Novel Multilocus Sequence Typing Scheme Reveals High Genetic Diversity of Human Pathogenic Members of the Fusarium incarnatum-F. equiseti and F. chlamydosporum Species Complexes within the United States

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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High genetic diversity and geographic subdivision of three lance nematode species ( Hoplolaimus spp.) in the United States

Ecology and Evolution ◽

10.1002/ece3.1568 ◽

2015 ◽

Vol 5 (14) ◽

pp. 2929-2944 ◽

Cited By ~ 4

Author(s):

Claudia M. Holguin ◽

Juan A. Baeza ◽

John D. Mueller ◽

Paula Agudelo

Keyword(s):

United States ◽

Genetic Diversity ◽

Nematode Species ◽

The United States ◽

High Genetic Diversity ◽

Lance Nematode

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Epidemiology of nosocomial bacteria resistant to antimicrobials

Colombia Medica ◽

10.25100/cm.v42i1.759 ◽

2011 ◽

pp. 117-125 ◽

Cited By ~ 4

Author(s):

Cristina E Cabrera ◽

Romel F Gómez ◽

Andrés E Zuñiga ◽

Raúl H Corral ◽

Bertha López ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Latin American ◽

The United States ◽

Epidemiological Studies ◽

Global Scale ◽

Multiresistant Pathogens ◽

High Genetic Diversity ◽

Gram Negative ◽

Enterococcus Spp

Nosocomial infections are a major challenge for public health because of the high rates of morbidity and mortality generated. It was considered that the excessive or inappropriate use of antibiotics triggers the emergence of resistant strains. Among the clinically important bacteria that most commonly cause nososcomial infections, Gram positive multiresistant pathogens stand out such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus spp (VRE), and the Gram negative strains of Klebsiella pneumoniae, Escherichia coli, Pseudomonas spp. and Acinetobacter baumannii producing expanded spectrum b-lactamases (ESbL). This review describes the behavior of the main bacterial pathogens resistant to antibiotics that cause infections in Europe, United States, and Latin America, emphasizing studies of molecular epidemiology on a global scale, including the major epidemiological studies in Colombia. The genetic structure of S. aureus and Enterococcus spp strains shows a clonal characteristic favored by the predominance of a small number of clones with the capacity to spread globally, due probably to cross-infection. However, the introduction of MRSA strains from the community encourages genetic diversity, tending to establish a genetic polyclonal endemic structure in places like the United States. In Gram negative bacteria, the high genetic diversity among isolates, mainly in Latin American countries, indicates that the polyclonal spread is influenced by horizontal transfer of plasmids, by excessive exposure to antibiotics, and prolonged hospital stays. In Colombia, there is information on nosocomial resistant pathogens, but molecular epidemiological information is still scarce.

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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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Carios kelleyi (Acari: Ixodida: Argasidae) Infected With Rickettsial Agents Documented Infesting Housing in Kansas, United States

Journal of Medical Entomology ◽

10.1093/jme/tjab069 ◽

2021 ◽

Author(s):

Robyn M Nadolny ◽

Ashley C Kennedy ◽

James M Rodgers ◽

Zachary T Vincent ◽

Hannah Cornman ◽

...

Keyword(s):

Public Health ◽

United States ◽

Health Center ◽

Human Disease ◽

Multilocus Sequence Typing ◽

The United States ◽

Rickettsia Species ◽

History Of ◽

Tick Borne Disease ◽

Blood Meals

Abstract During September–December 2018, 25 live ticks were collected on-post at Fort Leavenworth, Kansas, in a home with a history of bat occupancy. Nine ticks were sent to the Army Public Health Center Tick-Borne Disease Laboratory and were identified as Carios kelleyi (Cooley and Kohls, 1941), a species that seldom bites humans but that may search for other sources of blood meals, including humans, when bats are removed from human dwellings. The ticks were tested for numerous agents of human disease. Rickettsia lusitaniae was identified by multilocus sequence typing to be present in two ticks, marking the first detection of this Rickettsia agent in the United States and in this species of tick. Two other Rickettsia spp. were also detected, including an endosymbiont previously associated with C. kelleyi and a possible novel Rickettsia species. The potential roles of C. kelleyi and bats in peridomestic Rickettsia transmission cycles warrant further investigation.

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Population structure of Drosophila suzukii and signals of multiple invasions into the continental United States

10.1101/2021.03.14.435345 ◽

2021 ◽

Author(s):

Kyle M Lewald ◽

Antoine Abrieux ◽

Derek A Wilson ◽

Yoosook Lee ◽

William R Conner ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Population Structure ◽

Weather Conditions ◽

The United States ◽

Future Research ◽

Drosophila Suzukii ◽

Significant Damage ◽

Wide Range ◽

Multiple Invasions

Drosophila suzukii, or spotted-wing drosophila, is now an established pest in many parts of the world, causing significant damage to numerous fruit crop industries. Native to East Asia, D. suzukii infestations started in the United States a decade ago, occupying a wide range of climates. To better understand invasion ecology of this pest, knowledge of past migration events, population structure, and genetic diversity is needed. To improve on previous studies examining genetic structure of D. suzukii, we sequenced whole genomes of 237 individual flies collected across the continental U.S., as well as several representative sites in Europe, Brazil, and Asia, to identify hundreds of thousands of genetic markers for analysis. We analyzed these markers to detect population structure, to reconstruct migration events, and to estimate genetic diversity and differentiation within and among the continents. We observed strong population structure between West and East Coast populations in the U.S., but no evidence of any population structure North to South, suggesting there is no broad-scale adaptations occurring in response to the large differences in regional weather conditions. We also find evidence of repeated migration events from Asia into North America have provided increased levels of genetic diversity, which does not appear to be the case for Brazil or Europe. This large genomic dataset will spur future research into genomic adaptations underlying D. suzukii pest activity and development of novel control methods for this agricultural pest.

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A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States

Viruses ◽

10.3390/v14010104 ◽

2022 ◽

Vol 14 (1) ◽

pp. 104

Author(s):

Adam A. Capoferri ◽

Wei Shao ◽

Jon Spindler ◽

John M. Coffin ◽

Jason W. Rausch ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Rna Virus ◽

Viral Evolution ◽

The United States ◽

Virus Spread ◽

Immune Pressure ◽

Viral Genetic Diversity ◽

Genetic Sampling ◽

The U.S

COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced immune pressure and prior infections might be expected to influence viral evolution. Accordingly, we conducted a study to characterize the spread of SARS-CoV-2 in the U.S. pre-vaccination, investigate the depth and uniformity of genetic surveillance during this period, and measure and otherwise characterize changing viral genetic diversity, including by comparison with more recently emergent variants of concern (VOCs). In 2020, SARS-CoV-2 spread across the U.S. in three phases distinguishable by peaks in the numbers of infections and shifting geographical distributions. Virus was genetically sampled during this period at an overall rate of ~1.2%, though there was a substantial mismatch between case rates and genetic sampling nationwide. Viral genetic diversity tripled over this period but remained low in comparison to other widespread RNA virus pathogens, and although 54 amino acid changes were detected at frequencies exceeding 5%, linkage among them was not observed. Based on our collective observations, our analysis supports a targeted strategy for worldwide genetic surveillance as perhaps the most sensitive and efficient means of detecting new VOCs.

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Measurement of Genetic Diversity of Chinese Seashore Paspalum Resources through Morphological and Sequence-related Amplified Polymorphism Analysis

Journal of the American Society for Horticultural Science ◽

10.21273/jashs04700-19 ◽

2019 ◽

Vol 144 (6) ◽

pp. 379-386

Author(s):

Yan Liu ◽

Hailin Guo ◽

Yi Wang ◽

Jingang Shi ◽

Dandan Li ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Cluster Analysis ◽

Genetic Variation ◽

Genetic Distance ◽

Morphological Characteristics ◽

The United States ◽

Germplasm Resources ◽

Seashore Paspalum ◽

Chinese Germplasm

Seashore paspalum (Paspalum vaginatum) is a notable warm-season turfgrass. Certain germplasm resources are distributed in the southern regions of China. The objectives of this study were to investigate the genetic diversity and genetic variation of Chinese seashore paspalum resources. Morphological characteristics and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships and genetic variation among 36 germplasm resources from China and six cultivars from the United States. The results showed significant variation for 13 morphological characteristics among 42 tested seashore paspalum accessions, and that the phenotypic cv was, in turn, turf height > turf density > internode length > inflorescence density > leaf width > reproductive branch height > spikelet width > leaf length > spikelet number > inflorescence length > internode diameter > inflorescence width > spikelet length. According to the morphological characteristics and cluster analysis, 42 seashore paspalum accessions were divided into six morphological types. In total, 374 clear bands were amplified using 30 SRAP primer combinations; among these bands, 321 were polymorphic with 85.83% polymorphism. SRAP marker cluster analysis showed that 42 seashore paspalum accessions were grouped into seven major groups, with a genetic similarity coefficient ranging from 0.4385 to 0.9893 and genetic distance values ranging from 0.0108 to 0.8244. The high level of genetic diversity occurred among Chinese germplasm, and the genetic distance was relatively high between Chinese germplasm and cultivars introduced from the United States. The patterns in morphological trait variations and genetic diversity will be useful for the further exploitation and use of Chinese seashore paspalum resources.

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Fine-Scale Population Genetic Structure and Within-Tree Distribution of Mating Types of Venturia effusa, Cause of Pecan Scab in the United States

Phytopathology ◽

10.1094/phyto-02-18-0068-r ◽

2018 ◽

Vol 108 (11) ◽

pp. 1326-1336 ◽

Cited By ~ 5

Author(s):

Clive H. Bock ◽

Carolyn A. Young ◽

Katherine L. Stevenson ◽

Nikki D. Charlton

Keyword(s):

United States ◽

Genetic Diversity ◽

Asexual Reproduction ◽

Population Genetic ◽

Spatial Scales ◽

The United States ◽

Source Population ◽

Mating Types ◽

Fine Scale ◽

Scale Population

Scab (caused by Venturia effusa) is the major disease of pecan in the southeastern United States. There is no information available on the fine-scale population genetic diversity or the occurrence of clonal types at small spatial scales that provides insight into inoculum sources and dispersal mechanisms, and potential opportunity for sexual reproduction. To investigate fine-scale genetic diversity, four trees of cultivar Wichita (populations) were sampled hierarchically: within each tree canopy, four approximately evenly spaced terminals (subpopulations) were selected and up to six leaflets (sub-subpopulations) were sampled from different compound leaves on each terminal. All lesions (n = 1 to 8) on each leaflet were sampled. The isolates were screened against a panel of 29 informative microsatellite markers and the resulting multilocus genotypes (MLG) subject to analysis. Mating type was also determined for each isolate. Of 335 isolates, there were 165 MLG (clonal fraction 49.3%). Nei’s unbiased measure of genetic diversity for the clone-corrected data were moderate to high (0.507). An analysis of molecular variance demonstrated differentiation (P = 0.001) between populations on leaflets within individual terminals and between terminals within trees in the tree canopies, with 93.8% of variance explained among isolates within leaflet populations. Other analyses (minimum-spanning network, Bayesian, and discriminant analysis of principal components) all indicated little affinity of isolate for source population. Of the 335 isolates, most unique MLG were found at the stratum of the individual leaflets (n = 242), with similar total numbers of unique MLG observed at the strata of the terminal (n = 170), tree (n = 166), and orchard (n = 165). Thus, the vast majority of shared clones existed on individual leaflets on a terminal at the scale of 10s of centimeters or less, indicating a notable component of short-distance dispersal. There was significant linkage disequilibrium (P < 0.001), and an analysis of Psex showed that where there were multiple encounters of an MLG, they were most probably the result of asexual reproduction (P < 0.05) but there was no evidence that asexual reproduction was involved in single or first encounters of an MLG (P > 0.05). Overall, the MAT1-1-1 and MAT1-2-1 idiomorphs were at equilibrium (73:92) and in most populations, subpopulations, and sub-subpopulations. Both mating types were frequently observed on the same leaflet. The results provide novel information on the characteristics of populations of V. effusa at fine spatial scales, and provide insights into the dispersal of the organism within and between trees. The proximity of both mating idiomorphs on single leaflets is further evidence of opportunity for development of the sexual stage in the field.

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