Tag: rpoB

Why is strain identification for labeling accuracy of probiotic products important?5 answersStrain identification for labeling accuracy of probiotic products is important because probiotic health benefits are strain-specific. Different strains of probiotics have different effects on human health, and therefore it is crucial to include the correct strains in probiotic products…

Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef  PubMed  Google Scholar  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Arahal DR,…

Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020;70:5607–12. Article  PubMed  PubMed Central  Google Scholar  Saxena AK, Kumar M, Chakdar H, Anuroopa N, Bagyaraj DJ. Bacillus species in soil…

Construction of the VgrG database Encoded as a stand-alone gene or fused at the N-terminus of the toxin, the MIX domains can assist the delivery of their cognate T6SS effector19,20. As the central component of the spike complex, VgrG is a good marker to explore the potential conserved domains involved…

The 16S rRNA gene sequencing is insufficient to distinguish closely related Streptomyces species due to the large size of the Streptomyces genus. Strains with identical 16S rRNA gene sequences can have markedly different properties and be classified as different species. Multilocus sequence analysis (MLSA) based on atpD, gyrB, recA, rpoB,…

Introduction Infectious diseases are illnesses caused by pathogenic microbes such as bacteria, viruses, parasites, or fungus, which can be transmitted directly or indirectly from one person to another.1 Throughout human history, infectious illnesses have been a major cause of morbidity and mortality. One-third of all death worldwide is caused by…

Phase separation propensity of AMPs We retrieved the sequences of previously identified AMPs deposited into the Database of Antimicrobial Activity and Structure of Peptides (DBAASP)40 and in the APD3 antimicrobial peptide database41 to analyse their predicted propensities to undergo phase separation. Interestingly, we find that some AMPs possess features42,43,44 that…

Transcribed image text: 9.) A 2012 study was discussed in class providing evidence that recent horizontal gene transfer has contributed to the emergence of antibiotic resistance in human pathogenic bacteria such as Salmonella typhimurium. The study compared sequences of 16 S ribosomal RNA (rRNA) genes, rpoB genes, and various antibiotic resistance…

Zebra finches (Taeniopygia guttata) are laboratory animal species commonly used for modeling neurobiology and learning. Historically, using bacterial culture, biochemical analysis, and 16S ribosomal RNA gene sequencing, bacterial isolates from feces of finches housed at Massachusetts Institute of Technology had been presumptively diagnosed as Campylobacter jejuni, which is commonly isolated…

Global clinical results A total of 50,723 M. tuberculosis isolates with WGS and drug susceptibility test data from 64 countries were analysed, and encompassed all major lineages (L4 48.3%, L2 27.6%, L3 11.8%, L1 9.1%) (Table 1, Fig. 1B). Lineage 2.2.1 (Beijing strain-type) is the most prevalent in four of six…

Chloroplast genome features of four Polygonatum species In this phase of our study, we pursued the sequencing of four Polygonatum species namely P. filipes, P. cyrtonema, P. zanlanscianense and P. odoratum, using the Illumina HiSeq 2500 sequencing platform. This endeavour yielded a corpus of Illumina reads ranging from 15,915,998 to…

Study population Among the 60 cases, 28 were male (46.7%) and 32 were female (53.3%) ranging between 1.5 and 90 years of age; most patients were between 19 and 64 years (n = 26; 43.3%) or less than 9 years (n = 16; 26.7%). No difference in the proportion of stool submissions was observed by year, though…

Introduction The clinical symptoms and signs of pulmonary disease caused by nontuberculous mycobacteria (NTM) are very similar to tuberculosis, so differentiating the two becomes extremely challenging. Both diseases manifest cough, expectoration, hemoptysis, chest pain, and other respiratory symptoms, as well as systemic symptoms, such as fatigue and anorexia.1–3 Furthermore, NTM…

Introduction Klebsiella pneumoniae is a gram-negative opportunistic pathogen that can cause both community and hospital-acquired pneumonia, urinary tract infections, and bacteremia primarily in immunocompromised patients.1 Most experts agree that carbapenems are an effective treatment for serious infections brought on by Enterobacteriaceae that produce extended-spectrum beta-lactamases (ESBLs).2–4 Because of the wide…

Introduction According to the World Health Organization report 2022, the incidence rate of tuberculosis in China is 7.4%, with a year-on-year increase of 1.6%. China ranks third globally in terms of tuberculosis cases, with the top three countries being developing nations.1 It is worth noting that the tuberculosis mortality rate…

Hydrogeochemical properties of the arsenic-contaminated groundwater The hydrological and geochemical properties of the analyzed GW samples are summarized in Table 2. Temperature, pH, and dissolved oxygen (DO) levels were within acceptable limits for drinking water in all samples. The average temperature and pH of the As-contaminated GW samples were 27.33°C…

Nitrososphaeria AOA dominate archaeal and nitrifier assemblage throughout the year Nitrososphaeria AOA represented 79.4–100%, 75.4–98.0%, and 73.4–98.6% of total archaea and 2.8–7.6%, 1.0–1.8%, and 1.2–2.3% of total microbial communities in 16S rRNA gene amplicon, metagenome-recovered 16S rRNA genes, and prokaryotic rpoB-normalized amoA gene reads, respectively, throughout the year (Fig. 1A–C). Non-ammonia-oxidizing…

Introduction Tuberculosis is a threat to human health caused by Mycobacterium tuberculosis that affected lung and other extra-pulmonary sites. There was an estimated 10.0 million people fell ill with TB, 1.2 million TB deaths among HIV-negative people, and an additional 251,000 deaths among HIV-positive people in 2018 (World Health Organization,…

Pappas G, Papadimitriou P, Akritidis N, Christou L, Tsianos EV. The new global map of human brucellosis. Lancet Infect Dis. 2006;6(2):91–9. Article  PubMed  Google Scholar  Pappas G. The changing Brucella ecology: novel reservoirs, new threats. Int J Antimicrob Agents. 2010;36(Suppl 1):8–11. Article  Google Scholar  Wyatt HV. Lessons from the history…

Introduction Tuberculosis (TB), caused by etiological Mycobacterium tuberculosis (Mtb), remains a public health worldwide and the leading cause of death from a single infectious agent until the COVID-19 pandemic.1 Previous studies revealed that M. tuberculosis originated in Africa and spread with human migration worldwide, it developed to a contemporary phylogeny…

1. Introduction Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (MTB). According to the “Global Tuberculosis Report” published by the World Health Organization (WHO) in 2022, 10.6 million new cases of TB worldwide were estimated in 2021, and 1.4 million people died from the disease. That year, 3.6%…

Abedalthagafi M, Rosenberg O, Miller S (2014) First report of tenosynovitis in an immunocompetent person caused by Mycobacterium heraklionense. JMM Case Rep 1(2):e002071. doi.org/10.1099/jmmcr.0.002071 Ali ZI, Hanafy M, Hansen C, Saudi AM, Talaat AM (2021) Genotypic analysis of nontuberculous mycobacteria isolated from raw milk and human cases in Wisconsin. J Dairy…

Introduction Tuberculosis (TB) is one of the most common causes of death and the leading cause of a single infectious agent.1 According to the 2022 Global TB Report of the World Health Organization (WHO), 10.6 million people were infected with TB in 2021, and although the annual number of deaths…

Albert, T.J., Dailidiene, D., Dailide, G., Norton, J.E., Kalia, A., Richmond, T.A., Molla, M., Singh, J., Green, R.D., and Berg, D.E., Mutation discovery in bacterial genomes: metronidazole resistance in Helicobacter pylori, Nat. Methods, 2005, vol. 2, no. 12, pp. 951–953. Article  CAS  PubMed  Google Scholar  Ammor, M.S., Flórez, A.B., and…

Abstract Cotinus is an oligo‐specific ornamentally valuable genus with a disjunct distribution in the Northern Hemisphere. Traditionally, the taxonomy of Cotinus was mainly based on leaf morphological characteristics. However, the limited availability of genomic information greatly hindered the study of molecular evolution and phylogeny of this genus. This study sequenced…

1. Introduction Lactococcosis is a serious septicemic fish disease in Mediterranean countries. Lactococcus garvieae was considered the sole causative agent of lactococcosis until recently. L. garvieae has been isolated as a causative agent of the disease in several freshwater and marine species such as rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromis…

1. Introduction Since the beginning of extraterrestrial exploration by NASA, planetary protection (PP) has been an important effort to prevent biological forward contamination of non-Earth environments. The Committee on Space Research (COSPAR) has formulated a Planetary Protection Policy with associated implementation requirements as an international standard to protect against interplanetary biological…

Enrichment in ONT amplicon sequencing and adaptive sequencing The number of TB reads detected in clinical samples can vary from one to thousands, with over 90% human reads8,9. To simulate a simple TB metagenomic sample for enrichment evaluation using MinION amplicon sequencing and adaptive sequencing, we prepared a synthetic metagenomic…

Our choice of the shoestring fern H. ensiformis as a leptosporangiate fern for complete assembly of both organelle genomes was based on pronounced variability in mitochondrial RNA editing and intron (co-)evolution in the monilophyte family Pteridaceae and the sub-family Vittarioideae in particular22. We used next-generation sequencing (NGS) data to assemble…

Jagoueix, S., Bové, J. M. & Garnier, M. The phloem-limited bacterium of greening disease of citrus is a member of the α subdivision of the Proteobacteria. Int. J. Syst. Bacteriol. 44, 379–386 (1994). Article  CAS  PubMed  Google Scholar  Duan, Y. et al. Complete genome sequence of citrus huanglongbing bacterium, ‘Candidatus…

Introduction Klebsiella pneumoniae (KPN) is a common gram-negative bacterium that causes clinical infection, and studies have shown that it has the second-highest detection rate among all bacterial infections.1,2 Compared with common KPN (ie classic KPN [cKP]), hypervirulent KPN (HvKP) has the following characteristics: (1) Usually, HvKP colonies display a high-mucus…

Characteristics of the study population Among the 200 DR-TB cases, 146 (73.0%) cases were male, the median age was 66 (interquartile range = 55–78) years, 165 (82.5%) were new cases and 182 (91.0%) cases showed pulmonary TB (Table 1). The majority of DR-TB cases came from northern (74, 37.0%) Taiwan. Among the…

Isolation, phenotypic identification, pathogenicity and antibiogram profiling Enterococcus faecalis strains BFF1B1, BFFF11 and BFPS6 were cultured in Streptococcus selective agar media (Himedia, India). The culture characteristics such as colony, morphological, physiological and biochemical characteristics of these strains BFF1B1, BFFF11 and BFPS6 were summarized in the Supplementary Table S1. All of…

Introduction Klebsiella pneumoniae (Kp; K. pneumoniae) is an important hospital and community-acquired pathogen that primarily causes pneumonia, urinary tract infections, bloodstream-associated infections, meningitis, and pyogenic liver abscess.1–3 Carbapenem antibiotics represent the most important treatment for Enterobacteriaceae; however, with the widespread use of such antibiotics, carbapenem-resistant K. pneumoniae (CRKP) is increasingly…

1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9. PubMed  PubMed Central  CAS  Google Scholar  2. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A…

I am having trouble running the blastp command. When I run this command against the Swiss-prot database installed from the NCBI i get this error $ blastp -db swissprot -query Ecoli_rpoB.fasta -out TEST15.txt BLAST Database error: Error: Not a valid version 4 database. However, when I create my own database…

Introduction Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen and the leading cause of healthcare-associated infections.1 Multidrug-resistant (MDR) K. pneumoniae isolates are rapidly spreading, thus limiting the choice of antimicrobial agents for empiric treatment of infections caused by these microorganisms; hence, this is a public health challenge.2 Polymyxins are last-resort…

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

Introduction Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the top 10 causes of death worldwide and the leading cause of death from a single infectious agent (ranking above HIV/AIDS).1 In 2020, World Health Organization (WHO) reported that 7.1 million people with tuberculosis were newly diagnosed and notified in 2019,…