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Using Genotyping and Molecular Surveillance to Investigate Tuberculosis Transmission
Published in Lloyd N. Friedman, Martin Dedicoat, Peter D. O. Davies, Clinical Tuberculosis, 2020
Sarah Talarico, Laura F. Anderson, Benjamin J. Silk
The United Kingdom and United States both have recently implemented prospective WGS for all M. tuberculosis isolates for molecular surveillance purposes, which should allow for further insights via population-based surveillance studies. In addition, multilocus sequence typing (MLST) based on sequencing of the whole genome offers an opportunity to standardize a classification scheme. In one example, Kohl et al. used this gene-by-gene allele numbering approach to develop a core genome MLST (cgMLST) scheme that discriminated between isolates with a comparable resolution to that of whole-genome SNP analysis.32 Aside from use in epidemiological investigation, WGS has the additional advantage of providing species identification and detection of mutations that confer drug resistance. Although WGS of M. tuberculosis currently requires culturing, methods for sequencing directly from patient samples are being developed that will greatly reduce the time from sample collection to molecular epidemiology and antibiotic susceptibility results for a patient.33,34
Escherichia
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
Marta Rivas, Elizabeth Miliwebsky, Beatriz D'Astek, Luis Pianciola
Traditional culture techniques for pathogenic E. coli can be time consuming and laborious. The adoption of molecular techniques has allowed for more rapid detection and identification of the different pathotypes. Other methods have been developed to subtype isolates for phylogenetic analysis, outbreaks, and surveillance investigations. Pulsed-field gel electrophoresis (PFGE) is considered the gold standard for typing and is applied in epidemiological investigations to discriminate between outbreak isolates.18 The alternative method of multilocus variable-number tandem repeat analysis has been shown to discriminate between sporadic isolates and outbreaks.19 Multilocus sequence typing (MLST) has become a common method for typing pathogenic E. coli strains20 and establishing their relatedness. Whole genome sequencing (WGS) has proven to be a very powerful methodology, and there is an international agreement for its implementation for diagnosis and typing in public health due to additional improvement in bioinformatics tools and easy use in laboratories.21
Campylobacter Jejuni Infection
Published in Meera Chand, John Holton, Case Studies in Infection Control, 2018
At the reference laboratory, identification of the isolates was by species specific PCR and typing by multilocus sequence typing (MLST). The most common MLST type in the UK is ST-21. In this case, all the specimens from the patients, including the index case, were ST-45. This finding suggested that the index case was part of the same outbreak, although the patient did not eat the cannelloni in the hospital. Further epidemiological investigations into past behaviour identified a supplier of chicken liver paté with a positive culture of ST-45 Campylobacter from chicken liver collected from that supplier’s factory as the source of an extended regional outbreak. Frequently chicken liver paté is blended with other foods, and in this case it was included in the cannelloni.
Phenotypic whole-cell screening identifies a protective carbohydrate epitope on Klebsiella pneumoniae
Published in mAbs, 2022
Sophia K. Berry, Steven Rust, Carolina Caceres, Lorraine Irving, Josefin Bartholdson Scott, David E. Tabor, Gordon Dougan, Graham Christie, Paul Warrener, Ralph Minter, Andrew J. Grant
Clinical isolates were obtained from the International Health Management Associates (IHMA) as part of a collection from an international antibiotic resistance surveillance program. Basic demographic data (age, sex, hospital location, sample type, and length of stay) were provided for each isolate by the IHMA using a unique study number that was delinked from any patient identification. DNA was purified from bacterial cultures via bead beating followed by extraction using a PureLink Genomic DNA Mini Kit (ThermoFisher). Sequencing libraries were prepared by mechanical shearing of DNA (Covaris) followed by a NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs). Libraries were then run on an Illumina HiSeq, 2×150bp configuration. Sequence data was quality-trimmed, de-novo assembled and annotated using BugBuilder,30 and multilocus sequence typing (MLST) was performed using SRST2.31 In some cases, where whole genome sequences were unavailable, housekeeping genes used for MLST were PCR-amplified using methods described previously,32 with primers listed in Table S5, and then analyzed via the BIGSdb online server (http://bigsdb.pasteur.fr/klebsiella/klebsiella.html).
4CMenB vaccine and its role in preventing transmission and inducing herd immunity
Published in Expert Review of Vaccines, 2022
Mark McMillan, Helen S Marshall, Peter Richmond
The most accurate characterization of N. meningitidis is performed by conducting whole-genome sequencing [3]. Multilocus sequence typing (MLST) is used to assess variation at multiple genetic loci [3]. Neisseria spp. are incredibly diverse, with over 15,000 sequence types (STs) identified to date and hundreds of variants of the PorA OMP [3,90]. Although diverse, meningococci have been classified into groups that are closely related, called clonal complexes [91]. Whilst different from each other, a common origin can be identified, and these groups have been important in understanding the virulent lineages of meningococci [91]. These virulent hyper-invasive clonal complexes are responsible for a disproportionate number of IMD cases compared to their carriage prevalence in asymptomatic people [24,91]. The loss of the expression of their polysaccharide capsule enhances the ability of N. meningitidis to colonize the pharynx [92,93]. In carriage studies, up to half of the isolates from healthy carriers may not express a capsule [94]. However, multiple genetic mechanisms enable the meningococcus to change the expression of its polysaccharide capsule. This can occur through 1) on-off/off-on phase variation of capsule biosynthesis genes, 2) structural changes, or 3) changes in the amount of capsular polysaccharide expressed [93]. Unencapsulated disease-associated strains colonizing the pharynx, therefore have the ability to revert to encapsulated phenotypes once in the bloodstream [93].
Global epidemiology and changing clinical presentations of invasive meningococcal disease: a narrative review
Published in Infectious Diseases, 2022
Ala-Eddine Deghmane, Samy Taha, Muhamed-Kheir Taha
Meningococcal epidemiology remains unpredictable and can be linked to bacterial factors but also to environmental factors such as the association of meningococcal epidemics and the Harmattan sandy wind in sub-Saharan African countries and Santa Ana winds in Baja-California [5]. Due to meningococcal diversity, typing of Nm isolates has been a major challenge to explore this diversity. The MLST (MultiLocus Sequence Typing) method was first used to cluster the isolates on the basis of the partial sequences of 7 genes coding for enzymes of bacterial metabolism into diverse sequence types (ST) and the STs are grouped into clonal complexes (CC) according to the level of similarities of their allelic combinations [6]. Thereafter, whole-genome sequencing (WGS) allowed more resolution to resolve and monitor the spread of meningococcal genetic lineages [7].