scholarly journals Evaluating sub-typing methods for pathogenicYersinia enterocoliticato support outbreak investigations in New Zealand

2019 ◽  
Vol 147 ◽  
Author(s):  
H. Strydom ◽  
J. Wang ◽  
S. Paine ◽  
K. Dyet ◽  
K. Cullen ◽  
...  
Keyword(s):  
New Zealand ◽  
Variable Number Tandem Repeat ◽  
Epidemiological Data ◽  
Variable Number ◽  
Single Type ◽  
Snp Analysis ◽  
Single Nucleotide ◽  
Outbreak Investigations ◽  
Typing Methods ◽  
Mlva Typing

AbstractIncidence of human yersiniosis in New Zealand has increased between 2013 and 2017. For surveillance and outbreak investigations it is essential that an appropriate level of discrimination between pathogenicYersinia enterocoliticaisolates is provided, in order to support epidemiological linking of connected cases. Subtyping of 227Y. enterocoliticaisolates was performed using a range of different typing methods, including biotyping, serotyping and seven loci multiple-locus variable-number tandem-repeat analysis (MLVA). In addition, core genome single-nucleotide polymorphism (core SNP) analysis and multi-locus sequence typing were performed on a subset of 69 isolates. Sixty-seven different MLVA types were identified. One MLVA profile was associated with an outbreak in the Bay of Plenty region, supported by epidemiological data. Core SNP analysis showed that all the outbreak-related isolates clustered together. The subtyping and epidemiological evidence suggests that the outbreak of yersiniosis in the Bay of Plenty region between October and December 2016 could be attributed to a point source. However, subtyping results further suggest that the same clone was isolated from several regions between August 2016 and March 2017. Core SNP analysis and MLVA typing failed to differentiate betweenY. enterocoliticabiotype 2 and biotype 3. For this reason, we propose that these biotypes should be reported as a single type namely:Y. enterocoliticabiotype 2/3 and that the serotype should be prioritised as an indicator of prevalence.

Genome typing and epidemiology of human listeriosis in New Zealand 1999-2018

2021 ◽  
Author(s):  
Lucia Rivas ◽  
Shevaun Paine ◽  
Pierre-Yves Dupont ◽  
Audrey Tiong ◽  
Beverley Horn ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Zealand ◽  
Epidemiological Data ◽  
Common Source ◽  
Snp Analysis ◽  
Whole Genome ◽  
Single Nucleotide ◽  
Low Genetic Diversity ◽  
Geographical Regions ◽  
Sequence Types

This study describes the epidemiology of listeriosis in New Zealand (NZ) between 1999 and 2018, as well as the retrospective whole genome sequencing (WGS) of 453 Listeria monocytogenes isolates corresponding to 95% of the human cases within this period. The average notified rate of listeriosis was 0.5 cases per 100,000 population and non-pregnancy associated cases were more prevalent than pregnancy-associated cases (average 19 and 5 cases per annum, respectively). Analysis of WGS data was assessed using multi-locus sequencing typing (MLST), including core-genome and whole-genome MLST (cgMLST and wgMLST) and single-nucleotide polymorphism (SNP) analysis. Thirty-nine sequence types (STs) were identified, with the most common being, ST1 (21.9%), ST4 (13.2%), ST2 (11.3%), ST120 (6.1%) and ST155 (6.4%). A total of 291 different cgMLST types were identified, with the majority (n = 243) of types observed as a single isolate, consistent with the observation that listeriosis is predominately sporadic. Amongst the 49 cgMLST types containing two or more isolates, 18 cgMLST types contained 2-4 isolates (50 isolates in total, including three outbreak-associated isolates) that shared low genetic diversity (0-2 whole-genome alleles), some of which were dispersed in time or geographical regions. SNP-analysis also produced comparable results to wgMLST. The low genetic diversity within these clusters suggests a potential common source but incomplete epidemiological data impaired retrospective epidemiological investigations. Prospective use of WGS analysis, together with thorough exposure information from cases will potentially identify future outbreaks more rapidly and possibly those that have been undetected for some time over different geographically regions.

scholarly journals Anthrax among heroin users in Europe possibly caused by same Bacillus anthracis strain since 2000

2013 ◽  
Vol 18 (13) ◽  
Author(s):  
R Grunow ◽  
S R Klee ◽  
W Beyer ◽  
M George ◽  
D Grunow ◽  
...  
Keyword(s):  
United Kingdom ◽  
Fatal Case ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Snp Analysis ◽  
Single Nucleotide ◽  
Heroin Users ◽  
The United Kingdom ◽  
German Regions ◽  
Injecting Drug User

Injection anthrax was described first in 2000 in a heroin-injecting drug user in Norway. New anthrax cases among heroin consumers were detected in the United Kingdom (52 cases) and Germany (3 cases) in 2009-10. In June 2012, a fatal case occurred in Regensburg, Bavaria. As of December 2012, 13 cases had been reported in this new outbreak from Germany, Denmark, France and the United Kingdom. We analysed isolates from 2009-10 and 2012 as well as from the first injection anthrax case in Norway in 2000 by comparative molecular typing using a high resolution 31 marker multilocus variable-number tandem repeat analysis (MLVA) and a broad single nucleotide polymorphism (SNP) analysis. Our results show that all cases may be traced back to the same outbreak strain. They also indicate the probability of a single source contaminating heroin and that the outbreak could have lasted for at least a decade. However, an additional serological pilot study in two German regions conducted in 2011 failed to discover additional anthrax cases among 288 heroin users.

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 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 Molecular Epidemiology Characteristics of Brucella Abortus Strains in China and Their Relationships With World Lineages

2020 ◽  
Author(s):  
Xu-Ming Wang ◽  
Zhongzhi Zhao ◽  
Miao Wang ◽  
Buyun Cui ◽  
Zhiguo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Epidemiology ◽  
Brucella Abortus ◽  
Variable Number Tandem Repeat ◽  
Northern China ◽  
Variable Number ◽  
Snp Analysis ◽  
High Genetic Diversity ◽  
Geographic Origins ◽  
Epidemic Area

Abstract Background Brucella abortus is a facultative intracellular Gram-negative bacterium that causes chronic persistent infections in humans and livestock. In this study, conventional bio-typing, multiple-locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing-single-nucleotide polymorphism (WGS-SNP) were used to investigate the molecular epidemiology characteristics of Brucella abortus strains in China and their relationships to world lineages. Results A total of 100 strains were collected from 1953 to 2013, suggesting that B. abortus circulated in China in the past five decades. Moreover, most strains were mainly distributed in the Northwest areas, suggest that provinces in the Northwest were a dominant epidemic area of this disease. During this period, seven biovars were found, indicating that B. abortus had a high diversity of biovars and it is also a potential reason for the disease ongoing spread in the Northern provinces. Strains have high genetic diversity, and bruce07 is the most helpful locus for genotyping of this population. Moreover, 17 MLVA-11 genotypes were found; 13 of them are of known genotypes and four are unassigned genotypes, indicating that B. abortus in this study had several geographic origins. Still, strains from unassigned genotypes may originate from China. Many shared MLVA-16 genotypes were observed in strains from the same provinces in Northern China, which confirmed a B. abortus brucellosis outbreak within Northern regions. WGS-SNP analysis showed that eight Chinese strains formed a ladder-like phylogram (C. Ⅶ) with strains from nine countries, including Uganda, Iraq, Russia, Georgia, Spain, Italy, Egypt, Mongolia, and China; suggest that strains were introduced to these countries from a single source. Conclusions Chinese B. abortus strains had high biovars and genetic diversity as well as represent characteristics of multiple geographic origins, and B. abortus strains from several mainly epidemic areas were closely related to strains from Russia and Mongolia; frequent animal (cattle) trade and exchanges may promote this process. We will provide new and valuable information to strengthening surveillance and control of B. abortus brucellosis in China.

An Optimized Multilocus Variable-Number Tandem Repeat Analysis Typing Scheme for Listeria monocytogenes from Three Western Provinces in China

2018 ◽  
Vol 81 (12) ◽  
pp. 1956-1962
Author(s):  
RENDONG FANG ◽  
BING JIANG ◽  
JIANHUA XIE ◽  
ZICHUN WANG ◽  
WANGWANG LIANG ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Tandem Repeat ◽  
Multilocus Sequence Typing ◽  
Variable Number Tandem Repeat ◽  
Foodborne Pathogen ◽  
Variable Number ◽  
Western China ◽  
Typing Scheme ◽  
Repeat Analysis ◽  
Outbreak Investigations

ABSTRACT Listeria monocytogenes is a foodborne pathogen worldwide. Multilocus variable-number tandem repeat analysis (MLVA) has been used for listeriosis surveillance and outbreak investigations. MLVA typing schemes have been proposed, but their usefulness for typing isolates from the People's Republic of China has not been assessed. To this aim, all L. monocytogenes strains (79) isolated from 1,445 raw meat and abattoir environmental samples of three western provinces in China were characterized with PCR serogrouping, multilocus sequence typing, and MLVA. The isolates were typed into the four PCR serogroups IIb (38.0%), IIc (26.6%), IIa (24.0%), and IVb (11.4%), with a Simpson's index (SI) of 0.7235. With multilocus sequence typing, they were typed into 18 sequence types (STs), including two new STs, ST1029 and ST1011, with an SI of 0.8880. With the 14 MLVA loci from the previous five schemes, the isolates were typed into 39 MLVA genotypes, with an SI of 0.9656. The typing data indicated that MLVA had the highest typing capability among the three methods. A subsequent optimization analysis identified an optimal combination of eight loci (LMV2, LMV9, LMV1, Lm10, Lm11, Lm15, Lm23, and LMTR6) producing the same SI as that of the 14 loci. The present optimized combination shared only six loci with the optimal nine-loci combination proposed in Australia, verifying for the first time that the optimal combinations varied with the isolates' sets. The current optimal typing scheme was ideal for L. monocytogenes isolates from western China.

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