Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world

Nature Reviews Microbiology, Journal Year: 2024, Volume and Issue: 22(9), P. 543 - 555

Published: May 24, 2024

Language: Английский

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Differential roles of deterministic and stochastic processes in structuring soil bacterial ecotypes across terrestrial ecosystems

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 8, 2025

Soil bacteria are vital to ecosystem resilience and resistance, yet ecological attributes the drivers governing their composition distribution, especially for taxa varying in traits inhabiting different ecosystems, not fully understood. Here, we analyzed a large-scale bacterial community environmental dataset of 622 soil samples systematically collected by us from six major terrestrial ecosystems across United States. We show that diversity significantly differ among ecotypes partially determined few universal abiotic factors (e.g., pH, calcium, aluminum) several ecotype- or ecosystem-specific drivers. Co-occurrence network analysis suggests rare have stronger relevance than abundant taxa. Ecological models revealed deterministic processes shape assembly generalists, while stochastic played greater role specialists. Also, communities shrubland appear be more sensitive changes other evidenced lowest diversity, least connected network, strongest local selection driven surrounding land use. Overall, this study reveals mechanisms underlying biogeography nationwide highlights need preserve biosphere amid disturbance. Determinants microbial structure less well studied. Riddley et al. profile biogeographic patterns, identify key distinct roles shaping ecotype ecosystems.

Language: Английский

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Updated Parameters for Listeria monocytogenes Dose–Response Model Considering Pathogen Virulence and Age and Sex of Consumer

Foods, Journal Year: 2024, Volume and Issue: 13(5), P. 751 - 751

Published: Feb. 29, 2024

Better knowledge regarding the Listeria monocytogenes dose–response (DR) model is needed to refine assessment of risk foodborne listeriosis. In 2018, European Food Safety Agency (EFSA) derived a lognormal Poisson DR for 14 different age–sex sub-groups, marginally strain virulence. present study, new sets parameters are developed by integrating EFSA these sub-groups together with three classes virulence characteristics (“less virulent”, “virulent”, and “more virulent”). Considering leads estimated relative risks (RRs) listeriosis following ingestion 1000 bacteria “less virulent” vs. strains ranging from 21.6 24.1, depending on sub-group. These relatively low RRs when compared linked comorbidities described in literature suggest that influence comorbidity occurrence invasive given exposure much more important than strains. The updated allow better prediction across population interest, provided necessary data demographics proportional contribution food products interest available. An R package made available facilitate use models.

Language: Английский

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Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 19, 2024

Soil is an important reservoir of antibiotic resistance genes (ARGs) and understanding how corresponding environmental changes influence their emergence, evolution, spread crucial. The soil-dwelling bacterial genus Listeria, including L. monocytogenes, the causative agent listeriosis, serves as a key model for establishing this understanding. Here, we characterize ARGs in 594 genomes representing 19 Listeria species that previously isolated from soils natural environments across United States. Among five putatively functional identified, lin, which confers to lincomycin, most prevalent, followed by mprF, sul, fosX, norB. are predominantly found sensu stricto species, with those more closely related monocytogenes tending harbor ARGs. Notably, phylogenetic recombination analyses provide evidence recent horizontal gene transfer (HGT) all within and/or likely mediated transformation rather than conjugation transduction. In addition, richness genetic divergence associated conditions, particularly soil properties (e.g., aluminum magnesium) surrounding land use patterns forest coverage). Collectively, our data suggest HGT selection play vital role acquisition diversification environments. It remains elusive evolves spreads. Goh et al. analyzed nationwide genomic dataset find acting on evolution

Language: Английский

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Whole-Genome Sequencing Analysis Revealed High Genomic Variability, Recombination Events and Mobile Genetic Elements in Streptococcus uberis Strains Isolated from Bovine Mastitis in Colombian Dairy Herds

Antibiotics, Journal Year: 2025, Volume and Issue: 14(3), P. 297 - 297

Published: March 12, 2025

Introduction: Streptococcus uberis is a poorly controlled cause of bovine intramammary infections and common motivation for the use antibiotics in dairy farms worldwide. Therefore, studying genomic characteristics this pathogen fundamental to understand its complex epidemiology behavior against antimicrobials. Methods: A comparative analysis 10 S. strains was performed their antimicrobial susceptibility assessed. Results: Ten different novel sequence types were found, genes (tetM, tetO, patB, lnuC, lnuA, lsaE, ermB, ANT(6)-la) mobile genetic elements previously associated with resistance (repUS43, ISSag2, ISEnfa4) virulence (315.2 phage) detected. Additionally, our had highest relative rate recombination mutation (8.3) compared other isolated from continents (America: 7.7, Asia: 2.9, Europe: 5.4, Oceania: 6.6). Most (80%) tested showed phenotypic clindamycin 70% exhibited intermediate penicillin. Conclusions: The high heterogeneity observed presence factors linked represent challenge implementation surveillance measures focused on control elimination pathogen.

Language: Английский

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Diverse spore-forming bacterial populations in US organic raw milk are driven by climate region

Journal of Dairy Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Spore-forming bacteria pose significant challenges to the dairy industry, as they are present at high levels in natural environment and can cause finished product spoilage. To improve organic raw milk quality minimize spoilage caused by spore-forming bacteria, we used a farm-to-table approach, assessing diversity of various spore types through longitudinal studies United States (US) supplies, including (i) from 100 farms, (ii) intended for cheese production 5 processing plants, (iii) pasteurized (iv) powders 2 plants. Based on total 4,194 isolates characterized either rpoB or 16S rRNA gene sequencing, Bacillus spp. dominated aerobic spore-formers isolated farm milk, powders. Nonmetric multidimensional scaling revealed that spore-former populations differ significantly between climate zones genus, species, allelic type levels. The anaerobic/facultative anaerobic samples represented orders Clostridiales Bacillales. Evaluation gas produced showed varied clades, 1 Bacillales clade amounts were not different most clades. Overall, our data indicate substantial US supplies with predominant genera species similar conventional previously described; both facultative found produce gas; may affect milk.

Language: Английский

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Diverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment

International Journal of Food Microbiology, Journal Year: 2023, Volume and Issue: 410, P. 110479 - 110479

Published: Nov. 9, 2023

Listeria (L.) monocytogenes is of global concern for food safety as the listeriosis-causing pathogen widely distributed in processing environments, where it can survive a long time. Frozen vegetables contaminated with L. were recently identified source two large listeriosis outbreaks EU and US. So far, only few studies have investigated occurrence behavior frozen associated environment. This study investigates other spp. vegetable environment products. Using whole genome sequencing (WGS), distribution sequence types (MLST-STs) core (cgMLST-CT) assessed, in-house clones identified. Comparative genomic analyses phenotypical characterization different MLST-STs isolates performed, including growth ability under low temperatures, well survival freeze-thaw cycles. disseminated five namely ST451-CT4117, ST20-CT3737, ST8-CT1349, ST8-CT6243, ST224-CT5623 among present environmental swab samples. Subsequently, also detected product Conveyor belts major contamination A wide repertoire stress resistance markers supported colonization facility. The presence ArgB was significantly clones. Significant differences observed rate between at temperatures (4 °C 10 °C), but not non-in-house isolates. All harbored virulence genes such full length InlA InlB LIPI-1, yet there content. results this demonstrate that WGS strong tool tracing sources transmission routes, identifying Further research targeting co-occurring microbiota biofilms needed to fully understand mechanism persistence

Language: Английский

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What’s on a prophage: analysis of Salmonella spp. prophages identifies a diverse range of cargo with multiple virulence- and metabolism-associated functions

mSphere, Journal Year: 2024, Volume and Issue: 9(6)

Published: May 22, 2024

The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion a new environment, host. While previous studies have focused on identifying and characterizing genetic diversity analyses prophages carry not been extensively explored. We characterized prophage regions from 303

Language: Английский

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Comparative genomics analysis to explore the biodiversity and mining novel target genes of Listeria monocytogenes strains from different regions

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 15

Published: June 19, 2024

As a common foodborne pathogen, infection with L. monocytogenes poses significant threat to human life and health. The objective of this study was employ comparative genomics unveil the biodiversity evolutionary characteristics strains from different regions, screening for potential target genes mining novel genes, thus providing reference value specific molecular detection therapeutic targets strains. Pan-genomic analysis revealed that regions have open genomes, solid genetic basis adaptation environments. These contain numerous virulence contribute their high pathogenicity. They also exhibit relatively resistance phosphonic acid, glycopeptide, lincosamide, peptide antibiotics. results mobile elements indicate that, despite being located in geographical locations, there is certain degree similarity bacterial genome evolution environmental pressures. identified through pan-genomics are primarily associated fundamental activities invasion monocytogenes, including known such as inlB, which can be utilized purposes. After large number we further screened them using hub gene selection methods genes. present employed eight methods, ultimately identifying ten highly connected (bglF_1, davD, menE_1, tilS, dapX, iolC, gshAB, cysG, trpA, hisC), play crucial roles pathogenesis monocytogenes. pan-genomic showed evolution. PCR demonstrated excellent specificity bglF_1 davD Therefore, hold promise regions.

Language: Английский

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Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 27, 2024

Abstract Soil has been identified as an important reservoir of antibiotic resistance genes (ARGs) and there is a need to understand how corresponding environmental changes influence their emergence, evolution, spread. As soil-dwelling bacterial genus containing pathogens, Listeria, including L. monocytogenes , the causative agent listeriosis in humans, could serve key model for establishing this understanding. Notably, acquired among isolated from foods environment observed some regions over past decade. Here we characterized ARGs using 594 genomes representing 19 Listeria species that previously soils across United States. Among five putatively functional identified, lin which confers lincomycin, was most prevalent, followed by mprF, sul, fosX norB . were found be predominant sensu stricto more closely related tended harbor ARGs. lin, fosX, showed evidence recent horizontal gene transfer (HGT) species, likely through transformation opposed conjugation transduction, while mprF sul appear have undergone positive selection. In addition, soil properties surrounding land use factors associated with ARG richness genetic divergence, respectively. Using machine learning, demonstrated presence can predicted variables good accuracy (mean auROC 0.76). Collectively, our data suggest HGT selection played vital role acquisition diversification environment.

Language: Английский

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