Lutz Geue

The Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STECper) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STECspo) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STECper isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STECspo isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STECper isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STECspo isolates. Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STECper from STECspo isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level. IMPORTANCE Ruminants, especially cattle, are sources of food-borne infections by Shiga toxin-producing Escherichia coli (STEC) in humans. Some STEC strains persist in cattle for longer periods of time, while others are detected only sporadically. Persisting strains can serve as gene reservoirs that supply E. coli with virulence factors, thereby generating new outbreak strains. Attempts to reduce the human risk for acquiring STEC infections should therefore include strategies to control such persisting STEC strains. By analyzing representative genes of their core and accessory genomes, we show that bovine STEC with a persistent colonization type emerged independently from sporadically colonizing isolates and evolved in parallel evolutionary branches. However, persistent colonizing strains share similar sets of accessory genes. Defining the genetic patterns that distinguish persistent from sporadically colonizing STEC isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.

Decreased STEC shedding by cattle following passive and active vaccination based on recombinant Escherichia coli Shiga toxoids

The principal virulence factor of Shiga toxin (Stx)-producing Escherichia coli (STEC), the eponymous Stx, modulates cellular immune responses in cattle, the primary STEC reservoir. We examined whether immunization with genetically inactivated recombinant Shiga toxoids (rStx1MUT/rStx2MUT) influences STEC shedding in a calf cohort. A group of 24 calves was passively (colostrum from immunized cows) and actively (intra-muscularly at 5th and 8th week) vaccinated. Twenty-four calves served as unvaccinated controls (fed with low anti-Stx colostrum, placebo injected). Each group was divided according to the vitamin E concentration they received by milk replacer (moderate and high supplemented). The effective transfer of Stx-neutralizing antibodies from dams to calves via colostrum was confirmed by Vero cell assay. Serum antibody titers in calves differed significantly between the vaccinated and the control group until the 16th week of life. Using the expression of activation marker CD25 on CD4+CD45RO+ cells and CD8αhiCD45RO+ cells as flow cytometry based read-out, cells from vaccinated animals responded more pronounced than those of control calves to lysates of STEC and E. coli strains isolated from the farm as well as to rStx2MUT in the 16th week. Summarized for the entire observation period, less fecal samples from vaccinated calves were stx1 and/or stx2 positive than samples from control animals when calves were fed a moderate amount of vitamin E. This study provides first evidence, that transfer to and induction in young calves of Stx-neutralizing antibodies by Shiga toxoid vaccination offers the opportunity to reduce the incidence of stx-positive fecal samples in a calf cohort.

Effect of vitamin E supplementation in milk replacer and Shiga toxoid vaccination on serum α‐tocopherol, performance, haematology and blood chemistry in male Holstein calves

Vitamin E (vit E), an essential antioxidant for maintaining the stability of biological membranes and the function of the immune system, is considered to support adaptive immune responses and performance in cattle. The principal virulence factor of Shiga toxin (Stx)-producing Escherichia coli (STEC), the eponymous Stx, modulates cellular immune responses in cattle, the primary STEC reservoir. Active and passive immunization of calves with Shiga toxoids (rStxMUT ) was recently shown to reduce the STEC shedding. Here, we examined the influence of vit E on calves serum α-tocopherol, performance, haematology, blood chemistry and its interaction with rStxMUT immunization. Data from calves having received passive (colostrum from immunized cows) and active (intramuscularly at 5th and 8th weeks of life) vaccination with rStxMUT (nxa0=xa024) were compared to unvaccinated controls (nxa0=xa024; fed with low anti-Stx colostrum, placebo injected). For each vaccination group, data were analysed according to the level of vit E supplementation offered by milk replacer (188xa0IU all-rac-α-tocopheryl acetate daily [VitEM ] vs. 354xa0IU [VitEH ]). An increase by 79% in daily vit E supplementation led to slightly higher serum α-tocopherol level and earlier concentrate intake at the beginning of the experiment without significant differences in live weight gain, haematology, blood chemistry parameters and peripheral CD4+ and CD8+ T-cell subpopulations. rStxMUT vaccination modulated the CD4+ /CD8+ ratio irrespective of vit E supplementation but decreased concentrate intake in VitEH in a time-dependent manner. Results of our study indicate that an increase in daily vit E supplementation vastly fails to exert effects on laboratory parameters and growth performance. However, observed interactive effects of vit E supply and vaccination on the regulation of feed intake deserves further attention.

Pro-inflammatory capacity of Escherichia coli O104:H4 outbreak strain during colonization of intestinal epithelial cells from human and cattle

In 2011, Germany was struck by the largest outbreak of hemolytic uremic syndrome. The highly virulent E. coli O104:H4 outbreak strain LB226692 possesses a blended virulence profile combining genetic patterns of human adapted enteroaggregative E. coli (EAEC), rarely detected in animal hosts before, and enterohemorrhagic E. coli (EHEC), a subpopulation of Shiga toxin (Stx)-producing E. coli (STEC) basically adapted to the ruminant host. This study aimed at appraising the relative level of adaptation of the EAEC/EHEC hybrid strain LB226692 to humans and cattle. Adherence and invasion of the hybrid strain to intestinal (jejunal and colonic) epithelial cells (IEC) of human and bovine origin was compared to that of E. coli strains representative of different pathovars and commensal E. coli by means of light and electron microscopy and culture. Strain-specific host gene transcription profiles of selected cytokines and chemokines as well as host-induced transcription of bacterial virulence genes were assessed. The release of Stx upon host cell contact was quantified. The outbreak strains immunomodulation was assessed by cultivating primary bovine macrophages with conditioned supernatants from IEC infection studies with E. coli, serving as model for the innate immunity of the bovine gut. The outbreak strain adhered to IEC of both, human and bovine origin. Electron microscopy of infected cells revealed the strains particular affinity to human small IEC, in contrast to few interactions with bovine small IEC. The outbreak strain possessed a high-level of adhesive power, similar to human-associated E. coli strains and in contrast to bovine-associated STEC strains. The outbreak strain displayed a non-invasive phenotype, in contrast to some bovine-associated E. coli strains, which were invasive. The outbreak strain provoked some pro-inflammatory activity in human cells, but to a lower extent as compared to other pathotypes. In contrasts to bovine-associated E. coli strains, the outbreak strain induced marked pro-inflammatory activity when interacting with bovine host cells directly (IEC) and indirectly (macrophages). Among stx2-positive strains, the human-pathogenic strains (LB226692 and EHEC strain 86-24) released higher amounts of Stx compared to bovine-associated STEC. The findings imply that the outbreak strain is rather adapted to humans than to cattle. However, the outbreak strains potential to colonize IEC of both host species and the rather mixed reaction patterns observed for all strains under study indicate, that even STEC strains with an unusual genotype as the EHEC O104:H4 outbreak strain, i.e. with an EAEC genetic background, may be able to conquer other reservoir hosts.

Evaluation of applicability of DNA microarray–based characterization of bovine Shiga toxin–producing Escherichia coli isolates using whole genome sequence analysis

We assessed the ability of a commercial DNA microarray to characterize bovine Shiga toxin–producing Escherichia coli (STEC) isolates and evaluated the results using in silico hybridization of the microarray probes within whole genome sequencing scaffolds. From a total of 69,954 reactions (393 probes with 178 isolates), 68,706 (98.2%) gave identical results by DNA microarray and in silico probe hybridization. Results were more congruent when detecting the genoserotype (209 differing results from 19,758 in total; 1.1%) or antimicrobial resistance genes (AMRGs; 141 of 26,878; 0.5%) than when detecting virulence-associated genes (VAGs; 876 of 22,072; 4.0%). Owing to the limited coverage of O-antigens by the microarray, only 37.2% of the isolates could be genoserotyped. However, the microarray proved suitable to rapidly screen bovine STEC strains for the occurrence of high numbers of VAGs and AMRGs and is suitable for molecular surveillance workflows.

Complete Annotated Genome Sequences of Two Shiga Toxin-Producing Escherichia coli Strains and One Atypical Enteropathogenic E. coli Strain, Isolated from Naturally Colonized Cattle of German Origin

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) are important zoonotic enteric pathogens with the main reservoir in cattle. Here, we present the genomes of two STEC strains and one atypical enteropathogenic E. coli strain from cattle origin, obtained during a longitudinal study in German cattle herds.

Evidence for contemporary switching of the O-antigen gene cluster between Shiga toxin producing Escherichia coli strains colonizing cattle

Shiga toxin-producing Escherichia coli (STEC) comprise a group of zoonotic enteric pathogens with ruminants, especially cattle, as the main reservoir. O-antigens are instrumental for host colonization and bacterial niche adaptation. They are highly immunogenic and, therefore, targeted by the adaptive immune system. The O-antigen is one of the most diverse bacterial cell constituents and variation not only exists between different bacterial species, but also between individual isolates/strains within a single species. We recently identified STEC persistently infecting cattle and belonging to the different serotypes O156:H25 (n = 21) and O182:H25 (n = 15) that were of the MLST sequence types ST300 or ST688. These STs differ by a single nucleotide in purA only. Fitness-, virulence-associated genome regions, and CRISPR/CAS (clustered regularly interspaced short palindromic repeats/CRISPR associated sequence) arrays of these STEC O156:H25 and O182:H25 isolates were highly similar, and identical genomic integration sites for the stx converting bacteriophages and the core LEE, identical Shiga toxin converting bacteriophage genes for stx1a, identical complete LEE loci, and identical sets of chemotaxis and flagellar genes were identified. In contrast to this genomic similarity, the nucleotide sequences of the O-antigen gene cluster (O-AGC) regions between galF and gnd and very few flanking genes differed fundamentally and were specific for the respective serotype. Sporadic aEPEC O156:H8 isolates (n = 5) were isolated in temporal and spatial proximity. While the O-AGC and the corresponding 5′ and 3′ flanking regions of these aEPEC isolates were identical to the respective region in the STEC O156:H25 isolates, the core genome, the virulence associated genome regions and the CRISPR/CAS elements differed profoundly. Our cumulative epidemiological and molecular data suggests a recent switch of the O-AGC between isolates with O156:H8 strains having served as DNA donors. Such O-antigen switches can affect the evaluation of a strains pathogenic and virulence potential, suggesting that NGS methods might lead to a more reliable risk assessment.

Dynamics of total and Shiga-toxin (Stx) forming Escherichia coli shedding with faeces of dairy cows experiencing a change from a low to a high caloric diet

The aim of the experiment was to study the dynamics of Escherichia coli counts in faeces of Holstein cows in dependence on a diet change. The first 6xa0weeks served to change from a low-caloric diet (3.8xa0MJ NEL/kg DM, 100xa0% straw) to a high-caloric ration (7.5xa0MJ NEL/kg DM, 60xa0% of concentrate feed) subsequently fed for 10xa0weeks. Only a few E. coli colonies were detected at the beginning and decreased to 75 and 21xa0CFU/g in weeks 2 and 4, respectively. Thereafter, a steep increase to approximately 1.1E+05xa0CFU/g was found within 2xa0weeks, which was followed by a further, less pronounced, tenfold increase during the next 6xa0weeks. Seven out of the 8 cows were Stx-positive at the outset. Cows positively tested decreased continuously; 4 in weeks 2 and 4, 1 in week 6, 8 and 10. In week 12 all cows were negative while 4 cows turned to be Stx-positive in weeks 14 and 16. Each of the eight cows was tested to be Stx-positive at least once, and at a maximum of five times. In conclusion, feeding of a high-calorie diet increased the total E. coli without a parallel increase in Stx-positive CFU.ZusammenfassungDas Ziel des Versuchs bestand darin, die Dynamik der Konzentration von Escherichia coli im Kot von Holstein-Kühen in Abhängigkeit von einem Futterwechsel zu verfolgen. Die ersten 6xa0Wochen dienten dem Wechsel von einer Niedrig-kalorischen Ration (3,8xa0MJ NEL/kg DM, 100xa0% Stroh) auf eine hoch-kalorische Diät (7.5xa0MJ NEL/kg DM, 60xa0% Konzentratanteil) welche für weitere 10xa0Wochen gefüttert wurde. Zu Beginn waren nur wenige E. coli-Kolonien nachzuweisen, die in den Wochen 2 und 4 auf 75 bzw. 21xa0CFU/g absanken. Danach wurde ein starker Anstieg auf 1,1E+05xa0CFU/g innerhalb der nächsten 2xa0Wochen festgestellt, der gefolgt wurde von einem weniger stark ausgeprägten 10-fachen Anstieg während der nächsten 6xa0Wochen. Sieben der 8xa0Kühe waren Stx-positiv zu Versuchsbeginn. Der Anteil positiv getesteter Tiere sank kontinuierlich; 4 in den Wochen 2 und 4, 1 in den Wochen 6, 8 und 10. In Woche 12 waren alle Kühe negativ, während zu Versuchsende 4xa0Kühe in den Wochen 14 und 16 wieder positiv waren. Jede der 8xa0Kühe wurde wenigstens einmal und höchstens 5-mal Stx-positiv getestet. Es kann geschlussfolgert werden, dass die Fütterung einer hoch-kalorischen Diät die Gesamtzahl an E.coli erhöhte, was aber nicht von einem gleichgerichteten Anstieg Stx-positiver CFU begleitet war.

Genotypic characterization of bovine Shiga toxin-producing Escherichia coli (STEC) strains with persistent or sporadic colonization types

In food and food-producing animals monitoring of antimicrobial resistant bacteria is mostly conducted on commensal E. coli. From 2015 on in the EU also the selective isolation and subsequent resistance testing on ESBL/AmpC-producing E. coli is mandatory (2013/652/EU).Question: Domestic pigs and Eurasian wild boar (Sus scrofa) share several important viral and bacterial pathogens. Therefore, direct and indirect contacts between domestic pigs and wild boar present a risk of pathogen spill-over and can lead to long-term perpetuation of infection. Biological indicators could be a powerful tool to understand and characterize contacts between wild boar and domestic pigs. Here, faecal E. coli were explored as potential biological indicator under experimental conditions. nMethods: Within an animal trial domestic pigs (group 2, n=8) were brought into contact with faecal material of wild boar (group 1, n=8). Before and three to five weeks after transmission of faeces fecal samples of both groups were collected, coliforme bacteria isolated, and the bacteria tested by CHEF-PFGE for clonal relatedness. The study was meant as test and calibration phase for potential field studies. nResults: Eighty-eight individual E. coli clones were detected by XbaI restriction and PFGE analysis. Selecting only one isolates representing a distinct clone from an individual faecal sample, 123 E. coli isolates were further analysed. Overall, 17 different clones were found in several animals of a group (1 or 2) or both samples from one animal. Additionally, five clones were detected in group 1 as well as in contact group 2. nConclusions: The data gained in our pilot study suggest that faecal E. coli can be used as biological indicator of contact between wild boar and domestic pig. Based on these promising results, future field studies will especially target the practicability of E. coli microbiome molecular typing as surrogate of contacts at the nwildlife-livestock interface. nThis study is funded by the European Unions Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 311931 (ASFORCE).

Experimental evaluation of faecal Escherichia coli as biological indicator of contacts between domestic pigs and Eurasian wild boar

In food and food-producing animals monitoring of antimicrobial resistant bacteria is mostly conducted on commensal E. coli. From 2015 on in the EU also the selective isolation and subsequent resistance testing on ESBL/AmpC-producing E. coli is mandatory (2013/652/EU).Question: Domestic pigs and Eurasian wild boar (Sus scrofa) share several important viral and bacterial pathogens. Therefore, direct and indirect contacts between domestic pigs and wild boar present a risk of pathogen spill-over and can lead to long-term perpetuation of infection. Biological indicators could be a powerful tool to understand and characterize contacts between wild boar and domestic pigs. Here, faecal E. coli were explored as potential biological indicator under experimental conditions. nMethods: Within an animal trial domestic pigs (group 2, n=8) were brought into contact with faecal material of wild boar (group 1, n=8). Before and three to five weeks after transmission of faeces fecal samples of both groups were collected, coliforme bacteria isolated, and the bacteria tested by CHEF-PFGE for clonal relatedness. The study was meant as test and calibration phase for potential field studies. nResults: Eighty-eight individual E. coli clones were detected by XbaI restriction and PFGE analysis. Selecting only one isolates representing a distinct clone from an individual faecal sample, 123 E. coli isolates were further analysed. Overall, 17 different clones were found in several animals of a group (1 or 2) or both samples from one animal. Additionally, five clones were detected in group 1 as well as in contact group 2. nConclusions: The data gained in our pilot study suggest that faecal E. coli can be used as biological indicator of contact between wild boar and domestic pig. Based on these promising results, future field studies will especially target the practicability of E. coli microbiome molecular typing as surrogate of contacts at the nwildlife-livestock interface. nThis study is funded by the European Unions Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 311931 (ASFORCE).