BACKGROUND Strain typing is a tool for determining the diversity and epidemiology of infections. METHODS Treponema pallidum DNA was isolated from 158 patients with syphilis from the United States, China, Ireland, and Madagascar and from 15 T. pallidum isolates. Six typing targets were assessed: (1) the number of 60‐bp repeats in the acidic repeat protein gene, (2) restriction fragment length ...

The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framewor...

In this study, we present a trilocus sequence typing (TLST) scheme based on intragenic regions of two antigenic genes, ace and salA (encoding a collagen/laminin adhesin and a cell wall-associated antigen, respectively), and a gene associated with antibiotic resistance, lsa (encoding a putative ABC transporter), for subspecies differentiation of Enterococcus faecalis. Each of the alleles was ana...

Three molecular typing methods were used to study the relationships among 184 Campylobacter strains isolated from humans, cattle, and chickens. All strains were genotyped by amplified fragment length polymorphism (AFLP) analysis, multilocus sequence typing (MLST), and sequence analysis of a genomic region with short tandem repeats designated clustered regularly interspaced short palindromic rep...

Rotavirus is the leading causative agent of severe diarrhea among children.1 The rotavirus genome consists of 11 double-stranded RNA (dsRNA) segments enclosed in a double-shelled capsid. The outer shell is composed of a major glycoprotein (vp7), which defines the rotavirus serotype specificity. Nucleotide sequence analysis of vp7 cDNAs from different isolates indicates the presence of variable ...

BACKGROUND AND OBJECTIVES Although widely used, serological typing of HLA loci does not always produce uequivocal results. This may be particularly the case for cord blood since samples may be of small volume and poor quality, and contaminated. DESIGN AND METHODS We typed 220 cord blood units (CBU) for HLA class I antigens using the serological technique. For those samples giving doubtful res...

The aim of this paper is to introduce and study a new concept ofstrong double $(A)_ {Delta}$-convergent sequence offuzzy numbers with respect to an Orlicz function and also someproperties of the resulting sequence spaces of fuzzy   numbers areexamined. In addition, we define the double$(A,Delta)$-statistical convergence of fuzzy  numbers andestablish some connections between the spaces of stron...

Species limits within the clinically important Fusarium incarnatum-F. equiseti and F. chlamydosporum species complexes (FIESC and FCSC, respectively) were investigated using multilocus DNA sequence data. Maximum-parsimony and maximum-likelihood analyses of aligned DNA sequences from four loci resolved 28 species within the FIESC, within which the species were evenly divided among two clades des...

Sequence-based epidemiological typing of methicillin-resistant Staphylococcus aureus (MRSA) has recently been promoted because it results in unambiguous data sets that can be organized in local and global databases. The replacement of previous typing methods, such as the highly discriminatory pulsed-field gel electrophoresis (PFGE), has been attempted with various markers and typing schemes, in...

Vibrio cholerae is the etiological agent of cholera. Its natural reservoir is the aquatic environment. To date, practical typing of V. cholerae is mainly serological and requires about 200 antisera. Simple sequence repeats (SSR), also termed VNTR (for variable number of tandem repeats), provide a source of high genomic polymorphism used in bacterial typing. Here we describe an SSR-based typing ...