scholarly journals Ruminant-associated Listeria monocytogenes isolates belong preferentially to dairy-related hypervirulent clones: a longitudinal study in 19 farms

2021 ◽  
Author(s):  
Carla Palacios-Gorba ◽  
Alexandra MOURA ◽  
Jesús Gomis ◽  
Alexandre Leclercq ◽  
Ángel Gómez-Martín ◽  
...  
Keyword(s):  
Longitudinal Study ◽  
Listeria Monocytogenes ◽  
Environmental Samples ◽  
Large Scale ◽  
Foodborne Pathogen ◽  
Public Health Issue ◽  
Fecal Shedding ◽  
Lactating Cows ◽  
Cattle Farms ◽  
Sequence Types

The increasing prevalence of Listeria monocytogenes infections is a public health issue. Although studies have shown that ruminants constitute reservoirs of this foodborne pathogen, little is known about its epidemiology and genetic diversity within ruminant farms. Here we conducted a large-scale genomic and epidemiologic longitudinal study of Listeria spp. in dairy ruminants and their environments, comprising 19 farms monitored for three consecutive seasons (N=3251 samples). L. innocua was the most prevalent Listeria spp, followed by L. monocytogenes. L. monocytogenes was detected in 52.6% of farms (prevalence in feces samples 3.8%, in farm environment samples 2.5%) and more frequently in cattle (4.1%) and sheep (4.5%) than in goat farms (0.2%). Lineage I accounted for 69% of L. monocytogenes isolates. Among animal samples, the most prevalent sublineages (SL) and clonal complexes (CC) were SL1/CC1, SL219/CC4, SL26/CC26 and SL87/CC87, whereas SL666/CC666 was prevalent in environmental samples. 61 different L. monocytogenes CTs (cgMLST sequence types) were found, 17 of them (27.9%) common to different animals and/or surfaces within the same farms. L. monocytogenes prevalence was not affected by farm hygiene but by season: the overall prevalence of L. monocytogenes in cattle farms was higher during winter, and in sheep farms was higher during winter and spring. Cows in their second lactation had a higher probability of L. monocytogenes fecal shedding than other lactating cows. This study highlights that dairy farms constitute a reservoir for hypervirulent L. monocytogenes and the importance of continuous animal surveillance to reduce the burden of human listeriosis.

scholarly journals MentaLiST – A fast MLST caller for large MLST schemes

2017 ◽  
Author(s):  
Pedro Feijao ◽  
Hua-Ting Yao ◽  
Dan Fornika ◽  
Jennifer Gardy ◽  
Will Hsiao ◽  
...  
Keyword(s):  
Large Scale ◽  
Core Genome ◽  
Foodborne Pathogen ◽  
Simulated Data ◽  
Housekeeping Genes ◽  
Whole Genome ◽  
Large Size ◽  
Classic Technique ◽  
Computational Resources ◽  
Sequence Types

AbstractMLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing (WGS) data, MLST methods have evolved toward larger typing schemes, based on a few hundred genes (core genome MLST, cgMLST) to a few thousand genes (whole genome MLST, wgMLST). Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes.We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST scheme with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.

scholarly journals Whole-Genome Sequencing-Based Characterization of Listeria monocytogenes from Fish and Fish Production Environments in Poland

2020 ◽  
Vol 21 (24) ◽  
pp. 9419
Author(s):  
Kinga Wieczorek ◽  
Arkadiusz Bomba ◽  
Jacek Osek
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Foodborne Pathogen ◽  
Whole Genome ◽  
Antimicrobial Resistance Profile ◽  
Production Environments ◽  
Long Time ◽  
Sequence Types

Listeria monocytogenes, an important foodborne pathogen, may be present in different kinds of food and in food processing environments where it can persist for a long time. In this study, 28 L. monocytogenes isolates from fish and fish manufactures were characterized by whole genome sequencing (WGS). Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with publicly available genomes of L. monocytogenes strains recovered worldwide from food and from humans with listeriosis. All but one (96.4%) of the examined isolates belonged to molecular serogroup IIa, and one isolate (3.6%) was classified to serogroup IVb. The isolates of group IIa were mainly of MLST sequence types ST121 (13 strains) and ST8 (four strains) whereas the isolate of serogroup IVb was classified to ST1. Strains of serogroup IIa were further subtyped into eight different sublineages with the most numerous being SL121 (13; 48.1% strains) which belonged to six cgMLST types. The majority of strains, irrespective of the genotypic subtype, had the same antimicrobial resistance profile. The cluster analysis identified several molecular clones typical for L. monocytogenes isolated from similar sources in other countries; however, novel molecular cgMLST types not present in the Listeria database were also identified.

LIVESTOCK FARMING TECHNOLOGIES IN CASE OF LARGE-SCALE RADIOACTIVE CONTAMINATION (TO 35TH-ANNIVERSARY OF THE CHERNOBYL NPP ACCIDENT)

1970 ◽  
pp. 58-63
Author(s):  
A. V. Panov ◽  
N. N. Isamov ◽  
O. S. Gubareva ◽  
P. N. Tsygvintsev ◽  
А. N. Ratnikov ◽  
...  
Keyword(s):  
Radioactive Contamination ◽  
Large Scale ◽  
Animal Husbandry ◽  
Livestock Farming ◽  
Lactating Cows ◽  
Chernobyl Npp ◽  
Livestock Products ◽  
Cattle Farms

On the example of the Chernobyl NPP accident, the problems of animal husbandry in case of radioactive contamination of hayfields and pastures are shown. The factors determining the accumulation of radionuclides in milk and meat are presented. It is noted that the excess of radiological standards for the content of 137Cs in livestock products in the southwestern districts of the Bryansk region is long-term and requires continuation of rehabilitation work. A classification of countermeasures and technologies in animal husbandry carried out after the Chernobyl accident is given. It was shown that the most effective was the use of Cs-binding sorbents - hexacyanoferrates for lactating cows and fattening cattle. Farms in the southwestern districts of the Bryansk region have been identified, where until now there is a risk of exceeding the standards for the content of radionuclides in livestock products. For these farms, a scheme for the use of hexacyanoferrates was proposed depending on the levels of 137Cs contamination of grassland.

Predominance and Distribution of a Persistent Listeria monocytogenes Clone in a Commercial Fresh Mushroom Processing Environment

2015 ◽  
Vol 78 (11) ◽  
pp. 1988-1998 ◽  
Author(s):  
LATHA MURUGESAN ◽  
ZUZANA KUCEROVA ◽  
STEPHEN J. KNABEL ◽  
LUKE F. LaBORDE
Keyword(s):  
Longitudinal Study ◽  
Listeria Monocytogenes ◽  
Environmental Samples ◽  
Additional Research ◽  
Time Interval ◽  
Period 2

A longitudinal study was conducted to determine the prevalence of Listeria spp. in a commercial fresh mushroom slicing and packaging environment. Samples were collected at three different sampling periods within a 13-month time interval. Of the 255 environmental samples collected, 18.8% tested positive for L. monocytogenes, 4.3% for L. innocua, and 2.0% for L. grayi. L. monocytogenes was most often found on wet floors within the washing and slicing and packaging areas. Each of the 171 L. monocytogenes isolates found in the environment could be placed into one of three different serotypes; 1/2c was predominant (93.6%), followed by 1/2b (3.5%) and 1/2a (2.9%). Of 58 isolates subtyped using multi-virulence-locus sequence typing, all 1/2c isolates were identified as virulence type (VT) 11 (VT11), all 1/2b isolates were VT105, and 1/2a isolates were either VT107 or VT56. VT11 was designated as the predominant and persistent clone in the environment because it was isolated repeatedly at numerous locations throughout the study. The overall predominance and persistence of VT11 indicates that it likely colonized the mushroom processing environment. Areas adjacent to the trench drain in the washing and slicing area and a floor crack in the packaging area may represent primary harborage sites (reservoirs) for VT11. Improvements made to sanitation procedures by company management after period 2 coincided with a significant (P ≤ 0.001) reduction in the prevalence of L. monocytogenes from 17.8% in period 1 and 30.7% in period 2 to 8.5% in period 3. This suggests that targeted cleaning and sanitizing procedures can be effective in minimizing the occurrence of L. monocytogenes contamination in processing facilities. Additional research is needed to understand why VT11 was predominant and persistent in the mushroom processing environment.

scholarly journals Occurrence, Persistence, and Contamination Routes ofListeria monocytogenesGenotypes on Three Finnish Dairy Cattle Farms: a Longitudinal Study

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Hanna Castro ◽  
Anniina Jaakkonen ◽  
Marjaana Hakkinen ◽  
Hannu Korkeala ◽  
Miia Lindström
Keyword(s):  
Longitudinal Study ◽  
Listeria Monocytogenes ◽  
Dairy Cattle ◽  
Control Strategies ◽  
Dairy Farms ◽  
Bulk Tank Milk ◽  
Content Type ◽  
Bulk Tank ◽  
Contamination Routes ◽  
Cattle Farms

ABSTRACTThe molecular epidemiology ofListeria monocytogeneswas investigated in a longitudinal study of three Finnish dairy farms during 2013 to 2016. A total of 186 bulk tank milk (BTM), 224 milk filter sock (MFS), and 1,702 barn environment samples were analyzed, and isolates ofL. monocytogeneswere genotyped using pulsed-field gel electrophoresis.L. monocytogenesoccurred throughout the year in all sample types, and the prevalence in MFS increased significantly during the indoor season.L. monocytogeneswas more prevalent in MFS (29%) than in BTM (13%) samples. However, the prevalence ofL. monocytogenesvaried more between farms in samples of MFS (13 to 48%) than in BTM (10 to 16%). For each farm, theL. monocytogenesgenotypes detected were classified by persistence (defined as persistent if isolated from ≥3 samples during ≥6 months) and predominance (defined as predominant if >5% prevalence on at least one farm visit). The prevalence of sporadic genotypes was 4 to 5% on all three farms. In contrast, the prevalence of persistent predominant genotypes varied between farms by 4% to 16%. The highest prevalence of persistent predominant genotypes was observed on the farm with the poorest production hygiene. Persistent predominant genotypes were most prevalent on feeding surfaces, water troughs, and floors. Genotypes isolated from the milking system or from cow udders had a greater relative risk of occurring in BTM and MFS than genotypes that only occurred elsewhere in the farm, supporting the hypothesis thatL. monocytogenes is transmitted to milk from contamination on the udder surface or in the milking equipment.IMPORTANCEListeria monocytogenesis a ubiquitous environmental bacterium and the causative agent of a serious foodborne illness, listeriosis. Dairy products are common vehicles of listeriosis, and dairy cattle farms harborL. monocytogenesgenotypes associated with human listeriosis outbreaks. Indeed, dairy cattle farms act as a reservoir ofL. monocytogenes, and the organism is frequently detected in bulk tank milk (BTM) and in the feces of clinically healthy cows. The ecology ofL. monocytogenesin the farm environment is complex and poorly understood. Isolates of the sameL. monocytogenesgenotype can occur in the farm for years, but the factors contributing to the persistence of genotypes on dairy farms are unknown. Knowledge of the persistence patterns and contamination routes ofL. monocytogeneson dairy farms can improve management of the contamination pressure in the farm environment and aid in the development of focused control strategies to reduce BTM contamination.

10 K: a large‐scale prospective longitudinal study in Israel

2021 ◽  
Author(s):  
Smadar Shilo ◽  
Noam Bar ◽  
Ayya Keshet ◽  
Yeela Talmor-Barkan ◽  
Hagai Rossman ◽  
...  
Keyword(s):  
Longitudinal Study ◽  
Large Scale ◽  
Prospective Longitudinal Study ◽  
Prospective Longitudinal

Effect of cold temperature on the composition of different lipid classes of the foodborne pathogen Listeria monocytogenes: Focus on neutral lipids

2006 ◽  
Vol 23 (2) ◽  
pp. 184-194 ◽  
Author(s):  
S.K. Mastronicolis ◽  
A. Boura ◽  
A. Karaliota ◽  
P. Magiatis ◽  
N. Arvanitis ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Neutral Lipids ◽  
Foodborne Pathogen ◽  
Cold Temperature ◽  
Lipid Classes

scholarly journals Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

2014 ◽  
Vol 53 (1) ◽  
pp. 191-200 ◽  
Author(s):  
Walter Demczuk ◽  
Tarah Lynch ◽  
Irene Martin ◽  
Gary Van Domselaar ◽  
Morag Graham ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Large Scale ◽  
Epidemiological Studies ◽  
23S Rrna ◽  
Genome Comparison ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
High Level ◽  
Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

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