scholarly journals Linked seasonal outbreaks of Salmonella Typhimurium among passerine birds, domestic cats and humans, Sweden, 2009 to 2016

2019 ◽  
Vol 24 (34) ◽  
Author(s):  
Robert Söderlund ◽  
Cecilia Jernberg ◽  
Linda Trönnberg ◽  
Anna Pääjärvi ◽  
Erik Ågren ◽  
...  
Keyword(s):  
Historical Data ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Passerine Birds ◽  
Domestic Cats ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Repeat Analysis ◽  
Mass Migration ◽  
Bird Feeders

In 2016, an outbreak of Salmonella Typhimurium (STm) with multilocus variable-number tandem repeat analysis (MLVA) profiles historically associated with passerine birds (2-[11-15]-[3-4]-NA-212) occurred among passerines, cats and humans in Sweden. Our retrospective observational study investigated the outbreak and revisited historical data from 2009–16 to identify seasonality, phylogeography and other characteristics of this STm variant. Outbreak isolates were analysed by whole-genome single nucleotide polymorphism (SNP) typing. The number of notified cases of passerine-associated STm among passerines, cats and humans per month and county, and their MLVA profiles, were compared to birdwatchers’ counts of passerines. Seasonal trend decomposition and correlation analysis was performed. Outbreak isolates did not cluster by host on SNP level. Passerine-associated STm was seasonal for birds, cats and humans, with a peak in March. Cases and counts of passerines at bird feeders varied between years. The incidence of passerine-associated STm infections in humans was higher in the boreal north compared with the southern and capital regions, consistent with passerine population densities. Seasonal mass migration of passerines appears to cause STm outbreaks among cats certain years in Sweden, most likely via predation on weakened birds. Outbreaks among humans can follow, presumably caused by contact with cats or environmental contamination.

scholarly journals Retrospective Analysis of the Relationship between Two Anthrax Outbreaks in Kazakhstan Based on Genomic Data

2020 ◽  
Vol 9 (50) ◽  
Author(s):  
Alexandr Shevtsov ◽  
Gilles Vergnaud ◽  
Asylulan Amirgazin ◽  
Larissa Lukhnova ◽  
Uinkul Izbanova ◽  
...  
Keyword(s):  
Retrospective Analysis ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Repeat Analysis ◽  
Source Of Infection ◽  
Western Kazakhstan ◽  
Genome Wide ◽  
The Relationship

ABSTRACT We present a retrospective analysis of strains from two anthrax outbreaks in western Kazakhstan in 2009. The outbreaks occurred during the same period and in the same area located close to main roads, favoring a single source of infection. However, multilocus variable-number tandem-repeat analysis (MLVA), canonical single-nucleotide polymorphism (CanSNP) analysis, and genome-wide analysis demonstrated that the outbreaks were not connected.

scholarly journals Drug-resistant Mycobacterium tuberculosis and its genotypes isolated from an outbreak in western Thailand

2020 ◽  
Author(s):  
Janisara Rudeeaneksin ◽  
Benjawan Phetsuksiri ◽  
Chie Nakajima ◽  
Supranee Bunchoo ◽  
Krairerk Suthum ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Variable Number Tandem Repeat ◽  
Multidrug Resistant ◽  
Variable Number ◽  
Drug Resistant ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Extensively Drug Resistant ◽  
Mdr Tb ◽  
Vntr Analysis

Abstract Background Multidrug-resistant TB (MDR-TB) outbreaks have occurred in the Thamaka district, Kanchanaburi province in Thailand. Methods Seventy-two isolates, which included 7% mono-, 30.6% MDR and extensively drug-resistant TB (XDR-TB), were genotyped by spoligotyping, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) and single nucleotide polymorphism genotyping, and their drug resistance was analysed. Results The spoligotyping results showed that Beijing spoligo-international type (SIT)1 was predominant (n=38; 52.8%) while the remaining were non-Beijing sublineages (n=34). The MIRU-VNTR analysis showed that Beijing isolates, most of which belonged to the modern type (n=37), formed 5 clusters and 13 individual patterns. In katG, only mutation Ser315Thr was identified. In rpoB, Ser531Leu was predominant, except for His526Arg and Leu533Pro, which were found in two isolates. A cluster of 14 Beijing strains contained these common mutations and shared the MIRU-VNTR genotype with isolates in the Thamaka district that had spread previously. Two U SIT523 isolates contained the mutations A1400G in rrs and Asp94Gly in gyrA genes, indicating a spread of XDR-TB. Conclusions Most mutations were associated with drug resistance and the specific MDR Beijing and XDR-TB in U SIT523 isolates remain. This genotyping is a key tool for tracking TB transmission in the Thamaka district of Thailand.

scholarly journals Genetic Diversity among Bacillus anthracis Soil Isolates at Fine Geographic Scales

2012 ◽  
Vol 78 (18) ◽  
pp. 6433-6437 ◽  
Author(s):  
Chad W. Stratilo ◽  
Douglas E. Bader
Keyword(s):  
Bacillus Anthracis ◽  
National Park ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Phenotypic Characterization ◽  
Single Nucleotide ◽  
Content Type ◽  
Repeat Analysis ◽  
Typing Methods ◽  
Wood Buffalo National Park

ABSTRACTEnvironmental samples were collected from carcass sites during and after anthrax outbreaks in 2000 and 2001 in the bison (Bison bison) population within Wood Buffalo National Park and the Hook Lake Region north of Wood Buffalo National Park.Bacillus anthracisspores were isolated from these samples and confirmed using phenotypic characterization and real-time PCR. ConfirmedB. anthracisisolates were typed using multiple-locus variable-number tandem repeat analysis (MLVA15) and single-nucleotide-repeat analysis (SNRA).B. anthracisisolates split into two clades based on MLVA15, while SNRA allowed some isolates between carcass sites to be distinguished from each other. SNRA polymorphisms were also present within a single carcass site. Some isolates from different carcass sites having the same SNRA type had divergent MLVA types; this finding leads to questions about hierarchical typing methods and the robustness of the fine-scale typing ofBacillus anthracis.

Bangladesh anthrax outbreaks are probably caused by contaminated livestock feed

2012 ◽  
Vol 141 (5) ◽  
pp. 1021-1028 ◽  
Author(s):  
A. FASANELLA ◽  
G. GAROFOLO ◽  
M. J. HOSSAIN ◽  
M. SHAMSUDDIN ◽  
J. K. BLACKBURN ◽  
...  
Keyword(s):  
Genetic Variance ◽  
Monsoon Season ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Snp Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Major Lineage ◽  
Livestock Feed ◽  
Vntr Analysis

SUMMARYIn Bangladesh from 1 July to 30 September 2010 there were 104 animal cases of anthrax and 607 associated human cases. This investigation was conducted in Sirajganj district in December 2010, on eight farms where animal cases had occurred.Bacillus anthraciswas recovered from soil samples and turbinate bones on six farms. Canonical single nucleotide polymorphism (SNP) analysis showed that all the isolates belonged to the major lineage A, sublineage A.Br.001/002 of China and South East Asia while a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) with 15 VNTRs demonstrated three unique genotypes. The single nucleotide repeat (SNR) analyses showed two SNR types in 97 out of 99 isolates; nevertheless, due to its higher discriminatory power the presence of two isolates with different SNR-type polymorphisms were detected within two MLVA genotypes. The epidemic occurred during the monsoon season, a time of extensive flooding, suggesting that the source was contaminated feed, not grazing, which is supported by the genetic variance.

scholarly journals Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157

2019 ◽  
Vol 85 (17) ◽  
Author(s):  
Kenichi Lee ◽  
Hidemasa Izumiya ◽  
Sunao Iyoda ◽  
Makoto Ohnishi
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Core Genome ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Molecular Surveillance ◽  
Content Type ◽  
Repeat Analysis

ABSTRACT Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary. For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance. IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated. Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.

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