Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways

ABSTRACT Paenibacillus is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of Paenibacillus spp., we first used rpoB allelic typing data for a preexisting collection of 1,228 Paenibacillus species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented rpoB allelic types in the collection revealed that these isolates represent 21 different Paenibacillus spp., with P. odorifer being the predominant species. Further genomic characterization of P. odorifer isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all P. odorifer isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6°C, suggesting that psychrotolerance is conserved in P. odorifer. Overall, our data suggest that Paenibacillus spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage. IMPORTANCE Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.

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Genetic Diversity and Geographical Distribution of Indigenous Soybean-Nodulating Bradyrhizobia in the United States

Applied and Environmental Microbiology ◽

10.1128/aem.00236-13 ◽

2013 ◽

Vol 79 (12) ◽

pp. 3610-3618 ◽

Cited By ~ 35

Author(s):

Sokichi Shiro ◽

Syota Matsuura ◽

Rina Saiki ◽

Gilbert C. Sigua ◽

Akihiro Yamamoto ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Community Structure ◽

Geographical Distribution ◽

The United States ◽

23S Rrna ◽

Rrna Gene ◽

Scaling Analysis ◽

Internal Transcribed Spacer Region ◽

Content Type

ABSTRACTWe investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybeanRjgenotypes (non-Rj,Rj2Rj3, andRj4). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDABradyrhizobiumstrains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters wereBradyrhizobium japonicumBj123, in the northern United States, andBradyrhizobium elkanii, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging toB. elkaniithan for the cluster belonging toB. japonicum. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically.

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Genetic Diversity of Flavobacterium psychrophilum Isolates from Three Oncorhynchus spp. in the United States, as Revealed by Multilocus Sequence Typing

Applied and Environmental Microbiology ◽

10.1128/aem.00411-16 ◽

2016 ◽

Vol 82 (11) ◽

pp. 3246-3255 ◽

Cited By ~ 18

Author(s):

Danielle Van Vliet ◽

Gregory D. Wiens ◽

Thomas P. Loch ◽

Pierre Nicolas ◽

Mohamed Faisal

Keyword(s):

United States ◽

Genetic Diversity ◽

Rainbow Trout ◽

Chinook Salmon ◽

Host Species ◽

Cold Water ◽

The United States ◽

Content Type ◽

Flavobacterium Psychrophilum ◽

Bacterial Cold Water Disease

ABSTRACTThe use of a multilocus sequence typing (MLST) technique has identified the intraspecific genetic diversity of U.S.Flavobacterium psychrophilum, an important pathogen of salmonids worldwide. Prior to this analysis, little U.S.F. psychrophilumgenetic information was known; this is of importance when considering targeted control strategies, including vaccine development. Herein, MLST was used to investigate the genetic diversity of 96F. psychrophilumisolates recovered from rainbow trout (Oncorhynchus mykiss), coho salmon (Oncorhynchus kisutch), and Chinook salmon (Oncorhynchus tshawytscha) that originated from nine U.S. states. The isolates fell into 34 distinct sequence types (STs) that clustered in 5 clonal complexes (CCs) (n= 63) or were singletons (n= 33). The distribution of STs varied spatially, by host species, and in association with mortality events. Several STs (i.e., ST9, ST10, ST30, and ST78) were found in multiple states, whereas the remaining STs were localized to single states. With the exception of ST256, which was recovered from rainbow trout and Chinook salmon, all STs were found to infect a single host species. Isolates that were collected during bacterial cold water disease outbreaks most frequently belonged to CC-ST10 (e.g., ST10 and ST78). Collectively, the results of this study clearly demonstrate the genetic diversity ofF. psychrophilumwithin the United States and identify STs of clinical significance. Although the majority of STs described herein were novel, some (e.g., ST9, ST10, ST13, ST30, and ST31) were previously recovered on other continents, which demonstrates the transcontinental distribution ofF. psychrophilumgenotypes.IMPORTANCEFlavobacterium psychrophilumis the causative agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS) and is an important bacterial pathogen of wild and farmed salmonids worldwide. These infections are responsible for large economic losses globally, yet the genetic diversity of this pathogen remains to be fully investigated. Previous studies have identified the genetic diversity of this pathogen in other main aquaculture regions; however, little effort has been focused on the United States. In this context, this study aims to examine the genetic diversity ofF. psychrophilumfrom the United States, as this region remains important in salmonid aquaculture.

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Genotypic and Phenotypic Diversity of Staphylococcus aureus Isolates from Cystic Fibrosis Patient Lung Infections and Their Interactions with Pseudomonas aeruginosa

mBio ◽

10.1128/mbio.00735-20 ◽

2020 ◽

Vol 11 (3) ◽

Cited By ~ 2

Author(s):

Eryn E. Bernardy ◽

Robert A. Petit ◽

Vishnu Raghuram ◽

Ashley M. Alexander ◽

Timothy D. Read ◽

...

Keyword(s):

United States ◽

Cystic Fibrosis ◽

Staphylococcus Aureus ◽

Pseudomonas Aeruginosa ◽

Virulence Factors ◽

Phenotypic Diversity ◽

Laboratory Strain ◽

The United States ◽

Content Type ◽

Lung Infections

ABSTRACT Staphylococcus aureus has recently overtaken Pseudomonas aeruginosa as the most commonly recognized bacterial pathogen that infects the respiratory tracts of individuals with the genetic disease cystic fibrosis (CF) in the United States. Most studies of S. aureus in CF patient lung infections have focused on a few isolates, often exclusively laboratory-adapted strains, and how they are killed by P. aeruginosa. Less is known about the diversity of S. aureus CF patient lung isolates in terms of both their virulence and their interaction with P. aeruginosa. To begin to address this gap, we recently sequenced 64 clinical S. aureus isolates and a reference isolate, JE2. Here, we analyzed the antibiotic resistance genotypes, sequence types, clonal complexes, spa types, agr types, and presence/absence of other known virulence factor genes of these isolates. We hypothesized that virulence phenotypes of S. aureus, namely, toxin production and the mucoid phenotype, would be lost in these isolates due to adaptation in the CF patient lung. In contrast to these expectations, we found that most isolates can lyse both rabbit and sheep blood (67.7%) and produce polysaccharide (69.2%), suggesting that these phenotypes were not lost during adaptation to the CF lung. We also identified three distinct phenotypic groups of S. aureus based on their survival in the presence of nonmucoid P. aeruginosa laboratory strain PAO1 and its mucoid derivative. Altogether, our work provides greater insight into the diversity of S. aureus isolates from CF patients, specifically the distribution of important virulence factors and their interaction with P. aeruginosa, all of which have implications in patient health. IMPORTANCE Staphylococcus aureus is now the most frequently detected recognized pathogen in the lungs of individuals who have cystic fibrosis (CF) in the United States, followed closely by Pseudomonas aeruginosa. When these pathogens are found to coinfect the CF lung, patients have a significantly worse prognosis. While P. aeruginosa has been rigorously studied in the context of bacterial pathogenesis in CF, less is known about S. aureus. Here, we present an in-depth study of 64 S. aureus clinical isolates from CF patients, for which we investigated genetic diversity utilizing whole-genome sequencing, virulence phenotypes, and interactions with P. aeruginosa. We found that S. aureus isolated from CF lungs are phylogenetically diverse; most retain known virulence factors and vary in their interactions with P. aeruginosa (i.e., they range from being highly sensitive to P. aeruginosa to completely tolerant to it). Deepening our understanding of how S. aureus responds to its environment and other microbes in the CF lung will enable future development of effective treatments and preventative measures against these formidable infections.

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Genetic Diversity and Pathogenic Potential of Attaching and Effacing Escherichia coli O26:H11 Strains Recovered from Bovine Feces in the United States

Applied and Environmental Microbiology ◽

10.1128/aem.00397-15 ◽

2015 ◽

Vol 81 (11) ◽

pp. 3671-3678 ◽

Cited By ~ 14

Author(s):

Sarah A. Ison ◽

Sabine Delannoy ◽

Marie Bugarel ◽

Kendra K. Nightingale ◽

Hattie E. Webb ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

Genetic Diversity ◽

The United States ◽

Pathogenic Potential ◽

Content Type ◽

Genomic Plasticity ◽

E Coli ◽

Short Palindromic Repeat ◽

Bovine Feces

ABSTRACTEscherichia coliO26 has been identified as the most common non-O157 Shiga toxin-producingE. coli(STEC) serogroup to cause human illnesses in the United States and has been implicated in outbreaks around the world.E. colihas high genomic plasticity, which facilitates the loss or acquisition of virulence genes. Attaching and effacingE. coli(AEEC) O26 strains have frequently been isolated from bovine feces, and there is a need to better characterize the relatedness of these strains to defined molecular pathotypes and to describe the extent of their genetic diversity. High-throughput real-time PCR was used to screen 178E. coliO26 isolates from a single U.S. cattle feedlot, collected from May to July 2011, for the presence or absence of 25 O26 serogroup-specific and virulence-associated markers. The selected markers were capable of distinguishing these strains into molecularly defined groups (yielding 18 unique marker combinations). Analysis of the clustered regularly interspaced short palindromic repeat 1 (CRISPR1) and CRISPR2a loci further discriminated isolates into 24 CRISPR types. The combination of molecular markers and CRISPR typing provided 20.8% diversity. The recent CRISPR PCR target SP_O26-E, which was previously identified only instx2-positive O26:H11 human clinical strains, was identified in 96.4% (161/167 [95% confidence interval, 99.2 to 93.6%]) of thestx-negative AEEC O26:H11 bovine fecal strains. This supports that thesestx-negative strains may have previously contained a prophage carryingstxor could acquire this prophage, thus possibly giving them the potential to become pathogenic to humans. These results show that investigation of specific genetic markers may further elucidate our understanding of the genetic diversity of AEEC O26 strains in bovine feces.

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Multilaboratory Survey To Evaluate Salmonella Prevalence in Diarrheic and Nondiarrheic Dogs and Cats in the United States between 2012 and 2014

Journal of Clinical Microbiology ◽

10.1128/jcm.02137-16 ◽

2017 ◽

Vol 55 (5) ◽

pp. 1350-1368 ◽

Cited By ~ 21

Author(s):

Renate Reimschuessel ◽

Michael Grabenstein ◽

Jake Guag ◽

Sarah M. Nemser ◽

Kyunghee Song ◽

...

Keyword(s):

United States ◽

Susceptibility Testing ◽

Sequence Data ◽

The United States ◽

Pulsed Field Gel Electrophoresis ◽

Phenotypic Data ◽

Content Type ◽

Testing Laboratories ◽

Geographically Dispersed

ABSTRACT Eleven laboratories collaborated to determine the periodic prevalence of Salmonella in a population of dogs and cats in the United States visiting veterinary clinics. Fecal samples (2,965) solicited from 11 geographically dispersed veterinary testing laboratories were collected in 36 states between January 2012 and April 2014 and tested using a harmonized method. The overall study prevalence of Salmonella in cats (3 of 542) was <1%. The prevalence in dogs (60 of 2,422) was 2.5%. Diarrhea was present in only 55% of positive dogs; however, 3.8% of the all diarrheic dogs were positive, compared with 1.8% of the nondiarrheic dogs. Salmonella -positive dogs were significantly more likely to have consumed raw food ( P = 0.01), to have consumed probiotics ( P = 0.002), or to have been given antibiotics ( P = 0.01). Rural dogs were also more likely to be Salmonella positive than urban ( P = 0.002) or suburban ( P = 0.001) dogs. In the 67 isolates, 27 unique serovars were identified, with three dogs having two serovars present. Antimicrobial susceptibility testing of 66 isolates revealed that only four of the isolates were resistant to one or more antibiotics. Additional characterization of the 66 isolates was done using pulsed-field gel electrophoresis and whole-genome sequencing (WGS). Sequence data compared well to resistance phenotypic data and were submitted to the National Center for Biotechnology Information (NCBI). This study suggests an overall decline in prevalence of Salmonella -positive dogs and cats over the last decades and identifies consumption of raw food as a major risk factor for Salmonella infection. Of note is that almost half of the Salmonella -positive animals were clinically nondiarrheic.

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Investigation of Genotypes of Borrelia burgdorferi in Ixodes scapularis Ticks Collected during Surveillance in Canada

Applied and Environmental Microbiology ◽

10.1128/aem.02636-10 ◽

2011 ◽

Vol 77 (10) ◽

pp. 3244-3254 ◽

Cited By ~ 57

Author(s):

N. H. Ogden ◽

G. Margos ◽

D. M. Aanensen ◽

M. A. Drebot ◽

E. J. Feil ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

North America ◽

Lyme Disease ◽

Borrelia Burgdorferi ◽

Diagnostic Tests ◽

Ixodes Scapularis ◽

The United States ◽

Borrelia Miyamotoi ◽

Content Type

ABSTRACTThe genetic diversity ofBorrelia burgdorferisensu stricto, the agent of Lyme disease in North America, has consequences for the performance of serological diagnostic tests and disease severity. To investigateB. burgdorferidiversity in Canada, where Lyme disease is emerging, bacterial DNA in 309 infected adultIxodes scapularisticks collected in surveillance was characterized by multilocus sequence typing (MLST) and analysis of outer surface protein C gene (ospC) alleles. Six ticks carriedBorrelia miyamotoi, and one tick carried the novel speciesBorrelia kurtenbachii. 142 ticks carriedB. burgdorferisequence types (STs) previously described from the United States. Fifty-eight ticks carriedB. burgdorferiof 1 of 19 novel or undescribed STs, which were single-, double-, or triple-locus variants of STs first described in the United States. Clonal complexes with founder STs from the United States were identified. SeventeenospCalleles were identified in 309B. burgdorferi-infected ticks. Positive and negative associations in the occurrence of different alleles in the same tick supported a hypothesis of multiple-niche polymorphism forB. burgdorferiin North America. Geographic analysis of STs andospCalleles were consistent with south-to-north dispersion of infected ticks from U.S. sources on migratory birds. These observations suggest that the genetic diversity ofB. burgdorferiin eastern and central Canada corresponds to that in the United States, but there was evidence for founder events skewing the diversity in emerging tick populations. Further studies are needed to investigate the significance of these observations for the performance of diagnostic tests and clinical presentation of Lyme disease in Canada.

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NCSS notable trade book lesson plan: the girl who buried her dreams in a can

Social Studies Research and Practice ◽

10.1108/ssrp-03-2019-0015 ◽

2020 ◽

Vol 15 (2) ◽

pp. 121-126

Author(s):

Takisha Durm

Keyword(s):

United States ◽

Research Design ◽

Design Methodology ◽

Lesson Plan ◽

The United States ◽

Elementary Grades ◽

Effect Change ◽

Content Type ◽

Similarities And Differences ◽

Future Date

PurposeThe Girl Who Buried Her Dreams in a Can, written by Dr Tererai, profiles a cultural, yet global experience of the power of believing in one's dream. Through this study of the similarities and differences of how children in the United States and abroad live and dream of a better life, this lesson seeks to enhance students' understandings of the power and authority they possess to effect change not only within their own lives but also in the lives of countless others in world. After reading the text, students will work to create vision boards illustrating their plans to effect change within their homes, schools, communities, states or countries. They will present their plans to their peers. To culminate the lesson, the students will bury their dreams in can and collectively decide on a future date to revisit the can to determine how far they have progressed in accomplishing their goals.Design/methodology/approachThis is an elementary grades 3–6 lesson plan. There was no research design/methodology/approach included.FindingsAs this is a lesson plan and no actual research was represented, there are no findings.Originality/valueThis is an original lesson plan completed by the first author Takisha Durm.

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Molecular Analysis of a Plum pox virus W Isolate in Plum Germplasm Hand Carried into the USA from the Ukraine Shows a Close Relationship to a Latvian Isolate

Plant Disease ◽

10.1094/pdis-01-12-0104-re ◽

2013 ◽

Vol 97 (1) ◽

pp. 44-52 ◽

Cited By ~ 14

Author(s):

Vessela Mavrodieva ◽

Delano James ◽

Karen Williams ◽

Sarika Negi ◽

Aniko Varga ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

The United States ◽

Common Source ◽

Plum Pox Virus ◽

High Genetic Diversity ◽

Close Relationship ◽

The Usa ◽

Sequence Identities ◽

Germplasm Accessions

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

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Genetic Diversity of Wild Oat (Avena fatua)Populations from China and the United States

Weed Science ◽

10.1614/ws-06-108.1 ◽

2007 ◽

Vol 55 (2) ◽

pp. 95-101 ◽

Cited By ~ 21

Author(s):

Runzhi Li ◽

Shiwen Wang ◽

Liusheng Duan ◽

Zhaohu Li ◽

Michael J. Christoffers ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Gene Diversity ◽

Genetic Relationships ◽

The United States ◽

Mantel Test ◽

Wild Oat ◽

Chinese Populations ◽

Nei's Distance ◽

The Impact

Weed genetic diversity is important for understanding the ability of weeds to adapt to different environments and the impact of herbicide selection on weed populations. Genetic diversity within and among six wild oat populations in China varying in herbicide selection pressure and one population in North Dakota were surveyed using 64 polymorphic alleles resulting from 25 microsatellite loci. Mean Nei's gene diversity (h) for six wild oat populations from China was between 0.17 and 0.21, and total diversity (HT) was 0.23. A greater proportion of this diversity, however, was within (Hs= 0.19) rather than among (Gst= 0.15) populations. For the wild oat population from the United States,h= 0.24 andHT= 0.24 were comparable to the values for the six populations from China. Cluster analysis divided the seven populations into two groups, where one group was the United States population and the other group included the six Chinese populations. The genetic relationships among six populations from China were weakly correlated with their geographic distribution (r= 0.22) using the Mantel test. Minimal difference in gene diversity and small genetic distance (Nei's distance 0.07 or less) among six populations from China are consistent with wide dispersal of wild oat in the 1980s. Our results indicate that the wild oat populations in China are genetically diverse at a level similar to North America, and the genetic diversity of wild oat in the broad spatial scale is not substantially changed by environment, agronomic practices, or herbicide usage.

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Washington will rethink its foreign chip strategy

Emerald Expert Briefings ◽

10.1108/oxan-db265673 ◽

2021 ◽

Keyword(s):

United States ◽

Supply Chain ◽

The United States ◽

Export Controls ◽

Political Pressure ◽

Technical Standards ◽

Content Type ◽

The Us ◽

Technology Competition ◽

Business In China

Significance Follow-on action from Washington and responses from foreign actors will shape the US government’s adversarial policy towards China in semiconductors and other strategic technologies. Impacts The Biden administration will likely conclude that broad-based diversion of the semiconductor supply chain away from China is not feasible. The United States will rely on export controls and political pressure to prevent diffusion to China of cutting-edge chip technologies. The United States will focus on persuading foreign semiconductor leaders to help develop US capabilities, thereby staying ahead of China. Washington will focus on less direct approaches to strategic technology competition with China, notably technical standards-setting. Industry leaders in the semiconductor supply chain worldwide will continue expanding business in China in less politically sensitive areas.

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