Pathogen resistance to clinical antimicrobial agents is an urgent problem. The fungus Aspergillus fumigatus causes 300,000 life-threatening infections in susceptible humans annually. Azoles, which are widely used in both clinical and agricultural settings, are currently the most effective treatment, but resistance to clinical azoles is emerging worldwide. Here we report the isolation and analysis of azole-sensitive and azole-resistant A. fumigatus from agricultural environments in the southeastern United States (USA) and show that the USA pan-azole-resistant isolates form a clade with pan-azole-resistant isolates from the United Kingdom, the Netherlands, and India. We show that several pan-azole-resistant isolates from agricultural settings in the USA and India also carry alleles with mutations conferring resistance to agricultural fungicides from the benzimidazole (MBC) and quinone outside inhibitor (QoI) classes. We further show that pan-azole-resistant A. fumigatus isolates from patients in clinical settings in the USA, India and the Netherlands also carry alleles conferring resistance to MBC and QoI agricultural fungicides. The presence of markers for resistance to agricultural-use fungicides in clinical A. fumigatus isolates is strong evidence for an agricultural origin of pan-azole resistance in patients. The presence of multiple fungicide-resistance alleles in agricultural and clinical isolates further suggests that the unique genetics of the pan-azole-resistant clade enables the evolution and/or persistence of antimicrobial resistance mutations leading to the establishment of multi-fungicide-resistant isolates.

Corynespora cassiicola is a ubiquitous fungus causing emerging plant diseases worldwide, including target spot of cotton, soybean, and tomato, which have rapidly increased in incidence and severity throughout the southeastern United States. The objectives of this study were to understand the causes for the emerging target spot epidemics in the United States by comparing phylogenetic relationships of isolates from cotton, tomato, soybean, and other crop plants and ornamental hosts, and through the determination of the host range of isolates from emerging populations. Fifty-three isolates were sampled from plants in the southeastern United States and 1,380 nucleotides from four nuclear loci were sequenced. Additionally, sequences of the same loci from 23 isolates representing each of the distinct lineages of C. cassiicola described from previous studies were included. Isolates clustered based on host of origin, regardless of the geographic location of sampling. There was no genetic diversity detected among isolates from cotton, which were genetically distinct from isolates from other host species. Furthermore, pathogenicity and virulence assays of 40 isolates from various hosts onto cotton, soybean, tomato, and cucumber showed that isolates from cotton were more aggressive to cotton than those from other hosts. Soybean and tomato were most susceptible to isolates that originated from the same host, providing evidence of host specialization. These results suggest that emerging target spot epidemics in the United States are caused by either the introduction of host-specific isolates or the evolution of more aggressive strains on each host.

Corynespora cassiicola is a highly diverse fungal pathogen that can infect more than 500 species of plants, including many economically important crops such as cotton, soybean, tomato, and cucumber. In Florida, the number one vegetable crop by market value are fresh-market tomatoes, which generate nearly half a billion dollars annually. Florida’s subtropical to tropical climate is conducive to infection and development of the target spot pathogen on tomato caused by C. cassiicola. There is no varietal resistance available for target spot of tomato, and preventative fungicide treatments are the primary method for control. In the last decade, C. cassiicola has been more frequently reported by Florida tomato growers, appearing not only more aggressive but also increasingly insensitive to various fungicides. This review brings together the most recent C. cassiicola literature, providing a history and understanding of the immense pathogen diversity and its relevance to tomato. It also provides insight into fungicide resistance development and pathogen survivability, which are important factors in providing effective control recommendations and in understanding the epidemiology of this disease, respectively.

Fusarium wilt of watermelon, caused by Fusarium oxysporum f. sp. niveum (FON), occurs worldwide and is responsible for substantial yield losses in watermelon-producing areas of the southeastern United States. Management of this disease largely relies on the use of integrated pest management (i.e., fungicides, resistant cultivars, crop rotation, etc.). Knowledge about race structure and genetic diversity of FON in the southeastern US is limited. To determine genetic diversity of the pathogen, FON isolates were collected from symptomatic watermelon plants in commercial fields in Georgia and Florida, USA, and identified based on morphological characteristics and PCR analysis using FON-specific primers. Discriminant analysis of principal components (DAPC) of 99 isolates genotyped with 15 simple sequence repeat (SSR) markers grouped the isolates in eight distinct clusters with two prominent clusters (clusters 1 and 8). Cluster 1 consisted of a total of 14 isolates, out of which 85.7% of the isolates were collected in Florida. However, most of the isolates (92.4%) in cluster 8 were collected in Georgia. Both DAPC and pairwise population differentiation analysis (Ф PT ) revealed that the genetic groups were closely associated with geographical locations of pathogen collection. Three races of FON (races 0, 2 and 3) were identified in the phenotypic analysis; with race 3 identified for the first time in Georgia. Overall, 5.1%, 38.9% and 55.9% of the isolates were identified as race 0, race 2 and race 3, respectively. The majority of the isolates in cluster 1 and cluster 8 belonged to either race 2 (35.6%) or race 3 (45.8%). Additionally, no relationship between genetic cluster assignment and races of the isolates was observed. The information obtained on genotypic and phenotypic diversity of FON in the southeastern US will help in development of effective disease management programs to combat Fusarium wilt.

Corynespora cassiicola is a destructive plant-pathogenic fungus causing widespread target spot epidemics, including outbreaks on cotton, soybean, and tomato in the southeastern United States. Previous studies revealed that populations from the three hosts are genetically distinct and host specialized. Although variation in aggressiveness to cotton and tomato were observed, no genetic diversity was detected within populations sampled from each of these hosts. We aimed to gain a better understanding of the emerging target spot epidemics by developing microsatellite markers for C. cassiicola to assess genetic variation, population structure, and to infer modes of reproduction and mechanisms of dispersal. Two hundred sixty-five isolates from cotton, soybean, tomato, and other host plants were genotyped with 13 microsatellite markers. Genotypic diversity revealed genetic variation within each of the populations collected from different hosts, with the population from cotton dominated by clonal genotypes and showing the least genetic diversity. In addition, C. cassiicola populations on different host species were genetically distinct and structured based on host species. No association between genetic and geographic distances was identified in the tomato populations, and the association in cotton populations was low. However, significant regional geographic structure was detected in the soybean populations of C. cassiicola. These results further support previous findings of introduced host specialized isolates or the evolution of more aggressive strains on each host. The lack of geographic structure suggests that the clones on cotton and tomato spread rapidly, or similar founder populations were established by human-mediated dispersal, and that dispersal is not limited. However, regional geographic structure of populations on soybean suggests limited dispersal among more established populations of C. cassiicola, or genetic differences in founder populations that colonized different geographic areas.