Emergence d'infections à Escherichia coli de pathotype hybride, producteurs d'une Shiga toxine et associés à une virulence extra-intestinale : caractérisation moléculaire et optimisation de leur prévention et de leur prise en charge

The epidemiology of Enterohemorrhagic Escherichia coli (EHEC) involved in Hemolytic and Uremic Syndrome (HUS) has strongly changed in recent years. An atypical clone of serotype O80:H2 (Sequence-type ST301) responsible for HUS and invasive infections has recently emerged in Europe. This clone harbors both virulence factors (VFs) typical of EHEC (intimin - eae-ξ, Shiga toxin - stx, enterohemolysin - ehxA), characteristic VFs of Extra-intestinal pathogenic E. coli (ExPEC) and multi-drug resistance traits (MDR). The aim of this work is to perform a molecular and phenotypic characterization of this heteropathotype to understand its emergence and to contribute to the improvement of diagnosis, treatment and prevention of the infections caused by this pathogen. The EHEC O80:H2 clone acquired a mosaic plasmid (pR444_A) strongly related to the plasmid pS88, a major determinant of ExPEC virulence, carrying multiple extra-intestinal VFs and within which a MDR cassette inserted itself. This ExPEC/EHEC heteropathotype pattern is not restricted to this single serotype since at least 3 other serotypes (O55:H9, O45:H2 and O186:H2) carrying a similar plasmid have been identified within the ST301. A metabolic feature associated with a genetic scar highly specific of ST301, was exploited to develop a real-time PCR (Se=100%, Sp=98.4%) and a culture medium (Se=85%, Sp=85%) selective of these clones. In the case of invasive infections requiring antibiotherapy, the comparative production of Stx in presence of different antibiotics leads to recommend the combination of a beta-lactam and a protein synthesis inhibitor. Through an extensive characterization including phenotypic, genotypic, phylogenetic, molecular and metabolic analysis, this study contributes to the improvement of knowledge on ExPEC/EHEC heteropathotypes of ST301 and the management of their infections. The high capacity of these clones to acquire foreign genetic material underlines their extreme genomic plasticity whose the underlying genetic factors remain to be discovered. The use of these two new diagnostic methods in the food industry could help for identifying the still unknown reservoir of the O80:H2 clone and thus contribute to the prevention of these infections.L'épidémiologie des Escherichia coli entérohémorragiques (EHEC) responsables de Syndrome Hémolytique et Urémique (SHU), s'est considérablement modifiée ces dernières années. Un clone atypique de sérotype O80:H2 (Sequence-type ST301) responsable de SHU et d'infections invasives a récemment émergé en Europe. Ce clone possède à la fois des facteurs de virulence (FVs) typiques des EHEC (intimine - eae-xi, Shiga toxine - stx, entérohémolysine - ehxA), des FVs caractéristiques des E. coli pathogènes extra-intestinaux (ExPEC) et une multirésistance aux antibiotiques (ATB). L'objectif de ce travail est de caractériser sur le plan moléculaire et phénotypique cet hétéropathotype afin de comprendre son émergence et de contribuer à l'amélioration du diagnostic, du traitement et de la prévention des infections liées à ce pathogène. Le clone EHEC O80:H2 a acquis un plasmide mosaïque (pR444_A) hautement similaire au plasmide pS88, un déterminant majeur de la virulence des ExPEC, porteur de multiples FVs extra-intestinaux et au sein duquel une cassette de résistance aux ATB s'est insérée. Ce profil d'hétéropathotype ExPEC/EHEC n'est pas restreint à ce seul sérotype puisque au moins 3 autres sérotypes (O55:H9, O45:H2 et O186:H2) porteurs d'un plasmide similaire ont été identifiés au sein du ST301. Une particularité métabolique associée à une cicatrice génétique hautement spécifique du ST301, a été exploitée pour développer une PCR en temps réel (Se=100%, Sp=98,4%) et un milieu de culture (Se=85%, Sp=85%) sélectifs de ces clones. En cas d'infections invasives imposant une antibiothérapie, la production comparée de Stx en présence de différents ATB conduit à recommander l'association d'une béta-lactamine à un inhibiteur de la synthèse protéique. Au travers d'une caractérisation étendue incluant des analyses phénotypiques, génotypiques, phylogénétiques, moléculaires et métaboliques, ce travail participe à l'amélioration de la connaissance des hétéropathotypes ExPEC/EHEC de ST301 et de la prise en charge des infections liées à ces clones. L'importante capacité de ces clones à acquérir du matériel génétique étranger souligne leur extrême plasticité génomique dont les facteurs génétiques sous-jacents restent à découvrir. L'application de ces deux nouvelles méthodes diagnostiques dans l'industrie agro-alimentaire pourrait participer à l'identification du réservoir du clone O80:H2 inconnu jusqu'alors et ainsi contribuer à la prévention de ces infections

Emergence of infections with hybrid pathotype Escherichia coli producing a Shiga toxin and associated with extra-intestinal virulence : molecular characterization and improvement of their prevention and management

L'épidémiologie des Escherichia coli entérohémorragiques (EHEC) responsables de Syndrome Hémolytique et Urémique (SHU), s'est considérablement modifiée ces dernières années. Un clone atypique de sérotype O80:H2 (Sequence-type ST301) responsable de SHU et d'infections invasives a récemment émergé en Europe. Ce clone possède à la fois des facteurs de virulence (FVs) typiques des EHEC (intimine - eae-xi, Shiga toxine - stx, entérohémolysine - ehxA), des FVs caractéristiques des E. coli pathogènes extra-intestinaux (ExPEC) et une multirésistance aux antibiotiques (ATB). L'objectif de ce travail est de caractériser sur le plan moléculaire et phénotypique cet hétéropathotype afin de comprendre son émergence et de contribuer à l'amélioration du diagnostic, du traitement et de la prévention des infections liées à ce pathogène. Le clone EHEC O80:H2 a acquis un plasmide mosaïque (pR444_A) hautement similaire au plasmide pS88, un déterminant majeur de la virulence des ExPEC, porteur de multiples FVs extra-intestinaux et au sein duquel une cassette de résistance aux ATB s'est insérée. Ce profil d'hétéropathotype ExPEC/EHEC n'est pas restreint à ce seul sérotype puisque au moins 3 autres sérotypes (O55:H9, O45:H2 et O186:H2) porteurs d'un plasmide similaire ont été identifiés au sein du ST301. Une particularité métabolique associée à une cicatrice génétique hautement spécifique du ST301, a été exploitée pour développer une PCR en temps réel (Se=100%, Sp=98,4%) et un milieu de culture (Se=85%, Sp=85%) sélectifs de ces clones. En cas d'infections invasives imposant une antibiothérapie, la production comparée de Stx en présence de différents ATB conduit à recommander l'association d'une béta-lactamine à un inhibiteur de la synthèse protéique. Au travers d'une caractérisation étendue incluant des analyses phénotypiques, génotypiques, phylogénétiques, moléculaires et métaboliques, ce travail participe à l'amélioration de la connaissance des hétéropathotypes ExPEC/EHEC de ST301 et de la prise en charge des infections liées à ces clones. L'importante capacité de ces clones à acquérir du matériel génétique étranger souligne leur extrême plasticité génomique dont les facteurs génétiques sous-jacents restent à découvrir. L'application de ces deux nouvelles méthodes diagnostiques dans l'industrie agro-alimentaire pourrait participer à l'identification du réservoir du clone O80:H2 inconnu jusqu'alors et ainsi contribuer à la prévention de ces infections.The epidemiology of Enterohemorrhagic Escherichia coli (EHEC) involved in Hemolytic and Uremic Syndrome (HUS) has strongly changed in recent years. An atypical clone of serotype O80:H2 (Sequence-type ST301) responsible for HUS and invasive infections has recently emerged in Europe. This clone harbors both virulence factors (VFs) typical of EHEC (intimin - eae-ξ, Shiga toxin - stx, enterohemolysin - ehxA), characteristic VFs of Extra-intestinal pathogenic E. coli (ExPEC) and multi-drug resistance traits (MDR). The aim of this work is to perform a molecular and phenotypic characterization of this heteropathotype to understand its emergence and to contribute to the improvement of diagnosis, treatment and prevention of the infections caused by this pathogen. The EHEC O80:H2 clone acquired a mosaic plasmid (pR444_A) strongly related to the plasmid pS88, a major determinant of ExPEC virulence, carrying multiple extra-intestinal VFs and within which a MDR cassette inserted itself. This ExPEC/EHEC heteropathotype pattern is not restricted to this single serotype since at least 3 other serotypes (O55:H9, O45:H2 and O186:H2) carrying a similar plasmid have been identified within the ST301. A metabolic feature associated with a genetic scar highly specific of ST301, was exploited to develop a real-time PCR (Se=100%, Sp=98.4%) and a culture medium (Se=85%, Sp=85%) selective of these clones. In the case of invasive infections requiring antibiotherapy, the comparative production of Stx in presence of different antibiotics leads to recommend the combination of a beta-lactam and a protein synthesis inhibitor. Through an extensive characterization including phenotypic, genotypic, phylogenetic, molecular and metabolic analysis, this study contributes to the improvement of knowledge on ExPEC/EHEC heteropathotypes of ST301 and the management of their infections. The high capacity of these clones to acquire foreign genetic material underlines their extreme genomic plasticity whose the underlying genetic factors remain to be discovered. The use of these two new diagnostic methods in the food industry could help for identifying the still unknown reservoir of the O80:H2 clone and thus contribute to the prevention of these infections

Emergence d'infections à Escherichia coli de pathotype hybride, producteurs d'une Shiga toxine et associés à une virulence extra-intestinale : caractérisation moléculaire et optimisation de leur prévention et de leur prise en charge

The epidemiology of Enterohemorrhagic Escherichia coli (EHEC) involved in Hemolytic and Uremic Syndrome (HUS) has strongly changed in recent years. An atypical clone of serotype O80:H2 (Sequence-type ST301) responsible for HUS and invasive infections has recently emerged in Europe. This clone harbors both virulence factors (VFs) typical of EHEC (intimin - eae-ξ, Shiga toxin - stx, enterohemolysin - ehxA), characteristic VFs of Extra-intestinal pathogenic E. coli (ExPEC) and multi-drug resistance traits (MDR). The aim of this work is to perform a molecular and phenotypic characterization of this heteropathotype to understand its emergence and to contribute to the improvement of diagnosis, treatment and prevention of the infections caused by this pathogen. The EHEC O80:H2 clone acquired a mosaic plasmid (pR444_A) strongly related to the plasmid pS88, a major determinant of ExPEC virulence, carrying multiple extra-intestinal VFs and within which a MDR cassette inserted itself. This ExPEC/EHEC heteropathotype pattern is not restricted to this single serotype since at least 3 other serotypes (O55:H9, O45:H2 and O186:H2) carrying a similar plasmid have been identified within the ST301. A metabolic feature associated with a genetic scar highly specific of ST301, was exploited to develop a real-time PCR (Se=100%, Sp=98.4%) and a culture medium (Se=85%, Sp=85%) selective of these clones. In the case of invasive infections requiring antibiotherapy, the comparative production of Stx in presence of different antibiotics leads to recommend the combination of a beta-lactam and a protein synthesis inhibitor. Through an extensive characterization including phenotypic, genotypic, phylogenetic, molecular and metabolic analysis, this study contributes to the improvement of knowledge on ExPEC/EHEC heteropathotypes of ST301 and the management of their infections. The high capacity of these clones to acquire foreign genetic material underlines their extreme genomic plasticity whose the underlying genetic factors remain to be discovered. The use of these two new diagnostic methods in the food industry could help for identifying the still unknown reservoir of the O80:H2 clone and thus contribute to the prevention of these infections.L'épidémiologie des Escherichia coli entérohémorragiques (EHEC) responsables de Syndrome Hémolytique et Urémique (SHU), s'est considérablement modifiée ces dernières années. Un clone atypique de sérotype O80:H2 (Sequence-type ST301) responsable de SHU et d'infections invasives a récemment émergé en Europe. Ce clone possède à la fois des facteurs de virulence (FVs) typiques des EHEC (intimine - eae-xi, Shiga toxine - stx, entérohémolysine - ehxA), des FVs caractéristiques des E. coli pathogènes extra-intestinaux (ExPEC) et une multirésistance aux antibiotiques (ATB). L'objectif de ce travail est de caractériser sur le plan moléculaire et phénotypique cet hétéropathotype afin de comprendre son émergence et de contribuer à l'amélioration du diagnostic, du traitement et de la prévention des infections liées à ce pathogène. Le clone EHEC O80:H2 a acquis un plasmide mosaïque (pR444_A) hautement similaire au plasmide pS88, un déterminant majeur de la virulence des ExPEC, porteur de multiples FVs extra-intestinaux et au sein duquel une cassette de résistance aux ATB s'est insérée. Ce profil d'hétéropathotype ExPEC/EHEC n'est pas restreint à ce seul sérotype puisque au moins 3 autres sérotypes (O55:H9, O45:H2 et O186:H2) porteurs d'un plasmide similaire ont été identifiés au sein du ST301. Une particularité métabolique associée à une cicatrice génétique hautement spécifique du ST301, a été exploitée pour développer une PCR en temps réel (Se=100%, Sp=98,4%) et un milieu de culture (Se=85%, Sp=85%) sélectifs de ces clones. En cas d'infections invasives imposant une antibiothérapie, la production comparée de Stx en présence de différents ATB conduit à recommander l'association d'une béta-lactamine à un inhibiteur de la synthèse protéique. Au travers d'une caractérisation étendue incluant des analyses phénotypiques, génotypiques, phylogénétiques, moléculaires et métaboliques, ce travail participe à l'amélioration de la connaissance des hétéropathotypes ExPEC/EHEC de ST301 et de la prise en charge des infections liées à ces clones. L'importante capacité de ces clones à acquérir du matériel génétique étranger souligne leur extrême plasticité génomique dont les facteurs génétiques sous-jacents restent à découvrir. L'application de ces deux nouvelles méthodes diagnostiques dans l'industrie agro-alimentaire pourrait participer à l'identification du réservoir du clone O80:H2 inconnu jusqu'alors et ainsi contribuer à la prévention de ces infections

Shiga Toxin-Associated Hemolytic Uremic Syndrome: A Narrative Review

The severity of human infection by one of the many Shiga toxin-producing Escherichia coli (STEC) is determined by a number of factors: the bacterial genome, the capacity of human societies to prevent foodborne epidemics, the medical condition of infected patients (in particular their hydration status, often compromised by severe diarrhea), and by our capacity to devise new therapeutic approaches, most specifically to combat the bacterial virulence factors, as opposed to our current strategies that essentially aim to palliate organ deficiencies. The last major outbreak in 2011 in Germany, which killed more than 50 people in Europe, was evidence that an effective treatment was still lacking. Herein, we review the current knowledge of STEC virulence, how societies organize the prevention of human disease, and how physicians treat (and, hopefully, will treat) its potentially fatal complications. In particular, we focus on STEC-induced hemolytic and uremic syndrome (HUS), where the intrusion of toxins inside endothelial cells results in massive cell death, activation of the coagulation within capillaries, and eventually organ failure

Shiga Toxin-Associated Hemolytic Uremic Syndrome: Specificities of Adult Patients and Implications for Critical Care Management

International audienceShiga toxin-producing Escherichia coli-associated hemolytic uremic syndrome (STEC-HUS) is a form of thrombotic microangiopathy secondary to an infection by an enterohemorrhagic E. coli. Historically considered a pediatric disease, its presentation has been described as typical, with bloody diarrhea at the forefront. However, in adults, the clinical presentation is more diverse and makes the early diagnosis hazardous. In this review, we review the epidemiology, most important outbreaks, physiopathology, clinical presentation and prognosis of STEC-HUS, focusing on the differential features between pediatric and adult disease. We show that the clinical presentation of STEC-HUS in adults is far from typical and marked by the prevalence of neurological symptoms and a poorer prognosis. Of note, we highlight knowledge gaps and the need for studies dedicated to adult patients. The differences between pediatric and adult patients have implications for the treatment of this disease, which remains a public health threat and lack a specific treatment

Fatal Meningitis from Shiga Toxin–Producing Escherichia coli in 2 Full-Term Neonates, France

We report fatal meningitis in 2 neonates in France caused by Shiga toxin 1–producing Escherichia coli. Virulence factors capsular K1 antigen and salmochelin were present in both strains, potentially representing a new hybrid pathotype. Clinicians should remain aware of emerging pathotypes and design therapeutic strategies for neonatal E. coli infections

First Isolation of the Heteropathotype Shiga Toxin-Producing and Extra-Intestinal Pathogenic (STEC-ExPEC) E. coli O80:H2 in French Healthy Cattle: Genomic Characterization and Phylogenetic Position

International audienceThe emerging heteropathotype shigatoxigenic (STEC) and extra-intestinal pathogenic Escherichia coli (ExPEC) O80:H2 has been the second leading cause of pediatric HUS in France since the mid-2010s. In contrast with other highly pathogenic STEC serotypes, for which ruminants have clearly been identified as the main human infection source, this heteropathotype’s reservoir remains unknown. In this context, we describe for the first time the isolation of seven STEC O80:H2 strains from healthy cattle on a single cattle farm in France. This study aimed at (i) characterizing the genome and (ii) investigating the phylogenetic positions of these O80:H2 STEC strains. The virulomes, resistomes, and phylogenetic positions of the seven bovine isolates were investigated using in silico typing tools, antimicrobial susceptibility testing and cgMLST analysis after short-read whole genome sequencing (WGS). One representative isolate (A13P112V1) was also subjected to long-read sequencing. The seven isolates possessed ExPEC-related virulence genes on a pR444_A-like mosaic plasmid, previously described in strain RDEx444 and known to confer multi-drug resistance. All isolates were clonally related and clustered with human clinical strains from France and Switzerland with a range of locus differences of only one to five. In conclusion, our findings suggest that healthy cattle in France could potentially act as a reservoir of the STEC-ExPEC O80:H2 pathotype

Diagnostic challenge of gastrointestinal infection due to lactose-fermenting Salmonella enterica subsp. enterica serovar 4,5:I:-

International audienceHere, we describe a case of a nontyphoidal Salmonella disease caused by a Salmonella enterica serovar 4,5:i:- (monophasic Salmonella typhimurium) which acquired a Lac operon. This lactose-fermenting bacterium presents a major challenge for phenotypical detection of Salmonella. Only specific agar plates or molecular techniques allow reliable detection

Diagnostic Accuracy of Blind Bronchial Sample Testing by BioFire Pneumonia plus Panel in Pediatric Intensive Care Unit Patients and Its Impact in Early Adaptation of Antimicrobial Therapy: A Prospective Observational Study

International audienceBackground: Community-acquired and nosocomial lower-respiratory-tract infections in critically ill pediatric patients require early appropriate antibiotic therapy to optimize outcomes. Using blind bronchial samples, we assessed the diagnostic performance of the rapid-multiplex polymerase chain reaction (PCR) assay BioFire Pneumonia plus Panel vs. reference standard culturing with antimicrobial susceptibility testing. Methods: For this prospective observational study in a single pediatric intensive care unit, we included consecutive patients younger than 18 years admitted for suspected community-, hospital- or ventilator-associated pneumonia in 2021–2022. Sensitivity, specificity, positive predictive value and negative predictive value of the multiplex PCR assay were determined. The kappa coefficient was computed to assess agreement, and univariate analyses were done to identify factors associated with discrepancies between the 2 diagnostic methods. Results: Of the 36 included patients (median age, 1.4 years; interquartile range, 0.2–9.2), 41.7%, 27.8%, and 30.5% had community-, hospital- and ventilator-associated pneumonia, respectively. The overall κ was 0.74, indicating good agreement. Overall, the sensitivity of the multiplex PCR assay was 92% (95% CI: 77%–98%) and specificity 95% (95% CI: 92%–97%), with variations across microorganisms. The median time from sample collection to antimicrobial susceptibility test results was 3.9 (2.5–15) hours with the multiplex PCR assay and 60.5 (47.6–72.2) hours with the reference technique. Conclusion: The BioFire Pneumonia plus Panel used to test blind bronchial samples had satisfactory diagnostic performance in critically ill pediatric patients. The rapid results provided by this test may improve the appropriateness of antimicrobial therapy and help minimize the use of antibiotics