scholarly journals High genetic heterogeneity of Mycobacterium intracellulare isolated from respiratory specimens

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Nicoletta Lari ◽  
Laura Rindi
Keyword(s):  
Genetic Diversity ◽  
Respiratory Tract ◽  
Geographical Origin ◽  
Nontuberculous Mycobacteria ◽  
Geographical Area ◽  
Causative Pathogen ◽  
High Genetic Diversity ◽  
Mycobacterium Intracellulare ◽  
Vntr Analysis ◽  
Respiratory Specimens

Abstract Background M. intracellulare is a frequent causative pathogen of nontuberculous mycobacteria infection that causes infections in the respiratory tract, whose incidence is increasing in many countries. This study aimed at determining the VNTR-based genetic diversity of a collection of 39 M. intracellulare human strains isolated from respiratory specimens over the last 5 years. Results The VNTR analysis showed that M. intracellulare strains displayed a high genetic diversity, indicating that the M. intracellulare genotypes are quite heterogeneous in our geographical area. Moreover, a comparison with VNTR profiles of strains from other countries confirmed that genotypes of clinical strains of M. intracellulare are not related to geographical origin. Conclusions VNTR typing has proved to be a highly discriminatory method for better understanding the molecular epidemiology of M. intracellulare.

scholarly journals GENETIC DIVERSITY OF MYCOBACTERIUM AVIUM subsp. HOMINISSUIS STRAINS ISOLATED IN ITALY BASED ON VNTR LOCI ANALYSIS

2019 ◽  
Vol 8 (4) ◽  
pp. 441-446
Author(s):  
M. Menichini ◽  
F. Genua ◽  
N. Lari ◽  
L. Rindi
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Avium ◽  
Allelic Variation ◽  
Local Level ◽  
Geographical Area ◽  
Discriminatory Power ◽  
Mycobacterium Avium Subsp ◽  
Clinical Feature ◽  
Genetic Characteristics ◽  
Vntr Analysis

Abstract.Background.Mycobacterium avium subsp. hominissuis (MAH) is an important pathogen responsible for most of the human-associated nontuberculous mycobacteria infections. Over the past few decades the incidence of MAH infections is increasing in Italy, as in many countries worldwide. The present study is aimed to elucidate the genetic characteristics of MAH strains isolated from human patients using VNTR typing and to show the genetic relatedness among them.Methods.The genetic diversity of 108 human isolates of MAH was determined by VNTR analysis targeting 8 loci, coded 32, 292, X3, 25, 3, 7, 10 and 47.Results.The VNTR analysis revealed 25 distinct VNTR patterns; of these, 13 patterns were unique, while 12 patterns were shared by 2 or more isolates, thus yielding 12 clusters including a total of 95 isolates. The discriminatory power of our VNTR analysis yielded an HGDI of 0.990, indicating that VNTR typing has an excellent discriminatory power. No association of a particular VNTR pattern with a particular clinical feature, such as the disseminated, pulmonary or extrapulmonary type of infection, was observed. Minimum spanning tree analysis showed that 21 VNTR patterns, occurring either as clustered or unique isolates, differed from the nearest one for one allelic variation.Conclusions.The results obtained through the VNTR analysis showed that most MAH strains displayed a close genetic relationship. This high phylogenetic proximity of the VNTR loci over a long time period supports the concept that the MAH genotype is highly homogeneous in our geographical area, suggesting the hypothesis of the presence of possible sources of infection and transmission pathways at the local level.

Genetic diversity among geographically separated populations of Nepenthes mirabilis

Biologia ◽  
2006 ◽  
Vol 61 (3) ◽  
Author(s):  
Arunrat Chaveerach ◽  
Alongkod Tanomtong ◽  
Runglawan Sudmoon ◽  
Tawatchai Tanee
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Geographical Area ◽  
Inter Simple Sequence Repeat ◽  
Genetic Distances ◽  
High Genetic Diversity ◽  
Total Genetic Diversity ◽  
Environmental Variations ◽  
Diversity Profile ◽  
Great Genetic Diversity

AbstractThe distribution of Nepenthes mirabilis ranges from Northeast (NE) to South (S) Thailand. Eleven individuals from NE, S and Suen Jatujak market in Bangkok, Central (C) Thailand, were collected and divided into four populations according to their geographical areas. These four populations were analyzed to determine a genetic diversity profile using thirteen inter-simple sequence repeat markers. The individuals produced 75.18% polymorphic banding profiles. The Shannon’s index was used to estimate genetic diversity. Total genetic diversity (H T) and inter-population genetic diversity (H S) were 0.854 and 0.678, respectively. The degree of genetic differentiation (G ST) of the species populations is 0.206, whereas the gene flow (Nm) among all the various geographical area populations is 1.016. Both the dendrogram and the results of the Shannon’s diversity index suggest great genetic diversity. These results support the broad range of distribution sites of Nepenthes mirabilis, which would require high genetic diversity to adapt to the environmental variations that can be found between NE, C, and S Thailand. ANOVA shows that the genetic diversity in each population is not significantly different (P > 0.05). Mantel tests reveal that geographical distance is an important factor for affecting the genetic distances among populations.

scholarly journals Inter- and intra-variant genetic heterogeneity of human coronavirus OC43 strains in France

2006 ◽  
Vol 87 (11) ◽  
pp. 3349-3353 ◽  
Author(s):  
Astrid Vabret ◽  
Julia Dina ◽  
Thomas Mourez ◽  
Stéphanie Gouarin ◽  
Joëlle Petitjean ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cell Culture ◽  
Respiratory Tract ◽  
Respiratory Infections ◽  
Rt Pcr ◽  
Human Coronavirus ◽  
High Genetic Diversity ◽  
Close Relationship ◽  
Respiratory Tract Illness

Human coronavirus OC43 (HCoV-OC43) causes acute, self-limited respiratory infections. A close relationship between bovine coronaviruses (BCoVs) and HCoV-OC43 has recently been demonstrated. This study includes seven clinical, non-cell culture-adapted, contemporary HCoV-OC43 strains detected in France in 2003. By using RT-PCR and clonal sequencing of the S1 gene of HCoV-OC43, the inter-variant heterogeneity of the HCoV-OC43 circulating strains was studied and the intra-variant diversity was assessed by investigation of a quasispecies cloud. This paper brings to the forefront a high genetic diversity of circulating HCoV-OC43 variants. Genetically different groups are defined among the variants described in this study. One of these variants holds characteristics of an outlier and presents a deletion of 12 nt, also found in BCoV strains. Moreover, the presence of HCoV-OC43 as a quasispecies cloud in vivo during an acute respiratory-tract illness was discovered. It has also been revealed that quasispecies-cloud sizes are similar for the two viral populations tested.

scholarly journals Prevalence of Nontuberculous Mycobacteria in a Tertiary Hospital in Beijing, China, January 2013 to December 2018

2019 ◽  
Author(s):  
Jing-jing Huang ◽  
Ying-xing Li ◽  
Ying Zhao ◽  
Wen-hang Yang ◽  
Meng Xiao ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Nontuberculous Mycobacteria ◽  
Tertiary Hospital ◽  
Mycobacterium Abscessus ◽  
Mycobacterial Species ◽  
Aged Patients ◽  
Mycobacterium Chelonae ◽  
Microarray Chip ◽  
Mycobacterium Intracellulare ◽  
Beijing China

Abstract Background To investigate the species distribution of non-tuberculous mycobacteria (NTM) among tuberculosis (TB) specimens collected from January 2013 to December 2018 at Peking Union Medical Hospital (Beijing), China. NTM species identification was carried out by DNA microarray chip. Results Mycobacterial species were detected in 1514 specimens from 1508 patients, among which NTM accounted for 37.3% (565/1514), increasing from a prevalence of 15.6% in 2013 to 46.1% in 2018 ( P <0.001). Among the 565 NTM positive specimens, the majority (55.2%) were from female patients. Furthermore, patients aged 45-65 years accounted for 49.6% of the total patients tested. Among 223 NTM positive specimens characterized further, the majority (86.2%) were from respiratory tract, whilst 3.6% and 3.1% were from lymph nodes and pus, respectively. Mycobacterium intracellulare (31.8%) and Mycobacterium chelonae / Mycobacterium abscessus (21.5%) were the most frequently detected species, followed by M. avium (13.5%), M. gordonae (11.7%), M. kansasii (7.6%), and others. Conclusion The proportion of NTM among mycobacterial species detected in a tertiary hospital in Beijing, China, increased rapidly from year 2013 to 2018. Middle-aged patients are more likely to be infected with NTM, especially females. Mycobacterium intracellulare and Mycobacterium chelonae / Mycobacterium abscessus were the most frequently detected NTM pathogens. Accurate and timely identification of NTM is important for diagnosis and treatment.

Multilocus sequence typing (MLST) analysis of 104Clostridium difficilestrains isolated from China

2012 ◽  
Vol 141 (1) ◽  
pp. 195-199 ◽  
Author(s):  
Q. YAN ◽  
J. ZHANG ◽  
C. CHEN ◽  
H. ZHOU ◽  
P. DU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Clostridium Difficile ◽  
Multilocus Sequence Typing ◽  
Geographical Origin ◽  
Host Population ◽  
High Genetic Diversity ◽  
Dominant Type ◽  
Mlst Analysis ◽  
Phylogenetic Lineages ◽  
Sequence Types

SUMMARYThe phylogenetic and epidemic relationships of 104 clinical isolatesof Clostridium difficilefrom three hospitals of different geographical and population sources in China were investigated by multilocus sequence typing. Twenty-two sequence types (STs) were identified, four of which, ST117, ST118, ST119 and ST129, were novel. No geographically specific and host population-specific phylogenetic lineages were found and there was no correlation between geographical origin or host population and strain genotype. ST37 was the dominant type in our survey but the four novel STs underline the high genetic diversity and unique polymorphisms inC. difficilefrom China.

scholarly journals Prevalence of Nontuberculous Mycobacteria in a Tertiary Hospital in Beijing, China, January 2013 to December 2018

2020 ◽  
Author(s):  
Jing-jing HUANG ◽  
Ying-xing LI ◽  
Ying ZHAO ◽  
Wen-hang YANG ◽  
Meng XIAO ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Nontuberculous Mycobacteria ◽  
Tertiary Hospital ◽  
Mycobacterium Abscessus ◽  
Mycobacterial Species ◽  
Aged Patients ◽  
Mycobacterium Chelonae ◽  
Microarray Chip ◽  
Mycobacterium Intracellulare ◽  
Beijing China

Abstract Background To investigate the species distribution of non-tuberculous mycobacteria (NTM) among tuberculosis (TB) specimens collected from January 2013 to December 2018 at Peking Union Medical Hospital (Beijing), China. NTM species identification was carried out by DNA microarray chip. Results Mycobacterial species were detected in 1514 specimens from 1508 patients, among which NTM accounted for 37.3% (565/1514), increasing from a proportion of 15.6% in 2013 to 46.1% in 2018 ( P <0.001). Among the 565 NTM positive specimens, the majority (55.2%) were from female patients. Furthermore, patients aged 45-65 years accounted for 49.6% of the total patients tested. Among 223 NTM positive specimens characterized further, the majority (86.2%) were from respiratory tract, whilst 3.6% and 3.1% were from lymph nodes and pus, respectively. Mycobacterium intracellulare (31.8%) and Mycobacterium chelonae / Mycobacterium abscessus (21.5%) were the most frequently detected species, followed by M. avium (13.5%), M. gordonae (11.7%), M. kansasii (7.6%), and others. Conclusion The proportion of NTM among mycobacterial species detected in a tertiary hospital in Beijing, China, increased rapidly from year 2013 to 2018. Middle-aged patients are more likely to be infected with NTM, especially females. Mycobacterium intracellulare and Mycobacterium chelonae / Mycobacterium abscessus were the most frequently detected NTM pathogens. Accurate and timely identification of NTM is important for diagnosis and treatment.

scholarly journals High Genetic Diversity of Ciprofloxacin-Nonsusceptible Isolates of Streptococcus pneumoniae in Poland

2005 ◽  
Vol 49 (5) ◽  
pp. 2126-2129 ◽  
Author(s):  
Ewa Sadowy ◽  
Radosław Izdebski ◽  
Anna Skoczyńska ◽  
Marek Gniadkowski ◽  
Waleria Hryniewicz
Keyword(s):  
Genetic Diversity ◽  
Streptococcus Pneumoniae ◽  
Respiratory Tract ◽  
Gel Electrophoresis ◽  
Multilocus Sequence Typing ◽  
Pulsed Field Gel Electrophoresis ◽  
Respiratory Tract Diseases ◽  
High Genetic Diversity ◽  
Resistance Determinants ◽  
Great Genetic Diversity

ABSTRACT We have analyzed the susceptibility to ciprofloxacin of 697 pneumococcal isolates collected in 1998-2002 in Poland from patients with respiratory tract diseases. Thirty-one ciprofloxacin-nonsusceptible isolates (MICs, ≥4 μg/ml) were identified, of which two were resistant to levofloxacin (MIC, 8 μg/ml). Serotyping, pulsed-field gel electrophoresis, multilocus sequence typing, and the analysis of resistance determinants showed their great genetic diversity.

scholarly journals Genetic diversity ofPoa pratensisL. depending on geographical origin and compared with genetic markers

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2489 ◽  
Author(s):  
Magdalena Szenejko ◽  
Przemysław Śmietana ◽  
Edyta Stępień
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Geographical Origin ◽  
Poa Pratensis ◽  
Common Species ◽  
Multivariate Methods ◽  
Habitat Conditions ◽  
High Genetic Diversity ◽  
Rapd And Issr ◽  
Substantial Degree

BackgroundPoa pratensisis one of the most common species of meadow grass in Europe. Most cultivars of the species found in Poland were originally derived from its ecotypes. We compared the effectiveness of the RAPD and ISSR methods in assessing the genetic diversity of the selected populations ofP. pratensis. We examined whether these methods could be useful for detecting a possible link between the geographical origin of a given population and its assessed genetic variation.MethodsThe molecular markers RAPD and ISSR were used and their efficiency compared using, inter alia, statistical multivariate methods (UPGMA and PCA).ResultsThe low value of Dice’s coefficient (0.369) along with the significantly high percentage of polymorphic products indicates a substantial degree of genetic diversity among the studied populations. Our results found a correlation between the geographical origin of the studied populations and their genetic variations. For ISSR, which proved to be the more effective method in that respect, we selected primers with the greatest differentiating powers correlating to geographical origin.DiscussionThe populations evaluated in this study were characterized by a high genetic diversity. This seems to confirm the hypothesis that ecotypes ofP. pratensisoriginating from different regions of Central Europe with different terrain structures and habitat conditions can be a source of great genetic variability.

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