scholarly journals Evolution and Molecular Phylogeny of Listeria monocytogenes Isolated from Human and Animal Listeriosis Cases and Foods

2005 ◽  
Vol 187 (16) ◽  
pp. 5537-5551 ◽  
Author(s):  
K. K. Nightingale ◽  
K. Windham ◽  
M. Wiedmann
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Positive Selection ◽  
New York State ◽  
Housekeeping Genes ◽  
Acid Sites ◽  
Food Samples ◽  
Phylogenetic Lineages

ABSTRACT To probe the evolution and phylogeny of Listeria monocytogenes from defined host species and environments, L. monocytogenes isolates from human (n = 60) and animal (n = 30) listeriosis cases and food samples (n = 30) were randomly selected from a larger collection of isolates (n = 354) obtained in New York State between 1999 and 2001. Partial sequencing of four housekeeping genes (gap, prs, purM, and ribC), one stress response gene (sigB), and two virulence genes (actA and inlA) revealed between 11 (gap) and 33 (inlA) allelic types as well as 52 sequence types (unique combination of allelic types). actA, ribC, and purM demonstrated the highest levels of nucleotide diversity (π > 0.05). actA and inlA as well as prs and the hypervariable housekeeping genes ribC and purM showed evidence of horizontal gene transfer and recombination. actA and inlA also showed evidence of positive selection at specific amino acid sites. Maximum likelihood phylogenies for all seven genes confirmed that L. monocytogenes contains two deeply separated evolutionary lineages. Lineage I was found to be highly clonal, while lineage II showed greater diversity and evidence of horizontal gene transfer. Allelic types were exclusive to lineages, except for a single gap allele, and nucleotide distance within lineages was much lower than that between lineages, suggesting that genetic exchange between lineages is rare. Our data show that (i) L. monocytogenes is a highly diverse species with at least two distinct phylogenetic lineages differing in their evolutionary history and population structure and (ii) horizontal gene transfer as well as positive selection contributed to the evolution of L. monocytogenes.

scholarly journals Small produce farm environments can harbor diverse Listeria monocytogenes and Listeria spp. populations

2020 ◽  
Author(s):  
Alexandra M Belias ◽  
Laura K Strawn ◽  
Martin Wiedmann ◽  
Daniel Weller
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
Spatial Scale ◽  
New York State ◽  
Foodborne Pathogen ◽  
Pond Water ◽  
Positive Sample ◽  
Small Spatial Scale ◽  
Pathogen Diversity ◽  
Produce Contamination

A comprehensive understanding of foodborne pathogen diversity in pre-harvest environments is necessary to effectively track pathogens on farms and identify sources of produce contamination. As such, this study aimed to characterize Listeria diversity in wildlife feces and agricultural water collected from a New York State produce farm over a growing season. Water samples were collected from a pond (N=80) and stream (N=52). Fecal samples (N=77) were opportunistically collected from areas <5m from the water sources; all samples were collected from a <0.5km2 area. Overall, 41% (86/209) and 24% (50/209) of samples were positive for Listeria monocytogenes and Listeria spp. (excluding L. monocytogenes), respectively. For each positive sample, one L. monocytogenes or Listeria spp. isolate was speciated by sequencing the sigB gene, which allowed for additional characterization based on the sigB allelic type (AT). The 86 L. monocytogenes and 50 Listeria spp. isolates represented 8 and 23 different ATs, respectively. A subset of L. monocytogenes isolates (N=44) from pond water and pond-adjacent feces (representing a ~5,000m2 area) were further characterized by PFGE; these 44 isolates represented 22 PFGE types, which is indicative of considerable diversity at a small spatial scale. Ten PFGE types were isolated more than once, suggesting persistence or re-introduction of PFGE types in this area. Given the small spatial scale, the prevalence of L. monocytogenes and Listeria spp., as well as the considerable diversity amongst isolates, suggests traceback investigations may be challenging. For example, traceback of finished product or processing facility contamination with specific subtypes to pre-harvest sources may require collection of large sample sets, and characterization of a considerable number of isolates. Our data also support the adage, “absence of evidence does not equal evidence of absence” applies to L. monocytogenes traceback efforts at the pre-harvest level.

scholarly journals Erratum to: Spatially explicit uncertainty modeling of zoonotic pathogen distribution: a case of Listeria monocytogenes in New York State, USA

2017 ◽  
Vol 9 (2) ◽  
pp. 125-126
Author(s):  
Rita Mwima ◽  
Anthony Gidudu ◽  
Allan Mazimwe ◽  
Arika Ligmann-Zielinska ◽  
Samuel Majalija ◽  
...  
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
New York State ◽  
Uncertainty Modeling ◽  
Spatially Explicit ◽  
Zoonotic Pathogen ◽  
York State

scholarly journals Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael J. Ormsby ◽  
Robert L. Davies
Keyword(s):  
Rainbow Trout ◽  
Amino Acid ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Atlantic Salmon ◽  
Sequence Variation ◽  
Housekeeping Genes ◽  
Housekeeping Gene ◽  
Yersinia Ruckeri ◽  
Amino Acid Sequence Variation

AbstractYersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.

scholarly journals Evolution of land plant genes encoding L-Ala-D/L-Glu epimerases (AEEs) via horizontal gene transfer and positive selection

2013 ◽  
Vol 13 (1) ◽  
pp. 34 ◽  
Author(s):  
Zefeng Yang ◽  
Yifan Wang ◽  
Yong Zhou ◽  
Qingsong Gao ◽  
Enying Zhang ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Positive Selection ◽  
Land Plant ◽  
Genes Encoding ◽  
Plant Genes

Irrigation Is Significantly Associated with an Increased Prevalence of Listeria monocytogenes in Produce Production Environments in New York State

2015 ◽  
Vol 78 (6) ◽  
pp. 1132-1141 ◽  
Author(s):  
DANIEL WELLER ◽  
MARTIN WIEDMANN ◽  
LAURA K. STRAWN
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
Environmental Factors ◽  
Odds Ratio ◽  
Management Practices ◽  
New York State ◽  
Irrigation Level ◽  
York State ◽  
Listeria Species ◽  
Production Environments

Environmental (i.e., meteorological and landscape) factors and management practices can affect the prevalence of foodborne pathogens in produce production environments. This study was conducted to determine the prevalence of Listeria monocytogenes, Listeria species (including L. monocytogenes), Salmonella, and Shiga toxin–producing Escherichia coli (STEC) in produce production environments and to identify environmental factors and management practices associated with their isolation. Ten produce farms in New York State were sampled during a 6-week period in 2010, and 124 georeferenced samples (80 terrestrial, 33 water, and 11 fecal) were collected. L. monocytogenes, Listeria spp., Salmonella, and STEC were detected in 16, 44, 4, and 5% of terrestrial samples, 30, 58, 12, and 3% of water samples, and 45, 45, 27, and 9% of fecal samples, respectively. Environmental factors and management practices were evaluated for their association with terrestrial samples positive for L. monocytogenes or other Listeria species by univariate logistic regression; analysis was not conducted for Salmonella or STEC because the number of samples positive for these pathogens was low. Although univariate analysis identified associations between isolation of L. monocytogenes or Listeria spp. from terrestrial samples and various water-related factors (e.g., proximity to wetlands and precipitation), multivariate analysis revealed that only irrigation within 3 days of sample collection was significantly associated with isolation of L. monocytogenes (odds ratio = 39) and Listeria spp. (odds ratio = 5) from terrestrial samples. These findings suggest that intervention at the irrigation level may reduce the risk of produce contamination.

scholarly journals Molecular Ecology of Listeria monocytogenes: Evidence for a Reservoir in Milking Equipment on a Dairy Farm

2008 ◽  
Vol 75 (5) ◽  
pp. 1315-1323 ◽  
Author(s):  
Alejandra A. Latorre ◽  
Jo Ann S. Van Kessel ◽  
Jeffrey S. Karns ◽  
Michael J. Zurakowski ◽  
Abani K. Pradhan ◽  
...  
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
Environmental Samples ◽  
Molecular Ecology ◽  
New York State ◽  
Dairy Farm ◽  
Bulk Tank Milk ◽  
Fecal Samples ◽  
Milk Samples ◽  
Bulk Tank

ABSTRACT A longitudinal study aimed to detect Listeria monocytogenes on a New York State dairy farm was conducted between February 2004 and July 2007. Fecal samples were collected every 6 months from all lactating cows. Approximately 20 environmental samples were obtained every 3 months. Bulk tank milk samples and in-line milk filter samples were obtained weekly. Samples from milking equipment and the milking parlor environment were obtained in May 2007. Fifty-one of 715 fecal samples (7.1%) and 22 of 303 environmental samples (7.3%) were positive for L. monocytogenes. A total of 73 of 108 in-line milk filter samples (67.6%) and 34 of 172 bulk tank milk samples (19.7%) were positive for L. monocytogenes. Listeria monocytogenes was isolated from 6 of 40 (15%) sampling sites in the milking parlor and milking equipment. In-line milk filter samples had a greater proportion of L. monocytogenes than did bulk tank milk samples (P < 0.05) and samples from other sources (P < 0.05). The proportion of L. monocytogenes-positive samples was greater among bulk tank milk samples than among fecal or environmental samples (P < 0.05). Analysis of 60 isolates by pulsed-field gel electrophoresis (PFGE) yielded 23 PFGE types after digestion with AscI and ApaI endonucleases. Three PFGE types of L. monocytogenes were repeatedly found in longitudinally collected samples from bulk tank milk and in-line milk filters.

Prevalence, Distribution, and Diversity of Listeria monocytogenes in Retail Environments, Focusing on Small Establishments and Establishments with a History of Failed Inspections

2011 ◽  
Vol 74 (7) ◽  
pp. 1083-1095 ◽  
Author(s):  
KARIN HOELZER ◽  
BRIAN D. SAUDERS ◽  
MARIA D. SANCHEZ ◽  
PETER T. OLSEN ◽  
MICHELE M. PICKETT ◽  
...  
Keyword(s):  
New York ◽  
Listeria Monocytogenes ◽  
New York State ◽  
York State ◽  
Food Contact ◽  
Food Contact Surfaces ◽  
Increased Risk ◽  
History Of ◽  
Contact Surfaces ◽  
Retail Establishments

Despite growing concerns about cross-contamination of ready-to-eat foods with Listeria monocytogenes, our knowledge about the ecology and transmission of L. monocytogenes in retail establishments has remained limited. We conducted a cross-sectional study to characterize the prevalence, distribution, and subtype diversity of L. monocytogenes in 120 New York State retail deli establishments that were hypothesized to present an increased risk for environmental L. monocytogenes contamination (i.e., small establishments and establishments with a history of failed New York State Agriculture and Markets inspections). Analysis of these data along with previously reported data for 121 predominantly larger retail establishments in New York State identified establishment size, geographic location, and inspection history as significant predictors of L. monocytogenes presence and prevalence. The odds of an establishment being L. monocytogenes positive were approximately twice as high for large establishments, establishments located in New York City, or establishments with poor inspection history (as compared with establishments without these attributes), even though correlation between location and inspection history complicated interpretation of results. Within an establishment, L. monocytogenes was significantly more prevalent on nonfood contact surfaces than on food contact surfaces; prevalence was particularly high for floors and in floor drains, sinks, the dairy case, and milk crates. L. monocytogenes subtype diversity differed between sites, with lineage I isolates significantly associated with nonfood contact surfaces and lineage II isolates significantly associated with food contact surfaces. Isolates belonging to the same ribotype were often found dispersed across multiple sites within an operation.

scholarly journals Exploring Genetic Diversity and Signatures of Horizontal Gene Transfer in Nodule Bacteria Associated with Lotus japonicus in Natural Environments

2019 ◽  
Vol 32 (9) ◽  
pp. 1110-1120 ◽  
Author(s):  
Masaru Bamba ◽  
Seishiro Aoki ◽  
Tadashi Kajita ◽  
Hiroaki Setoguchi ◽  
Yasuyuki Watano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Lotus Japonicus ◽  
Population Expansion ◽  
Housekeeping Genes ◽  
Natural Environments ◽  
Symbiotic Genes ◽  
Nodule Bacteria ◽  
Wide Range

To investigate the genetic diversity and understand the process of horizontal gene transfer (HGT) in nodule bacteria associated with Lotus japonicus, we analyzed sequences of three housekeeping and five symbiotic genes using samples from a geographically wide range in Japan. A phylogenetic analysis of the housekeeping genes indicated that L. japonicus in natural environments was associated with diverse lineages of Mesorhizobium spp., whereas the sequences of symbiotic genes were highly similar between strains, resulting in remarkably low nucleotide diversity at both synonymous and nonsynonymous sites. Guanine-cytosine content values were lower in symbiotic genes, and relative frequencies of recombination between symbiotic genes were also lower than those between housekeeping genes. An analysis of molecular variance showed significant genetic differentiation among populations in both symbiotic and housekeeping genes. These results confirm that the Mesorhizobium genes required for symbiosis with L. japonicus behave as a genomic island (i.e., a symbiosis island) and suggest that this island has spread into diverse genomic backgrounds of Mesorhizobium via HGT events in natural environments. Furthermore, our data compilation revealed that the genetic diversity of symbiotic genes in L. japonicus-associated symbionts was among the lowest compared with reports of other species, which may be related to the recent population expansion proposed in Japanese populations of L. japonicus.

scholarly journals Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State Using Two Web-based Platforms: National Center for Biotechnology Information-Pathogen Detection and FDA-GalaxyTrakr

2020 ◽  
Author(s):  
Jaclyn Carey ◽  
Jocelyn Cole ◽  
Sai Laxmi Gubbala Venkata ◽  
Hannah Hoyt ◽  
Lisa Mingle ◽  
...  
Keyword(s):  
New York ◽  
Clostridium Perfringens ◽  
Pathogen Detection ◽  
New York State ◽  
The United States ◽  
Food Samples ◽  
Whole Genome Sequence ◽  
Web Based ◽  
Phylogenetic Clustering ◽  
York State

Clostridium perfringens is the second-leading cause of bacterial foodborne illness in the United States. The Wadsworth Center (WC) at the New York State Department of Health enumerates infectious dose from primary patient and food samples and until recently, identified C. perfringens to the species level only. We investigated whether whole-genome sequence-based subtyping could benefit epidemiological investigations of this pathogen, as it has with other enteric organisms. We retrospectively sequenced 76 patient and food samples received between May 2010-February 2020, including 52 samples linked epidemiologically to 13 outbreaks and 24 sporadic samples not linked to other samples. Phylogenetic trees were built using two web-based platforms; National Centers for Biotechnology Information Pathogen Detection (NCBI-PD) and GalaxyTrakr (a Galaxy instance supported by the GenomeTrakr initiative). For GalaxyTrakr analyses single nucleotide polymorphism (SNP) matrices and maximum likelihood (ML) trees were generated using 3 different reference genomes. Across the four separate analyses phylogenetic clustering was generally concordant with epidemiologically-identified outbreaks. SNP diversity among phylogenetically-linked samples in an outbreak ranged from 0-20 SNPs, excepting one outbreak ranging from 4-62 SNPs. Importantly, four of the 13 outbreaks harbored one or more samples that were phylogenetic outliers, and for two outbreaks, no samples were closely related. Three specimens were found harboring two distinct genotypes. For samples below CDC enumeration dose threshold, phylogenetic clustering was robust and linked patient and/or food samples. We concluded that WGS phylogenetic clusters are: 1) largely concordant with epidemiologically-defined outbreaks, irrespective of analysis platform or reference genome we employed; 2) have limited pairwise SNP diversity, allowing phylogenetic clusters to be distinguished from sporadic cases; 3) can aid in epidemiological investigations by identifying outlier and polyclonal samples.

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