Pathogenic specialisation within Colletotrichum trifolii in Australia, and lucerne cultivar reactions to all known Australian pathotypes

Anthracnose and crown rot, caused by Colletotrichum trifolii, are serious diseases of lucerne (Medicago saliva L.) in humid regions of the world. A race survey was conducted by inoculating individual lucerne clones (genotypes) with C. trifolii isolates collected from a range of Medicago hosts, locations, and years in south-eastern Queensland. This survey revealed for the first time in Australia the presence of race 2 (virulence on anthracnose resistance gene An I) and the first world report of race 4 (virulence on An(2)). A collection of North American race I and race 2 C. trifolii isolates, when inoculated onto the Australian differential clones, gave responses that were in agreement with their North American reactions. A RAPD analysis was conducted on 9 Australian C. trifolii isolates including races 1, 2, and 4; two C. destructivum and one C. gloeosporioides isolate were included as known outliers. For the C. trifolii isolates, 94.6% similarity was found regardless of host origin or race, compared with 2.2% similarity between this group and the C. gloeosporioides and C. destructivum isolates, confirming that the new races belong to C. trifolii. Currently, it is hypothesised that only plants carrying genes An, and An2 are resistant to the 3 races. Of 22 cultivars screened against the 3 races, only UQL-1, Hallmark, and Pioneer 54Q53 had >30% of plants resistant to the 3 races in separate screenings. The research highlights the need to find new sources of resistance to C. trifolii in lucerne.

Genetic relationship of diarrheagenic Escherichia coli pathotypes among the enteropathogenic Escherichia coli O serogroup

The genetic relationship among the Escherichia coli pathotypes was investigated. We used random amplified polymorphic DNA (RAPD) data for constructing a dendrogram of 73 strains of diarrheagenic E. coli. A phylogenetic tree encompassing 15 serotypes from different pathotypes was constructed using multilocus sequence typing data. Phylogram clusters were used for validating RAPD data on the clonality of enteropathogenic E. coli (EPEC) O serogroup strains. Both analyses showed very similar topologies, characterized by the presence of two major groups: group A includes EPEC H6 and H34 strains and group B contains the other EPEC strains plus all serotypes belonging to atypical EPEC, enteroaggregative E. coli (EAEC) and enterohemorrhagic E. coli (EHEC). These results confirm the existence of two evolutionary divergent groups in EPEC: one is genetically and serologically very homogeneous whereas the other harbors EPEC and non-EPEC serotypes. The same situation was found for EAEC and EHEC.

Identification of Phaeoisariopsis griseola pathotypes from five States in Brazil

Due to the increased importance of angular leaf spot of common bean (Phaseolus vulgaris) in Brazil, monitoring the pathogenic variability of its causal agent (Phaeoisariopsis griseola) is the best strategy for a breeding program aimed at developing resistant genotypes. Fifty one isolates of P. griseola collected in five Brazilian States were tested on a set of 12 international differential cultivars in the greenhouse. When inoculated plants showed symptoms but no sporulation was observed, they were transferred to a moist chamber for approximately 20-24 h. After this period of time, if no sporulation was observed, the plants were considered resistant; otherwise, they were considered susceptible. From the fifty-one tested isolates, seven different pathotypes were identified. No Andean pathotypes were identified; consequently, all isolates were classified as Middle American pathotypes. Pathotype 63-31 was the most widespread. Pathotype 63-63 overcame resistance genes present in all differential cultivars and also the resistance gene(s) present in the cultivar AND 277. This fact has important implications for breeding angular leaf spot resistance in beans, and suggests that searching for new resistance genes to angular leaf spot must be pursued.

A classification of Pepper yellow mosaic virus isolates into pathotypes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pathotypes and probiotics: response to a commentary on the detection of a Shiga toxin producing Escherichia coli in a Crohn’s disease patient

A recent report on the detection in a Crohn's disease (CD) patient of an adherent and invasive Shiga toxin producing Escherichia coli (STEC) (Gut pathogens 2015, 7:2) prompted a commentary expressing some skepticism on the significance of the paper findings (Gut pathogens 2015, 7:15). Besides focusing on recurrent issues concerning the difficulties in defining a pathogen, the opinion considers recent data demonstrating the presence of virulence factors in a commercial probiotic. In response to the commentary's observations, additional information on the described STEC strain, as well as a short discussion on CD associated E. coli are presented here.

Escherichia coli from Crohn’s disease patient displays virulence features of enteroinvasive (EIEC), enterohemorragic (EHEC), and enteroaggregative (EAEC) pathotypes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

P-220-Escherichia coli displaying virulence features of multiple diarrheogenic pathotypes detected in a Crohn's disease patient

Background: The number of Escherichia coli in the gut of Crohn's disease (CD) patients is higher than that of normal subjects, but the virulence potential of these bacteria is not fully known. Previous studies have shown that these E. coli are closely related to extraintestinal pathogenic categories (ExPEC), are able to invade epithelial cells, and usually do not produce exotoxins. We report here the detection, in a CD patient, of an E. coli which belongs to a classical enteropathogenic (EPEC) serotype and displays virulence markers of enteroinvasive (EIEC), enteroaggregative (EAEC) and enterohemorrhagic (EHEC) pathotypes. Methods: The E. coli strain was isolated, in 2009, by classical bacteriological procedures from a 56 year old woman who underwent ileo-terminal resection 1 year before, due to intestinal obstruction. The bacterial characterization was carried out by in vitro adhesion and invasion assays to cultured epithelial cells and macrophages and screening by PCR to identify virulence genetic markers of diarrheogenic E. coli (DEC) and to detect one of the gene combinations which define the phylogroups of the E. coli reference (EcoR) collection. The strain was also tested for the ability to produce biofilm and shiga cytotoxins and had its whole genome sequenced by Ion Torrent Sequencing Technology. Results: The studied strain, which was detected both in ileum biopsies and the stools of the patient, displayed the aggregative adherence (AA) phenotype to Hep-2 cells and an ability to enter Caco-2 cells 3x as high as that of EIEC reference strain and 89% of that of the prototype AIEC LF82 strain. Although it could invade cultured macrophages, the strain was unable to replicate inside these cells. PCR screening revealed the presence of eae, aggR and stx1. Tests with bacterial culture supernatants in Vero cells demonstrating cytotoxicity suggested the production of Stx1. In addition, the strain revealed to be a strong biofilm producer, belonged to the B2 EcoR phylogroup, to the O126:H27 serogroup and to the multilocus sequencing type (MLST) ST3057. The 2 later features were deduced from the whole genome sequence of the strain. Conclusions: The characterization of this E. coli isolate from a CD patient revealed a combination of virulence markers of distinct DEC pathotypes, namely eae and stx1 of EHEC, AA, aggR and biofilm formation of EAEC, and invasiveness of EIEC. These features along with its serotype and phylogroup identity seem to suggest a potential to be involved in CD, an observation which should be tested with additional studies.

Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range

Abstract Background Citrus bacterial canker is a disease that has severe economic impact on citrus industries worldwide and is caused by a few species and pathotypes of Xanthomonas. X. citri subsp. citri strain 306 (XccA306) is a type A (Asiatic) strain with a wide host range, whereas its variant X. citri subsp. citri strain Aw12879 (Xcaw12879, Wellington strain) is restricted to Mexican lime. Results To characterize the mechanism for the differences in host range of XccA and Xcaw, the genome of Xcaw12879 that was completed recently was compared with XccA306 genome. Effectors xopAF and avrGf1 are present in Xcaw12879, but were absent in XccA306. AvrGf1 was shown previously for Xcaw to cause hypersensitive response in Duncan grapefruit. Mutation analysis of xopAF indicates that the gene contributes to Xcaw growth in Mexican lime but does not contribute to the limited host range of Xcaw. RNA-Seq analysis was conducted to compare the expression profiles of Xcaw12879 and XccA306 in Nutrient Broth (NB) medium and XVM2 medium, which induces hrp gene expression. Two hundred ninety two and 281 genes showed differential expression in XVM2 compared to in NB for XccA306 and Xcaw12879, respectively. Twenty-five type 3 secretion system genes were up-regulated in XVM2 for both XccA and Xcaw. Among the 4,370 common genes of Xcaw12879 compared to XccA306, 603 genes in NB and 450 genes in XVM2 conditions were differentially regulated. Xcaw12879 showed higher protease activity than XccA306 whereas Xcaw12879 showed lower pectate lyase activity in comparison to XccA306. Conclusions Comparative genomic analysis of XccA306 and Xcaw12879 identified strain specific genes. Our study indicated that AvrGf1 contributes to the host range limitation of Xcaw12879 whereas XopAF contributes to virulence. Transcriptome analyses of XccA306 and Xcaw12879 presented insights into the expression of the two closely related strains of X. citri subsp. citri. Virulence genes including genes encoding T3SS components and effectors are induced in XVM2 medium. Numerous genes with differential expression in Xcaw12879 and XccA306 were identified. This study provided the foundation to further characterize the mechanisms for virulence and host range of pathotypes of X. citri subsp. citri.

Pathotypes and serogroups of enterotoxigenic Escherichia coli isolated from pre-weaning pigs in north Vietnam

The contribution of enterotoxigenic Escherichia coli (ETEC) to pre-weaning diarrhoea was investigated over a 6 month period at five selected commercial piggeries (CPs) in north Vietnam with at least 100 sows each. Diarrhoea was found to affect 71(.)5% of the litters born during the period of study. Of 406 faecal specimens submitted for bacteriological culture, 200 (49(.)3%) yielded a heavy pure culture of E coli and 126(31 %)were confirmed by PCR to carry at least one of eight porcine ETEC virulence genes. ETEC was responsible for 43% of cases of diarrhoea in neonatal pigs during the first 4 days of life and 23(.)9% of the remaining cases up until the age of weaning. Pathotypes were determined by PCR for the 126 ETEC isolates together with 44 ETEC isolates obtained from village pigs (VPs) raised by smallholder farmers. The CP isolates belonged to five pathotypes, four of which were also identified in VP isolates. Haemolytic serogroup O149: K91 isolates that belonged to F4/STa/STb/LT were most commonly identified in both CPs (33 % of isolates) and VPs (45(.)5%). Other combinations identified in both production systems included O64 (F5/STa), O101 (F4/STa/STb) and O-nontypable (F-/STb). A high proportion of CP isolates (22(.)3 %) possessed all three enterotoxins (STa/STWLT), lacked the genes for all five tested fimbriae (F4, F5, F6, F41 and F18) and belonged to serogroup O8. These unusual 08 F- isolates were haemolytic and were isolated from all ages of diarrhoeic piglets at each CP, suggesting that they have pathogenic potential.

Caractérisation des pathotypes d'Escherichia coli dans les eaux des Grands Lacs à l'aide d'une biopuce d'ADN

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Caractérisation des pathotypes d'Escherichia coli dans les eaux des Grands Lacs à l'aide d'une biopuce d'ADN

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Assessment of virulence factors characteristic of human Escherichia coli pathotypes and antimicrobial resistance in O157:H7 and non-O157:H7 isolates from livestock in Spain

The distribution of virulence factors (VFs) typical of diarrheagenic Escherichia coli and the antimicrobial resistance (AMR) profiles were assessed in 780 isolates from healthy pigs, broilers, and cattle from Spain. VF distribution was broader than expected, although at low prevalence for most genes, with AMR being linked mainly to host species.

Atypical enteropathogenic Escherichia coli genomic background allows the acquisition of non-EPEC virulence factors

Atypical enteropathogenic Escherichia coli (aEPEC) has been associated with infantile diarrhea in many countries. The clonal structure of aEPEC is the object of active investigation but few works have dealt with its genetic relationship with other diarrheagenic E. coli (DEC). This study aimed to evaluate the genetic relationship of aEPEC with other DEC pathotypes. The phylogenetic relationships of DEC strains were evaluated by multilocus sequence typing. Genetic diversity was assessed by pulsed-field gel electrophoresis (PFGE). The phylogram showed that aEPEC strains were distributed in four major phylogenetic groups (A, B1, B2 and D). Cluster I ( group B1) contains the majority of the strains and other pathotypes [enteroaggregative, enterotoxigenic and enterohemorrhagic E. coli ( EHEC)]; cluster II ( group A) also contains enteroaggregative and diffusely adherent E. coli; cluster III ( group B2) has atypical and typical EPEC possessing H6 or H34 antigen; and cluster IV ( group D) contains aEPEC O55:H7 strains and EHEC O157:H7 strains. PFGE analysis confirmed that these strains encompass a great genetic diversity. These results indicate that aEPEC clonal groups have a particular genomic background - especially the strains of phylogenetic group B1 that probably made possible the acquisition and expression of virulence factors derived from non-EPEC pathotypes.