scholarly journals Markers to Rapidly Distinguish Bacillus paralicheniformis From the Very Close Relative, Bacillus licheniformis

2021 ◽  
Vol 11 ◽  
Author(s):  
Atinuke M. Olajide ◽  
Shu Chen ◽  
Gisèle LaPointe
Keyword(s):  
Bacillus Licheniformis ◽  
Ribosomal Rna ◽  
Close Relative ◽  
Rrna Gene ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ionization Time ◽  
Bacillus Paralicheniformis ◽  
Rrna Gene Sequencing ◽  
Close Relatives

As close relatives, Bacillus paralicheniformis is often wrongly identified as Bacillus licheniformis. In this study, two genetic markers are presented based on fenC and fenD from the fengycin operon of B. paralicheniformis to rapidly distinguish it from B. licheniformis. The fengycin operon is one of the few present in B. paralicheniformis but absent in B. lichenformis up to date. Using these markers, two presumptive B. paralicheniformis isolates each were recovered from a set of isolates previously identified as B. licheniformis by Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) or identified only to genus level as Bacillus by 16S ribosomal RNA (rRNA) gene sequencing, respectively. Whole genome sequencing of the four isolates confirmed their identity as B. paralicheniformis having the closest similarity with B. paralicheniformis ATCC 9945a (GenBank: CP005965.1) with a 7,682 k-mer score and 97.22% Average Nucleotide Identity (ANI). ANI of 100% suggests that the four isolates are highly similar. Further analysis will be necessary to determine if finer differences exist among these isolates at the level of single nucleotide polymorphisms.

scholarly journals Evaluation of a Custom SNP Panel for Identifying and Rectifying of Misjudged Paternity in Deficiency Cases

2021 ◽  
Vol 12 ◽  
Author(s):  
Liao Chang ◽  
Huiyun Yu ◽  
Xinyao Miao ◽  
Siqi Wen ◽  
Bao Zhang ◽  
...  
Keyword(s):  
Individual Identification ◽  
Close Relative ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Parentage Testing ◽  
Snp Panel ◽  
Custom Panel ◽  
Close Relatives ◽  
Short Tandem ◽  
Deficiency Cases

Parentage testing is routinely performed by genotyping short tandem repeat (STR) through capillary electrophoresis in the present. However, ambiguous or even misjudged paternity based on STRs happens from time to time in cases where only one putative parent is available. We analyzed STR data of 7,818,969 unrelated pairs and 75 close-relative pairs and found that although the probability of a random false match between non-relatives was 4.22 × 10–6, the incidence of false or ambiguous paternity results between children and first-degree relatives of their true parent was as high as 18.67%. These results highlight the risk of false inclusion of a relative or even non-relatives in parentage testing with STRs. We then validated all ambiguous STR results by targeted sequencing with a custom panel containing 4,830 individual identification single nucleotide polymorphisms (IISNP), found that the ratio of mismatch loci to total SNPs was 1.78–6.95% in close relatives compared with 10.93–13.49% in unrelated pairs. Last, we reported three real cases with undetermined paternity by STRs and rectified them by dissecting with our IISNP panel. These results suggested that high-density IISNP panel can be used to identify and rectify misjudged cases effectively.

scholarly journals Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry in diagnosis of clinical Nocardia species

2019 ◽  
Vol 43 (3) ◽  
pp. 157-162
Author(s):  
Gülşen Hasçelik ◽  
Markus Kostrzewa ◽  
Hamit Kaan Müştak ◽  
Celalettin Uner ◽  
Kadir Serdar Diker
Keyword(s):  
Species Level ◽  
Rrna Gene ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Maldi Biotyper ◽  
Rrna Gene Sequencing ◽  
Tof Ms

Abstract Background The routine identification to the species level of Nocardia genus by conventional methods is a fastidious and time-consuming process owing to the limited biochemical reactivity of these microorganisms, often requiring 1 or more days to complete identification. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a new technology for definitive and rapid species identification. Methods We evaluated the MALDI-TOF MS for the identification of 44 clinical isolates of Nocardia species in comparison to 16S ribosomal RNA (rRNA) gene sequencing. Nocardia isolates were identified by microbiological examination, phenotypical tests and MALDI-TOF MS and the results were compared by 16S rRNA gene sequencing. Results Of the 44 Nocardia strains, the identification of 28 isolates was determined with MALDI Biotyper database. According to this, 16 isolates (57.1%) of the strain log scores were ≥2. Two (7.1%) were identified to the species level (log scores of ≥2) as Nocardia otitidiscaviarum. The addition of a newly established Nocardia database (16 new Nocardia strains included to the original database) did significantly improve the scores. The results were 43 (97.7%) correct identification to the species level (log scores of ≥2). Conclusions This study showed that the identification of clinical Nocardia isolates by the Bruker MALDI Biotyper is highly reliable, whereas identification rates are generally lower than those for some Gram-negative bacteria and Gram-positive cocci. Based on our data, the identification rates can be improved by validated new database entries and the results can be confirmed with nucleic acid sequence analysis.

scholarly journals Association of ATM Gene Polymorphism with PTC Metastasis in Female Patients

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Yulu Gu ◽  
Xiaoli Liu ◽  
Yaqin Yu ◽  
Jieping Shi ◽  
Lizhe Ai ◽  
...  
Keyword(s):  
Northern China ◽  
Dna Lesions ◽  
Nucleotide Polymorphisms ◽  
Ataxia Telangiectasia Mutated ◽  
Single Nucleotide ◽  
Ionization Time ◽  
Flight Mass Spectrometry ◽  
Codominant Model ◽  
Atm Gene ◽  
Gender Specific

Ataxia telangiectasia mutated (ATM) gene is critical in the process of recognizing and repairing DNA lesions and is related to invasion and metastasis of malignancy. The incidence rate of papillary thyroid cancer (PTC) has increased for several decades and is higher in females than males. In this study, we want to investigate whether ATM polymorphisms are associated with gender-specific metastasis of PTC. 358 PTC patients in Northern China, including 109 males and 249 females, were included in our study. Four ATM single nucleotide polymorphisms (SNPs) were genotyped using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS). Association between genotypes and the gender-specific risk of metastasis was assessed by odds ratios (OR) and 95% confidence intervals (CI) under the unconditional logistic regression analysis. Significant associations were observed between rs189037 and metastasis of PTC in females under different models of inheritance (codominant model:OR=0.15, 95% CI 0.04–0.56,P=0.01for GA versus GG andOR=0.08, 95% CI 0.01–0.74,P=0.03for AA versus GG, resp.; dominant model:OR=0.49, 95% CI 0.25–0.98,P=0.04; overdominant model:OR=0.47, 95% CI 0.25–0.89,P=0.02). However, no association remained significant after Bonferroni correction. Our findings suggest a possible association between ATM rs189037 polymorphisms and metastasis in female PTCs.

scholarly journals Six species of non-tuberculosis mycobacteria carry non-identical 16S rRNA gene copies

2018 ◽  
Author(s):  
Keita Takeda ◽  
Kinuyo Chikamatsu ◽  
Yuriko Igarashi ◽  
Yuta Morishige ◽  
Yoshiro Murase ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Target Sequence ◽  
Nucleotide Polymorphisms ◽  
16S Rrna Gene Sequences ◽  
Cloning And Sequencing ◽  
Single Nucleotide ◽  
Gene Copies ◽  
The 16S Rrna Gene

AbstractNon-tuberculosis mycobacteria (NTM) can carry two or more 16S rRNA gene copies that are, in some instances, non-identical. In this study, we used a combined cloning and sequencing approach to analyze the 16S rRNA gene sequences of six NTM species,Mycobacterium cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, andM. xenopi. The approach facilitated the identification of two distinct gene copies in each species. The twoM. cosmeticumgenes had a single nucleotide difference, whereas two nucleotide polymorphisms were identified inM. hodleri, M. flavescens, andM. xenopi. M. pallenshad a difference in four nucleotides andM. crocinumin 23. Hence, we showed that the six NTM species possess at least two non-identical 16S rRNA gene copies.ImportanceThe presence of multiple 16S rRNA gene copies with nucleotide polymorphisms represents a challenge for species identification using 16S rRNA as the target sequence. Our analysis was focused on six NTM species,M. cosmeticum, M. pallens, M. hodleri, M. crocinum, M. flavescens, andM. xenopi. As a result, we generated the full-length sequences of two non-identical 16S rRNA copies for each NTM species. The data will be helpful for the sequence analysis of specimens or other samples.

scholarly journals The Evolution of Multidrug Resistance in an Isolated Pseudomonas Strain

2020 ◽  
Vol 17 (3) ◽  
pp. 41-50
Author(s):  
Allison Grodnick ◽  
Ashley Fink ◽  
Timothy Johnson ◽  
David Mitchell
Keyword(s):  
Multidrug Resistance ◽  
Bacterial Strain ◽  
Acquired Resistance ◽  
16S Rrna Gene Sequencing ◽  
Multidrug Resistant ◽  
Rrna Gene ◽  
Nucleotide Polymorphisms ◽  
Forest Environment ◽  
Antibiotic Drugs ◽  
Rrna Gene Sequencing

As an unintentional result of the extensive use of antibiotics in healthcare and agriculture, antibiotics have become an increasingly prevalent selective pressure on bacteria. This forces bacteria to evolve and acquire antibiotic-resistant genes or mutations in order to survive. Suppose a bacterial strain acquires resistance to three or more antibiotics. In that case, it is deemed multidrug-resistant (MDR), and it becomes a potentially more serious problem to solve in the context of healthcare. This study aims to evaluate the acquisition of resistance to multiple antibiotic drugs by an initially susceptible isolated bacterium from a Minnesota forest environment. The bacterium was found to be Pseudomonas by 16s rRNA gene sequencing. Three antibiotics, neomycin, ciprofloxacin, and imipenem, each from a different drug class, were selected to see if this isolate could become resistant over time and exposure. The bacterial strain developed resistance to the selected antibiotics through a series of sequential exposures to increasing concentrations of each drug in this order. As determined by a disc susceptibility test, the initial isolate acquired resistance to all three selected antibiotics. Single nucleotide polymorphisms (SNPs) between the original isolate and the final resistant strain were identified. These SNPs suggest that mutations to efflux transporters and antibiotic protein targets play a role in acquiring and maintaining antibiotic resistance. KEYWORDS: Multidrug Resistance; Antibiotics; Neomycin; Ciprofloxacin; Imipenem; Pseudomonas; Evolution; MDR; Minnesota Environment

scholarly journals Evidence of adoption, monozygotic twinning, and low inbreeding rates in a large genetic pedigree of polar bears

2015 ◽  
Author(s):  
René M. Malenfant ◽  
David W. Coltman ◽  
Evan S. Richardson ◽  
Nicholas J. Lunn ◽  
Ian Stirling ◽  
...  
Keyword(s):  
Mating Systems ◽  
Parentage Analysis ◽  
Hudson Bay ◽  
Polar Bears ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Monozygotic Twinning ◽  
Close Relatives ◽  
Free Ranging ◽  
First Time

Multigenerational pedigrees have been developed for free-ranging populations of many species, are frequently used to describe mating systems, and are used in studies of quantitative genetics. Here, we document the development of a 4449-individual pedigree for the Western Hudson Bay subpopulation of polar bears (Ursus maritimus), created from relationships inferred from field and genetic data collected over six generations of bears sampled between 1966 and 2011. Microsatellite genotypes for 22-25 loci were obtained for 2945 individuals, and parentage analysis was performed using the program FRANZ, including additional offspring-dam associations known only from capture data. Parentage assignments for a subset of 859 individuals were confirmed using an independent medium-density set of single nucleotide polymorphisms. To account for unsampled males in our population, we performed half-sib/full-sib analysis to reconstruct males using the program COLONY, resulting in a final pedigree containing 2957 assigned maternities and 1861 assigned paternities with only one observed case of inbreeding between close relatives. During genotyping, we identified two independently captured two-year-old males with identical genotypes at all 25 loci, showing--for the first time--a case of monozygotic twinning among polar bears. In addition, we documented six new cases of cub adoption, which we attribute to cub misidentification or misdirected maternal care by a female bereaved of her young. Importantly, none of these adoptions could be attributed to reduced female vigilance caused by immobilization to facilitate scientific handling, as has previously been suggested.

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