Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates.

Background: Oxford Nanopore provides high throughput sequencing platforms able to reconstruct complete bacterial genomes with 99.95% accuracy. However, even small levels of error can obscure the phylogenetic relationships between closely related isolates.

Prospective Genomic Surveillance Reveals Cryptic MRSA Outbreaks with Local to International Origins among NICU Patients.

Methicillin-resistant Staphylococcus aureus (MRSA) infections cause substantive morbidity and mortality in neonates. Using publicly available resources from the National Center of Biotechnology Information (NCBI) and Food and Drug Administration's (FDA) GalaxyTrakr pipeline, we illustrate the dynamics of MRSA colonization and infection in neonates. Over 217 days of prospective surveillance, analyses revealed concurrent MRSA transmission chains affecting 11 of 17 MRSA-colonized patients (65%), with two clusters that demonstrated intervals of more than a month among the appearance of isolates.

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.

Background: The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification.

Induction of the Viable-but-Nonculturable State in Contaminating Dried Fruit.

Salmonella can become viable but nonculturable (VBNC) in response to environmental stressors, but the induction of the VBNC state in Salmonella contaminating ready-to-eat dried fruit is poorly characterized. Dried apples, strawberries, and raisins were mixed with a five-strain cocktail of Salmonella at 4% volume per weight of dried fruit at 10 CFU/g. The inoculated dried fruit were then dried in desiccators at 25°C until the water activity () approximated that of the uninoculated dried fruit.

Identification of Novel Genes Mediating Survival of on Low-Moisture Foods via Transposon Sequencing Analysis.

is the leading foodborne pathogen associated with outbreaks involving low-moisture foods (LMFs). However, the genes involved in s long-term survival on LMFs remain poorly characterized. In this study, in-shell pistachios were inoculated with Tnbased mutant libraries of .

Validation of an ampicillin selection protocol to enrich for mutants of Listeria monocytogenes unable to replicate on fresh produce.

Several outbreaks of listeriosis have implicated fresh produce but genetic factors required for growth of Listeria monocytogenes on produce remain poorly characterized. Based on the fact that β-lactam antibiotics only kill bacterial cells that are growing, we hypothesized that ampicillin selection can enrich for L. monocytogenes mutants unable to grow on produce.

Predicting the Growth of Listeria monocytogenes and Salmonella Typhimurium in Diced Celery, Onions, and Tomatoes during Simulated Commercial Transport, Retail Storage, and Display.

Temperature is arguably the most important factor affecting microbial proliferation in fresh-cut produce. In this study, growth of Listeria monocytogenes in diced onions and celery and Salmonella Typhimurium in diced tomatoes was determined in modified atmosphere packages and snap-fit containers using three fluctuating temperature scenarios for transport, retail storage, and display. As expected, L.

The Listeria monocytogenes Key Virulence Determinants hly and prfA are involved in Biofilm Formation and Aggregation but not Colonization of Fresh Produce.

has been extensively studied as a model facultative intracellular pathogen. While the roles of major virulence factors in host-pathogen interactions have been extensively characterized, recent work suggests that some of these factors can also contribute to environmental proliferation of this pathogen. In this study, we characterized two non-hemolytic transposon mutants of strain 2011L-2858 (serotype 1/2b), implicated in the 2011 listeriosis outbreak via whole cantaloupe, for their capacity to form biofilms on polystyrene, aggregate, and colonize cantaloupe rind.

Novel Cadmium Resistance Determinant in Listeria monocytogenes.

is a foodborne pathogen that can cause severe disease (listeriosis) in susceptible individuals. It is ubiquitous in the environment and often exhibits resistance to heavy metals. One of the determinants that enables to tolerate exposure to cadmium is the efflux system, with CadA being a P-type ATPase.

Capacity of Listeria monocytogenes Strains from the 2011 Cantaloupe Outbreak To Adhere, Survive, and Grow on Cantaloupe.

The 2011 listeriosis outbreak attributed to whole cantaloupe involved several genetically distinct strains of serotypes 1/2a and 1/2b that had not been previously reported in invasive listeriosis outbreaks. Here we investigated the potential of strains from the 2011 cantaloupe outbreak to adhere, survive, and grow on cantaloupe rind and flesh and in juice extracted from cantaloupe at different temperatures (4, 8, and 25°C). All strains were able to adhere and grow, with ∼10-fold increases after 7 days at 4 or 8°C and after 24 h at 25°C, with a propensity for more growth on rind than on flesh or in extract.