 (30.8%) were considered MBL-positive. Among 81 strains resistant to carbapenems, genes encoding FimH, rmpA, and mrkD were detected in 87.6% (71/81), 11.1% (9/81), and 67.95% (55/81) of the isolates, respectively. Besides, TEM and SHV as antibiotic resistance genes were detected in 49.3% (40/81) and 80.2% (65/81) of the isolates. But, magA was not detected in any of the tested isolates. The PCR results revealed that blaVIM-1 was the most prevalent gene (13.6%; 11/81), while both blaIMP-1 and blaNDM-1 were only detected in two isolates. Multilocus sequence typing demonstrated that 15 MBL producers belonged to three sequence types (ST): 11 to ST23, two to ST1147, and two to ST15. Finally, rep-PCR typing showed similar fingerprints with MLST, except for ST23, such that ST23 was discriminated in two clonal groups, suggesting the greater discriminatory power of rep-PCR. Conclusions: Here, we reported the emergence of MBL-producing K. pneumoniae in clinical centers of Isfahan, Iran. The findings are alarming and represent the urgent need for the application of infection control programs.

Detection of viruses by electron microscopy: Increased sensitivity by direct micro-ultracentrifugation of samples

1987 ◽  
Vol 45 ◽  
pp. 908-909
Author(s):  
Alain R. Trudel ◽  
M. Trudel
Keyword(s):  
Electron Microscopy ◽  
Fold Increase ◽  
Observation Time ◽  
Clinical Samples ◽  
Maximum Speed ◽  
Viral Particles ◽  
Structural Details ◽  
Latex Spheres ◽  
Increased Sensitivity ◽  
Size Of Particles

AirfugeR (Beckman) direct ultracentrifugation of viral samples on electron microscopy grids offers a rapid way to concentrate viral particles or subunits and facilitate their detection and study. Using the A-100 fixed angle rotor (30°) with a K factor of 19 at maximum speed (95 000 rpm), samples up to 240 μl can be prepared for electron microscopy observation in a few minutes: observation time is decreased and structural details are highlighted. Using latex spheres to calculate the increase in sensitivity compared to the inverted drop procedure, we obtained a 10 to 40 fold increase in sensitivity depending on the size of particles. This technique also permits quantification of viral particles in samples if an aliquot is mixed with latex spheres of known concentration.Direct ultracentrifugation for electron microscopy can be performed on laboratory samples such as gradient or column fractions, infected cell supernatant, or on clinical samples such as urine, tears, cephalo-rachidian liquid, etc..

External Validity of SCORS-G Ratings of Thematic Apperception Test Narratives in a Sample of Outpatients and Inpatients

2015 ◽  
Vol 36 (1) ◽  
pp. 58-81 ◽  
Author(s):  
Michelle B. Stein ◽  
Jenelle Slavin-Mulford ◽  
Caleb J. Siefert ◽  
Samuel Justin Sinclair ◽  
Michaela Smith ◽  
...  
Keyword(s):  
Life Events ◽  
Psychiatric Hospitalization ◽  
Clinical Care ◽  
Thematic Apperception Test ◽  
Clinical Samples ◽  
Cross Sectional ◽  
Conduct Disordered ◽  
Global Ratings ◽  
Thematic Apperception ◽  
History Of

Abstract. The Social Cognition and Object Relations Scale-Global Ratings Method (SCORS-G; Stein, Hilsenroth, Slavin-Mulford, & Pinsker-Aspen, 2011 ) is a reliable system for coding narrative data, such as Thematic Apperception Test (TAT) stories. This study employs a cross-sectional, correlational design to examine associations between SCORS-G dimensions and life events in two clinical samples. Samples were composed of 177 outpatients and 57 inpatients who completed TAT protocols as part of routine clinical care. Two experienced raters coded narratives with the SCORS-G. Data on the following clinically relevant life events were collected: history of psychiatric hospitalization, suicidality, self-harming behavior, drug/alcohol abuse, conduct-disordered behavior, trauma, and education level. As expected, the clinical life event variable associated with the largest number of SCORS-G dimensions was Suicidality. Identity and Coherence of Self was related to self-harm history across samples. Emotional Investment in Relationships and Complexity of Representations were also associated with several life events. Clinical applications, limitations of the study, and future directions are reviewed.

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