scholarly journals Current Methods in the Molecular Typing ofMycobacterium tuberculosisand Other Mycobacteria

2014 ◽  
Vol 2014 ◽  
pp. 1-21 ◽  
Author(s):  
Tomasz Jagielski ◽  
Jakko van Ingen ◽  
Nalin Rastogi ◽  
Jarosław Dziadek ◽  
Paweł K. Mazur ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Human Disease ◽  
Molecular Typing ◽  
Phylogenetic Analyses ◽  
Research Question ◽  
Strain Typing ◽  
Critical Importance ◽  
Source Of Infection ◽  
Typing Methods ◽  
Transmission Studies

In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individualMycobacteriumstrains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on theMycobacteriumspecies under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing ofM. tuberculosisand some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.

scholarly journals Circulation of DistinctTreponema pallidumStrains in Individuals with Heterosexual Orientation and Men Who Have Sex with Men

2018 ◽  
Vol 57 (1) ◽  
Author(s):  
Yoko Kojima ◽  
Keiichi Furubayashi ◽  
Takuya Kawahata ◽  
Haruyo Mori ◽  
Jun Komano
Keyword(s):  
Molecular Typing ◽  
Treponema Pallidum ◽  
Adult Women ◽  
Strain Typing ◽  
Young Adult Women ◽  
Content Type ◽  
Global Trend ◽  
Typing Methods ◽  
Males And Females ◽  
Sex With Men

ABSTRACTHuman treponematosis is caused by various pathogenicTreponema pallidumsubspecies, includingT. pallidumsubsp.pallidum,T. pallidumsubsp.pertenue,T. pallidumsubsp.endemicum, andTreponema carateum. The global prevalence of syphilis has been increasing since the 2000s. Men account for more than 90% of the cases, with the majority being men who have sex with men (MSM). In Japan, the increase in the number of syphilis patients began in 2011, a 10-year delay from the global trend. In 2017, a total of 5,829 syphilis cases (3,934 men and 1,895 women) were reported, with an outstanding increase in cases among young adult women; the number reported for women age 15 to 20 years was 1,100. Hence, a molecular epidemiological study was conducted on circulatingT. pallidumstrains using two strain typing methods, the enhanced CDC method and sequencing-based molecular typing. Clinical specimens from 95 adults suspected of syphilis were collected from September 2013 to August 2017 in Osaka, Japan.T. pallidumDNA was detected in specimens from 25 males and 11 females, including seven MSM. The majority of the heterosexual patients (66.7% and 90.9% of males and females, respectively) were positive for 14d/f-SSR8. In contrast, the genotypes identified in the MSM group were significantly divergent.T. pallidumsubsp.endemicumwas notably identified in two MSM patients. Macrolide-sensitive or Nichols-like strains were significantly associated with the MSM group. These data suggest that distinctT. pallidumstrains were circulating in the heterosexual and MSM groups. Our findings imply that independent factors may contribute to the increased syphilis prevalence in heterosexual and MSM populations.

Evaluation of Molecular Typing Methods for Escherichia coli O157:H7 Isolates from Cattle, Food, and Humans

2004 ◽  
Vol 67 (4) ◽  
pp. 651-657 ◽  
Author(s):  
STEVEN L. FOLEY ◽  
SHABBIR SIMJEE ◽  
JIANGHONG MENG ◽  
DAVID G. WHITE ◽  
PATRICK F. McDERMOTT ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Foodborne Pathogens ◽  
Molecular Typing ◽  
Housekeeping Gene ◽  
Escherichia Coli O157 ◽  
E Coli ◽  
Source Of Infection ◽  
Life Threatening ◽  
Typing Methods

Escherichia coli O157:H7, a Shiga toxin–producing E. coli, has been the causative agent of many cases of severe, often life-threatening foodborne illness. Because of the importance of E. coli O157:H7 to public health, many molecular typing methods have been developed to determine its transmission routes and source of infection during epidemiological investigations. Pulsed-field gel electrophoresis (PFGE) is currently used by public health organizations to track infections of E. coli O157:H7 and other foodborne pathogens. In this study, we compared the ability of PFGE, multilocus sequence typing (MLST), and repetitive-element PCR (Rep-PCR) to distinguish among 92 E. coli O157:H7 isolates from cattle, food, and infected humans. Several virulence genes, including the intimin gene (eaeA), the hemolysin gene (hlyA), and the H7 fimbrial gene (fliC), and a housekeeping gene for β-glucuronidase (uidA) were included in MLST. Rep-PCR reactions were performed using a commercially available typing kit (Bacterial Barcodes Inc., Houston, Tex.) with the provided Uprime-RI primer set. Results of the study indicated that PFGE provided the most discrimination among the techniques, identifying 72 distinct PFGE profiles for the isolates; Rep-PCR elucidated 14 different profiles, whereas MLST generated five profiles. Additionally, there did not appear to be any correlation among the typing methods examined in this study. Therefore, to date, PFGE remains the technique of choice for molecular subtyping of E. coli O157:H7.

The Role of Free-Living Amoebae Occurring in Heated Effluents as Causative Agents of Human Disease

1983 ◽  
Vol 15 (10) ◽  
pp. 135-147
Author(s):  
Maurice A Shapiro ◽  
Meryl H Karol ◽  
Georg Keleti ◽  
Jan L Sykora ◽  
A J Martinez
Keyword(s):  
Human Disease ◽  
Power Plants ◽  
Elevated Temperatures ◽  
Human Subjects ◽  
Cooling Towers ◽  
Free Living ◽  
Cooling Systems ◽  
Delayed Onset ◽  
Source Of Infection ◽  
Causative Agents

It has been shown that several pathogenic organisms may be frequently found in thermal effluents and cooling systems of coal fired power plants. One of them is pathogenic Naegleria fowleri, the causative agent of an acute fatal human disease - primary amoebic meningoencephalitis (PAM). In our study two out of eight power plants investigated, harbored pathogenic N. fowleri in heated water or cooling towers. The occurrence of this organism was related to elevated temperatures. No significant correlation was found for other biological and chemical parameters. In addition, pathogenic Acanthamoeba which causes granulomatous amoebic encephalitis (GAE) was found in the tested heated effluents from coal fired power plants. Non-pathogenic strains of N. fowleri as well as other free-living and “harmless” amoebae were also very abundant in effluents from all investigated coal fired power plants and cooling towers. It has been reported that several species of nonpathogenic amoebae were isolated from humidifiers and air conditioning systems. Serological testing of symptomatic human subjects has indicated that these organisms may be one of the causative agents of hypersensitivity pneumonitis. An experimental study performed in our laboratory involved testing of guinea pigs sensitized by injection of axenic, non-pathogenic N. gruberi. Delayed onset skin reactivity was apparent in all animals injected with the antigen. Antibodies were detected in all sensitized animals. Bronchial provocation challenge employed to investigate pulmonary hypersensitivity was also used, and yielded positive results. All the sensitized animals displayed delayed onset respiratory responses. The results of this study indicate that not only pathogenic but also non-pathogenic free-living amoebae may be important causative agents of human disease. The occurrence of these organisms in cooling systems from coal fired power plants indicates that these facilities may be an important source of infection.

Outbreak ofStenotrophomonas maltophiliaBacteremia Among Patients Undergoing Bone Marrow Transplantation: Association With Faulty Replacement of Handwashing Soap

1999 ◽  
Vol 20 (11) ◽  
pp. 756-758 ◽  
Author(s):  
Jeffrey D. Klausner ◽  
Carol Zukerman ◽  
Ajit P. Limaye ◽  
Lawrence Corey
Keyword(s):  
Bone Marrow ◽  
Bone Marrow Transplantation ◽  
Healthcare Worker ◽  
Molecular Typing ◽  
Marrow Transplantation ◽  
Stenotrophomonas Maltophilia ◽  
Marrow Transplant ◽  
Hand Washing ◽  
Transplant Patients ◽  
Typing Methods

AbstractUsing molecular typing methods, we confirmed an outbreak ofStenotrophomonas maltophiliaamong bone marrow transplant patients. The likely source was a healthcare worker who may have washed with moisturizer instead of soap between patients. Hospital epidemiologists need to go beyond antibiograms when evaluating outbreaks and be vigilant about all aspects of hand washing.

Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽  
2021 ◽  
Vol 4952 (2) ◽  
pp. 331-353
Author(s):  
CHAO YANG ◽  
LE ZHAO ◽  
QINGXIONG WANG ◽  
HAO YUAN ◽  
XUEJUAN LI ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Gene Rearrangement ◽  
Phylogenetic Analyses ◽  
Protein Coding ◽  
Comparative Analyses ◽  
Protein Coding Genes ◽  
Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies. 

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

scholarly journals Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses

2003 ◽  
Vol 77 (13) ◽  
pp. 7202-7213 ◽  
Author(s):  
Marco Salemi ◽  
Tulio De Oliveira ◽  
Valerie Courgnaud ◽  
Vincent Moulton ◽  
Barbara Holland ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Decomposition Analysis ◽  
Phylogeny Reconstruction ◽  
Origin And Evolution ◽  
Immunodeficiency Virus ◽  
Primate Lentiviruses ◽  
Recombinant Fragments ◽  
Clustering Patterns

ABSTRACT To clarify the origin and evolution of the primate lentiviruses (PLVs), which include human immunodeficiency virus types 1 and 2 as well as their simian relatives, simian immunodeficiency viruses (SIVs), isolated from several host species, we investigated the phylogenetic relationships among the six supposedly nonrecombinant PLV lineages for which the full genome sequences are available. Employing bootscanning as an exploratory tool, we located several regions in the PLV genome that seem to have uncertain or conflicting phylogenetic histories. Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns. Split decomposition analysis also shows that phylogenetic relationships among PLVs may be better represented by network-based graphs, such as the ones produced by SplitsTree. Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts.

scholarly journals Review on Molecular Typing Methods of Pathogens

2014 ◽  
Vol 04 (03) ◽  
pp. 147-152 ◽  
Author(s):  
Tiehao Lin ◽  
Liying Lin ◽  
Fan Zhang
Keyword(s):  
Molecular Typing ◽  
Typing Methods

scholarly journals Pyrenochaetopsis kuksensis (Pyrenochaetopsidaceae), a new species associated with an ornamental boxwood in the Czech Republic

Phytotaxa ◽  
2021 ◽  
Vol 498 (3) ◽  
pp. 177-185
Author(s):  
MILAN ŠPETÍK ◽  
AKILA BERRAF-TEBBAL ◽  
ROBERT POKLUDA ◽  
ALEŠ EICHMEIER
Keyword(s):  
Czech Republic ◽  
New Species ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
New Taxon ◽  
The Czech Republic ◽  
Buxus Sempervirens ◽  
Fungal Microbiome ◽  
A New Species

During the investigation of fungal microbiome associated with boxwood in the Czech Republic, samples from Buxus sempervirens L. (Buxaceae) plants were collected and used for isolation. Two fungal strains were proposed as a new species Pyrenochaetopsis kuksensis based on morphology as well as phylogenetic analyses of ITS, LSU, rpb2, and tub2 sequence data. Detailed descriptions and phylogenetic relationships of the new taxon are provided.

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