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International Journal of Infectious... Jul 2020Clostridioides difficile is the major cause of infectious nosocomial diarrhoea in industrialized nations. Data on the occurrence of C. difficile in Africa, ribotype (RT)...
BACKGROUND
Clostridioides difficile is the major cause of infectious nosocomial diarrhoea in industrialized nations. Data on the occurrence of C. difficile in Africa, ribotype (RT) distribution, antimicrobial susceptibility patterns and potential zoonotic transmission are scarce.
METHODS
80 Zimbabwean C. difficile isolates from different sources (chicken [n=30], soil [n=21] and humans [n=29]) were investigated using ribotyping, toxin gene detection, resistance testing, multiple-locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing (WGS).
RESULTS
Among chicken isolates, the most common RTs were RT103 (6/30), RT025 (5/30) and RT070 (4/30). Within soil samples, RT025 and RT056 were most common (3/21 each). In contrast, the non-toxigenic RT084 was most frequently found in human isolates (4/29). Toxin genes were detected in only 19/29 human isolates. Susceptibility testing showed no resistance against metronidazole and vancomycin, and resistance against macrolides and rifampicin was scarce (3/80 and 2/80, respectively); however, 26/80 isolates showed moxifloxacin resistance. MLVA and WGS of strains with identical RTs stemming from different sources revealed clustering of RT025 and RT084 isolates from human und non-human samples.
CONCLUSION
No "hypervirulent" strains were found. The detected clusters between human, chicken and soil isolates indicate ongoing transmission between humans and environmental sources and might point towards a zoonotic potential.
Topics: Animals; Chickens; Clostridioides difficile; Drug Resistance, Bacterial; Humans; Minisatellite Repeats; Ribotyping; Soil Microbiology; Zimbabwe
PubMed: 32311450
DOI: 10.1016/j.ijid.2020.04.026 -
Microbial Genomics May 2021Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is...
Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is , which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of in Ethiopia. A total of 134 . isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of , based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.
Topics: Animals; Bacterial Typing Techniques; Cattle; Ethiopia; Europe; Genotype; Livestock; Minisatellite Repeats; Mycobacterium bovis; Sequence Analysis; Tuberculosis, Bovine; Whole Genome Sequencing
PubMed: 33945462
DOI: 10.1099/mgen.0.000539 -
Nutrients Jul 2020The dopamine D4 receptor (DRD4) has a predominant expression in the prefrontal cortex (PFC), brain area strictly involved in the modulation of reward processes related... (Review)
Review
The dopamine D4 receptor (DRD4) has a predominant expression in the prefrontal cortex (PFC), brain area strictly involved in the modulation of reward processes related to both food and drug consumption. Additionally, the human DRD4 gene is characterized by a variable number of tandem repeats (VNTR) in the exon 3 and, among the polymorphic variants, the 7-repeat (7R) allele appears as a contributing factor in the neurobiological mechanisms underlying drug abuse, aberrant eating behaviors and related comorbidities. The 7R variant encodes for a receptor with a blunted intracellular response to dopamine, and carriers of this polymorphism might be more tempted to enhance dopamine levels in the brain, through the overconsumption of drugs of abuse or palatable food, considering their reinforcing properties. Moreover, the presence of this polymorphism seems to increase the susceptibility of individuals to engage maladaptive eating patterns in response to negative environmental stimuli. This review is focused on the role of DRD4 and DRD4 genetic polymorphism in these neuropsychiatric disorders in both clinical and preclinical studies. However, further research is needed to better clarify the complex DRD4 role, by using validated preclinical models and novel compounds more selective for DRD4.
Topics: Alleles; Animals; Brain; Dopamine; Exons; Feeding and Eating Disorders; Genetic Predisposition to Disease; Humans; Minisatellite Repeats; Polymorphism, Genetic; Receptors, Dopamine D4; Substance-Related Disorders
PubMed: 32751662
DOI: 10.3390/nu12082288 -
International Journal of... 2021Paratuberculosis is an enteric disease caused by Mycobacterium avium sp. paratuberculosis (MAP) that affects mainly ruminant producing losses to the livestock industry....
Genetic diversity of sp. paratuberculosis by mycobacterial interspersed repetitive Unit-Variable number tandem repeat and multi-locus short-sequence repeat one-sentence summary: Genetic diversity of sp. paratuberculosis isolates.
BACKGROUND
Paratuberculosis is an enteric disease caused by Mycobacterium avium sp. paratuberculosis (MAP) that affects mainly ruminant producing losses to the livestock industry. Many molecular epidemiological methods have been used to discriminate MAP isolates.
METHOD
The aim of this study was to describe the genetic diversity of the Argentinean MAP isolates using a combination of two molecular systems, the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) ("automated and "non-automated") and the multi-locus short-sequence repeat (MLSSR) system.
RESULTS
Thirty-two isolates were identified as MAP of C type by IS900 polymerase chain reaction (PCA) and IS1311 PCA-restriction enzyme analysis. The main patterns found by both MIRU-VNTR systems were INMV1 (54.5%), INMV2 (24.2%) and INMV11 (9.1%). The INMV5, INMV8 and INMV16 were represented with one isolate each (3.0%). Only 4 MIRU-VNTR loci were polymorphic.
CONCLUSION
Those isolates sharing the same INMV patterns were analyzed by MLSSR, being locus 2 the most polymorphic one showing isolates with 9, 10, 11, and more than 11 "G" repeats. Besides, the global discriminatory power among isolates could be increased using both techniques. Based on these results, a short version of the "automated" MIRU-VNTR could be used as a screening tool to group isolates genetically related and subsequently perform the SSR using locus 2 on those isolates sharing the same INMV pattern.
Topics: Animals; Bacterial Typing Techniques; Genetic Variation; Genotype; Humans; Minisatellite Repeats; Mycobacterium avium subsp. paratuberculosis; Paratuberculosis
PubMed: 33707372
DOI: 10.4103/ijmy.ijmy_229_20 -
Transboundary and Emerging Diseases Sep 2022Eastern Siberia (Russia) and Mongolia are borderline regions in Asia with a high incidence of tuberculosis (TB). In this study, we investigated the transborder...
Eastern Siberia (Russia) and Mongolia are borderline regions in Asia with a high incidence of tuberculosis (TB). In this study, we investigated the transborder transmission of Mycobacterium tuberculosis with a focus on endemic and epidemic clones and drug resistance. M. tuberculosis isolates (287 from Mongolia and 754 from Russia) were collected using cross-sectional population-based surveys between 2010 and 2016. The isolates were genotyped using 24 variable number of tandem repeat loci and by testing of the key markers to discriminate within the Beijing genotype. All isolates were divided into 427 mycobacterial interspersed repetitive units types that were assigned to Lineage 2 (Beijing) and Lineage 4 (Ural, Haarlem, Latin American-Mediterranean [LAM], S, unclassified). The Beijing genotype was dominant in both countries (69% in Russia, 75% in Mongolia). However, the Beijing isolates differed significantly between the countries, in terms of the identified subtypes. LAM was the most common non-Beijing genotype (11.1% in Mongolia and 14.9% in Russia) and LAM isolates mostly belonged to the LAM-RUS branch in both countries. The multidrug-resistance (MDR) rate was higher in Russia than in Mongolia among newly diagnosed patients: 29.4% versus 5.6% (p < .001). In Mongolia, the MDR rate was similar in Beijing (29.7%) and non-Beijing (27.5%) genotypes. In Russia, a higher MDR rate was observed in (i) Beijing compared with non-Beijing (48.7% versus 38.3%, p = .03) and (ii) Beijing B0/W148 compared with Beijing Central Asian/Russian (63.4% versus 37.3%, p < .001). In conclusion, the M. tuberculosis population structure in Mongolia was shaped by mainly historical interaction with China (dominance of the Beijing genotype) and Northern Eurasia (presence of the LAM-RUS branch). In contrast, the transborder transmission of M. tuberculosis since the 1990s between Mongolia and its neighbours has been negligible, and the adverse trends of MDR-TB in Russia did not impact the current situation in Mongolia.
Topics: Animals; Antitubercular Agents; Cross-Sectional Studies; Genotype; Minisatellite Repeats; Mongolia; Mycobacterium tuberculosis; Russia; Siberia; Tuberculosis; Tuberculosis, Multidrug-Resistant
PubMed: 35294112
DOI: 10.1111/tbed.14515 -
PloS One 2020Candida kefyr causes invasive candidiasis in immunocompromised patients, particularly among those with oncohematological diseases. This study determined the prevalence...
OBJECTIVE
Candida kefyr causes invasive candidiasis in immunocompromised patients, particularly among those with oncohematological diseases. This study determined the prevalence of C. kefyr among yeast isolates collected during 2011-2018 in Kuwait. Antifungal susceptibility testing (AST) and genotypic heterogeneity among C. kefyr was also studied.
METHODS
Clinical C. kefyr isolates recovered from bloodstream and other specimens during 2011 to 2018 were retrospectively analyzed. All C. kefyr isolates were identified by CHROMagar Candida, Vitek2 and PCR amplification of rDNA. AST was performed by Etest. Molecular basis of resistance to fluconazole and echinocandins was studied by PCR-sequencing of ERG11 and FKS1, respectively. Genotypic heterogeneity was determined with microsatellite-/minisatellite-based primers and for 27 selected isolates by PCR-sequencing of IGS1 region of rDNA.
RESULTS
Among 8257 yeast strains, 69 C. kefyr (including four bloodstream) isolates were detected by phenotypic and molecular methods. Isolation from urine and respiratory samples from female and male patients was significantly different (P = 0.001). Four isolates showed reduced susceptibility to amphotericin B and one isolate to all (amphotericin B, fluconazole, voriconazole and caspofungin/micafungin) antifungals tested. Fluconazole-resistant isolate contained only synonymous mutations in ERG11. Echinocandin-resistant isolate contained wild-type hotspot-1 and hotspot-2 of FKS1. Fingerprinting with microsatellite-/minisatellite-based primers identified only three types. IGS1 sequencing identified seven haplotypes among 27 selected isolates.
CONCLUSIONS
The overall prevalence of C. kefyr among clinical yeast isolates and among candidemia cases was recorded as 0.83% and 0.32%, respectively. The frequency of isolation of C. kefyr from bloodstream and other invasive samples was stable during the study period. The C. kefyr isolates grown from invasive (bloodstream, bronchoalveolar lavage, abdominal drain fluid, peritonial fluid and gastric fluid) samples and amphotericin B-resistant isolates were genotypically heterogeneous strains.
Topics: Antifungal Agents; Blood; Candida; Candidiasis, Invasive; Drug Resistance, Fungal; Echinocandins; Female; Fluconazole; Fungal Proteins; Genetic Heterogeneity; Haplotypes; Humans; Kuwait; Male; Microsatellite Repeats; Phylogeny; Prevalence; Retrospective Studies; Sequence Analysis, DNA
PubMed: 33108361
DOI: 10.1371/journal.pone.0240426 -
Microbiology and Molecular Biology... Feb 2021Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative... (Review)
Review
Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.
Topics: Animals; Base Pairing; Cell Line, Tumor; Chromosome Fragile Sites; DNA; DNA Mismatch Repair; G-Quadruplexes; HeLa Cells; Humans; Minisatellite Repeats; Sequence Inversion; Trinucleotide Repeats
PubMed: 33361270
DOI: 10.1128/MMBR.00110-20 -
PloS One 2022Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB)....
INTRODUCTION
Mycobacterial Interspersed Repetitive Units-Variable Tandem Repeats (MIRU-VNTR) typing has been widely used for molecular epidemiological studies of tuberculosis (TB). However, genotyping tools for Mycobacterium tuberculosis (Mtb) may be limiting in some settings due to high cost and workload. In this study developed a customized stepwise MIRU-VNTR typing that prioritizes high discriminatory loci and validated this method using penitentiary system cohort in the country of Georgia.
METHODS
We used a previously generated MIRU-VNTR dataset from recurrent TB cases (32 cases) in Georgia and a new dataset of TB cases from the penitentiary system (102 cases) recruited from 2014 to 2015. A Hunter-Gaston Discriminatory Index (HGDI) was calculated utilizing a 24 standard loci panel, to select high discriminatory power loci, subsequently defined as the customized Georgia-specific set of loci for initial typing. The remaining loci were scored and hierarchically grouped for second and third step typing of the cohort. We then compared the processing time and costs of the customized stepwise method to the standard 24-loci method.
RESULTS
For the customized Georgia-specific set that was used for initial typing, 10 loci were selected with a minimum value of 0.32 to the highest HGDI score locus. Customized 10 loci (step 1) typing of 102 Mtb patient isolates revealed 35.7% clustered cases. This proportion was reduced to 19.5% after hierarchical application of 2nd and 3rd step typing with the corresponding groups of loci. Our customized stepwise MIRU-VNTR genotyping approach reduced the quantity of samples to be typed and therefore overall processing time and costs by 42.6% each.
CONCLUSION
Our study shows that our customized stepwise MIRU-VNTR typing approach is a valid alternative of standard MIRI-VNTR typing panels for molecular epidemiological investigation in Georgia that saves time, workload and costs. Similar approaches could be developed for other settings.
Topics: Bacterial Typing Techniques; DNA, Bacterial; Genotype; Georgia; Humans; Minisatellite Repeats; Molecular Epidemiology; Mycobacterium tuberculosis; Tuberculosis
PubMed: 35231041
DOI: 10.1371/journal.pone.0264472 -
Life Science Alliance Apr 2023The dopamine transporter gene, , has received substantial attention in genetic association studies of various phenotypes. Although some variable number tandem repeats...
The dopamine transporter gene, , has received substantial attention in genetic association studies of various phenotypes. Although some variable number tandem repeats (VNTRs) present in have been tested in genetic association studies, results have not been consistent. VNTRs in that have not been examined genetically were characterized. The Tandem Repeat Annotation Library was used to characterize the VNTRs of 64 unrelated long-read haplotype-phased sequences. Sequence similarity of each repeat unit of the five VNTRs is reported, along with the correlations of SNP-SNP, SNP-VNTR, and VNTR-VNTR alleles across the gene. One of these VNTRs is a novel hyper-VNTR (hyVNTR) in intron 8 of , which contains a range of 3.4-133.4 repeat copies and has a consensus sequence length of 38 bp, with 82% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. In addition, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it might be a recombination hotspot.
Topics: Alleles; Dopamine Plasma Membrane Transport Proteins; Haplotypes; Introns; Minisatellite Repeats; Humans
PubMed: 36754567
DOI: 10.26508/lsa.202201677 -
Forensic Science International. Genetics Nov 2021Opium poppy, a member of the Papaveraceae family, is an ancient herbaceous plant and well-known medical resource in the pharmaceutical industry. However, opium poppies...
Opium poppy, a member of the Papaveraceae family, is an ancient herbaceous plant and well-known medical resource in the pharmaceutical industry. However, opium poppies are grown worldwide for producing illicit drugs, significantly increasing the incidence of narcotic drug abuse. Since the narcotic poppy has not yet been genetically investigated, we characterized a novel variable number tandem repeat (VNTR) marker of forensically important poppy species based on the genetic analysis of 164 samples collected from two locations spanning the Jeolla province and Jeju island of South Korea. Comparing analysis of the chloroplast (cp) genome sequences for four representative species of Papaver (Papaver somniferum, Papaver somniferum subs. setigerum, Papaver orientale, and Papaver rhoeas) revealed a unique region with 1-3 repeats for 16 nucleotide motifs in the genome inverted repeat A (IRA, positions 128,651 to 128,698) region. For 16 nucleotide motifs, 3 repeats were found in P. somniferum, and 2 repeats were found in P. somniferum subs. setigerum. Therefore, 10 known and the 133 unknown, seized Papaver species were compared to determine whether the species could be identified via variations in the repeat units. The sizes of a novel VNTR ranged from 181 to 252 bp between the species. Phylogenetic analysis confirmed that a novel VNTR, which we named Pscp1, could clearly distinguish between the narcotic and non-narcotic types of Papaver species based on the patterns of sequence variation. Interestingly, we found that Pscp1 could also distinguish between P. somniferum and P. somniferum subs. setigerum. The regions of eight non-narcotic species displayed similar patterns and also differences were found due to the nucleotide substitution and deletion events. The structural differences of Pscp1 were observed within the two narcotic species or between the narcotic and non-narcotic species, suggesting that these variations may act as a genetic marker. We, therefore, developed a new Pscp1 PCR-capillary electrophoresis (CE) method that can reliably identify the narcotic type of Papaver species. Taken together, our findings suggest that the newly developed Pscp1 can be used as an identification marker of opium poppy, and establish that the Pscp1 genotyping method by PCR-CE is an effective primary screening tool that can also contribute to species discrimination in the field of forensic diagnosis and applications.
Topics: Genetic Markers; Humans; Minisatellite Repeats; Papaver; Phylogeny; Polymerase Chain Reaction
PubMed: 34517229
DOI: 10.1016/j.fsigen.2021.102581