Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters

This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differ ences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across differentMycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis —a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance.
Source: PLoS Computational Biology - Category: Biology Authors: Source Type: research

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Publication date: Available online 17 February 2020Source: Clinical Epidemiology and Global HealthAuthor(s): Krishna Prasad Acharya, Niran Adhikari, Muhammad TariqAbstractThe agro-climatic conditions, socio-economic situation, poor sanitation, low hygiene and health standards in Nepal are major contributing factors to the emergence of scrub typhus in Nepal. These outbreaks, along with poor diagnostic facilities, can lead to severe economic losses in a resource-limited country like Nepal. Diseases like avian influenza, leptospirosis, brucellosis, tuberculosis and rabies, that cause heavy socio-economic burden, have received...
Source: Clinical Epidemiology and Global Health - Category: Epidemiology Source Type: research
K. K. Tibbetts et al.
Source: Emerging Infectious Diseases Journal - Category: Infectious Diseases Source Type: research
Tuberculosis disproportionately affects the Canadian Inuit. To address this, it is imperative we understand transmission dynamics in this population. We investigate whether 'deep' sequencing can provide additional resolution compared to standard sequencing, using a well-characterized outbreak from the Arctic (2011-2012, 50 cases). Samples were sequenced to ~500-1000x and reads were aligned to a novel local reference genome generated with PacBio SMRT sequencing. Consensus and heterogeneous variants were identified and compared across genomes. In contrast with previous genomic analyses using ~50x depth, deep sequencing allow...
Source: eLife - Category: Biomedical Science Tags: Epidemiology and Global Health Source Type: research
Sandro Cinquetti Risk perception has a significant impact on decisions people make when facing a threat: a mismatch between actual hazard and perceived risk can lead to inappropriate behaviours and suboptimal compliance to recommended public health measures. The present study was conducted in the aftermath of a tuberculosis (TB) outbreak that occurred in 2019 in a primary school in Italy. The aim was to evaluate the impact of communication measures implemented by local health authorities (including face-to-face meetings between LHAs and the local population, weekly press announcements, implementation of a telephone ho...
Source: International Journal of Environmental Research and Public Health - Category: Environmental Health Authors: Tags: Article Source Type: research
per S Abstract The genotyping is applied to analyse tuberculosis detected in Aragon, Spain, since 2004. The new sequencing technologies were applied to analyse an outbreak which, the first time the responsible Myocbacterium tuberculosis strain of the outbreak appeared was in 2014, spreading to 14 patients in the next three years. We perform whole-genome sequencing (WGS) to characterise the strain and try to elucidate the transmission chain. The WGS results showed that this strain belonged to the Linage 4.3.3 and was genetically susceptible to anti-tuberculosis drugs. We found scarce variability between the isolate...
Source: Infection, Genetics and Evolution - Category: Genetics & Stem Cells Authors: Tags: Infect Genet Evol Source Type: research
Demystifying Medicine Lecture Series Ebola, swine flu, drug-resistant tuberculosis, diarrheal diseases, and just about anything carried by mosquitoes … These are but a few of the infectious diseases that keep Drs. Fauci and Glass awake at night. Oh, and ticks, too. Threats are everywhere. Every day, it seems, brings outbreaks and the potential for a pandemic. And yet, remarkably, scientists and healthcare providers on the frontlines manage to keep billions of people relatively safe. This Demystifying Medicine lecture by two of the biggest names in global health will provide a broad perspective on the myriad infectio...
Source: Videocast - All Events - Category: General Medicine Tags: Upcoming Events Source Type: video
Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions presen...
Source: BMC Infectious Diseases - Category: Infectious Diseases Authors: Tags: Research article Source Type: research
ng;B Abstract OBJECTIVES: Recurrent tuberculosis (TB) is defined by more than one TB episode per patient and is caused by reinfection with a new M. tuberculosis (Mtb) strain or relapse with the previous strain. In Denmark, a major TB outbreak caused by one specific Mtb genotype "DKC2" is ongoing. Of the 892 patients infected with DKC2 between 1992 and 2014, 32 had recurrent TB with 67 TB episodes in total. METHODS: The 32 cases were evaluated in terms of number of single-nucleotide polymorphism (SNP) differences and time between episodes derived from whole-genome sequencing data. RESULTS: For...
Source: Infection, Genetics and Evolution - Category: Genetics & Stem Cells Authors: Tags: Infect Genet Evol Source Type: research
Demystifying Medicine Lecture Series Ebola, swine flu, drug-resistant tuberculosis, diarrheal diseases, and just about anything carried by mosquitoes … These are but a few of the infectious diseases that keep Drs. Fauci and Glass awake at night. Oh, and ticks, too. Threats are everywhere. Every day, it seems, brings outbreaks and the potential for a pandemic. And yet, remarkably, scientists and healthcare providers on the frontlines manage to keep billions of people relatively safe. This Demystifying Medicine lecture by two of the biggest names in global health will provide a broad perspective on the myriad infectio...
Source: Videocast - All Events - Category: General Medicine Tags: Upcoming Events Source Type: video
In 2016, water lines at a children's dental clinic in Orange County, California were contaminated with Mycobacterium abscessus (MA), a non-tuberculosis rapidly-growing mycobacterium, leading to the largest MA outbreak ever reported. Mandatory reporting and active case finding directed by the Public Health Department was conducted in collaboration with community Pediatric Infectious Disease physicians for patients who underwent dental pulpotomies at the contaminated Dental Clinic from January 1 to September 6, 2016. Seventy-one cases (22 confirmed and 49 probable) were identified. One case that required extensive debridemen...
Source: Journal of Craniofacial Surgery - Category: Surgery Tags: Clinical Studies Source Type: research
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