Draft Genome Sequences of Paenibacillus alvei A6-6i and TS-15

Luo, Yan; Wang, Charles; Allard, Sarah; Strain, Errol; Allard, Marc W.; Brown, Eric W.; Zheng, Jie

doi:10.1128/genomea.00673-13

Cited by 6 publications

(9 citation statements)

References 6 publications

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“…Frequently, antagonistic microorganisms are co-enriched along with target pathogens [21]. For example, Paenibacillus spp ., which are capable of inhibiting and killing Salmonella [22, 23] , were also enriched using protocols outlined in the FDA BAM to recover Salmonella from tomatoes [21, 24] and cilantro [25]. Thus, continued optimization of reference enrichment protocols is still needed.…”

Section: Discussionmentioning

confidence: 99%

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak

et al. 2016

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BackgroundMicrobiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA). Enrichment cultures were analyzed using DNA extraction and sequencing from samples taken every 4 h throughout 48 h of enrichment. Resphera Insight and CosmosID analysis tools were employed for high-resolution profiling of 16S rRNA amplicons and whole genome shotgun data, respectively.ResultsDuring enrichment, other bacterial taxa were identified, including Anoxybacillus, Geobacillus, Serratia, Pseudomonas, Erwinia, and Streptococcus spp. Surprisingly, incidence of L. monocytogenes was proportionally greater at hour 0 than when tested 4, 8, and 12 h later with all three enrichment schemes. The corresponding increase in Anoxybacillus and Geobacillus spp.indicated these taxa co-enriched in competition with L. monocytogenes during early enrichment hours. L. monocytogenes became dominant after 24 h in all three enrichments. DNA sequences obtained from shotgun metagenomic data of Listeria monocytogenes at 48 h were assembled to produce a consensus draft genome which appeared to have a similar tracking utility to pure culture isolates of L. monocytogenes.ConclusionsAll three methods performed equally well for enrichment of Listeria monocytogenes. The observation of potential competitive exclusion of L. mono by Anoxybacillus and Geobacillus in early enrichment hours provided novel information that may be used to further optimize enrichment formulations. Application of Resphera Insight for high-resolution analysis of 16S amplicon sequences accurately identified L. monocytogenes. Both shotgun and 16S rRNA data supported the presence of three slightly variable genomes of L. monocytogenes. Moreover, the draft assembly of a consensus genome of L. monocytogenes from shotgun metagenomic data demonstrated the potential utility of this approach to expedite trace-back of outbreak-associated strains, although further validation will be needed to confirm this utility.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-016-0894-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak

et al. 2016

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“…Results from the Bioscreen and agar plug assays, however, indicate that the inhibitory (i.e., bacteriostatic and bactericidal) effects of this antagonist on food-borne pathogens can be attributed mainly to its antimicrobial activities. Whole-genome sequencing was performed to help identify di- verse antibiotic biosynthetic genes present in these two isolates (39). A few novel antimicrobial agents with activities against many food-borne pathogens, including Salmonella spp., E. coli O157: H7, L. monocytogenes, S. dysenteriae, C. sakazakii, and drug-resistant S. aureus, were discovered in our laboratory (our unpublished data).…”

Section: Discussionmentioning

confidence: 99%

In Situ Evaluation of Paenibacillus alvei in Reducing Carriage of Salmonella enterica Serovar Newport on Whole Tomato Plants

Allard

Enurah

Strain

et al. 2014

Appl Environ Microbiol

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dRecently, tomatoes have been implicated as a primary vehicle in food-borne outbreaks of Salmonella enterica serovar Newport and other Salmonella serovars. Long-term intervention measures to reduce Salmonella prevalence on tomatoes remain elusive for growing and postharvest environments. A naturally occurring bacterium identified by 16S rRNA gene sequencing as Paenibacillus alvei was isolated epiphytically from plants native to the Virginia Eastern Shore tomato-growing region. After initial antimicrobial activity screening against Salmonella and 10 other bacterial pathogens associated with the human food supply, strain TS-15 was further used to challenge an attenuated strain of S. Newport on inoculated fruits, leaves, and blossoms of tomato plants in an insect-screened high tunnel with a split-plot design. Survival of Salmonella after inoculation was measured for groups with and those without the antagonist at days 0, 1, 2, and 3 and either day 5 for blossoms or day 6 for fruits and leaves. Strain TS-15 exhibited broad-range antimicrobial activity against both major food-borne pathogens and major bacterial phytopathogens of tomato. After P. alvei strain TS-15 was applied onto the fruits, leaves, and blossoms of tomato plants, the concentration of S. Newport declined significantly (P < 0.05) compared with controls. Astonishingly, >90% of the plants had no detectable levels of Salmonella by day 5 for blossoms. The naturally occurring antagonist strain TS-15 is highly effective in reducing the carriage of Salmonella Newport on whole tomato plants. The application of P. alvei strain TS-15 is a promising approach for reducing the risk of Salmonella contamination during tomato production.

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“…The 10-kb continuous-long-read (CLR) data were de novo assembled using the PacBio hierarchical genome assembly process (HGAP)/ Quiver software package, followed by Minimus 2, and were polished with Quiver [27]. The assembled contigs were annotated with the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/ Pipeline.html) [5].…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

“…Of particular interest is biocontrol of crop production for food safety applications, where pathogens, including fungal and bacterial growth, can be minimized or prevented by using a bacterial strain or compounds produced by bacteria that are native to the environment and exhibit antibiotic properties [3,4]. Previously, two naturally-occurring gram-positive bacteria identified as Paenibacillus alvei were isolated from plants native to the Virginia Eastern Shore tomato growing region [5,6]. Both strains showed broad-spectrum antimicrobial activity against gram-negative and gram-positive foodborne pathogens.…”

Section: Introductionmentioning

confidence: 99%

“…Here, we present the detection and identification of broadspectrum antimicrobial compounds produced by an environmentally isolated Paenibacillus alvei strain from plants native in the U.S. to the Virginia Eastern Shore tomato growing region [5,6]. Compounds were first fractionated by off-line ultra-performance liquid chromatography (UPLC), and the bioactivity of each fraction was assessed against gramnegative and -positive bacteria.…”

Section: Introductionmentioning

confidence: 99%

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Identification and Structural Characterization of Naturally-Occurring Broad-Spectrum Cyclic Antibiotics Isolated from Paenibacillus

Knolhoff

Zheng

McFarland

et al. 2015

J. Am. Soc. Mass Spectrom.

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Abstract. The rise of antimicrobial resistance necessitates the discovery and/or production of novel antibiotics. Isolated strains of Paenibacillus alvei were previously shown to exhibit antimicrobial activity against a number of pathogens, such as E. coli, Salmonella, and methicillin-resistant Staphylococcus aureus (MRSA). The responsible antimicrobial compounds were isolated from these Paenibacillus strains and a combination of low and high resolution mass spectrometry with multiple-stage tandem mass spectrometry was used for identification. A group of closely related cyclic lipopeptides was identified, differing primarily by fatty acid chain length and one of two possible amino acid substitutions. Variation in the fatty acid length resulted in mass differences of 14 Da and yielded groups of related MS n spectra. Despite the inherent complexity of MS/MS spectra of cyclic compounds, straightforward analysis of these spectra was accomplished by determining differences in complementary product ion series between compounds that differ in molecular weight by 14 Da. The primary peptide sequence assignment was confirmed through genome mining; the combination of these analytical tools represents a workflow that can be used for the identification of complex antibiotics. The compounds also share amino acid sequence similarity to a previously identified broad-spectrum antibiotic isolated from Paenibacillus. The presence of such a wide distribution of related compounds produced by the same organism represents a novel class of broad-spectrum antibiotic compounds.

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Draft Genome Sequences of Paenibacillus alvei A6-6i and TS-15

Cited by 6 publications

References 6 publications

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak

Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak

In Situ Evaluation of Paenibacillus alvei in Reducing Carriage of Salmonella enterica Serovar Newport on Whole Tomato Plants

Identification and Structural Characterization of Naturally-Occurring Broad-Spectrum Cyclic Antibiotics Isolated from Paenibacillus

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